Diff of the two buildlogs: -- --- b1/build.log 2025-08-14 12:44:21.407893633 +0000 +++ b2/build.log 2025-08-14 13:14:47.950049898 +0000 @@ -1,6 +1,6 @@ I: pbuilder: network access will be disabled during build -I: Current time: Thu Aug 14 00:09:06 -12 2025 -I: pbuilder-time-stamp: 1755173346 +I: Current time: Thu Sep 17 09:07:54 +14 2026 +I: pbuilder-time-stamp: 1789585674 I: Building the build Environment I: extracting base tarball [/var/cache/pbuilder/unstable-reproducible-base.tgz] I: copying local configuration @@ -36,53 +36,85 @@ 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/3735765/tmp/hooks/D02_print_environment starting +I: user script /srv/workspace/pbuilder/3072577/tmp/hooks/D01_modify_environment starting +debug: Running on codethink03-arm64. +I: Changing host+domainname to test build reproducibility +I: Adding a custom variable just for the fun of it... +I: Changing /bin/sh to bash +'/bin/sh' -> '/bin/bash' +lrwxrwxrwx 1 root root 9 Sep 16 19:08 /bin/sh -> /bin/bash +I: Setting pbuilder2's login shell to /bin/bash +I: Setting pbuilder2's GECOS to second user,second room,second work-phone,second home-phone,second other +I: user script /srv/workspace/pbuilder/3072577/tmp/hooks/D01_modify_environment finished +I: user script /srv/workspace/pbuilder/3072577/tmp/hooks/D02_print_environment starting I: set - BUILDDIR='/build/reproducible-path' - BUILDUSERGECOS='first user,first room,first work-phone,first home-phone,first other' - BUILDUSERNAME='pbuilder1' - BUILD_ARCH='arm64' - DEBIAN_FRONTEND='noninteractive' + BASH=/bin/sh + BASHOPTS=checkwinsize:cmdhist:complete_fullquote:extquote:force_fignore:globasciiranges:globskipdots:hostcomplete:interactive_comments:patsub_replacement:progcomp:promptvars:sourcepath + BASH_ALIASES=() + BASH_ARGC=() + BASH_ARGV=() + BASH_CMDS=() + BASH_LINENO=([0]="12" [1]="0") + BASH_LOADABLES_PATH=/usr/local/lib/bash:/usr/lib/bash:/opt/local/lib/bash:/usr/pkg/lib/bash:/opt/pkg/lib/bash:. + BASH_SOURCE=([0]="/tmp/hooks/D02_print_environment" [1]="/tmp/hooks/D02_print_environment") + BASH_VERSINFO=([0]="5" [1]="2" [2]="37" [3]="1" [4]="release" [5]="aarch64-unknown-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=arm64 + DEBIAN_FRONTEND=noninteractive DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=12 ' - DISTRIBUTION='unstable' - HOME='/root' - HOST_ARCH='arm64' + DIRSTACK=() + DISTRIBUTION=unstable + EUID=0 + FUNCNAME=([0]="Echo" [1]="main") + GROUPS=() + HOME=/root + HOSTNAME=i-capture-the-hostname + HOSTTYPE=aarch64 + HOST_ARCH=arm64 IFS=' ' - INVOCATION_ID='6156587f43464f7fa94ab86bb6be7ccf' - 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='3735765' - PS1='# ' - PS2='> ' + INVOCATION_ID=53a197f8152a4804beac21540bb66925 + LANG=C + LANGUAGE=nl_BE:nl + LC_ALL=C + MACHTYPE=aarch64-unknown-linux-gnu + MAIL=/var/mail/root + OPTERR=1 + OPTIND=1 + OSTYPE=linux-gnu + PATH=/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/i/capture/the/path + PBCURRENTCOMMANDLINEOPERATION=build + PBUILDER_OPERATION=build + PBUILDER_PKGDATADIR=/usr/share/pbuilder + PBUILDER_PKGLIBDIR=/usr/lib/pbuilder + PBUILDER_SYSCONFDIR=/etc + PIPESTATUS=([0]="0") + POSIXLY_CORRECT=y + PPID=3072577 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.TI27lAaZ/pbuilderrc_zduH --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.TI27lAaZ/b1 --logfile b1/build.log rdkit_202503.1-5.dsc' - SUDO_GID='109' - SUDO_HOME='/var/lib/jenkins' - SUDO_UID='104' - SUDO_USER='jenkins' - TERM='unknown' - TZ='/usr/share/zoneinfo/Etc/GMT+12' - USER='root' - _='/usr/bin/systemd-run' - http_proxy='http://192.168.101.4:3128' + PWD=/ + SHELL=/bin/bash + SHELLOPTS=braceexpand:errexit:hashall:interactive-comments:posix + SHLVL=3 + SUDO_COMMAND='/usr/bin/timeout -k 24.1h 24h /usr/bin/ionice -c 3 /usr/bin/nice -n 11 /usr/bin/unshare --uts -- /usr/sbin/pbuilder --build --configfile /srv/reproducible-results/rbuild-debian/r-b-build.TI27lAaZ/pbuilderrc_stRO --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.TI27lAaZ/b2 --logfile b2/build.log rdkit_202503.1-5.dsc' + SUDO_GID=109 + SUDO_HOME=/var/lib/jenkins + SUDO_UID=104 + SUDO_USER=jenkins + TERM=unknown + TZ=/usr/share/zoneinfo/Etc/GMT-14 + UID=0 + USER=root + _='I: set' + http_proxy=http://192.168.101.4:3128 I: uname -a - Linux codethink04-arm64 6.12.41+deb13-cloud-arm64 #1 SMP Debian 6.12.41-1 (2025-08-12) aarch64 GNU/Linux + Linux i-capture-the-hostname 6.12.41+deb13-cloud-arm64 #1 SMP Debian 6.12.41-1 (2025-08-12) aarch64 GNU/Linux I: ls -l /bin - lrwxrwxrwx 1 root root 7 Aug 10 12:30 /bin -> usr/bin -I: user script /srv/workspace/pbuilder/3735765/tmp/hooks/D02_print_environment finished + lrwxrwxrwx 1 root root 7 Aug 10 2025 /bin -> usr/bin +I: user script /srv/workspace/pbuilder/3072577/tmp/hooks/D02_print_environment finished -> Attempting to satisfy build-dependencies -> Creating pbuilder-satisfydepends-dummy package Package: pbuilder-satisfydepends-dummy @@ -576,7 +608,7 @@ Get: 369 http://deb.debian.org/debian unstable/main arm64 texlive-latex-recommended all 2024.20250309-1 [8745 kB] Get: 370 http://deb.debian.org/debian unstable/main arm64 texlive-pictures all 2024.20250309-1 [17.0 MB] Get: 371 http://deb.debian.org/debian unstable/main arm64 texlive-latex-extra all 2024.20250309-2 [25.2 MB] -Fetched 399 MB in 3s (148 MB/s) +Fetched 399 MB in 3s (141 MB/s) Preconfiguring packages ... Selecting previously unselected package m4. (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 20002 files and directories currently installed.) @@ -1768,8 +1800,8 @@ Setting up tzdata (2025b-5) ... Current default time zone: 'Etc/UTC' -Local time is now: Thu Aug 14 12:10:13 UTC 2025. -Universal Time is now: Thu Aug 14 12:10:13 UTC 2025. +Local time is now: Wed Sep 16 19:09:06 UTC 2026. +Universal Time is now: Wed Sep 16 19:09:06 UTC 2026. Run 'dpkg-reconfigure tzdata' if you wish to change it. Setting up libboost-atomic1.83.0:arm64 (1.83.0-4.2) ... @@ -1934,11 +1966,6 @@ Setting up pandoc (3.1.11.1+ds-3) ... Setting up libfreetype6:arm64 (2.13.3+dfsg-1) ... Setting up ssl-cert (1.1.3) ... -hostname: Name or service not known -make-ssl-cert: Could not get FQDN, using 'codethink04-arm64'. -make-ssl-cert: You may want to fix your /etc/hosts and/or DNS setup and run -make-ssl-cert: 'make-ssl-cert generate-default-snakeoil --force-overwrite' -make-ssl-cert: again. Setting up libboost-date-time1.83-dev:arm64 (1.83.0-4.2) ... Setting up shared-mime-info (2.4-5+b2) ... Setting up libp11-kit0:arm64 (0.25.5-3) ... @@ -2160,7 +2187,11 @@ 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_202503.1-5_source.changes +I: user script /srv/workspace/pbuilder/3072577/tmp/hooks/A99_set_merged_usr starting +Not re-configuring usrmerge for unstable +I: user script /srv/workspace/pbuilder/3072577/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_202503.1-5_source.changes dpkg-buildpackage: info: source package rdkit dpkg-buildpackage: info: source version 202503.1-5 dpkg-buildpackage: info: source distribution unstable @@ -2284,8 +2315,8 @@ command to set the policy and suppress this warning. This warning is for project developers. Use -Wno-dev to suppress it. --- Configuring done (2.7s) --- Generating done (1.2s) +-- Configuring done (2.8s) +-- Generating done (1.0s) CMake Warning: Manually-specified variables were not used by the project: @@ -2361,114 +2392,114 @@ make[3]: Entering directory '/build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu' make -f External/INCHI-API/CMakeFiles/inchi_support.dir/build.make External/INCHI-API/CMakeFiles/inchi_support.dir/depend make -f Code/RDGeneral/CMakeFiles/RDGeneral.dir/build.make Code/RDGeneral/CMakeFiles/RDGeneral.dir/depend -make[4]: Entering directory '/build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu' -cd /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202503.1 /build/reproducible-path/rdkit-202503.1/External/INCHI-API /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu 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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 -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT External/GA/CMakeFiles/ga.dir/ga/IntegerStringChromosomePolicy.cpp.o -MF CMakeFiles/ga.dir/ga/IntegerStringChromosomePolicy.cpp.o.d -o CMakeFiles/ga.dir/ga/IntegerStringChromosomePolicy.cpp.o -c /build/reproducible-path/rdkit-202503.1/External/GA/ga/IntegerStringChromosomePolicy.cpp -[ 3%] Linking C shared library ../../../../lib/libRDKithc.so +[ 2%] Linking C shared library ../../../../lib/libRDKithc.so cd /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/ML/Cluster/Murtagh && /usr/bin/cmake -E cmake_link_script CMakeFiles/hc.dir/link.txt --verbose=1 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3%] Building CXX object Code/RDGeneral/CMakeFiles/RDGeneral.dir/LocaleSwitcher.cpp.o +cd /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/RDGeneral && /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 -DRDGeneral_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_RDGENERAL_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_BUILD_XYZ2MOL_SUPPORT -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_BOOST_STACKTRACE -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 -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/RDGeneral/CMakeFiles/RDGeneral.dir/LocaleSwitcher.cpp.o -MF CMakeFiles/RDGeneral.dir/LocaleSwitcher.cpp.o.d -o CMakeFiles/RDGeneral.dir/LocaleSwitcher.cpp.o -c /build/reproducible-path/rdkit-202503.1/Code/RDGeneral/LocaleSwitcher.cpp [ 3%] Building CXX object Code/RDGeneral/CMakeFiles/RDGeneral.dir/versions.cpp.o cd /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/RDGeneral && /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 -DRDGeneral_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_RDGENERAL_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_BUILD_XYZ2MOL_SUPPORT 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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 -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT External/GA/CMakeFiles/ga.dir/util/RandomUtil.cpp.o -MF CMakeFiles/ga.dir/util/RandomUtil.cpp.o.d -o CMakeFiles/ga.dir/util/RandomUtil.cpp.o -c /build/reproducible-path/rdkit-202503.1/External/GA/util/RandomUtil.cpp -[ 3%] Building CXX object External/GA/CMakeFiles/ga.dir/util/Util.cpp.o -cd /build/reproducible-path/rdkit-202503.1/obj-aarch64-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 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-D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,--dependency-file=CMakeFiles/RDStreams.dir/link.d -Wl,-z,relro -Wl,-z,now -shared -Wl,-soname,libRDKitRDStreams.so.1 -o ../../lib/libRDKitRDStreams.so.1.2025.03.1 CMakeFiles/RDStreams.dir/streams.cpp.o /usr/lib/aarch64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_iostreams.so.1.83.0 @@ -2482,201 +2513,196 @@ make[4]: Leaving directory '/build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu' [ 3%] Built target RDGeneral make -f Code/DataStructs/CMakeFiles/DataStructs.dir/build.make Code/DataStructs/CMakeFiles/DataStructs.dir/depend -make[4]: Entering directory '/build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu' -cd /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" 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make -f Code/RDGeneral/CMakeFiles/testConcurrentQueue.dir/build.make Code/RDGeneral/CMakeFiles/testConcurrentQueue.dir/depend +cd /build/reproducible-path/rdkit-202503.1/obj-aarch64-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-aarch64-linux-gnu /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/RDGeneral /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/RDGeneral/CMakeFiles/testRDValue.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-aarch64-linux-gnu' +cd /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202503.1 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-I/build/reproducible-path/rdkit-202503.1/External -I/build/reproducible-path/rdkit-202503.1/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/DataStructs/CMakeFiles/DataStructs.dir/ExplicitBitVect.cpp.o -MF CMakeFiles/DataStructs.dir/ExplicitBitVect.cpp.o.d -o CMakeFiles/DataStructs.dir/ExplicitBitVect.cpp.o -c /build/reproducible-path/rdkit-202503.1/Code/DataStructs/ExplicitBitVect.cpp +make[4]: Entering directory '/build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu' +[ 4%] Building CXX object Code/RDGeneral/CMakeFiles/testDict.dir/testDict.cpp.o make[4]: Leaving directory '/build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu' 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-I/usr/lib/aarch64-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 -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/ML/Cluster/Murtagh/CMakeFiles/Clustering.dir/Clustering.cpp.o -MF CMakeFiles/Clustering.dir/Clustering.cpp.o.d -o CMakeFiles/Clustering.dir/Clustering.cpp.o -c /build/reproducible-path/rdkit-202503.1/Code/ML/Cluster/Murtagh/Clustering.cpp -[ 6%] Linking CXX executable testQuery -cd /build/reproducible-path/rdkit-202503.1/obj-aarch64-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=. 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pickersTestsCatch -cd /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/SimDivPickers && /usr/bin/cmake -E cmake_link_script CMakeFiles/pickersTestsCatch.dir/link.txt --verbose=1 -/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/pickersTestsCatch.dir/link.d CMakeFiles/pickersTestsCatch.dir/catch_tests.cpp.o -o pickersTestsCatch ../RDGeneral/librdkitCatch.a ../../lib/libRDKitSimDivPickers.so.1.2025.03.1 ../../lib/libRDKitDataStructs.so.1.2025.03.1 /usr/lib/libCatch2.a ../../lib/libRDKithc.so.1.2025.03.1 ../../lib/libRDKitRDGeneral.so.1.2025.03.1 /usr/lib/aarch64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl -make[4]: Leaving directory '/build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu' -[ 8%] Built target pickersTestsCatch +[ 8%] Building CXX object Code/ML/InfoTheory/Wrap/CMakeFiles/rdInfoTheory.dir/BitCorrMatGenerator.cpp.o +cd /build/reproducible-path/rdkit-202503.1/obj-aarch64-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_BUILD_XYZ2MOL_SUPPORT -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION 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Code/DataStructs/Wrap/CMakeFiles/cDataStructs.dir/wrap_FPB.cpp.o +cd /build/reproducible-path/rdkit-202503.1/obj-aarch64-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_BUILD_XYZ2MOL_SUPPORT -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DcDataStructs_EXPORTS -I/build/reproducible-path/rdkit-202503.1/External -I/build/reproducible-path/rdkit-202503.1/Code -I/usr/lib/aarch64-linux-gnu/python3-numpy/numpy/_core/include -isystem /usr/include/python3.13 -isystem /usr/include/eigen3 -g -O2 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Code/Geometry/CMakeFiles/RDGeometryLib.dir/UniformRealValueGrid3D.cpp.o -cd /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/Geometry && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDGeometryLib_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_RDGEOMETRYLIB_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_BUILD_XYZ2MOL_SUPPORT -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 -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/Geometry/CMakeFiles/RDGeometryLib.dir/UniformRealValueGrid3D.cpp.o -MF CMakeFiles/RDGeometryLib.dir/UniformRealValueGrid3D.cpp.o.d -o CMakeFiles/RDGeometryLib.dir/UniformRealValueGrid3D.cpp.o -c /build/reproducible-path/rdkit-202503.1/Code/Geometry/UniformRealValueGrid3D.cpp -[ 8%] Linking CXX shared module ../../../../rdkit/DataManip/Metric/rdMetricMatrixCalc.so -cd /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/DataManip/MetricMatrixCalc/Wrap && /usr/bin/cmake -E cmake_link_script CMakeFiles/rdMetricMatrixCalc.dir/link.txt --verbose=1 -/usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -g -fwrapv -O2 -Wl,--dependency-file=CMakeFiles/rdMetricMatrixCalc.dir/link.d -Wl,-z,relro -Wl,-z,now -shared -o ../../../../rdkit/DataManip/Metric/rdMetricMatrixCalc.so CMakeFiles/rdMetricMatrixCalc.dir/rdMetricMatrixCalc.cpp.o ../../../../lib/libRDKitDataStructs.so.1.2025.03.1 ../../../../lib/libRDKitRDBoost.so.1.2025.03.1 /usr/lib/aarch64-linux-gnu/libboost_numpy313.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_python313.so.1.83.0 ../../../../lib/libRDKitRDGeneral.so.1.2025.03.1 /usr/lib/aarch64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl -make[4]: Leaving directory '/build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu' -[ 8%] Built target rdMetricMatrixCalc -[ 8%] Building CXX object Code/ML/InfoTheory/Wrap/CMakeFiles/rdInfoTheory.dir/BitCorrMatGenerator.cpp.o -cd /build/reproducible-path/rdkit-202503.1/obj-aarch64-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_BUILD_XYZ2MOL_SUPPORT -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/aarch64-linux-gnu/python3-numpy/numpy/_core/include -isystem /usr/include/python3.13 -isystem /usr/include/eigen3 -g -O2 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-fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/CMakeFiles/GraphMol.dir/Bond.cpp.o -MF CMakeFiles/GraphMol.dir/Bond.cpp.o.d -o CMakeFiles/GraphMol.dir/Bond.cpp.o -c /build/reproducible-path/rdkit-202503.1/Code/GraphMol/Bond.cpp make -f Code/Numerics/Alignment/CMakeFiles/Alignment.dir/build.make Code/Numerics/Alignment/CMakeFiles/Alignment.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu' cd /build/reproducible-path/rdkit-202503.1/obj-aarch64-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-aarch64-linux-gnu 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/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 -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/DataStructs/Wrap/CMakeFiles/cDataStructs.dir/wrap_FPB.cpp.o -MF CMakeFiles/cDataStructs.dir/wrap_FPB.cpp.o.d -o CMakeFiles/cDataStructs.dir/wrap_FPB.cpp.o -c /build/reproducible-path/rdkit-202503.1/Code/DataStructs/Wrap/wrap_FPB.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 -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -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/aarch64-linux-gnu/libboost_numpy313.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_python313.so.1.83.0 ../../../../lib/libRDKitRDGeneral.so.1.2025.03.1 /usr/lib/aarch64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl -make[4]: Leaving directory '/build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu' -[ 11%] Built target rdInfoTheory +[ 10%] Building CXX object Code/GraphMol/CMakeFiles/GraphMol.dir/MolOps.cpp.o +cd /build/reproducible-path/rdkit-202503.1/obj-aarch64-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_BUILD_XYZ2MOL_SUPPORT -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 -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 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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 -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/Geometry/CMakeFiles/testGrid.dir/testGrid.cpp.o -MF CMakeFiles/testGrid.dir/testGrid.cpp.o.d -o CMakeFiles/testGrid.dir/testGrid.cpp.o -c /build/reproducible-path/rdkit-202503.1/Code/Geometry/testGrid.cpp +[ 11%] Linking CXX shared library ../../../lib/libRDKitAlignment.so +cd /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/Numerics/Alignment && /usr/bin/cmake -E cmake_link_script CMakeFiles/Alignment.dir/link.txt --verbose=1 +/usr/bin/c++ -fPIC -g -O2 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'/build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu' [ 11%] Building CXX object Code/Geometry/CMakeFiles/testRealValueGrid.dir/testRealValueGrid.cpp.o cd /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/Geometry && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_BUILD_XYZ2MOL_SUPPORT -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 -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/Geometry/CMakeFiles/testRealValueGrid.dir/testRealValueGrid.cpp.o -MF CMakeFiles/testRealValueGrid.dir/testRealValueGrid.cpp.o.d -o CMakeFiles/testRealValueGrid.dir/testRealValueGrid.cpp.o -c /build/reproducible-path/rdkit-202503.1/Code/Geometry/testRealValueGrid.cpp -[ 11%] Linking CXX shared library ../../../lib/libRDKitAlignment.so -cd /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/Numerics/Alignment && /usr/bin/cmake -E cmake_link_script CMakeFiles/Alignment.dir/link.txt --verbose=1 -/usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,--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/aarch64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl -cd /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/Numerics/Alignment && /usr/bin/cmake -E cmake_symlink_library ../../../lib/libRDKitAlignment.so.1.2025.03.1 ../../../lib/libRDKitAlignment.so.1 ../../../lib/libRDKitAlignment.so -make[4]: Leaving directory '/build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu' -[ 11%] Built target Alignment +[ 11%] Building CXX object 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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/CMakeFiles/GraphMol.dir/FindRings.cpp.o -MF CMakeFiles/GraphMol.dir/FindRings.cpp.o.d -o CMakeFiles/GraphMol.dir/FindRings.cpp.o -c /build/reproducible-path/rdkit-202503.1/Code/GraphMol/FindRings.cpp make -f Code/Geometry/CMakeFiles/geometryTestsCatch.dir/build.make Code/Geometry/CMakeFiles/geometryTestsCatch.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu' cd /build/reproducible-path/rdkit-202503.1/obj-aarch64-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-aarch64-linux-gnu /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/Geometry 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-Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/Numerics/Alignment/CMakeFiles/testAlignment.dir/testAlignment.cpp.o -MF CMakeFiles/testAlignment.dir/testAlignment.cpp.o.d -o CMakeFiles/testAlignment.dir/testAlignment.cpp.o -c /build/reproducible-path/rdkit-202503.1/Code/Numerics/Alignment/testAlignment.cpp [ 12%] Building CXX object Code/Geometry/Wrap/CMakeFiles/rdGeometry.dir/UniformGrid3D.cpp.o cd /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/Geometry/Wrap && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_NUMPY_DYN_LINK -DBOOST_NUMPY_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT 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-c /build/reproducible-path/rdkit-202503.1/Code/Geometry/Wrap/UniformGrid3D.cpp [ 12%] Linking CXX executable geometryTestsCatch @@ -2982,36 +3050,13 @@ /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/geometryTestsCatch.dir/link.d CMakeFiles/geometryTestsCatch.dir/catch_tests.cpp.o -o geometryTestsCatch ../RDGeneral/librdkitCatch.a ../../lib/libRDKitRDGeometryLib.so.1.2025.03.1 /usr/lib/libCatch2.a ../../lib/libRDKitDataStructs.so.1.2025.03.1 ../../lib/libRDKitRDGeneral.so.1.2025.03.1 /usr/lib/aarch64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_serialization.so.1.83.0 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Code/GraphMol/CMakeFiles/GraphMol.dir/PeriodicTable.cpp.o +cd /build/reproducible-path/rdkit-202503.1/obj-aarch64-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_BUILD_XYZ2MOL_SUPPORT -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 -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/CMakeFiles/GraphMol.dir/PeriodicTable.cpp.o -MF CMakeFiles/GraphMol.dir/PeriodicTable.cpp.o.d -o CMakeFiles/GraphMol.dir/PeriodicTable.cpp.o -c /build/reproducible-path/rdkit-202503.1/Code/GraphMol/PeriodicTable.cpp [ 12%] Linking CXX executable testRealValueGrid cd /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/Geometry && /usr/bin/cmake -E cmake_link_script CMakeFiles/testRealValueGrid.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 -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now 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-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_BUILD_XYZ2MOL_SUPPORT -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DrdGeometry_EXPORTS -I/build/reproducible-path/rdkit-202503.1/External -I/build/reproducible-path/rdkit-202503.1/Code -I/usr/lib/aarch64-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 -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/Geometry/Wrap/CMakeFiles/rdGeometry.dir/UniformRealValueGrid3D.cpp.o -MF CMakeFiles/rdGeometry.dir/UniformRealValueGrid3D.cpp.o.d -o CMakeFiles/rdGeometry.dir/UniformRealValueGrid3D.cpp.o -c /build/reproducible-path/rdkit-202503.1/Code/Geometry/Wrap/UniformRealValueGrid3D.cpp -[ 12%] Linking CXX shared module ../../../rdkit/SimDivFilters/rdSimDivPickers.so -cd /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/SimDivPickers/Wrap && /usr/bin/cmake -E cmake_link_script CMakeFiles/rdSimDivPickers.dir/link.txt --verbose=1 -/usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -g -fwrapv -O2 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'/build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu' -[ 12%] Building CXX object Code/Numerics/Alignment/CMakeFiles/testAlignment.dir/testAlignment.cpp.o -cd /build/reproducible-path/rdkit-202503.1/obj-aarch64-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_BUILD_XYZ2MOL_SUPPORT -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 -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/Numerics/Alignment/CMakeFiles/testAlignment.dir/testAlignment.cpp.o -MF CMakeFiles/testAlignment.dir/testAlignment.cpp.o.d -o CMakeFiles/testAlignment.dir/testAlignment.cpp.o -c /build/reproducible-path/rdkit-202503.1/Code/Numerics/Alignment/testAlignment.cpp make -f Code/Numerics/Alignment/Wrap/CMakeFiles/rdAlignment.dir/build.make Code/Numerics/Alignment/Wrap/CMakeFiles/rdAlignment.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu' cd /build/reproducible-path/rdkit-202503.1/obj-aarch64-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/Wrap /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/Numerics/Alignment/Wrap /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/Numerics/Alignment/Wrap/CMakeFiles/rdAlignment.dir/DependInfo.cmake "--color=" @@ -3020,15 +3065,25 @@ make[4]: Entering directory '/build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu' [ 12%] Building CXX object Code/Numerics/Alignment/Wrap/CMakeFiles/rdAlignment.dir/rdAlignment.cpp.o cd /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/Numerics/Alignment/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_BUILD_XYZ2MOL_SUPPORT -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DrdAlignment_EXPORTS -I/build/reproducible-path/rdkit-202503.1/External -I/build/reproducible-path/rdkit-202503.1/Code -I/usr/lib/aarch64-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 -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/Numerics/Alignment/Wrap/CMakeFiles/rdAlignment.dir/rdAlignment.cpp.o -MF CMakeFiles/rdAlignment.dir/rdAlignment.cpp.o.d -o CMakeFiles/rdAlignment.dir/rdAlignment.cpp.o -c /build/reproducible-path/rdkit-202503.1/Code/Numerics/Alignment/Wrap/rdAlignment.cpp -[ 12%] Building CXX object Code/GraphMol/CMakeFiles/GraphMol.dir/Bond.cpp.o -cd /build/reproducible-path/rdkit-202503.1/obj-aarch64-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_BUILD_XYZ2MOL_SUPPORT -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 -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/CMakeFiles/GraphMol.dir/Bond.cpp.o -MF CMakeFiles/GraphMol.dir/Bond.cpp.o.d -o CMakeFiles/GraphMol.dir/Bond.cpp.o -c /build/reproducible-path/rdkit-202503.1/Code/GraphMol/Bond.cpp -[ 12%] Building CXX object Code/GraphMol/CMakeFiles/GraphMol.dir/MolOps.cpp.o -cd /build/reproducible-path/rdkit-202503.1/obj-aarch64-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_BUILD_XYZ2MOL_SUPPORT -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 -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/CMakeFiles/GraphMol.dir/MolOps.cpp.o -MF CMakeFiles/GraphMol.dir/MolOps.cpp.o.d -o CMakeFiles/GraphMol.dir/MolOps.cpp.o -c /build/reproducible-path/rdkit-202503.1/Code/GraphMol/MolOps.cpp +[ 12%] Linking CXX shared module ../../../rdkit/DataStructs/cDataStructs.so +cd /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/DataStructs/Wrap && /usr/bin/cmake -E cmake_link_script CMakeFiles/cDataStructs.dir/link.txt --verbose=1 +In file included from /usr/include/c++/14/bits/stl_algobase.h:64, + from /usr/include/c++/14/bits/stl_tree.h:63, + from /usr/include/c++/14/map:62, + from /build/reproducible-path/rdkit-202503.1/Code/GraphMol/PeriodicTable.h:14, + from /build/reproducible-path/rdkit-202503.1/Code/GraphMol/PeriodicTable.cpp:11: +/usr/include/c++/14/bits/stl_pair.h: In instantiation of 'constexpr std::pair::type>::__type, typename std::__strip_reference_wrapper::type>::__type> std::make_pair(_T1&&, _T2&&) [with _T1 = double&; _T2 = double&; typename __strip_reference_wrapper::type>::__type = double; typename decay<_Tp>::type = double; typename __strip_reference_wrapper::type>::__type = double; typename decay<_Tp2>::type = double]': +/build/reproducible-path/rdkit-202503.1/Code/GraphMol/PeriodicTable.cpp:96:57: required from here + 96 | adata.d_isotopeInfoMap[isotope] = std::make_pair(mass, abundance); + | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~ +/usr/include/c++/14/bits/stl_pair.h:1132:5: note: parameter passing for argument of type 'std::pair' when C++17 is enabled changed to match C++14 in GCC 10.1 + 1132 | make_pair(_T1&& __x, _T2&& __y) + | ^~~~~~~~~ [ 12%] Linking CXX executable testAlignment +/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 -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -g -fwrapv -O2 -Wl,--dependency-file=CMakeFiles/cDataStructs.dir/link.d -Wl,-z,relro -Wl,-z,now -shared -o ../../../rdkit/DataStructs/cDataStructs.so CMakeFiles/cDataStructs.dir/DataStructs.cpp.o CMakeFiles/cDataStructs.dir/DiscreteValueVect.cpp.o CMakeFiles/cDataStructs.dir/SparseIntVect.cpp.o CMakeFiles/cDataStructs.dir/RealValueVect.cpp.o CMakeFiles/cDataStructs.dir/wrap_SparseBV.cpp.o CMakeFiles/cDataStructs.dir/wrap_ExplicitBV.cpp.o CMakeFiles/cDataStructs.dir/wrap_BitOps.cpp.o CMakeFiles/cDataStructs.dir/wrap_FPB.cpp.o CMakeFiles/cDataStructs.dir/wrap_Utils.cpp.o ../../../lib/libRDKitDataStructs.so.1.2025.03.1 ../../../lib/libRDKitRDBoost.so.1.2025.03.1 /usr/lib/aarch64-linux-gnu/libboost_numpy313.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_python313.so.1.83.0 ../../../lib/libRDKitRDGeneral.so.1.2025.03.1 /usr/lib/aarch64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl cd /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/Numerics/Alignment && /usr/bin/cmake -E cmake_link_script CMakeFiles/testAlignment.dir/link.txt --verbose=1 -/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now -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/aarch64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl make[4]: Leaving directory '/build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu' -[ 12%] Built target testAlignment +[ 12%] Built target cDataStructs make -f Code/Features/CMakeFiles/testBaseFeatures.dir/build.make Code/Features/CMakeFiles/testBaseFeatures.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu' cd /build/reproducible-path/rdkit-202503.1/obj-aarch64-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-aarch64-linux-gnu /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/Features /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/Features/CMakeFiles/testBaseFeatures.dir/DependInfo.cmake "--color=" @@ -3037,8 +3092,11 @@ make[4]: Entering directory '/build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu' [ 12%] Building CXX object Code/Features/CMakeFiles/testBaseFeatures.dir/testFeatures.cpp.o cd /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/Features && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_BUILD_XYZ2MOL_SUPPORT -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 -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/Features/CMakeFiles/testBaseFeatures.dir/testFeatures.cpp.o -MF CMakeFiles/testBaseFeatures.dir/testFeatures.cpp.o.d -o CMakeFiles/testBaseFeatures.dir/testFeatures.cpp.o -c /build/reproducible-path/rdkit-202503.1/Code/Features/testFeatures.cpp -[ 12%] Building CXX object Code/GraphMol/CMakeFiles/GraphMol.dir/FindRings.cpp.o -cd /build/reproducible-path/rdkit-202503.1/obj-aarch64-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_BUILD_XYZ2MOL_SUPPORT -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 -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/CMakeFiles/GraphMol.dir/FindRings.cpp.o -MF CMakeFiles/GraphMol.dir/FindRings.cpp.o.d -o CMakeFiles/GraphMol.dir/FindRings.cpp.o -c /build/reproducible-path/rdkit-202503.1/Code/GraphMol/FindRings.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 -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now -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/aarch64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl +make[4]: Leaving directory '/build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu' +[ 12%] Built target testAlignment +[ 12%] Building CXX object Code/Geometry/Wrap/CMakeFiles/rdGeometry.dir/UniformRealValueGrid3D.cpp.o +cd /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/Geometry/Wrap && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_NUMPY_DYN_LINK -DBOOST_NUMPY_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_BUILD_XYZ2MOL_SUPPORT -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DrdGeometry_EXPORTS -I/build/reproducible-path/rdkit-202503.1/External -I/build/reproducible-path/rdkit-202503.1/Code -I/usr/lib/aarch64-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 -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/Geometry/Wrap/CMakeFiles/rdGeometry.dir/UniformRealValueGrid3D.cpp.o -MF CMakeFiles/rdGeometry.dir/UniformRealValueGrid3D.cpp.o.d -o CMakeFiles/rdGeometry.dir/UniformRealValueGrid3D.cpp.o -c /build/reproducible-path/rdkit-202503.1/Code/Geometry/Wrap/UniformRealValueGrid3D.cpp [ 13%] Linking CXX executable testConrec cd /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/Numerics && /usr/bin/cmake -E cmake_link_script CMakeFiles/testConrec.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/testConrec.dir/link.d CMakeFiles/testConrec.dir/testConrec.cpp.o -o testConrec ../RDGeneral/librdkitCatch.a ../../lib/libRDKitRDGeometryLib.so.1.2025.03.1 /usr/lib/libCatch2.a ../../lib/libRDKitDataStructs.so.1.2025.03.1 ../../lib/libRDKitRDGeneral.so.1.2025.03.1 /usr/lib/aarch64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl @@ -3052,102 +3110,75 @@ make[4]: Entering directory '/build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu' [ 13%] Building CXX object Code/ChemicalFeatures/CMakeFiles/ChemicalFeatures.dir/FreeChemicalFeature.cpp.o cd /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/ChemicalFeatures && /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 -DChemicalFeatures_EXPORTS -DRDKIT_CHEMICALFEATURES_BUILD -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_BUILD_XYZ2MOL_SUPPORT -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED 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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 -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/CMakeFiles/GraphMol.dir/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 -[ 14%] Building CXX object Code/GraphMol/CMakeFiles/GraphMol.dir/QueryOps.cpp.o -cd /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB 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/usr/lib/aarch64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_iostreams.so.1.83.0 +make[4]: Leaving directory '/build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu' +[ 14%] Built target testBaseFeatures +[ 14%] Building CXX object Code/GraphMol/CMakeFiles/GraphMol.dir/Canon.cpp.o +[ 14%] Building CXX object Code/GraphMol/CMakeFiles/GraphMol.dir/AtomIterators.cpp.o +cd /build/reproducible-path/rdkit-202503.1/obj-aarch64-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_BUILD_XYZ2MOL_SUPPORT -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 -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/CMakeFiles/GraphMol.dir/AtomIterators.cpp.o -MF CMakeFiles/GraphMol.dir/AtomIterators.cpp.o.d -o CMakeFiles/GraphMol.dir/AtomIterators.cpp.o -c /build/reproducible-path/rdkit-202503.1/Code/GraphMol/AtomIterators.cpp +cd /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK 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CMakeFiles/GraphMol.dir/Canon.cpp.o -c /build/reproducible-path/rdkit-202503.1/Code/GraphMol/Canon.cpp [ 15%] Linking CXX shared module ../../../../rdkit/Numerics/rdAlignment.so cd /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/Numerics/Alignment/Wrap && /usr/bin/cmake -E cmake_link_script CMakeFiles/rdAlignment.dir/link.txt --verbose=1 -In file included from /usr/include/c++/14/bits/stl_algobase.h:64, - from /usr/include/c++/14/bits/stl_tree.h:63, - from /usr/include/c++/14/map:62, - from /build/reproducible-path/rdkit-202503.1/Code/GraphMol/PeriodicTable.h:14, - from /build/reproducible-path/rdkit-202503.1/Code/GraphMol/PeriodicTable.cpp:11: -/usr/include/c++/14/bits/stl_pair.h: In instantiation of 'constexpr std::pair::type>::__type, typename std::__strip_reference_wrapper::type>::__type> std::make_pair(_T1&&, _T2&&) [with _T1 = double&; _T2 = double&; typename __strip_reference_wrapper::type>::__type = double; typename decay<_Tp>::type = double; typename __strip_reference_wrapper::type>::__type = double; typename decay<_Tp2>::type = double]': -/build/reproducible-path/rdkit-202503.1/Code/GraphMol/PeriodicTable.cpp:96:57: required from here - 96 | adata.d_isotopeInfoMap[isotope] = std::make_pair(mass, abundance); - | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~ -/usr/include/c++/14/bits/stl_pair.h:1132:5: note: parameter passing for argument of type 'std::pair' when C++17 is enabled changed to match C++14 in GCC 10.1 - 1132 | make_pair(_T1&& __x, _T2&& __y) - | ^~~~~~~~~ /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 -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -g -fwrapv -O2 -Wl,--dependency-file=CMakeFiles/rdAlignment.dir/link.d -Wl,-z,relro -Wl,-z,now -shared -o ../../../../rdkit/Numerics/rdAlignment.so CMakeFiles/rdAlignment.dir/rdAlignment.cpp.o ../../../../lib/libRDKitAlignment.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/aarch64-linux-gnu/libboost_numpy313.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_python313.so.1.83.0 ../../../../lib/libRDKitRDGeneral.so.1.2025.03.1 /usr/lib/aarch64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl make[4]: Leaving directory '/build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu' [ 15%] Built target rdAlignment -[ 15%] Building CXX object Code/GraphMol/CMakeFiles/GraphMol.dir/MolPickler.cpp.o -cd /build/reproducible-path/rdkit-202503.1/obj-aarch64-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_BUILD_XYZ2MOL_SUPPORT -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 -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/CMakeFiles/GraphMol.dir/MolPickler.cpp.o -MF CMakeFiles/GraphMol.dir/MolPickler.cpp.o.d -o CMakeFiles/GraphMol.dir/MolPickler.cpp.o -c /build/reproducible-path/rdkit-202503.1/Code/GraphMol/MolPickler.cpp -[ 15%] Building CXX object Code/GraphMol/CMakeFiles/GraphMol.dir/Canon.cpp.o -cd /build/reproducible-path/rdkit-202503.1/obj-aarch64-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_BUILD_XYZ2MOL_SUPPORT -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 -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/CMakeFiles/GraphMol.dir/Canon.cpp.o -MF 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%] Building CXX object Code/GraphMol/CMakeFiles/GraphMol.dir/AtomIterators.cpp.o -cd /build/reproducible-path/rdkit-202503.1/obj-aarch64-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 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Code/GraphMol/CMakeFiles/GraphMol.dir/BondIterators.cpp.o cd /build/reproducible-path/rdkit-202503.1/obj-aarch64-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_BUILD_XYZ2MOL_SUPPORT -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 -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/CMakeFiles/GraphMol.dir/BondIterators.cpp.o -MF CMakeFiles/GraphMol.dir/BondIterators.cpp.o.d -o CMakeFiles/GraphMol.dir/BondIterators.cpp.o -c /build/reproducible-path/rdkit-202503.1/Code/GraphMol/BondIterators.cpp +[ 15%] Linking CXX shared module ../../../rdkit/rdBase.so +cd /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/RDBoost/Wrap && /usr/bin/cmake -E cmake_link_script CMakeFiles/rdBase.dir/link.txt --verbose=1 +/usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -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/aarch64-linux-gnu/libboost_numpy313.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_python313.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_iostreams.so.1.83.0 +make[4]: Leaving directory '/build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu' +[ 15%] Built target rdBase [ 15%] Linking CXX executable testChemicalFeatures cd /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/ChemicalFeatures && /usr/bin/cmake -E cmake_link_script CMakeFiles/testChemicalFeatures.dir/link.txt --verbose=1 -/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong 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/build/reproducible-path/rdkit-202503.1/Code/GraphMol/ConjugHybrid.cpp -[ 15%] Linking CXX shared module ../../../rdkit/rdBase.so -cd /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/RDBoost/Wrap && /usr/bin/cmake -E cmake_link_script CMakeFiles/rdBase.dir/link.txt --verbose=1 -/usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -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/aarch64-linux-gnu/libboost_numpy313.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_python313.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_iostreams.so.1.83.0 -make[4]: Leaving directory '/build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu' -[ 15%] Built target rdBase [ 15%] Building CXX object Code/GraphMol/CMakeFiles/GraphMol.dir/AddHs.cpp.o cd /build/reproducible-path/rdkit-202503.1/obj-aarch64-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_BUILD_XYZ2MOL_SUPPORT -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED 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-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_BUILD_XYZ2MOL_SUPPORT -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 -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/CMakeFiles/GraphMol.dir/Matrices.cpp.o -MF CMakeFiles/GraphMol.dir/Matrices.cpp.o.d -o CMakeFiles/GraphMol.dir/Matrices.cpp.o -c /build/reproducible-path/rdkit-202503.1/Code/GraphMol/Matrices.cpp [ 16%] Building CXX object Code/GraphMol/CMakeFiles/GraphMol.dir/Chirality.cpp.o cd /build/reproducible-path/rdkit-202503.1/obj-aarch64-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_BUILD_XYZ2MOL_SUPPORT -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 -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/CMakeFiles/GraphMol.dir/Chirality.cpp.o -MF CMakeFiles/GraphMol.dir/Chirality.cpp.o.d -o CMakeFiles/GraphMol.dir/Chirality.cpp.o -c /build/reproducible-path/rdkit-202503.1/Code/GraphMol/Chirality.cpp +[ 16%] Linking CXX shared module ../../../rdkit/Geometry/rdGeometry.so +cd /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/Geometry/Wrap && /usr/bin/cmake -E cmake_link_script CMakeFiles/rdGeometry.dir/link.txt --verbose=1 +/usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard 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+make[4]: Leaving directory '/build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu' +[ 16%] Built target rdGeometry [ 16%] Building CXX object Code/GraphMol/CMakeFiles/GraphMol.dir/RingInfo.cpp.o cd /build/reproducible-path/rdkit-202503.1/obj-aarch64-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_BUILD_XYZ2MOL_SUPPORT -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 -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/CMakeFiles/GraphMol.dir/RingInfo.cpp.o -MF CMakeFiles/GraphMol.dir/RingInfo.cpp.o.d -o CMakeFiles/GraphMol.dir/RingInfo.cpp.o -c /build/reproducible-path/rdkit-202503.1/Code/GraphMol/RingInfo.cpp [ 16%] Building CXX object Code/GraphMol/CMakeFiles/GraphMol.dir/Conformer.cpp.o @@ -3184,281 +3215,236 @@ [ 17%] Built target GraphMol make -f Code/GraphMol/MolTransforms/CMakeFiles/MolTransforms.dir/build.make Code/GraphMol/MolTransforms/CMakeFiles/MolTransforms.dir/depend make -f Code/GraphMol/SmilesParse/CMakeFiles/SmilesParse.dir/build.make Code/GraphMol/SmilesParse/CMakeFiles/SmilesParse.dir/depend -make[4]: Entering directory '/build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu' -cd /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202503.1 /build/reproducible-path/rdkit-202503.1/Code/GraphMol/MolTransforms /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/MolTransforms /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/MolTransforms/CMakeFiles/MolTransforms.dir/DependInfo.cmake "--color=" make -f Code/GraphMol/GenericGroups/CMakeFiles/GenericGroups.dir/build.make Code/GraphMol/GenericGroups/CMakeFiles/GenericGroups.dir/depend make -f Code/GraphMol/Trajectory/CMakeFiles/Trajectory.dir/build.make Code/GraphMol/Trajectory/CMakeFiles/Trajectory.dir/depend +make -f Code/GraphMol/CIPLabeler/CMakeFiles/CIPLabeler.dir/build.make Code/GraphMol/CIPLabeler/CMakeFiles/CIPLabeler.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu' -cd /build/reproducible-path/rdkit-202503.1/obj-aarch64-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-aarch64-linux-gnu /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/SmilesParse /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/SmilesParse/CMakeFiles/SmilesParse.dir/DependInfo.cmake "--color=" +cd /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202503.1 /build/reproducible-path/rdkit-202503.1/Code/GraphMol/MolTransforms /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/MolTransforms 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/build/reproducible-path/rdkit-202503.1 /build/reproducible-path/rdkit-202503.1/Code/GraphMol/CIPLabeler /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/CIPLabeler /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/CIPLabeler/CMakeFiles/CIPLabeler.dir/DependInfo.cmake "--color=" +cd /build/reproducible-path/rdkit-202503.1/obj-aarch64-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-aarch64-linux-gnu /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/SmilesParse /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/SmilesParse/CMakeFiles/SmilesParse.dir/DependInfo.cmake "--color=" make -f Code/GraphMol/Subgraphs/CMakeFiles/Subgraphs.dir/build.make 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'/build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu' cd /build/reproducible-path/rdkit-202503.1/obj-aarch64-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-aarch64-linux-gnu /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/CMakeFiles/tableTestsCatch.dir/DependInfo.cmake "--color=" make[4]: Entering directory '/build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu' +make[4]: Entering directory '/build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu' +cd /build/reproducible-path/rdkit-202503.1/obj-aarch64-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 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directory '/build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu' +make -f Code/GraphMol/MolInterchange/CMakeFiles/MolInterchange.dir/build.make Code/GraphMol/MolInterchange/CMakeFiles/MolInterchange.dir/depend cd /build/reproducible-path/rdkit-202503.1/obj-aarch64-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 /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/MolCatalog /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/MolCatalog/CMakeFiles/MolCatalog.dir/DependInfo.cmake "--color=" -make[4]: Leaving directory '/build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu' make[4]: Entering directory '/build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu' -make -f Code/GraphMol/MolTransforms/CMakeFiles/MolTransforms.dir/build.make Code/GraphMol/MolTransforms/CMakeFiles/MolTransforms.dir/build cd /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202503.1 /build/reproducible-path/rdkit-202503.1/Code/GraphMol/MolInterchange /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/MolInterchange /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/MolInterchange/CMakeFiles/MolInterchange.dir/DependInfo.cmake "--color=" +make -f Code/GraphMol/SLNParse/CMakeFiles/SLNParse.dir/build.make Code/GraphMol/SLNParse/CMakeFiles/SLNParse.dir/depend +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-aarch64-linux-gnu' +make[4]: Entering directory '/build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu' +cd /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202503.1 /build/reproducible-path/rdkit-202503.1/Code/GraphMol/SLNParse /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/SLNParse /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/SLNParse/CMakeFiles/SLNParse.dir/DependInfo.cmake "--color=" +cd /build/reproducible-path/rdkit-202503.1/obj-aarch64-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-aarch64-linux-gnu /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/Wrap 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Code/GraphMol/SLNParse/CMakeFiles/SLNParse.dir/build.make Code/GraphMol/SLNParse/CMakeFiles/SLNParse.dir/build +make -f Code/GraphMol/SmilesParse/CMakeFiles/SmilesParse.dir/build.make Code/GraphMol/SmilesParse/CMakeFiles/SmilesParse.dir/build +make[4]: Leaving directory '/build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu' make[4]: Entering directory '/build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu' +make[4]: Entering directory '/build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu' +make -f Code/GraphMol/MolInterchange/CMakeFiles/MolInterchange.dir/build.make Code/GraphMol/MolInterchange/CMakeFiles/MolInterchange.dir/build make[4]: Leaving directory '/build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu' +make -f Code/GraphMol/GenericGroups/CMakeFiles/GenericGroups.dir/build.make Code/GraphMol/GenericGroups/CMakeFiles/GenericGroups.dir/build +[ 17%] Building CXX object Code/GraphMol/MolTransforms/CMakeFiles/MolTransforms.dir/MolTransforms.cpp.o +cd /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/MolTransforms && /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 -DMolTransforms_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_MOLTRANSFORMS_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_BUILD_XYZ2MOL_SUPPORT -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 -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 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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 -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/Subgraphs/CMakeFiles/Subgraphs.dir/Subgraphs.cpp.o -MF CMakeFiles/Subgraphs.dir/Subgraphs.cpp.o.d -o CMakeFiles/Subgraphs.dir/Subgraphs.cpp.o -c /build/reproducible-path/rdkit-202503.1/Code/GraphMol/Subgraphs/Subgraphs.cpp [ 18%] Building CXX object Code/GraphMol/Trajectory/CMakeFiles/Trajectory.dir/Trajectory.cpp.o -cd /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/MolTransforms && /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 -DMolTransforms_EXPORTS 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-mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/GenericGroups/CMakeFiles/GenericGroups.dir/GenericGroups.cpp.o -MF CMakeFiles/GenericGroups.dir/GenericGroups.cpp.o.d -o CMakeFiles/GenericGroups.dir/GenericGroups.cpp.o -c /build/reproducible-path/rdkit-202503.1/Code/GraphMol/GenericGroups/GenericGroups.cpp -cd /build/reproducible-path/rdkit-202503.1/obj-aarch64-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_BUILD_XYZ2MOL_SUPPORT -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 -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/SmilesParse/CMakeFiles/SmilesParse.dir/SmilesParseOps.cpp.o -MF CMakeFiles/SmilesParse.dir/SmilesParseOps.cpp.o.d -o CMakeFiles/SmilesParse.dir/SmilesParseOps.cpp.o -c /build/reproducible-path/rdkit-202503.1/Code/GraphMol/SmilesParse/SmilesParseOps.cpp -cd /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/SmilesParse && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK 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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-aarch64-linux-gnu/Code/GraphMol/Trajectory && /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_TRAJECTORY_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_BUILD_XYZ2MOL_SUPPORT -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DTrajectory_EXPORTS -I/build/reproducible-path/rdkit-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 -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/Trajectory/CMakeFiles/Trajectory.dir/Trajectory.cpp.o -MF CMakeFiles/Trajectory.dir/Trajectory.cpp.o.d -o CMakeFiles/Trajectory.dir/Trajectory.cpp.o -c /build/reproducible-path/rdkit-202503.1/Code/GraphMol/Trajectory/Trajectory.cpp -cd /build/reproducible-path/rdkit-202503.1/obj-aarch64-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 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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 -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/MolInterchange/CMakeFiles/MolInterchange.dir/Parser.cpp.o -MF CMakeFiles/MolInterchange.dir/Parser.cpp.o.d -o CMakeFiles/MolInterchange.dir/Parser.cpp.o -c /build/reproducible-path/rdkit-202503.1/Code/GraphMol/MolInterchange/Parser.cpp +[ 18%] Building CXX object Code/GraphMol/SLNParse/CMakeFiles/SLNParse.dir/SLNParse.cpp.o cd /build/reproducible-path/rdkit-202503.1/obj-aarch64-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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-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 -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/SLNParse/CMakeFiles/SLNParse.dir/SLNParse.cpp.o -MF CMakeFiles/SLNParse.dir/SLNParse.cpp.o.d -o CMakeFiles/SLNParse.dir/SLNParse.cpp.o -c /build/reproducible-path/rdkit-202503.1/Code/GraphMol/SLNParse/SLNParse.cpp -[ 20%] Building CXX object Code/GraphMol/MolCatalog/CMakeFiles/MolCatalog.dir/MolCatalogParams.cpp.o -cd /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/MolCatalog && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK 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CMakeFiles/MolCatalog.dir/MolCatalogParams.cpp.o.d -o CMakeFiles/MolCatalog.dir/MolCatalogParams.cpp.o -c /build/reproducible-path/rdkit-202503.1/Code/GraphMol/MolCatalog/MolCatalogParams.cpp -[ 20%] Linking CXX shared library ../../../lib/libRDKitTrajectory.so +[ 19%] Built target MolCatalog +[ 19%] Building CXX object Code/GraphMol/MolInterchange/CMakeFiles/MolInterchange.dir/Writer.cpp.o +cd /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/MolInterchange && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DMolInterchange_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_MOLINTERCHANGE_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_BUILD_XYZ2MOL_SUPPORT -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/External/rapidjson-1.1.0/include -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 -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/MolInterchange/CMakeFiles/MolInterchange.dir/Writer.cpp.o -MF CMakeFiles/MolInterchange.dir/Writer.cpp.o.d -o CMakeFiles/MolInterchange.dir/Writer.cpp.o -c /build/reproducible-path/rdkit-202503.1/Code/GraphMol/MolInterchange/Writer.cpp +[ 19%] Linking CXX shared library ../../../lib/libRDKitTrajectory.so cd /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/Trajectory && 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-ldl cd /build/reproducible-path/rdkit-202503.1/obj-aarch64-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 make[4]: Leaving directory '/build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu' -[ 20%] Built target Trajectory -[ 20%] Building CXX object Code/GraphMol/SLNParse/CMakeFiles/SLNParse.dir/SLNAttribs.cpp.o -cd /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/SLNParse && /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_SLNPARSE_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_BUILD_XYZ2MOL_SUPPORT -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DSLNParse_EXPORTS -I/build/reproducible-path/rdkit-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 -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/SLNParse/CMakeFiles/SLNParse.dir/SLNAttribs.cpp.o -MF CMakeFiles/SLNParse.dir/SLNAttribs.cpp.o.d -o CMakeFiles/SLNParse.dir/SLNAttribs.cpp.o -c /build/reproducible-path/rdkit-202503.1/Code/GraphMol/SLNParse/SLNAttribs.cpp -[ 20%] Linking CXX shared library ../../../lib/libRDKitMolCatalog.so -cd /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/MolCatalog && /usr/bin/cmake -E cmake_link_script 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/usr/lib/aarch64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl -cd /build/reproducible-path/rdkit-202503.1/obj-aarch64-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 +[ 19%] Built target Trajectory +make -f Code/ChemicalFeatures/Wrap/CMakeFiles/rdChemicalFeatures.dir/build.make Code/ChemicalFeatures/Wrap/CMakeFiles/rdChemicalFeatures.dir/depend +make[4]: Entering directory '/build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu' +cd /build/reproducible-path/rdkit-202503.1/obj-aarch64-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-aarch64-linux-gnu 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-Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/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 [ 20%] Linking CXX shared library ../../../lib/libRDKitPartialCharges.so cd /build/reproducible-path/rdkit-202503.1/obj-aarch64-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 -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing 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-fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/CIPLabeler/CMakeFiles/CIPLabeler.dir/Mancude.cpp.o -MF CMakeFiles/CIPLabeler.dir/Mancude.cpp.o.d -o CMakeFiles/CIPLabeler.dir/Mancude.cpp.o -c /build/reproducible-path/rdkit-202503.1/Code/GraphMol/CIPLabeler/Mancude.cpp [ 20%] Linking CXX shared library ../../../lib/libRDKitMolTransforms.so cd /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/MolTransforms && /usr/bin/cmake -E cmake_link_script CMakeFiles/MolTransforms.dir/link.txt --verbose=1 /usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 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-I/build/reproducible-path/rdkit-202503.1/Code -I/usr/lib/aarch64-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 -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/Wrap/CMakeFiles/rdqueries.dir/Queries.cpp.o -MF CMakeFiles/rdqueries.dir/Queries.cpp.o.d -o CMakeFiles/rdqueries.dir/Queries.cpp.o -c /build/reproducible-path/rdkit-202503.1/Code/GraphMol/Wrap/Queries.cpp -[ 20%] Building CXX object Code/GraphMol/CIPLabeler/CMakeFiles/CIPLabeler.dir/Mancude.cpp.o -cd /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/CIPLabeler && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB 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-fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/SLNParse/CMakeFiles/SLNParse.dir/SLNAttribs.cpp.o -MF CMakeFiles/SLNParse.dir/SLNAttribs.cpp.o.d -o CMakeFiles/SLNParse.dir/SLNAttribs.cpp.o -c /build/reproducible-path/rdkit-202503.1/Code/GraphMol/SLNParse/SLNAttribs.cpp +[ 20%] Linking CXX shared library ../../../lib/libRDKitOptimizer.so +cd /build/reproducible-path/rdkit-202503.1/obj-aarch64-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 -mbranch-protection=standard -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 -I/usr/lib/aarch64-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 -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/MolTransforms/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 [ 21%] Building CXX object Code/GraphMol/CIPLabeler/CMakeFiles/CIPLabeler.dir/Edge.cpp.o cd 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-I/usr/lib/aarch64-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 -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/Wrap/CMakeFiles/rdtrajectory.dir/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 -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-aarch64-linux-gnu' -cd 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-Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/CIPLabeler/CMakeFiles/CIPLabeler.dir/rules/Rule1a.cpp.o -MF CMakeFiles/CIPLabeler.dir/rules/Rule1a.cpp.o.d -o CMakeFiles/CIPLabeler.dir/rules/Rule1a.cpp.o -c /build/reproducible-path/rdkit-202503.1/Code/GraphMol/CIPLabeler/rules/Rule1a.cpp -[ 23%] Linking CXX shared module ../../../rdkit/Chem/rdChemicalFeatures.so -cd /build/reproducible-path/rdkit-202503.1/obj-aarch64-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 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function 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'/build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu' -[ 23%] Built target rdChemicalFeatures -[ 23%] Building CXX object Code/GraphMol/CIPLabeler/CMakeFiles/CIPLabeler.dir/rules/Rule1b.cpp.o -cd /build/reproducible-path/rdkit-202503.1/obj-aarch64-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_BUILD_XYZ2MOL_SUPPORT -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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-fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/ShapeHelpers/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 -[ 23%] Building CXX object Code/GraphMol/CIPLabeler/CMakeFiles/CIPLabeler.dir/rules/Rule3.cpp.o -cd /build/reproducible-path/rdkit-202503.1/obj-aarch64-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 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directory '/build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu' -[ 24%] Built target rdPartialCharges +[ 22%] Built target rdPartialCharges +[ 22%] Building CXX object Code/GraphMol/SmilesParse/CMakeFiles/SmilesParse.dir/CanonicalizeStereoGroups.cpp.o +cd /build/reproducible-path/rdkit-202503.1/obj-aarch64-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_BUILD_XYZ2MOL_SUPPORT -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 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-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%] Linking CXX shared library ../../../lib/libRDKitSmilesParse.so -cd /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/SmilesParse && /usr/bin/cmake -E cmake_link_script CMakeFiles/SmilesParse.dir/link.txt --verbose=1 -[ 24%] Building CXX object Code/GraphMol/CIPLabeler/CMakeFiles/CIPLabeler.dir/rules/Rule6.cpp.o -cd /build/reproducible-path/rdkit-202503.1/obj-aarch64-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_BUILD_XYZ2MOL_SUPPORT -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 -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/CIPLabeler/CMakeFiles/CIPLabeler.dir/rules/Rule6.cpp.o -MF CMakeFiles/CIPLabeler.dir/rules/Rule6.cpp.o.d -o CMakeFiles/CIPLabeler.dir/rules/Rule6.cpp.o -c 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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/aarch64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl -cd /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/SmilesParse && /usr/bin/cmake -E cmake_symlink_library ../../../lib/libRDKitSmilesParse.so.1.2025.03.1 ../../../lib/libRDKitSmilesParse.so.1 ../../../lib/libRDKitSmilesParse.so +[ 23%] Building CXX object Code/GraphMol/Wrap/CMakeFiles/rdtrajectory.dir/Trajectory.cpp.o +cd /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/Wrap && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB 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-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 -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/SmilesParse/CMakeFiles/SmilesParse.dir/smiles.tab.cpp.o -MF CMakeFiles/SmilesParse.dir/smiles.tab.cpp.o.d -o CMakeFiles/SmilesParse.dir/smiles.tab.cpp.o -c /build/reproducible-path/rdkit-202503.1/Code/GraphMol/SmilesParse/smiles.tab.cpp +[ 24%] Linking CXX shared module ../../../../rdkit/Chem/rdMolTransforms.so +cd 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../../../../lib/libRDKitDataStructs.so.1.2025.03.1 ../../../../lib/libRDKitEigenSolvers.so.1.2025.03.1 /usr/lib/aarch64-linux-gnu/libboost_numpy313.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_python313.so.1.83.0 ../../../../lib/libRDKitRDGeneral.so.1.2025.03.1 /usr/lib/aarch64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl +make[4]: Leaving directory '/build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu' +[ 24%] Built target rdMolTransforms make -f Code/Numerics/Optimizer/CMakeFiles/testOptimizer.dir/build.make Code/Numerics/Optimizer/CMakeFiles/testOptimizer.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu' cd /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202503.1 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-cd /build/reproducible-path/rdkit-202503.1/obj-aarch64-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_BUILD_XYZ2MOL_SUPPORT -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 -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 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24%] Building CXX object Code/GraphMol/CIPLabeler/CMakeFiles/CIPLabeler.dir/rules/Rule3.cpp.o +cd /build/reproducible-path/rdkit-202503.1/obj-aarch64-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_BUILD_XYZ2MOL_SUPPORT -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 -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 -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/SmilesParse/CMakeFiles/SmilesParse.dir/lex.yysmarts.cpp.o -MF CMakeFiles/SmilesParse.dir/lex.yysmarts.cpp.o.d -o CMakeFiles/SmilesParse.dir/lex.yysmarts.cpp.o -c /build/reproducible-path/rdkit-202503.1/Code/GraphMol/SmilesParse/lex.yysmarts.cpp +[ 25%] Linking CXX executable testOptimizer +cd /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/Numerics/Optimizer && /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 -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/CIPLabeler/CMakeFiles/CIPLabeler.dir/rules/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 +[ 25%] Linking CXX shared module ../../../../rdkit/Chem/rdMolCatalog.so +cd /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/MolCatalog/Wrap && /usr/bin/cmake -E cmake_link_script CMakeFiles/rdMolCatalog.dir/link.txt --verbose=1 +[ 25%] Linking 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/build/reproducible-path/rdkit-202503.1/Code/ForceField/MMFF/OopBend.cpp +[ 28%] Linking CXX shared module ../../../../rdkit/Chem/rdSLNParse.so +cd /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/SLNParse/Wrap && /usr/bin/cmake -E cmake_link_script CMakeFiles/rdSLNParse.dir/link.txt --verbose=1 make -f Code/GraphMol/CMakeFiles/graphmolcpTest.dir/build.make Code/GraphMol/CMakeFiles/graphmolcpTest.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu' cd /build/reproducible-path/rdkit-202503.1/obj-aarch64-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-aarch64-linux-gnu /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol 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CMakeFiles/graphmolIterTest.dir/itertest.cpp.o -c /build/reproducible-path/rdkit-202503.1/Code/GraphMol/itertest.cpp +[ 28%] Building CXX object Code/ForceField/CMakeFiles/ForceField.dir/MMFF/Nonbonded.cpp.o +cd /build/reproducible-path/rdkit-202503.1/obj-aarch64-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_BUILD_XYZ2MOL_SUPPORT -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 -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/ForceField/CMakeFiles/ForceField.dir/MMFF/Nonbonded.cpp.o -MF CMakeFiles/ForceField.dir/MMFF/Nonbonded.cpp.o.d -o CMakeFiles/ForceField.dir/MMFF/Nonbonded.cpp.o -c /build/reproducible-path/rdkit-202503.1/Code/ForceField/MMFF/Nonbonded.cpp +[ 28%] Linking CXX shared library ../../../lib/libRDKitSubstructMatch.so +cd /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/Substruct && /usr/bin/cmake -E cmake_link_script CMakeFiles/SubstructMatch.dir/link.txt --verbose=1 +/build/reproducible-path/rdkit-202503.1/Code/ForceField/MMFF/StretchBend.cpp: In function 'std::pair ForceFields::MMFF::Utils::calcStbnForceConstants(const ForceFields::MMFF::MMFFStbn*)': +/build/reproducible-path/rdkit-202503.1/Code/ForceField/MMFF/StretchBend.cpp:23:35: note: parameter passing for argument of type 'std::pair' when C++17 is enabled changed to match C++14 in GCC 10.1 + 23 | const MMFFStbn *mmffStbnParams) { + | ^ +/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 -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,--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/aarch64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl +cd /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/Substruct && /usr/bin/cmake -E cmake_symlink_library ../../../lib/libRDKitSubstructMatch.so.1.2025.03.1 ../../../lib/libRDKitSubstructMatch.so.1 ../../../lib/libRDKitSubstructMatch.so +make[4]: Leaving directory '/build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu' +[ 28%] Built target SubstructMatch make -f Code/GraphMol/CMakeFiles/graphmolMemTest1.dir/build.make Code/GraphMol/CMakeFiles/graphmolMemTest1.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu' cd /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu && 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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 -[ 24%] Linking CXX shared library ../../../lib/libRDKitShapeHelpers.so -cd /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/ShapeHelpers && /usr/bin/cmake -E cmake_link_script CMakeFiles/ShapeHelpers.dir/link.txt --verbose=1 -/usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,--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 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/usr/lib/aarch64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl -make[4]: Leaving directory '/build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu' -[ 27%] Built target graphmolcpTest -[ 27%] Building CXX object Code/GraphMol/FilterCatalog/CMakeFiles/FilterCatalog.dir/FilterCatalog.cpp.o -cd /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FilterCatalog && /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 -DFilterCatalog_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_FILTERCATALOG_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_BUILD_XYZ2MOL_SUPPORT -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 -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/FilterCatalog/CMakeFiles/FilterCatalog.dir/FilterCatalog.cpp.o -MF CMakeFiles/FilterCatalog.dir/FilterCatalog.cpp.o.d -o CMakeFiles/FilterCatalog.dir/FilterCatalog.cpp.o -c /build/reproducible-path/rdkit-202503.1/Code/GraphMol/FilterCatalog/FilterCatalog.cpp -[ 27%] Linking CXX shared module ../../../../rdkit/Chem/rdMolInterchange.so -cd /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/MolInterchange/Wrap && /usr/bin/cmake -E cmake_link_script 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/usr/lib/aarch64-linux-gnu/libboost_python313.so.1.83.0 ../../../../lib/libRDKitRDGeneral.so.1.2025.03.1 /usr/lib/aarch64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl -make[4]: Leaving directory '/build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu' -[ 27%] Built target rdMolInterchange 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-aarch64-linux-gnu' cd /build/reproducible-path/rdkit-202503.1/obj-aarch64-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-aarch64-linux-gnu /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/SmilesParse 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Code/ForceField/CMakeFiles/ForceField.dir/PositionConstraint.cpp.o -cd /build/reproducible-path/rdkit-202503.1/obj-aarch64-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_BUILD_XYZ2MOL_SUPPORT -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 -mbranch-protection=standard -Wdate-time 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CMakeFiles/FilterCatalog.dir/FilterCatalog.cpp.o.d -o CMakeFiles/FilterCatalog.dir/FilterCatalog.cpp.o -c /build/reproducible-path/rdkit-202503.1/Code/GraphMol/FilterCatalog/FilterCatalog.cpp +[ 28%] Linking CXX executable smiTest2 +cd /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/SmilesParse && /usr/bin/cmake -E cmake_link_script CMakeFiles/smiTest2.dir/link.txt --verbose=1 +/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/smiTest2.dir/link.d CMakeFiles/smiTest2.dir/test2.cpp.o -o smiTest2 ../../../lib/libRDKitSmilesParse.so.1.2025.03.1 ../../../lib/libRDKitGraphMol.so.1.2025.03.1 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/build/reproducible-path/rdkit-202503.1/Code/GraphMol/Fingerprints/RDKitFPGenerator.cpp -/build/reproducible-path/rdkit-202503.1/Code/ForceField/MMFF/StretchBend.cpp: In function 'std::pair ForceFields::MMFF::Utils::calcStbnForceConstants(const ForceFields::MMFF::MMFFStbn*)': -/build/reproducible-path/rdkit-202503.1/Code/ForceField/MMFF/StretchBend.cpp:23:35: note: parameter passing for argument of type 'std::pair' when C++17 is enabled changed to match C++14 in GCC 10.1 - 23 | const MMFFStbn *mmffStbnParams) { - | ^ -[ 32%] Building CXX object Code/ForceField/CMakeFiles/ForceField.dir/MMFF/TorsionAngle.cpp.o -cd /build/reproducible-path/rdkit-202503.1/obj-aarch64-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 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Code/GraphMol/FragCatalog/CMakeFiles/FragCatalog.dir/FragCatParams.cpp.o +cd /build/reproducible-path/rdkit-202503.1/obj-aarch64-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 -DRDKIT_FRAGCATALOG_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_BUILD_XYZ2MOL_SUPPORT -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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object Code/GraphMol/MolChemicalFeatures/CMakeFiles/MolChemicalFeatures.dir/MolChemicalFeatureFactory.cpp.o +[ 33%] Linking CXX shared library ../../../lib/libRDKitFilterCatalog.so +cd /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FilterCatalog && /usr/bin/cmake -E cmake_link_script CMakeFiles/FilterCatalog.dir/link.txt --verbose=1 +/usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,--dependency-file=CMakeFiles/FilterCatalog.dir/link.d -Wl,-z,relro -Wl,-z,now -shared -Wl,-soname,libRDKitFilterCatalog.so.1 -o ../../../lib/libRDKitFilterCatalog.so.1.2025.03.1 CMakeFiles/FilterCatalog.dir/Filters.cpp.o CMakeFiles/FilterCatalog.dir/FilterCatalog.cpp.o 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/build/reproducible-path/rdkit-202503.1/Code/GraphMol/Fingerprints/FingerprintUtil.cpp +[ 33%] Building CXX object Code/GraphMol/MolChemicalFeatures/CMakeFiles/MolChemicalFeatures.dir/MolChemicalFeatureFactory.cpp.o cd /build/reproducible-path/rdkit-202503.1/obj-aarch64-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_BUILD_XYZ2MOL_SUPPORT -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202503.1/External -I/build/reproducible-path/rdkit-202503.1/Code -isystem /usr/include/eigen3 -g -O2 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/build/reproducible-path/rdkit-202503.1/Code/GraphMol/ReducedGraphs/ReducedGraphs.cpp +[ 33%] Building CXX object Code/GraphMol/MolChemicalFeatures/CMakeFiles/MolChemicalFeatures.dir/FeatureParser.cpp.o +cd /build/reproducible-path/rdkit-202503.1/obj-aarch64-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_BUILD_XYZ2MOL_SUPPORT -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 -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/MolChemicalFeatures/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 +[ 34%] Linking CXX executable smaTest1 +cd /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/SmilesParse && /usr/bin/cmake -E cmake_link_script CMakeFiles/smaTest1.dir/link.txt --verbose=1 make -f Code/GraphMol/SLNParse/CMakeFiles/testSLNParse.dir/build.make Code/GraphMol/SLNParse/CMakeFiles/testSLNParse.dir/depend make[4]: 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-c /build/reproducible-path/rdkit-202503.1/Code/GraphMol/SLNParse/test.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 -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now -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/aarch64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl +make[4]: Leaving directory '/build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu' +[ 34%] Built target smaTest1 make -f Code/GraphMol/Abbreviations/CMakeFiles/Abbreviations.dir/build.make Code/GraphMol/Abbreviations/CMakeFiles/Abbreviations.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu' cd /build/reproducible-path/rdkit-202503.1/obj-aarch64-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 /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/Abbreviations /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/Abbreviations/CMakeFiles/Abbreviations.dir/DependInfo.cmake "--color=" @@ -3918,48 +3971,43 @@ cd 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Code/GraphMol/ForceFieldHelpers/CMakeFiles/ForceFieldHelpers.dir/UFF/AtomTyper.cpp.o -MF CMakeFiles/ForceFieldHelpers.dir/UFF/AtomTyper.cpp.o.d -o CMakeFiles/ForceFieldHelpers.dir/UFF/AtomTyper.cpp.o -c /build/reproducible-path/rdkit-202503.1/Code/GraphMol/ForceFieldHelpers/UFF/AtomTyper.cpp -[ 34%] Linking CXX shared library ../../../lib/libRDKitReducedGraphs.so -cd /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/ReducedGraphs && /usr/bin/cmake -E cmake_link_script CMakeFiles/ReducedGraphs.dir/link.txt --verbose=1 [ 34%] Building CXX object Code/GraphMol/FilterCatalog/Wrap/CMakeFiles/rdfiltercatalog.dir/FilterCatalog.cpp.o cd /build/reproducible-path/rdkit-202503.1/obj-aarch64-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_BUILD_XYZ2MOL_SUPPORT -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/aarch64-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 -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/FilterCatalog/Wrap/CMakeFiles/rdfiltercatalog.dir/FilterCatalog.cpp.o -MF CMakeFiles/rdfiltercatalog.dir/FilterCatalog.cpp.o.d -o CMakeFiles/rdfiltercatalog.dir/FilterCatalog.cpp.o -c /build/reproducible-path/rdkit-202503.1/Code/GraphMol/FilterCatalog/Wrap/FilterCatalog.cpp +[ 34%] Linking CXX shared library ../../../lib/libRDKitReducedGraphs.so +cd /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/ReducedGraphs && /usr/bin/cmake -E cmake_link_script CMakeFiles/ReducedGraphs.dir/link.txt --verbose=1 /usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,--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/aarch64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl cd /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/ReducedGraphs && /usr/bin/cmake -E cmake_symlink_library ../../../lib/libRDKitReducedGraphs.so.1.2025.03.1 ../../../lib/libRDKitReducedGraphs.so.1 ../../../lib/libRDKitReducedGraphs.so make[4]: Leaving directory '/build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu' -[ 34%] Linking CXX executable moliteratorTestsCatch -cd /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol && /usr/bin/cmake -E cmake_link_script CMakeFiles/moliteratorTestsCatch.dir/link.txt --verbose=1 [ 34%] Built target ReducedGraphs +[ 35%] Building CXX object Code/GraphMol/ForceFieldHelpers/CMakeFiles/ForceFieldHelpers.dir/UFF/Builder.cpp.o +cd /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/ForceFieldHelpers && /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 -DForceFieldHelpers_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_FORCEFIELDHELPERS_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_BUILD_XYZ2MOL_SUPPORT -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED 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make[4]: Entering directory '/build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu' cd /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202503.1 /build/reproducible-path/rdkit-202503.1/Code/GraphMol/ReducedGraphs /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/ReducedGraphs /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/ReducedGraphs/CMakeFiles/testReducedGraphs.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu' make -f Code/GraphMol/ReducedGraphs/CMakeFiles/testReducedGraphs.dir/build.make Code/GraphMol/ReducedGraphs/CMakeFiles/testReducedGraphs.dir/build make[4]: Entering directory '/build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu' -[ 34%] Building CXX object 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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 -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 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Code/GraphMol/ForceFieldHelpers/CMakeFiles/ForceFieldHelpers.dir/MMFF/AtomTyper.cpp.o +cd /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/ForceFieldHelpers && /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 -DForceFieldHelpers_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_FORCEFIELDHELPERS_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_BUILD_XYZ2MOL_SUPPORT -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 -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/ForceFieldHelpers/CMakeFiles/ForceFieldHelpers.dir/MMFF/AtomTyper.cpp.o -MF CMakeFiles/ForceFieldHelpers.dir/MMFF/AtomTyper.cpp.o.d -o CMakeFiles/ForceFieldHelpers.dir/MMFF/AtomTyper.cpp.o -c /build/reproducible-path/rdkit-202503.1/Code/GraphMol/ForceFieldHelpers/MMFF/AtomTyper.cpp make -f Code/GraphMol/ReducedGraphs/Wrap/CMakeFiles/rdReducedGraphs.dir/build.make Code/GraphMol/ReducedGraphs/Wrap/CMakeFiles/rdReducedGraphs.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu' cd /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202503.1 /build/reproducible-path/rdkit-202503.1/Code/GraphMol/ReducedGraphs/Wrap 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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/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 -[ 35%] Building CXX object Code/GraphMol/ForceFieldHelpers/CMakeFiles/ForceFieldHelpers.dir/UFF/Builder.cpp.o -cd /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/ForceFieldHelpers && /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 -DForceFieldHelpers_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_FORCEFIELDHELPERS_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D 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'/build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu' [ 35%] Built target Abbreviations +[ 35%] Building CXX object Code/GraphMol/ForceFieldHelpers/CMakeFiles/ForceFieldHelpers.dir/MMFF/Builder.cpp.o +cd /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/ForceFieldHelpers && /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 -DForceFieldHelpers_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_FORCEFIELDHELPERS_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_BUILD_XYZ2MOL_SUPPORT -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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-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/aarch64-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 -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/Abbreviations/Wrap/CMakeFiles/rdAbbreviations.dir/rdAbbreviations.cpp.o -MF CMakeFiles/rdAbbreviations.dir/rdAbbreviations.cpp.o.d -o CMakeFiles/rdAbbreviations.dir/rdAbbreviations.cpp.o -c /build/reproducible-path/rdkit-202503.1/Code/GraphMol/Abbreviations/Wrap/rdAbbreviations.cpp -/usr/bin/c++ -fPIC -g -O2 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../../../lib/libRDKitRDGeometryLib.so.1.2025.03.1 ../../../lib/libRDKitDataStructs.so.1.2025.03.1 ../../../lib/libRDKitRDGeneral.so.1.2025.03.1 /usr/lib/aarch64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl -cd /build/reproducible-path/rdkit-202503.1/obj-aarch64-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 +[ 35%] Linking CXX shared library ../../../lib/libRDKitMolAlign.so +cd /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/MolAlign && /usr/bin/cmake -E cmake_link_script CMakeFiles/MolAlign.dir/link.txt --verbose=1 +/usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat 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/usr/lib/aarch64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl +cd /build/reproducible-path/rdkit-202503.1/obj-aarch64-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-aarch64-linux-gnu' -[ 35%] Built target MolChemicalFeatures +[ 35%] Built target MolAlign +[ 35%] Building CXX object Code/GraphMol/ForceFieldHelpers/CMakeFiles/ForceFieldHelpers.dir/CrystalFF/TorsionPreferences.cpp.o +cd /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/ForceFieldHelpers && /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 -DForceFieldHelpers_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_FORCEFIELDHELPERS_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_BUILD_XYZ2MOL_SUPPORT -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 -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/ForceFieldHelpers/CMakeFiles/ForceFieldHelpers.dir/CrystalFF/TorsionPreferences.cpp.o -MF CMakeFiles/ForceFieldHelpers.dir/CrystalFF/TorsionPreferences.cpp.o.d -o CMakeFiles/ForceFieldHelpers.dir/CrystalFF/TorsionPreferences.cpp.o -c /build/reproducible-path/rdkit-202503.1/Code/GraphMol/ForceFieldHelpers/CrystalFF/TorsionPreferences.cpp +[ 35%] Linking CXX executable testReducedGraphs +cd /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/ReducedGraphs && /usr/bin/cmake -E cmake_link_script CMakeFiles/testReducedGraphs.dir/link.txt --verbose=1 +/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/testReducedGraphs.dir/link.d CMakeFiles/testReducedGraphs.dir/test1.cpp.o -o testReducedGraphs ../../../lib/libRDKitReducedGraphs.so.1.2025.03.1 ../../../lib/libRDKitSubstructMatch.so.1.2025.03.1 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Code/GraphMol/MolChemicalFeatures/Wrap/CMakeFiles/rdMolChemicalFeatures.dir/rdMolChemicalFeatures.cpp.o -MF CMakeFiles/rdMolChemicalFeatures.dir/rdMolChemicalFeatures.cpp.o.d -o CMakeFiles/rdMolChemicalFeatures.dir/rdMolChemicalFeatures.cpp.o -c /build/reproducible-path/rdkit-202503.1/Code/GraphMol/MolChemicalFeatures/Wrap/rdMolChemicalFeatures.cpp -[ 35%] Building CXX object Code/GraphMol/ForceFieldHelpers/CMakeFiles/ForceFieldHelpers.dir/MMFF/AtomTyper.cpp.o -cd /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/ForceFieldHelpers && /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 -DForceFieldHelpers_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_FORCEFIELDHELPERS_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_BUILD_XYZ2MOL_SUPPORT -DRDK_HAS_EIGEN3 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../../../lib/libRDKitDataStructs.so.1.2025.03.1 ../../../lib/libRDKitRDGeneral.so.1.2025.03.1 /usr/lib/aarch64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl -make[4]: Leaving directory '/build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu' -[ 35%] Built target testReducedGraphs -[ 35%] Building CXX object Code/GraphMol/ForceFieldHelpers/CMakeFiles/ForceFieldHelpers.dir/MMFF/Builder.cpp.o -cd /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/ForceFieldHelpers && /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 -DForceFieldHelpers_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_FORCEFIELDHELPERS_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS 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/build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/MolAlign && /usr/bin/cmake -E cmake_link_script CMakeFiles/MolAlign.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 -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,--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/aarch64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl -cd /build/reproducible-path/rdkit-202503.1/obj-aarch64-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-aarch64-linux-gnu' -[ 35%] Built target MolAlign -[ 35%] Building CXX object Code/GraphMol/MolChemicalFeatures/Wrap/CMakeFiles/rdMolChemicalFeatures.dir/MolChemicalFeature.cpp.o -cd 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Code/GraphMol/MolChemicalFeatures/Wrap/CMakeFiles/rdMolChemicalFeatures.dir/MolChemicalFeatureFactory.cpp.o -MF CMakeFiles/rdMolChemicalFeatures.dir/MolChemicalFeatureFactory.cpp.o.d -o CMakeFiles/rdMolChemicalFeatures.dir/MolChemicalFeatureFactory.cpp.o -c /build/reproducible-path/rdkit-202503.1/Code/GraphMol/MolChemicalFeatures/Wrap/MolChemicalFeatureFactory.cpp [ 36%] Linking CXX executable graphmolqueryTest cd /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol && /usr/bin/cmake -E cmake_link_script CMakeFiles/graphmolqueryTest.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now 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-ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/ForceFieldHelpers/CMakeFiles/ForceFieldHelpers.dir/CrystalFF/TorsionAngleContribs.cpp.o -MF CMakeFiles/ForceFieldHelpers.dir/CrystalFF/TorsionAngleContribs.cpp.o.d -o CMakeFiles/ForceFieldHelpers.dir/CrystalFF/TorsionAngleContribs.cpp.o -c /build/reproducible-path/rdkit-202503.1/Code/GraphMol/ForceFieldHelpers/CrystalFF/TorsionAngleContribs.cpp [ 36%] Linking CXX shared module ../../../../rdkit/Chem/rdAbbreviations.so cd /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/Abbreviations/Wrap && /usr/bin/cmake -E cmake_link_script CMakeFiles/rdAbbreviations.dir/link.txt --verbose=1 -[ 36%] Building CXX object 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../../../../lib/libRDKitRDGeneral.so.1.2025.03.1 /usr/lib/aarch64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl make[4]: Leaving directory '/build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu' [ 36%] Built target rdAbbreviations -[ 36%] Linking CXX shared module ../../../../rdkit/Chem/rdFingerprintGenerator.so -cd /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/Fingerprints/Wrap && /usr/bin/cmake -E cmake_link_script CMakeFiles/rdFingerprintGenerator.dir/link.txt --verbose=1 -/usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -shared -Wl,-O1 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/usr/lib/aarch64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl -make[4]: Leaving directory '/build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu' -[ 36%] Built target rdFingerprintGenerator -[ 36%] Linking CXX shared module ../../../../rdkit/Chem/rdMolChemicalFeatures.so -cd /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/MolChemicalFeatures/Wrap && /usr/bin/cmake -E cmake_link_script CMakeFiles/rdMolChemicalFeatures.dir/link.txt --verbose=1 -/usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -g -fwrapv -O2 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/usr/lib/aarch64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl -make[4]: Leaving directory '/build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu' -[ 36%] Built target rdMolChemicalFeatures -[ 36%] Linking CXX shared library ../../../lib/libRDKitForceFieldHelpers.so -cd /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/ForceFieldHelpers && /usr/bin/cmake -E cmake_link_script CMakeFiles/ForceFieldHelpers.dir/link.txt --verbose=1 -/usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,--dependency-file=CMakeFiles/ForceFieldHelpers.dir/link.d -Wl,-z,relro 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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 -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/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-aarch64-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 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/build/reproducible-path/rdkit-202503.1/Code/DistGeom/DistGeomUtils.cpp +[ 37%] Building CXX object Code/DistGeom/CMakeFiles/DistGeometry.dir/DistViolationContribs.cpp.o +cd /build/reproducible-path/rdkit-202503.1/obj-aarch64-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_BUILD_XYZ2MOL_SUPPORT -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 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../../../../lib/libRDKitRDGeneral.so.1.2025.03.1 /usr/lib/aarch64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl +make[4]: Leaving directory '/build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu' +[ 37%] Built target rdMHFPFingerprint [ 37%] Building CXX object Code/DistGeom/CMakeFiles/DistGeometry.dir/ChiralViolationContribs.cpp.o cd /build/reproducible-path/rdkit-202503.1/obj-aarch64-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_BUILD_XYZ2MOL_SUPPORT -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS 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/build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/DistGeom && /usr/bin/cmake -E cmake_symlink_library ../../lib/libRDKitDistGeometry.so.1.2025.03.1 ../../lib/libRDKitDistGeometry.so.1 ../../lib/libRDKitDistGeometry.so +make[4]: Leaving directory '/build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu' +[ 37%] Built target DistGeometry +make -f Code/GraphMol/DistGeomHelpers/CMakeFiles/DistGeomHelpers.dir/build.make Code/GraphMol/DistGeomHelpers/CMakeFiles/DistGeomHelpers.dir/depend +make -f Code/DistGeom/CMakeFiles/testDistGeom.dir/build.make Code/DistGeom/CMakeFiles/testDistGeom.dir/depend +make -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-aarch64-linux-gnu' +cd /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202503.1 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/usr/lib/aarch64-linux-gnu/libcoordgen.so ../../../lib/libRDKitMolAlign.so.1.2025.03.1 ../../../lib/libRDKitSmilesParse.so.1.2025.03.1 ../../../lib/libRDKitSubstructMatch.so.1.2025.03.1 ../../../lib/libRDKitGenericGroups.so.1.2025.03.1 ../../../lib/libRDKitMolTransforms.so.1.2025.03.1 ../../../lib/libRDKitEigenSolvers.so.1.2025.03.1 ../../../lib/libRDKitGraphMol.so.1.2025.03.1 ../../../lib/libRDKitAlignment.so.1.2025.03.1 ../../../lib/libRDKitRDGeometryLib.so.1.2025.03.1 ../../../lib/libRDKitDataStructs.so.1.2025.03.1 ../../../lib/libRDKitRDGeneral.so.1.2025.03.1 /usr/lib/aarch64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl @@ -4214,95 +4284,49 @@ [ 37%] Built target Depictor make -f External/INCHI-API/CMakeFiles/RDInchiLib.dir/build.make External/INCHI-API/CMakeFiles/RDInchiLib.dir/depend make -f Code/GraphMol/ChemTransforms/CMakeFiles/ChemTransforms.dir/build.make 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[ 39%] Linking CXX shared library ../../../lib/libRDKitMolInteractionFields.so cd /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/MolInteractionFields && /usr/bin/cmake -E cmake_link_script CMakeFiles/MolInteractionFields.dir/link.txt --verbose=1 -[ 39%] Linking CXX shared module ../../../../rdkit/Chem/rdForceFieldHelpers.so -cd /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/ForceFieldHelpers/Wrap && /usr/bin/cmake -E cmake_link_script CMakeFiles/rdForceFieldHelpers.dir/link.txt --verbose=1 /usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,--dependency-file=CMakeFiles/MolInteractionFields.dir/link.d -Wl,-z,relro -Wl,-z,now -shared 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cmake_symlink_library ../../../lib/libRDKitMolInteractionFields.so.1.2025.03.1 ../../../lib/libRDKitMolInteractionFields.so.1 ../../../lib/libRDKitMolInteractionFields.so make[4]: Leaving directory '/build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu' [ 39%] Built target MolInteractionFields -[ 39%] Building CXX object Code/GraphMol/DistGeomHelpers/CMakeFiles/DistGeomHelpers.dir/Embedder.cpp.o -cd /build/reproducible-path/rdkit-202503.1/obj-aarch64-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_BUILD_XYZ2MOL_SUPPORT -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS 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/usr/lib/aarch64-linux-gnu/libboost_numpy313.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_python313.so.1.83.0 ../../../../lib/libRDKitRDGeneral.so.1.2025.03.1 /usr/lib/aarch64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl -make[4]: Leaving directory '/build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu' -[ 39%] Built target rdForceFieldHelpers -make -f Code/DistGeom/Wrap/CMakeFiles/DistGeom.dir/build.make Code/DistGeom/Wrap/CMakeFiles/DistGeom.dir/depend +make -f Code/GraphMol/MolHash/CMakeFiles/MolHash.dir/build.make Code/GraphMol/MolHash/CMakeFiles/MolHash.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu' -cd /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202503.1 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-DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_BUILD_XYZ2MOL_SUPPORT -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 -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/MolHash/CMakeFiles/MolHash.dir/hashfunctions.cpp.o -MF CMakeFiles/MolHash.dir/hashfunctions.cpp.o.d -o CMakeFiles/MolHash.dir/hashfunctions.cpp.o -c 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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-aarch64-linux-gnu' cd /build/reproducible-path/rdkit-202503.1/obj-aarch64-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/Wrap /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/MolInteractionFields/Wrap /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/MolInteractionFields/Wrap/CMakeFiles/rdMIF.dir/DependInfo.cmake "--color=" @@ -4311,32 +4335,36 @@ make[4]: Entering directory '/build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu' [ 39%] Building CXX object Code/GraphMol/MolInteractionFields/Wrap/CMakeFiles/rdMIF.dir/rdMIF.cpp.o 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/usr/lib/aarch64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl +make[4]: Leaving directory '/build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu' +[ 39%] Built target rdForceFieldHelpers +[ 39%] Building CXX object Code/GraphMol/ChemTransforms/CMakeFiles/ChemTransforms.dir/MolFragmenter.cpp.o +cd /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/ChemTransforms && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DChemTransforms_EXPORTS -DRDKIT_CHEMTRANSFORMS_BUILD -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_BUILD_XYZ2MOL_SUPPORT -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 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'/build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu' -make -f Code/GraphMol/MolHash/Wrap/CMakeFiles/rdMolHash.dir/build.make Code/GraphMol/MolHash/Wrap/CMakeFiles/rdMolHash.dir/build -make[4]: Entering directory '/build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu' -[ 39%] Building CXX object Code/GraphMol/MolHash/Wrap/CMakeFiles/rdMolHash.dir/rdMolHash.cpp.o -cd /build/reproducible-path/rdkit-202503.1/obj-aarch64-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_BUILD_XYZ2MOL_SUPPORT -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/aarch64-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 -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/MolHash/Wrap/CMakeFiles/rdMolHash.dir/rdMolHash.cpp.o -MF CMakeFiles/rdMolHash.dir/rdMolHash.cpp.o.d -o CMakeFiles/rdMolHash.dir/rdMolHash.cpp.o -c /build/reproducible-path/rdkit-202503.1/Code/GraphMol/MolHash/Wrap/rdMolHash.cpp -[ 39%] Linking CXX executable testDistGeom -cd /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/DistGeom && /usr/bin/cmake -E cmake_link_script CMakeFiles/testDistGeom.dir/link.txt --verbose=1 -/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/testDistGeom.dir/link.d CMakeFiles/testDistGeom.dir/testDistGeom.cpp.o -o testDistGeom ../../lib/libRDKitDistGeometry.so.1.2025.03.1 ../../lib/libRDKitEigenSolvers.so.1.2025.03.1 ../../lib/libRDKitForceFieldHelpers.so.1.2025.03.1 ../../lib/libRDKitForceField.so.1.2025.03.1 ../../lib/libRDKitOptimizer.so.1.2025.03.1 ../../lib/libRDKitTrajectory.so.1.2025.03.1 ../../lib/libRDKitSmilesParse.so.1.2025.03.1 ../../lib/libRDKitSubstructMatch.so.1.2025.03.1 ../../lib/libRDKitGenericGroups.so.1.2025.03.1 ../../lib/libRDKitGraphMol.so.1.2025.03.1 ../../lib/libRDKitRDGeometryLib.so.1.2025.03.1 ../../lib/libRDKitDataStructs.so.1.2025.03.1 ../../lib/libRDKitRDGeneral.so.1.2025.03.1 /usr/lib/aarch64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/aarch64-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 -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,--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/aarch64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl +cd /build/reproducible-path/rdkit-202503.1/obj-aarch64-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 +[ 39%] Built target rdfiltercatalog make[4]: Leaving directory '/build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu' -[ 39%] Built target testDistGeom +[ 39%] Built target DistGeomHelpers [ 39%] Linking CXX shared library ../../lib/libRDKitRDInchiLib.so cd /build/reproducible-path/rdkit-202503.1/obj-aarch64-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 -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,--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/aarch64-linux-gnu/libinchi.so ../../lib/libRDKitDepictor.so.1.2025.03.1 /usr/lib/aarch64-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/aarch64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl @@ -4351,20 +4379,42 @@ make[4]: Entering directory '/build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu' [ 39%] Building CXX object External/INCHI-API/Wrap/CMakeFiles/rdinchi.dir/pyInchi.cpp.o cd /build/reproducible-path/rdkit-202503.1/obj-aarch64-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_BUILD_XYZ2MOL_SUPPORT -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/aarch64-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 -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT 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 +[ 39%] Linking CXX shared library ../../../lib/libRDKitMolHash.so +cd /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/MolHash && /usr/bin/cmake -E cmake_link_script CMakeFiles/MolHash.dir/link.txt --verbose=1 +/usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,--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/aarch64-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/aarch64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl +cd /build/reproducible-path/rdkit-202503.1/obj-aarch64-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-aarch64-linux-gnu' +[ 39%] Built target MolHash +make -f Code/GraphMol/MolHash/Wrap/CMakeFiles/rdMolHash.dir/build.make 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Building CXX object Code/GraphMol/MolHash/Wrap/CMakeFiles/rdMolHash.dir/rdMolHash.cpp.o +cd /build/reproducible-path/rdkit-202503.1/obj-aarch64-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_BUILD_XYZ2MOL_SUPPORT -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/aarch64-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 -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/MolHash/Wrap/CMakeFiles/rdMolHash.dir/rdMolHash.cpp.o -MF CMakeFiles/rdMolHash.dir/rdMolHash.cpp.o.d -o CMakeFiles/rdMolHash.dir/rdMolHash.cpp.o -c /build/reproducible-path/rdkit-202503.1/Code/GraphMol/MolHash/Wrap/rdMolHash.cpp [ 39%] Linking CXX shared module ../../../../rdkit/Chem/rdDepictor.so cd /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/Depictor/Wrap && /usr/bin/cmake -E cmake_link_script CMakeFiles/rdDepictor.dir/link.txt --verbose=1 /usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -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/aarch64-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/aarch64-linux-gnu/libboost_numpy313.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_python313.so.1.83.0 ../../../../lib/libRDKitRDGeneral.so.1.2025.03.1 /usr/lib/aarch64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl make[4]: Leaving directory '/build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu' [ 39%] Built target rdDepictor -[ 39%] Linking CXX shared module ../../../rdkit/DistanceGeometry/DistGeom.so -cd /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/DistGeom/Wrap && /usr/bin/cmake -E cmake_link_script CMakeFiles/DistGeom.dir/link.txt --verbose=1 -/usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security 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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/aarch64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl cd /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/ChemTransforms && /usr/bin/cmake -E cmake_symlink_library ../../../lib/libRDKitChemTransforms.so.1.2025.03.1 ../../../lib/libRDKitChemTransforms.so.1 ../../../lib/libRDKitChemTransforms.so make[4]: Leaving directory '/build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu' @@ -4375,49 +4425,30 @@ make[4]: Leaving directory '/build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu' make -f Code/GraphMol/FileParsers/CMakeFiles/FileParsers.dir/build.make Code/GraphMol/FileParsers/CMakeFiles/FileParsers.dir/build make[4]: Entering directory 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Code/GraphMol/FileParsers/CMakeFiles/FileParsers.dir/CDXMLParser.cpp.o -MF CMakeFiles/FileParsers.dir/CDXMLParser.cpp.o.d -o CMakeFiles/FileParsers.dir/CDXMLParser.cpp.o -c /build/reproducible-path/rdkit-202503.1/Code/GraphMol/FileParsers/CDXMLParser.cpp +cd /build/reproducible-path/rdkit-202503.1/obj-aarch64-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_BUILD_XYZ2MOL_SUPPORT -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 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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 -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/FileParsers/CMakeFiles/FileParsers.dir/MolFileWriter.cpp.o -MF CMakeFiles/FileParsers.dir/MolFileWriter.cpp.o.d -o CMakeFiles/FileParsers.dir/MolFileWriter.cpp.o -c /build/reproducible-path/rdkit-202503.1/Code/GraphMol/FileParsers/MolFileWriter.cpp +cd /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK 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CMakeFiles/FileParsers.dir/SDMolSupplier.cpp.o -c /build/reproducible-path/rdkit-202503.1/Code/GraphMol/FileParsers/SDMolSupplier.cpp cd /build/reproducible-path/rdkit-202503.1/obj-aarch64-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_BUILD_XYZ2MOL_SUPPORT -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 -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/FileParsers/CMakeFiles/FileParsers.dir/SDWriter.cpp.o -MF CMakeFiles/FileParsers.dir/SDWriter.cpp.o.d -o CMakeFiles/FileParsers.dir/SDWriter.cpp.o -c /build/reproducible-path/rdkit-202503.1/Code/GraphMol/FileParsers/SDWriter.cpp -[ 40%] Linking CXX shared module ../../../rdkit/Chem/rdinchi.so -cd /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/External/INCHI-API/Wrap && /usr/bin/cmake -E cmake_link_script CMakeFiles/rdinchi.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 -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated 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/usr/lib/aarch64-linux-gnu/libboost_numpy313.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_python313.so.1.83.0 ../../../lib/libRDKitRDGeneral.so.1.2025.03.1 /usr/lib/aarch64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl -make[4]: Leaving directory '/build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu' -[ 40%] Built target rdinchi [ 40%] Building CXX object Code/GraphMol/FileParsers/CMakeFiles/FileParsers.dir/SmilesMolSupplier.cpp.o -cd /build/reproducible-path/rdkit-202503.1/obj-aarch64-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 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../../../../rdkit/Chem/rdMIF.so -cd /build/reproducible-path/rdkit-202503.1/obj-aarch64-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 -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -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 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/build/reproducible-path/rdkit-202503.1/obj-aarch64-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_BUILD_XYZ2MOL_SUPPORT -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 -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/FileParsers/CMakeFiles/FileParsers.dir/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 [ 40%] Building CXX object Code/GraphMol/FileParsers/CMakeFiles/FileParsers.dir/TDTWriter.cpp.o @@ -4465,99 +4496,99 @@ make -f External/CoordGen/CMakeFiles/testCoordGen.dir/build.make External/CoordGen/CMakeFiles/testCoordGen.dir/depend make -f Code/ForceField/UFF/CMakeFiles/testUFFForceField.dir/build.make Code/ForceField/UFF/CMakeFiles/testUFFForceField.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu' -make[4]: Entering directory '/build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu' -make -f 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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-aarch64-linux-gnu /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/CMakeFiles/testSGroup.dir/DependInfo.cmake "--color=" -make -f Code/ForceField/UFF/CMakeFiles/testUFFForceField.dir/build.make Code/ForceField/UFF/CMakeFiles/testUFFForceField.dir/build +make -f Code/GraphMol/CMakeFiles/test-valgrind.dir/build.make Code/GraphMol/CMakeFiles/test-valgrind.dir/depend +make[4]: Entering directory '/build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu' +cd /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202503.1 /build/reproducible-path/rdkit-202503.1/Code/GraphMol 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/build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol && /usr/bin/cmake -E cmake_link_script CMakeFiles/test-valgrind.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/test-valgrind.dir/link.d "CMakeFiles/test-valgrind.dir/test-valgrind.cpp.o" -o test-valgrind ../../lib/libRDKitFileParsers.so.1.2025.03.1 ../../lib/libRDKitChemTransforms.so.1.2025.03.1 ../../lib/libRDKitDepictor.so.1.2025.03.1 /usr/lib/aarch64-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/aarch64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl /usr/lib/aarch64-linux-gnu/libmaeparser.so @@ -4584,11 +4615,13 @@ make[4]: Entering directory '/build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu' [ 45%] Building CXX object Code/GraphMol/CMakeFiles/graphmolOrganometallicsCatch.dir/catch_organometallics.cpp.o cd /build/reproducible-path/rdkit-202503.1/obj-aarch64-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_BUILD_XYZ2MOL_SUPPORT -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 -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/GraphMol/CMakeFiles/graphmolOrganometallicsCatch.dir/catch_organometallics.cpp.o -MF CMakeFiles/graphmolOrganometallicsCatch.dir/catch_organometallics.cpp.o.d -o CMakeFiles/graphmolOrganometallicsCatch.dir/catch_organometallics.cpp.o -c /build/reproducible-path/rdkit-202503.1/Code/GraphMol/catch_organometallics.cpp +[ 45%] Linking CXX executable graphmoltestPicklerGlobalSetting +cd /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol && /usr/bin/cmake -E cmake_link_script CMakeFiles/graphmoltestPicklerGlobalSetting.dir/link.txt --verbose=1 [ 45%] Linking CXX executable resMolSupplierTest cd /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol && /usr/bin/cmake -E cmake_link_script CMakeFiles/resMolSupplierTest.dir/link.txt --verbose=1 -/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/resMolSupplierTest.dir/link.d CMakeFiles/resMolSupplierTest.dir/resMolSupplierTest.cpp.o -o resMolSupplierTest ../../lib/libRDKitFileParsers.so.1.2025.03.1 ../../lib/libRDKitChemTransforms.so.1.2025.03.1 ../../lib/libRDKitDepictor.so.1.2025.03.1 /usr/lib/aarch64-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/aarch64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl /usr/lib/aarch64-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 -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/graphmoltestPicklerGlobalSetting.dir/link.d 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/aarch64-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/aarch64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl /usr/lib/aarch64-linux-gnu/libmaeparser.so make[4]: Leaving directory '/build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu' -[ 45%] Built target resMolSupplierTest +[ 45%] Built target graphmoltestPicklerGlobalSetting make -f Code/GraphMol/CMakeFiles/graphmolSGroupCatch.dir/build.make Code/GraphMol/CMakeFiles/graphmolSGroupCatch.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu' cd /build/reproducible-path/rdkit-202503.1/obj-aarch64-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-aarch64-linux-gnu /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/CMakeFiles/graphmolSGroupCatch.dir/DependInfo.cmake "--color=" @@ -4597,11 +4630,9 @@ make[4]: Entering directory '/build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu' [ 45%] Building CXX object Code/GraphMol/CMakeFiles/graphmolSGroupCatch.dir/catch_sgroups.cpp.o cd /build/reproducible-path/rdkit-202503.1/obj-aarch64-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_BUILD_XYZ2MOL_SUPPORT -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 -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/GraphMol/CMakeFiles/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 -[ 45%] Linking CXX executable testUFFForceField -cd /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/ForceField/UFF && /usr/bin/cmake -E cmake_link_script CMakeFiles/testUFFForceField.dir/link.txt --verbose=1 -/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now -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/aarch64-linux-gnu/libcoordgen.so ../../../lib/libRDKitMolAlign.so.1.2025.03.1 ../../../lib/libRDKitSmilesParse.so.1.2025.03.1 ../../../lib/libRDKitSubstructMatch.so.1.2025.03.1 ../../../lib/libRDKitGenericGroups.so.1.2025.03.1 ../../../lib/libRDKitMolTransforms.so.1.2025.03.1 ../../../lib/libRDKitEigenSolvers.so.1.2025.03.1 ../../../lib/libRDKitGraphMol.so.1.2025.03.1 ../../../lib/libRDKitAlignment.so.1.2025.03.1 ../../../lib/libRDKitRDGeometryLib.so.1.2025.03.1 ../../../lib/libRDKitDataStructs.so.1.2025.03.1 ../../../lib/libRDKitRDGeneral.so.1.2025.03.1 /usr/lib/aarch64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl /usr/lib/aarch64-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 -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/resMolSupplierTest.dir/link.d CMakeFiles/resMolSupplierTest.dir/resMolSupplierTest.cpp.o -o resMolSupplierTest ../../lib/libRDKitFileParsers.so.1.2025.03.1 ../../lib/libRDKitChemTransforms.so.1.2025.03.1 ../../lib/libRDKitDepictor.so.1.2025.03.1 /usr/lib/aarch64-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/aarch64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl /usr/lib/aarch64-linux-gnu/libmaeparser.so make[4]: Leaving directory '/build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu' -[ 45%] Built target testUFFForceField +[ 45%] Built target resMolSupplierTest make -f Code/GraphMol/CMakeFiles/graphmolAdjustQueryCatch.dir/build.make Code/GraphMol/CMakeFiles/graphmolAdjustQueryCatch.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu' cd /build/reproducible-path/rdkit-202503.1/obj-aarch64-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-aarch64-linux-gnu /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/CMakeFiles/graphmolAdjustQueryCatch.dir/DependInfo.cmake "--color=" @@ -4610,13 +4641,11 @@ make[4]: Entering directory '/build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu' [ 45%] Building CXX object Code/GraphMol/CMakeFiles/graphmolAdjustQueryCatch.dir/catch_adjustquery.cpp.o cd /build/reproducible-path/rdkit-202503.1/obj-aarch64-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_BUILD_XYZ2MOL_SUPPORT -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 -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/GraphMol/CMakeFiles/graphmolAdjustQueryCatch.dir/catch_adjustquery.cpp.o -MF CMakeFiles/graphmolAdjustQueryCatch.dir/catch_adjustquery.cpp.o.d -o CMakeFiles/graphmolAdjustQueryCatch.dir/catch_adjustquery.cpp.o -c /build/reproducible-path/rdkit-202503.1/Code/GraphMol/catch_adjustquery.cpp -[ 45%] Linking CXX executable hanoiTest -cd /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol && /usr/bin/cmake -E cmake_link_script CMakeFiles/hanoiTest.dir/link.txt --verbose=1 -[ 45%] Linking CXX executable graphmoltestPicklerGlobalSetting -cd /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol && /usr/bin/cmake -E cmake_link_script CMakeFiles/graphmoltestPicklerGlobalSetting.dir/link.txt --verbose=1 -/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/hanoiTest.dir/link.d CMakeFiles/hanoiTest.dir/hanoitest.cpp.o -o hanoiTest ../../lib/libRDKitFileParsers.so.1.2025.03.1 ../../lib/libRDKitChemTransforms.so.1.2025.03.1 ../../lib/libRDKitDepictor.so.1.2025.03.1 /usr/lib/aarch64-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/aarch64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl /usr/lib/aarch64-linux-gnu/libmaeparser.so +[ 45%] Linking CXX executable testCoordGen +cd /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/External/CoordGen && /usr/bin/cmake -E cmake_link_script CMakeFiles/testCoordGen.dir/link.txt --verbose=1 +/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/testCoordGen.dir/link.d CMakeFiles/testCoordGen.dir/test.cpp.o -o testCoordGen /usr/lib/aarch64-linux-gnu/libcoordgen.so ../../lib/libRDKitFileParsers.so.1.2025.03.1 ../../lib/libRDKitChemTransforms.so.1.2025.03.1 ../../lib/libRDKitDepictor.so.1.2025.03.1 /usr/lib/aarch64-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/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 -ldl /usr/lib/aarch64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_iostreams.so.1.83.0 /usr/lib/aarch64-linux-gnu/libmaeparser.so make[4]: Leaving directory '/build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu' -[ 45%] Built target hanoiTest +[ 45%] Built target testCoordGen 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-aarch64-linux-gnu' cd /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202503.1 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/usr/lib/aarch64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl /usr/lib/aarch64-linux-gnu/libmaeparser.so make[4]: Leaving directory '/build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu' -[ 45%] Built target graphmoltestPicklerGlobalSetting +[ 45%] Built target testUFFForceField make -f Code/GraphMol/CMakeFiles/canonTestsCatch.dir/build.make Code/GraphMol/CMakeFiles/canonTestsCatch.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu' cd /build/reproducible-path/rdkit-202503.1/obj-aarch64-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-aarch64-linux-gnu /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol 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../../lib/libRDKitRDGeneral.so.1.2025.03.1 -ldl /usr/lib/aarch64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_iostreams.so.1.83.0 /usr/lib/aarch64-linux-gnu/libmaeparser.so +[ 45%] Linking CXX executable hanoiTest +cd /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol && /usr/bin/cmake -E cmake_link_script CMakeFiles/hanoiTest.dir/link.txt --verbose=1 +/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/hanoiTest.dir/link.d CMakeFiles/hanoiTest.dir/hanoitest.cpp.o -o hanoiTest ../../lib/libRDKitFileParsers.so.1.2025.03.1 ../../lib/libRDKitChemTransforms.so.1.2025.03.1 ../../lib/libRDKitDepictor.so.1.2025.03.1 /usr/lib/aarch64-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/aarch64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl /usr/lib/aarch64-linux-gnu/libmaeparser.so make[4]: Leaving directory '/build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu' -[ 45%] Built target testCoordGen +[ 45%] Built target hanoiTest 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-aarch64-linux-gnu' cd /build/reproducible-path/rdkit-202503.1/obj-aarch64-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-aarch64-linux-gnu /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/CMakeFiles/pickleTestsCatch.dir/DependInfo.cmake "--color=" @@ -4662,24 +4693,24 @@ make[4]: Entering directory '/build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu' [ 45%] Building CXX object Code/GraphMol/CMakeFiles/molopsTestsCatch.dir/catch_molops.cpp.o cd /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol && /usr/bin/c++ 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-MF CMakeFiles/molopsTestsCatch.dir/catch_molops.cpp.o.d -o CMakeFiles/molopsTestsCatch.dir/catch_molops.cpp.o -c /build/reproducible-path/rdkit-202503.1/Code/GraphMol/catch_molops.cpp -[ 46%] Linking CXX executable testSGroup -cd /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol && /usr/bin/cmake -E cmake_link_script CMakeFiles/testSGroup.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 -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/testSGroup.dir/link.d CMakeFiles/testSGroup.dir/testSGroup.cpp.o -o testSGroup ../../lib/libRDKitFileParsers.so.1.2025.03.1 ../../lib/libRDKitChemTransforms.so.1.2025.03.1 ../../lib/libRDKitDepictor.so.1.2025.03.1 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/usr/lib/aarch64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl /usr/lib/aarch64-linux-gnu/libmaeparser.so +[ 46%] Linking CXX executable graphmolAdjustQueryCatch +cd /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol && /usr/bin/cmake -E cmake_link_script CMakeFiles/graphmolAdjustQueryCatch.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 -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/graphmolAdjustQueryCatch.dir/link.d CMakeFiles/graphmolAdjustQueryCatch.dir/catch_adjustquery.cpp.o -o graphmolAdjustQueryCatch ../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/aarch64-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/aarch64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl /usr/lib/aarch64-linux-gnu/libmaeparser.so make[4]: Leaving directory '/build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu' -[ 47%] Built target pickleTestsCatch +[ 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/build/reproducible-path/rdkit-202503.1/Code/GraphMol/Depictor /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/Depictor /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/Depictor/CMakeFiles/testDepictor.dir/DependInfo.cmake "--color=" @@ -4727,13 +4758,11 @@ make[4]: Entering directory '/build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu' [ 47%] Building CXX object Code/GraphMol/Depictor/CMakeFiles/testDepictor.dir/testDepictor.cpp.o cd /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/Depictor && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DIN_COORDGEN -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_BUILD_XYZ2MOL_SUPPORT -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 -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/GraphMol/Depictor/CMakeFiles/testDepictor.dir/testDepictor.cpp.o -MF CMakeFiles/testDepictor.dir/testDepictor.cpp.o.d -o CMakeFiles/testDepictor.dir/testDepictor.cpp.o -c /build/reproducible-path/rdkit-202503.1/Code/GraphMol/Depictor/testDepictor.cpp -[ 47%] Linking CXX executable graphmolAdjustQueryCatch -cd 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../../lib/libRDKitDepictor.so.1.2025.03.1 /usr/lib/aarch64-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/aarch64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl /usr/lib/aarch64-linux-gnu/libmaeparser.so +[ 47%] Linking CXX executable canonTestsCatch +cd /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol && /usr/bin/cmake -E cmake_link_script 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../../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/aarch64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl /usr/lib/aarch64-linux-gnu/libmaeparser.so make[4]: Leaving directory '/build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu' -[ 47%] Built target graphmoltestPickler +[ 47%] Built target canonTestsCatch make -f Code/GraphMol/Depictor/CMakeFiles/depictorCatch.dir/build.make Code/GraphMol/Depictor/CMakeFiles/depictorCatch.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu' cd /build/reproducible-path/rdkit-202503.1/obj-aarch64-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-aarch64-linux-gnu /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/Depictor /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/Depictor/CMakeFiles/depictorCatch.dir/DependInfo.cmake "--color=" @@ -4742,9 +4771,11 @@ make[4]: Entering directory '/build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu' [ 47%] Building CXX object Code/GraphMol/Depictor/CMakeFiles/depictorCatch.dir/catch_tests.cpp.o cd /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/Depictor && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DIN_COORDGEN -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_BUILD_XYZ2MOL_SUPPORT -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 -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/GraphMol/Depictor/CMakeFiles/depictorCatch.dir/catch_tests.cpp.o -MF CMakeFiles/depictorCatch.dir/catch_tests.cpp.o.d -o CMakeFiles/depictorCatch.dir/catch_tests.cpp.o -c /build/reproducible-path/rdkit-202503.1/Code/GraphMol/Depictor/catch_tests.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 -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/graphmolAdjustQueryCatch.dir/link.d CMakeFiles/graphmolAdjustQueryCatch.dir/catch_adjustquery.cpp.o -o graphmolAdjustQueryCatch ../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/aarch64-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/aarch64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl /usr/lib/aarch64-linux-gnu/libmaeparser.so +[ 47%] Linking CXX executable molopsTestsCatch +cd /build/reproducible-path/rdkit-202503.1/obj-aarch64-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 -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/molopsTestsCatch.dir/link.d CMakeFiles/molopsTestsCatch.dir/catch_molops.cpp.o -o molopsTestsCatch ../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/aarch64-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/aarch64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl /usr/lib/aarch64-linux-gnu/libmaeparser.so make[4]: Leaving directory '/build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu' -[ 47%] Built target graphmolAdjustQueryCatch +[ 47%] Built target molopsTestsCatch make -f Code/GraphMol/FileParsers/CMakeFiles/fileParsersTest1.dir/build.make Code/GraphMol/FileParsers/CMakeFiles/fileParsersTest1.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu' cd /build/reproducible-path/rdkit-202503.1/obj-aarch64-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-aarch64-linux-gnu /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/CMakeFiles/fileParsersTest1.dir/DependInfo.cmake "--color=" @@ -4753,11 +4784,11 @@ make[4]: Entering directory '/build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu' [ 47%] Building CXX object Code/GraphMol/FileParsers/CMakeFiles/fileParsersTest1.dir/test1.cpp.o cd /build/reproducible-path/rdkit-202503.1/obj-aarch64-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_BUILD_XYZ2MOL_SUPPORT -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 -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/GraphMol/FileParsers/CMakeFiles/fileParsersTest1.dir/test1.cpp.o -MF CMakeFiles/fileParsersTest1.dir/test1.cpp.o.d -o CMakeFiles/fileParsersTest1.dir/test1.cpp.o -c /build/reproducible-path/rdkit-202503.1/Code/GraphMol/FileParsers/test1.cpp -[ 47%] Linking CXX executable molopsTestsCatch -cd /build/reproducible-path/rdkit-202503.1/obj-aarch64-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 -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/molopsTestsCatch.dir/link.d CMakeFiles/molopsTestsCatch.dir/catch_molops.cpp.o -o molopsTestsCatch ../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/aarch64-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/aarch64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl /usr/lib/aarch64-linux-gnu/libmaeparser.so +[ 47%] Linking CXX executable graphmoltestPickler +cd /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol && /usr/bin/cmake -E cmake_link_script CMakeFiles/graphmoltestPickler.dir/link.txt --verbose=1 +/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/graphmoltestPickler.dir/link.d CMakeFiles/graphmoltestPickler.dir/testPickler.cpp.o -o graphmoltestPickler ../../lib/libRDKitFileParsers.so.1.2025.03.1 ../../lib/libRDKitChemTransforms.so.1.2025.03.1 ../../lib/libRDKitDepictor.so.1.2025.03.1 /usr/lib/aarch64-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/aarch64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl /usr/lib/aarch64-linux-gnu/libmaeparser.so make[4]: Leaving directory '/build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu' -[ 47%] Built target molopsTestsCatch +[ 47%] Built target graphmoltestPickler make -f Code/GraphMol/FileParsers/CMakeFiles/testAtropisomers.dir/build.make Code/GraphMol/FileParsers/CMakeFiles/testAtropisomers.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu' cd /build/reproducible-path/rdkit-202503.1/obj-aarch64-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-aarch64-linux-gnu /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/CMakeFiles/testAtropisomers.dir/DependInfo.cmake "--color=" @@ -4794,11 +4825,13 @@ make[4]: Entering directory '/build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu' [ 48%] Building CXX object Code/GraphMol/FileParsers/CMakeFiles/testMolSupplier.dir/testMolSupplier.cpp.o cd /build/reproducible-path/rdkit-202503.1/obj-aarch64-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_BUILD_XYZ2MOL_SUPPORT -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 -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/GraphMol/FileParsers/CMakeFiles/testMolSupplier.dir/testMolSupplier.cpp.o -MF CMakeFiles/testMolSupplier.dir/testMolSupplier.cpp.o.d -o CMakeFiles/testMolSupplier.dir/testMolSupplier.cpp.o -c /build/reproducible-path/rdkit-202503.1/Code/GraphMol/FileParsers/testMolSupplier.cpp -[ 48%] Linking CXX executable testAtropisomers -cd /build/reproducible-path/rdkit-202503.1/obj-aarch64-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 -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now -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/aarch64-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 ../../../lib/libRDKitRDGeneral.so.1.2025.03.1 /usr/lib/aarch64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl /usr/lib/aarch64-linux-gnu/libmaeparser.so +[ 48%] Building CXX object Code/GraphMol/ChemReactions/CMakeFiles/ChemReactions.dir/DaylightParser.cpp.o +cd /build/reproducible-path/rdkit-202503.1/obj-aarch64-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_BUILD_XYZ2MOL_SUPPORT -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 -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/ChemReactions/CMakeFiles/ChemReactions.dir/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 +[ 48%] Linking CXX executable testSquiggleDoubleBonds +cd /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers && /usr/bin/cmake -E cmake_link_script CMakeFiles/testSquiggleDoubleBonds.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 -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/testSquiggleDoubleBonds.dir/link.d CMakeFiles/testSquiggleDoubleBonds.dir/testSquiggleDoubleBonds.cpp.o -o testSquiggleDoubleBonds ../../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/aarch64-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 ../../../lib/libRDKitRDGeneral.so.1.2025.03.1 /usr/lib/aarch64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl /usr/lib/aarch64-linux-gnu/libmaeparser.so make[4]: Leaving directory '/build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu' -[ 48%] Built target testAtropisomers +[ 48%] Built target testSquiggleDoubleBonds 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-aarch64-linux-gnu' cd /build/reproducible-path/rdkit-202503.1/obj-aarch64-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-aarch64-linux-gnu /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/CMakeFiles/testGeneralFileReader.dir/DependInfo.cmake "--color=" @@ -4807,11 +4840,11 @@ make[4]: Entering directory '/build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu' [ 48%] Building CXX object Code/GraphMol/FileParsers/CMakeFiles/testGeneralFileReader.dir/testGeneralFileReader.cpp.o cd /build/reproducible-path/rdkit-202503.1/obj-aarch64-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_BUILD_XYZ2MOL_SUPPORT -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 -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/GraphMol/FileParsers/CMakeFiles/testGeneralFileReader.dir/testGeneralFileReader.cpp.o -MF CMakeFiles/testGeneralFileReader.dir/testGeneralFileReader.cpp.o.d -o CMakeFiles/testGeneralFileReader.dir/testGeneralFileReader.cpp.o -c /build/reproducible-path/rdkit-202503.1/Code/GraphMol/FileParsers/testGeneralFileReader.cpp -[ 48%] Linking CXX executable testSquiggleDoubleBonds -cd /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers && /usr/bin/cmake -E cmake_link_script CMakeFiles/testSquiggleDoubleBonds.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 -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/testSquiggleDoubleBonds.dir/link.d CMakeFiles/testSquiggleDoubleBonds.dir/testSquiggleDoubleBonds.cpp.o -o testSquiggleDoubleBonds ../../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/aarch64-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 ../../../lib/libRDKitRDGeneral.so.1.2025.03.1 /usr/lib/aarch64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl /usr/lib/aarch64-linux-gnu/libmaeparser.so +[ 48%] Linking CXX executable testAtropisomers +cd /build/reproducible-path/rdkit-202503.1/obj-aarch64-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 -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now -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/aarch64-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 ../../../lib/libRDKitRDGeneral.so.1.2025.03.1 /usr/lib/aarch64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl /usr/lib/aarch64-linux-gnu/libmaeparser.so make[4]: Leaving directory '/build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu' -[ 48%] Built target testSquiggleDoubleBonds +[ 48%] Built target testAtropisomers 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-aarch64-linux-gnu' cd /build/reproducible-path/rdkit-202503.1/obj-aarch64-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-aarch64-linux-gnu /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/CMakeFiles/testMultithreadedMolSupplier.dir/DependInfo.cmake "--color=" @@ -4820,8 +4853,6 @@ make[4]: Entering directory '/build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu' [ 48%] Building CXX object Code/GraphMol/FileParsers/CMakeFiles/testMultithreadedMolSupplier.dir/testMultithreadedMolSupplier.cpp.o cd /build/reproducible-path/rdkit-202503.1/obj-aarch64-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_BUILD_XYZ2MOL_SUPPORT -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 -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/GraphMol/FileParsers/CMakeFiles/testMultithreadedMolSupplier.dir/testMultithreadedMolSupplier.cpp.o -MF CMakeFiles/testMultithreadedMolSupplier.dir/testMultithreadedMolSupplier.cpp.o.d -o CMakeFiles/testMultithreadedMolSupplier.dir/testMultithreadedMolSupplier.cpp.o -c /build/reproducible-path/rdkit-202503.1/Code/GraphMol/FileParsers/testMultithreadedMolSupplier.cpp -[ 48%] Building CXX object Code/GraphMol/ChemReactions/CMakeFiles/ChemReactions.dir/DaylightParser.cpp.o -cd /build/reproducible-path/rdkit-202503.1/obj-aarch64-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_BUILD_XYZ2MOL_SUPPORT -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 -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/ChemReactions/CMakeFiles/ChemReactions.dir/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 [ 49%] Linking CXX executable testDepictor cd /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/Depictor && /usr/bin/cmake -E cmake_link_script CMakeFiles/testDepictor.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/testDepictor.dir/link.d CMakeFiles/testDepictor.dir/testDepictor.cpp.o -o testDepictor ../../../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 /usr/lib/aarch64-linux-gnu/libcoordgen.so ../../../lib/libRDKitMolTransforms.so.1.2025.03.1 ../../../lib/libRDKitEigenSolvers.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/aarch64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl /usr/lib/aarch64-linux-gnu/libmaeparser.so @@ -4837,115 +4868,121 @@ cd /build/reproducible-path/rdkit-202503.1/obj-aarch64-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_BUILD_XYZ2MOL_SUPPORT -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 -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/GraphMol/FileParsers/CMakeFiles/testMolWriter.dir/testMolWriter.cpp.o -MF CMakeFiles/testMolWriter.dir/testMolWriter.cpp.o.d -o CMakeFiles/testMolWriter.dir/testMolWriter.cpp.o -c /build/reproducible-path/rdkit-202503.1/Code/GraphMol/FileParsers/testMolWriter.cpp [ 49%] Building CXX object Code/GraphMol/ChemReactions/CMakeFiles/ChemReactions.dir/ReactionPickler.cpp.o cd /build/reproducible-path/rdkit-202503.1/obj-aarch64-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_BUILD_XYZ2MOL_SUPPORT -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 -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/ChemReactions/CMakeFiles/ChemReactions.dir/ReactionPickler.cpp.o -MF CMakeFiles/ChemReactions.dir/ReactionPickler.cpp.o.d -o CMakeFiles/ChemReactions.dir/ReactionPickler.cpp.o -c /build/reproducible-path/rdkit-202503.1/Code/GraphMol/ChemReactions/ReactionPickler.cpp -[ 50%] Linking CXX executable testGeneralFileReader -cd /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers && /usr/bin/cmake -E cmake_link_script CMakeFiles/testGeneralFileReader.dir/link.txt --verbose=1 -[ 50%] Linking CXX executable testMultithreadedMolSupplier +[ 49%] Linking CXX executable testMultithreadedMolSupplier cd /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers && /usr/bin/cmake -E cmake_link_script CMakeFiles/testMultithreadedMolSupplier.dir/link.txt --verbose=1 -/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/testGeneralFileReader.dir/link.d CMakeFiles/testGeneralFileReader.dir/testGeneralFileReader.cpp.o -o testGeneralFileReader ../../../lib/libRDKitFileParsers.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/aarch64-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 -ldl /usr/lib/aarch64-linux-gnu/libmaeparser.so /usr/lib/aarch64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_iostreams.so.1.83.0 +/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/testMultithreadedMolSupplier.dir/link.d CMakeFiles/testMultithreadedMolSupplier.dir/testMultithreadedMolSupplier.cpp.o -o testMultithreadedMolSupplier ../../../lib/libRDKitFileParsers.so.1.2025.03.1 ../../../lib/libRDKitFingerprints.so.1.2025.03.1 ../../../lib/libRDKitRDStreams.so.1.2025.03.1 ../../../lib/libRDKitChemTransforms.so.1.2025.03.1 ../../../lib/libRDKitDepictor.so.1.2025.03.1 /usr/lib/aarch64-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/aarch64-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/aarch64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_iostreams.so.1.83.0 make[4]: Leaving directory '/build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu' -[ 50%] Built target testGeneralFileReader +[ 49%] Built target testMultithreadedMolSupplier make -f Code/GraphMol/FileParsers/CMakeFiles/testTplParser.dir/build.make Code/GraphMol/FileParsers/CMakeFiles/testTplParser.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu' cd /build/reproducible-path/rdkit-202503.1/obj-aarch64-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-aarch64-linux-gnu /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/CMakeFiles/testTplParser.dir/DependInfo.cmake "--color=" +[ 50%] Linking CXX executable testGeneralFileReader +cd /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers && /usr/bin/cmake -E cmake_link_script CMakeFiles/testGeneralFileReader.dir/link.txt --verbose=1 make[4]: Leaving directory '/build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu' make -f Code/GraphMol/FileParsers/CMakeFiles/testTplParser.dir/build.make Code/GraphMol/FileParsers/CMakeFiles/testTplParser.dir/build make[4]: Entering directory '/build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu' [ 50%] Building CXX object Code/GraphMol/FileParsers/CMakeFiles/testTplParser.dir/testTpls.cpp.o cd /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers && /usr/bin/c++ 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+make[4]: Leaving directory '/build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu' +[ 51%] Built target testTplParser 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-aarch64-linux-gnu' cd /build/reproducible-path/rdkit-202503.1/obj-aarch64-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-aarch64-linux-gnu /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/CMakeFiles/testMol2ToMol.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu' make -f 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--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 -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/depictorCatch.dir/link.d CMakeFiles/depictorCatch.dir/catch_tests.cpp.o -o depictorCatch ../../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/aarch64-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 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-DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202503.1/External -I/build/reproducible-path/rdkit-202503.1/Code -I/build/reproducible-path/rdkit-202503.1/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/ChemReactions/CMakeFiles/ChemReactions.dir/ReactionDepict.cpp.o -MF CMakeFiles/ChemReactions.dir/ReactionDepict.cpp.o.d -o CMakeFiles/ChemReactions.dir/ReactionDepict.cpp.o -c /build/reproducible-path/rdkit-202503.1/Code/GraphMol/ChemReactions/ReactionDepict.cpp -[ 50%] Linking CXX executable testTplParser -cd 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CMakeFiles/ChemReactions.dir/ReactionRunner.cpp.o.d -o CMakeFiles/ChemReactions.dir/ReactionRunner.cpp.o -c /build/reproducible-path/rdkit-202503.1/Code/GraphMol/ChemReactions/ReactionRunner.cpp +[ 51%] Linking CXX executable smiTest1 +cd /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/SmilesParse && /usr/bin/cmake -E cmake_link_script CMakeFiles/smiTest1.dir/link.txt --verbose=1 +/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/smiTest1.dir/link.d CMakeFiles/smiTest1.dir/test.cpp.o -o smiTest1 ../../../lib/libRDKitFileParsers.so.1.2025.03.1 ../../../lib/libRDKitChemTransforms.so.1.2025.03.1 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../../../lib/libRDKitChemTransforms.so.1.2025.03.1 ../../../lib/libRDKitDepictor.so.1.2025.03.1 /usr/lib/aarch64-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 -ldl /usr/lib/aarch64-linux-gnu/libmaeparser.so /usr/lib/aarch64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_iostreams.so.1.83.0 +[ 51%] Linking CXX executable testMol2ToMol +cd /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers && /usr/bin/cmake -E cmake_link_script CMakeFiles/testMol2ToMol.dir/link.txt --verbose=1 +/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/testMol2ToMol.dir/link.d CMakeFiles/testMol2ToMol.dir/testMol2ToMol.cpp.o -o testMol2ToMol ../../../lib/libRDKitFileParsers.so.1.2025.03.1 ../../../lib/libRDKitChemTransforms.so.1.2025.03.1 ../../../lib/libRDKitDepictor.so.1.2025.03.1 /usr/lib/aarch64-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/aarch64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl /usr/lib/aarch64-linux-gnu/libmaeparser.so make[4]: Leaving directory '/build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu' -[ 51%] Built target testMolSupplier +[ 51%] Built target testMol2ToMol make -f Code/GraphMol/FileParsers/CMakeFiles/XYZFileParserCatchTest.dir/build.make Code/GraphMol/FileParsers/CMakeFiles/XYZFileParserCatchTest.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu' cd /build/reproducible-path/rdkit-202503.1/obj-aarch64-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-aarch64-linux-gnu /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/CMakeFiles/XYZFileParserCatchTest.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu' make -f Code/GraphMol/FileParsers/CMakeFiles/XYZFileParserCatchTest.dir/build.make Code/GraphMol/FileParsers/CMakeFiles/XYZFileParserCatchTest.dir/build make[4]: Entering directory '/build/reproducible-path/rdkit-202503.1/obj-aarch64-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 -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/chiralityTestsCatch.dir/link.d CMakeFiles/chiralityTestsCatch.dir/catch_chirality.cpp.o -o chiralityTestsCatch ../RDGeneral/librdkitCatch.a ../../lib/libRDKitCIPLabeler.so.1.2025.03.1 ../../lib/libRDKitFileParsers.so.1.2025.03.1 /usr/lib/libCatch2.a ../../lib/libRDKitChemTransforms.so.1.2025.03.1 ../../lib/libRDKitDepictor.so.1.2025.03.1 /usr/lib/aarch64-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/aarch64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl /usr/lib/aarch64-linux-gnu/libmaeparser.so -make[4]: Leaving directory '/build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu' [ 51%] Building CXX object Code/GraphMol/FileParsers/CMakeFiles/XYZFileParserCatchTest.dir/XYZFileParserCatchTest.cpp.o cd /build/reproducible-path/rdkit-202503.1/obj-aarch64-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_BUILD_XYZ2MOL_SUPPORT -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 -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/GraphMol/FileParsers/CMakeFiles/XYZFileParserCatchTest.dir/XYZFileParserCatchTest.cpp.o -MF CMakeFiles/XYZFileParserCatchTest.dir/XYZFileParserCatchTest.cpp.o.d -o CMakeFiles/XYZFileParserCatchTest.dir/XYZFileParserCatchTest.cpp.o -c /build/reproducible-path/rdkit-202503.1/Code/GraphMol/FileParsers/XYZFileParserCatchTest.cpp -[ 51%] Building CXX object Code/GraphMol/ChemReactions/CMakeFiles/ChemReactions.dir/ReactionUtils.cpp.o -cd /build/reproducible-path/rdkit-202503.1/obj-aarch64-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_BUILD_XYZ2MOL_SUPPORT -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 -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/ChemReactions/CMakeFiles/ChemReactions.dir/ReactionUtils.cpp.o -MF CMakeFiles/ChemReactions.dir/ReactionUtils.cpp.o.d -o CMakeFiles/ChemReactions.dir/ReactionUtils.cpp.o -c /build/reproducible-path/rdkit-202503.1/Code/GraphMol/ChemReactions/ReactionUtils.cpp -[ 51%] Built target chiralityTestsCatch +[ 51%] Linking CXX executable testMolWriter +cd /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers && /usr/bin/cmake -E cmake_link_script CMakeFiles/testMolWriter.dir/link.txt --verbose=1 +/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/testMolWriter.dir/link.d CMakeFiles/testMolWriter.dir/testMolWriter.cpp.o -o testMolWriter ../../../lib/libRDKitFileParsers.so.1.2025.03.1 ../../../lib/libRDKitChemTransforms.so.1.2025.03.1 ../../../lib/libRDKitDepictor.so.1.2025.03.1 /usr/lib/aarch64-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/aarch64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl /usr/lib/aarch64-linux-gnu/libmaeparser.so +make[4]: Leaving directory '/build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu' +[ 51%] Built target testMolWriter make -f Code/GraphMol/FileParsers/CMakeFiles/cdxmlParserCatchTest.dir/build.make Code/GraphMol/FileParsers/CMakeFiles/cdxmlParserCatchTest.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu' cd /build/reproducible-path/rdkit-202503.1/obj-aarch64-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-aarch64-linux-gnu /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/CMakeFiles/cdxmlParserCatchTest.dir/DependInfo.cmake "--color=" @@ -4954,11 +4991,11 @@ make[4]: Entering directory '/build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu' [ 51%] Building CXX object Code/GraphMol/FileParsers/CMakeFiles/cdxmlParserCatchTest.dir/cdxml_parser_catch.cpp.o cd /build/reproducible-path/rdkit-202503.1/obj-aarch64-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_BUILD_XYZ2MOL_SUPPORT -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 -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/GraphMol/FileParsers/CMakeFiles/cdxmlParserCatchTest.dir/cdxml_parser_catch.cpp.o -MF CMakeFiles/cdxmlParserCatchTest.dir/cdxml_parser_catch.cpp.o.d -o CMakeFiles/cdxmlParserCatchTest.dir/cdxml_parser_catch.cpp.o -c /build/reproducible-path/rdkit-202503.1/Code/GraphMol/FileParsers/cdxml_parser_catch.cpp -[ 51%] Linking CXX executable smiTest1 -cd /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/SmilesParse && /usr/bin/cmake -E cmake_link_script CMakeFiles/smiTest1.dir/link.txt --verbose=1 -/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/smiTest1.dir/link.d CMakeFiles/smiTest1.dir/test.cpp.o -o smiTest1 ../../../lib/libRDKitFileParsers.so.1.2025.03.1 ../../../lib/libRDKitChemTransforms.so.1.2025.03.1 ../../../lib/libRDKitDepictor.so.1.2025.03.1 /usr/lib/aarch64-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/aarch64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl /usr/lib/aarch64-linux-gnu/libmaeparser.so +[ 51%] Linking CXX executable testSequence +cd /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers && /usr/bin/cmake -E cmake_link_script CMakeFiles/testSequence.dir/link.txt --verbose=1 +/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/testSequence.dir/link.d CMakeFiles/testSequence.dir/testSequence.cpp.o -o testSequence ../../../lib/libRDKitFileParsers.so.1.2025.03.1 ../../../lib/libRDKitChemTransforms.so.1.2025.03.1 ../../../lib/libRDKitDepictor.so.1.2025.03.1 /usr/lib/aarch64-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/aarch64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl /usr/lib/aarch64-linux-gnu/libmaeparser.so make[4]: Leaving directory '/build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu' -[ 51%] Built target smiTest1 +[ 51%] Built target testSequence make -f Code/GraphMol/FileParsers/CMakeFiles/molfileStereoCatchTest.dir/build.make Code/GraphMol/FileParsers/CMakeFiles/molfileStereoCatchTest.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu' cd /build/reproducible-path/rdkit-202503.1/obj-aarch64-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-aarch64-linux-gnu /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/CMakeFiles/molfileStereoCatchTest.dir/DependInfo.cmake "--color=" @@ -4969,62 +5006,37 @@ cd /build/reproducible-path/rdkit-202503.1/obj-aarch64-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_BUILD_XYZ2MOL_SUPPORT -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 -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/GraphMol/FileParsers/CMakeFiles/molfileStereoCatchTest.dir/molfile_stereo_catch.cpp.o -MF CMakeFiles/molfileStereoCatchTest.dir/molfile_stereo_catch.cpp.o.d -o CMakeFiles/molfileStereoCatchTest.dir/molfile_stereo_catch.cpp.o -c /build/reproducible-path/rdkit-202503.1/Code/GraphMol/FileParsers/molfile_stereo_catch.cpp [ 51%] Linking CXX executable testExtendedStereoParsing cd /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers && /usr/bin/cmake -E cmake_link_script CMakeFiles/testExtendedStereoParsing.dir/link.txt --verbose=1 +[ 52%] Linking CXX executable chiralityTestsCatch +cd /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol && /usr/bin/cmake -E cmake_link_script CMakeFiles/chiralityTestsCatch.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/testExtendedStereoParsing.dir/link.d CMakeFiles/testExtendedStereoParsing.dir/testExtendedStereoParsing.cpp.o -o testExtendedStereoParsing ../../../lib/libRDKitFileParsers.so.1.2025.03.1 ../../../lib/libRDKitChemTransforms.so.1.2025.03.1 ../../../lib/libRDKitDepictor.so.1.2025.03.1 /usr/lib/aarch64-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/aarch64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl /usr/lib/aarch64-linux-gnu/libmaeparser.so make[4]: Leaving directory '/build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu' -[ 51%] Built target testExtendedStereoParsing +[ 52%] Built target testExtendedStereoParsing make -f Code/GraphMol/FileParsers/CMakeFiles/connectTheDotsTest.dir/build.make Code/GraphMol/FileParsers/CMakeFiles/connectTheDotsTest.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu' cd /build/reproducible-path/rdkit-202503.1/obj-aarch64-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-aarch64-linux-gnu /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/CMakeFiles/connectTheDotsTest.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu' make -f Code/GraphMol/FileParsers/CMakeFiles/connectTheDotsTest.dir/build.make Code/GraphMol/FileParsers/CMakeFiles/connectTheDotsTest.dir/build make[4]: Entering directory '/build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu' -[ 51%] Building CXX object Code/GraphMol/FileParsers/CMakeFiles/connectTheDotsTest.dir/connectTheDots_catch.cpp.o +[ 52%] Building CXX object Code/GraphMol/FileParsers/CMakeFiles/connectTheDotsTest.dir/connectTheDots_catch.cpp.o cd /build/reproducible-path/rdkit-202503.1/obj-aarch64-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_BUILD_XYZ2MOL_SUPPORT -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 -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/GraphMol/FileParsers/CMakeFiles/connectTheDotsTest.dir/connectTheDots_catch.cpp.o -MF CMakeFiles/connectTheDotsTest.dir/connectTheDots_catch.cpp.o.d -o CMakeFiles/connectTheDotsTest.dir/connectTheDots_catch.cpp.o -c /build/reproducible-path/rdkit-202503.1/Code/GraphMol/FileParsers/connectTheDots_catch.cpp -[ 51%] Linking CXX executable testMolWriter -cd /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers && /usr/bin/cmake -E cmake_link_script CMakeFiles/testMolWriter.dir/link.txt --verbose=1 -/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. 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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 -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/GraphMol/FileParsers/CMakeFiles/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 -[ 51%] Linking CXX executable smiTestCatch -cd /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/SmilesParse && /usr/bin/cmake -E cmake_link_script CMakeFiles/smiTestCatch.dir/link.txt --verbose=1 -/usr/bin/c++ -g -O2 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../../../lib/libRDKitGenericGroups.so.1.2025.03.1 ../../../lib/libRDKitGraphMol.so.1.2025.03.1 ../../../lib/libRDKitRDGeometryLib.so.1.2025.03.1 ../../../lib/libRDKitDataStructs.so.1.2025.03.1 ../../../lib/libRDKitRDGeneral.so.1.2025.03.1 /usr/lib/aarch64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl /usr/lib/aarch64-linux-gnu/libmaeparser.so -make[4]: Leaving directory '/build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu' -[ 51%] Built target smiTestCatch -[ 52%] Building CXX object Code/GraphMol/ChemReactions/CMakeFiles/ChemReactions.dir/MoleculeParser.cpp.o -cd /build/reproducible-path/rdkit-202503.1/obj-aarch64-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 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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 -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/ChemReactions/CMakeFiles/ChemReactions.dir/ReactionRunner.cpp.o -MF CMakeFiles/ChemReactions.dir/ReactionRunner.cpp.o.d -o CMakeFiles/ChemReactions.dir/ReactionRunner.cpp.o -c /build/reproducible-path/rdkit-202503.1/Code/GraphMol/ChemReactions/ReactionRunner.cpp -[ 52%] Building CXX object Code/GraphMol/ChemReactions/CMakeFiles/ChemReactions.dir/PreprocessRxn.cpp.o -cd /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/ChemReactions && /usr/bin/c++ 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-fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/ChemReactions/CMakeFiles/ChemReactions.dir/PreprocessRxn.cpp.o -MF CMakeFiles/ChemReactions.dir/PreprocessRxn.cpp.o.d -o CMakeFiles/ChemReactions.dir/PreprocessRxn.cpp.o -c /build/reproducible-path/rdkit-202503.1/Code/GraphMol/ChemReactions/PreprocessRxn.cpp -[ 52%] Linking CXX executable connectTheDotsTest -cd /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers && /usr/bin/cmake -E cmake_link_script CMakeFiles/connectTheDotsTest.dir/link.txt --verbose=1 -/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/connectTheDotsTest.dir/link.d 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../../../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/aarch64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl /usr/lib/aarch64-linux-gnu/libmaeparser.so +[ 52%] Linking CXX executable XYZFileParserCatchTest +cd /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers && /usr/bin/cmake -E cmake_link_script CMakeFiles/XYZFileParserCatchTest.dir/link.txt --verbose=1 +/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now -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/aarch64-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/aarch64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl /usr/lib/aarch64-linux-gnu/libmaeparser.so make[4]: Leaving directory '/build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu' -[ 52%] Built target cdxmlParserCatchTest +[ 52%] Built target XYZFileParserCatchTest make -f Code/GraphMol/FileParsers/CMakeFiles/atropisomersCatch.dir/build.make Code/GraphMol/FileParsers/CMakeFiles/atropisomersCatch.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu' cd /build/reproducible-path/rdkit-202503.1/obj-aarch64-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-aarch64-linux-gnu /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/CMakeFiles/atropisomersCatch.dir/DependInfo.cmake "--color=" @@ -5050,16 +5058,11 @@ make[4]: Entering directory '/build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu' [ 52%] Building CXX object Code/GraphMol/FileParsers/CMakeFiles/atropisomersCatch.dir/atropisomers_catch.cpp.o cd /build/reproducible-path/rdkit-202503.1/obj-aarch64-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_BUILD_XYZ2MOL_SUPPORT -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 -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/GraphMol/FileParsers/CMakeFiles/atropisomersCatch.dir/atropisomers_catch.cpp.o -MF CMakeFiles/atropisomersCatch.dir/atropisomers_catch.cpp.o.d -o CMakeFiles/atropisomersCatch.dir/atropisomers_catch.cpp.o -c /build/reproducible-path/rdkit-202503.1/Code/GraphMol/FileParsers/atropisomers_catch.cpp -/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/v2MolSuppliers.dir/link.d CMakeFiles/v2MolSuppliers.dir/v2_suppliers_catch.cpp.o -o v2MolSuppliers ../../RDGeneral/librdkitCatch.a ../../../lib/libRDKitFileParsers.so.1.2025.03.1 /usr/lib/libCatch2.a ../../../lib/libRDKitChemTransforms.so.1.2025.03.1 ../../../lib/libRDKitDepictor.so.1.2025.03.1 /usr/lib/aarch64-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/aarch64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl /usr/lib/aarch64-linux-gnu/libmaeparser.so -make[4]: Leaving directory '/build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu' -[ 52%] Built target v2MolSuppliers -[ 52%] Building CXX object Code/GraphMol/ChemReactions/CMakeFiles/ChemReactions.dir/Enumerate/EnumerationPickler.cpp.o -cd /build/reproducible-path/rdkit-202503.1/obj-aarch64-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_BUILD_XYZ2MOL_SUPPORT -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 -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/ChemReactions/CMakeFiles/ChemReactions.dir/Enumerate/EnumerationPickler.cpp.o -MF CMakeFiles/ChemReactions.dir/Enumerate/EnumerationPickler.cpp.o.d -o CMakeFiles/ChemReactions.dir/Enumerate/EnumerationPickler.cpp.o -c /build/reproducible-path/rdkit-202503.1/Code/GraphMol/ChemReactions/Enumerate/EnumerationPickler.cpp -[ 52%] Linking CXX executable graphmolMolOpsTest -cd /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol && /usr/bin/cmake -E cmake_link_script CMakeFiles/graphmolMolOpsTest.dir/link.txt --verbose=1 -/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now -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/aarch64-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/aarch64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl /usr/lib/aarch64-linux-gnu/libmaeparser.so +[ 52%] Linking CXX executable connectTheDotsTest +cd /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers && /usr/bin/cmake -E cmake_link_script CMakeFiles/connectTheDotsTest.dir/link.txt --verbose=1 +/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/connectTheDotsTest.dir/link.d CMakeFiles/connectTheDotsTest.dir/connectTheDots_catch.cpp.o -o connectTheDotsTest ../../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/aarch64-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/aarch64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl /usr/lib/aarch64-linux-gnu/libmaeparser.so make[4]: Leaving directory '/build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu' -[ 52%] Built target graphmolMolOpsTest +[ 52%] Built target connectTheDotsTest make -f Code/GraphMol/FileParsers/CMakeFiles/multithreadedSupplierCatchTest.dir/build.make Code/GraphMol/FileParsers/CMakeFiles/multithreadedSupplierCatchTest.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu' cd /build/reproducible-path/rdkit-202503.1/obj-aarch64-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-aarch64-linux-gnu /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/CMakeFiles/multithreadedSupplierCatchTest.dir/DependInfo.cmake "--color=" @@ -5068,13 +5071,11 @@ make[4]: Entering directory '/build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu' [ 52%] Building CXX object Code/GraphMol/FileParsers/CMakeFiles/multithreadedSupplierCatchTest.dir/multithreaded_supplier_catch.cpp.o cd /build/reproducible-path/rdkit-202503.1/obj-aarch64-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_BUILD_XYZ2MOL_SUPPORT -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 -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/GraphMol/FileParsers/CMakeFiles/multithreadedSupplierCatchTest.dir/multithreaded_supplier_catch.cpp.o -MF CMakeFiles/multithreadedSupplierCatchTest.dir/multithreaded_supplier_catch.cpp.o.d -o CMakeFiles/multithreadedSupplierCatchTest.dir/multithreaded_supplier_catch.cpp.o -c /build/reproducible-path/rdkit-202503.1/Code/GraphMol/FileParsers/multithreaded_supplier_catch.cpp -[ 52%] Linking CXX executable testPropertyLists -cd /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers && /usr/bin/cmake -E cmake_link_script CMakeFiles/testPropertyLists.dir/link.txt --verbose=1 -[ 52%] Building CXX object Code/GraphMol/ChemReactions/CMakeFiles/ChemReactions.dir/Enumerate/EvenSamplePairs.cpp.o -cd /build/reproducible-path/rdkit-202503.1/obj-aarch64-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_BUILD_XYZ2MOL_SUPPORT -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 -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/ChemReactions/CMakeFiles/ChemReactions.dir/Enumerate/EvenSamplePairs.cpp.o -MF CMakeFiles/ChemReactions.dir/Enumerate/EvenSamplePairs.cpp.o.d -o CMakeFiles/ChemReactions.dir/Enumerate/EvenSamplePairs.cpp.o -c /build/reproducible-path/rdkit-202503.1/Code/GraphMol/ChemReactions/Enumerate/EvenSamplePairs.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 -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/testPropertyLists.dir/link.d CMakeFiles/testPropertyLists.dir/testPropertyLists.cpp.o -o testPropertyLists ../../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/aarch64-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/aarch64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl /usr/lib/aarch64-linux-gnu/libmaeparser.so +[ 52%] Linking CXX executable v2FileParsersCatchTest +cd /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers && /usr/bin/cmake -E cmake_link_script CMakeFiles/v2FileParsersCatchTest.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 -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now -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/aarch64-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/aarch64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl /usr/lib/aarch64-linux-gnu/libmaeparser.so make[4]: Leaving directory '/build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu' -[ 52%] Built target testPropertyLists +[ 52%] Built target v2FileParsersCatchTest 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-aarch64-linux-gnu' cd /build/reproducible-path/rdkit-202503.1/obj-aarch64-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-aarch64-linux-gnu /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/Substruct /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/Substruct/CMakeFiles/testSubstructMatch.dir/DependInfo.cmake "--color=" @@ -5083,6 +5084,27 @@ make[4]: Entering directory '/build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu' [ 52%] Building CXX object Code/GraphMol/Substruct/CMakeFiles/testSubstructMatch.dir/test1.cpp.o cd /build/reproducible-path/rdkit-202503.1/obj-aarch64-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_BUILD_XYZ2MOL_SUPPORT -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 -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/GraphMol/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 +[ 52%] Linking CXX executable molfileStereoCatchTest +cd /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers && /usr/bin/cmake -E cmake_link_script CMakeFiles/molfileStereoCatchTest.dir/link.txt --verbose=1 +/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now -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/aarch64-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/aarch64-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/aarch64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl +make[4]: Leaving directory '/build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu' +[ 52%] Built target molfileStereoCatchTest +[ 52%] Building CXX object Code/GraphMol/ChemReactions/CMakeFiles/ChemReactions.dir/PNGParser.cpp.o +cd /build/reproducible-path/rdkit-202503.1/obj-aarch64-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_BUILD_XYZ2MOL_SUPPORT -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 -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/ChemReactions/CMakeFiles/ChemReactions.dir/PNGParser.cpp.o -MF CMakeFiles/ChemReactions.dir/PNGParser.cpp.o.d -o CMakeFiles/ChemReactions.dir/PNGParser.cpp.o -c /build/reproducible-path/rdkit-202503.1/Code/GraphMol/ChemReactions/PNGParser.cpp +[ 52%] Building CXX object Code/GraphMol/ChemReactions/CMakeFiles/ChemReactions.dir/CDXMLParser.cpp.o +cd /build/reproducible-path/rdkit-202503.1/obj-aarch64-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_BUILD_XYZ2MOL_SUPPORT -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 -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/ChemReactions/CMakeFiles/ChemReactions.dir/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 +[ 52%] Linking CXX executable testPropertyLists +cd /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers && /usr/bin/cmake -E cmake_link_script CMakeFiles/testPropertyLists.dir/link.txt --verbose=1 +/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/testPropertyLists.dir/link.d CMakeFiles/testPropertyLists.dir/testPropertyLists.cpp.o -o testPropertyLists ../../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/aarch64-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/aarch64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl /usr/lib/aarch64-linux-gnu/libmaeparser.so +make[4]: Leaving directory '/build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu' +[ 52%] Built target testPropertyLists +[ 52%] Building CXX object Code/GraphMol/ChemReactions/CMakeFiles/ChemReactions.dir/Enumerate/Enumerate.cpp.o +cd /build/reproducible-path/rdkit-202503.1/obj-aarch64-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_BUILD_XYZ2MOL_SUPPORT -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 -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -fpermissive -MD -MT Code/GraphMol/ChemReactions/CMakeFiles/ChemReactions.dir/Enumerate/Enumerate.cpp.o -MF CMakeFiles/ChemReactions.dir/Enumerate/Enumerate.cpp.o.d -o CMakeFiles/ChemReactions.dir/Enumerate/Enumerate.cpp.o -c /build/reproducible-path/rdkit-202503.1/Code/GraphMol/ChemReactions/Enumerate/Enumerate.cpp +[ 52%] Linking CXX executable v2MolSuppliers +cd /build/reproducible-path/rdkit-202503.1/obj-aarch64-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 -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/v2MolSuppliers.dir/link.d CMakeFiles/v2MolSuppliers.dir/v2_suppliers_catch.cpp.o -o v2MolSuppliers ../../RDGeneral/librdkitCatch.a ../../../lib/libRDKitFileParsers.so.1.2025.03.1 /usr/lib/libCatch2.a ../../../lib/libRDKitChemTransforms.so.1.2025.03.1 ../../../lib/libRDKitDepictor.so.1.2025.03.1 /usr/lib/aarch64-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/aarch64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl /usr/lib/aarch64-linux-gnu/libmaeparser.so +make[4]: Leaving directory '/build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu' +[ 52%] Built target v2MolSuppliers 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-aarch64-linux-gnu' cd /build/reproducible-path/rdkit-202503.1/obj-aarch64-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-aarch64-linux-gnu /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/Substruct /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/Substruct/CMakeFiles/substructTestCatch.dir/DependInfo.cmake "--color=" @@ -5091,11 +5113,13 @@ make[4]: Entering directory '/build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu' [ 52%] Building CXX object Code/GraphMol/Substruct/CMakeFiles/substructTestCatch.dir/catch_tests.cpp.o cd /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/Substruct && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK 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CMakeFiles/substructTestCatch.dir/catch_tests.cpp.o -c /build/reproducible-path/rdkit-202503.1/Code/GraphMol/Substruct/catch_tests.cpp -[ 52%] Linking CXX executable v2FileParsersCatchTest -cd /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers && /usr/bin/cmake -E cmake_link_script CMakeFiles/v2FileParsersCatchTest.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 -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now -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/aarch64-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/aarch64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl /usr/lib/aarch64-linux-gnu/libmaeparser.so +[ 52%] Linking CXX executable graphmolMolOpsTest +cd /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol && /usr/bin/cmake -E cmake_link_script CMakeFiles/graphmolMolOpsTest.dir/link.txt --verbose=1 +[ 52%] Linking CXX executable cdxmlParserCatchTest +cd /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers && /usr/bin/cmake -E cmake_link_script CMakeFiles/cdxmlParserCatchTest.dir/link.txt --verbose=1 +/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now -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/aarch64-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/aarch64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl /usr/lib/aarch64-linux-gnu/libmaeparser.so make[4]: Leaving directory '/build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu' -[ 52%] Built target v2FileParsersCatchTest +[ 52%] Built target graphmolMolOpsTest make -f Code/GraphMol/ChemTransforms/CMakeFiles/testChemTransforms.dir/build.make Code/GraphMol/ChemTransforms/CMakeFiles/testChemTransforms.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu' cd /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202503.1 /build/reproducible-path/rdkit-202503.1/Code/GraphMol/ChemTransforms /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/ChemTransforms /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/ChemTransforms/CMakeFiles/testChemTransforms.dir/DependInfo.cmake "--color=" @@ -5104,6 +5128,9 @@ make[4]: Entering directory '/build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu' [ 52%] Building CXX object Code/GraphMol/ChemTransforms/CMakeFiles/testChemTransforms.dir/testChemTransforms.cpp.o cd /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/ChemTransforms && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_BUILD_XYZ2MOL_SUPPORT -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 -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/GraphMol/ChemTransforms/CMakeFiles/testChemTransforms.dir/testChemTransforms.cpp.o -MF CMakeFiles/testChemTransforms.dir/testChemTransforms.cpp.o.d -o CMakeFiles/testChemTransforms.dir/testChemTransforms.cpp.o -c /build/reproducible-path/rdkit-202503.1/Code/GraphMol/ChemTransforms/testChemTransforms.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 -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/cdxmlParserCatchTest.dir/link.d CMakeFiles/cdxmlParserCatchTest.dir/cdxml_parser_catch.cpp.o -o cdxmlParserCatchTest ../../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/aarch64-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/aarch64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl /usr/lib/aarch64-linux-gnu/libmaeparser.so +make[4]: Leaving directory '/build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu' +[ 52%] Built target cdxmlParserCatchTest make -f Code/GraphMol/ChemTransforms/CMakeFiles/chemTransformsTestCatch.dir/build.make Code/GraphMol/ChemTransforms/CMakeFiles/chemTransformsTestCatch.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu' cd /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202503.1 /build/reproducible-path/rdkit-202503.1/Code/GraphMol/ChemTransforms /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/ChemTransforms /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/ChemTransforms/CMakeFiles/chemTransformsTestCatch.dir/DependInfo.cmake "--color=" @@ -5112,6 +5139,8 @@ make[4]: Entering directory '/build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu' [ 52%] Building CXX object Code/GraphMol/ChemTransforms/CMakeFiles/chemTransformsTestCatch.dir/catch_tests.cpp.o cd /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/ChemTransforms && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_BUILD_XYZ2MOL_SUPPORT -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 -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/GraphMol/ChemTransforms/CMakeFiles/chemTransformsTestCatch.dir/catch_tests.cpp.o -MF CMakeFiles/chemTransformsTestCatch.dir/catch_tests.cpp.o.d -o CMakeFiles/chemTransformsTestCatch.dir/catch_tests.cpp.o -c /build/reproducible-path/rdkit-202503.1/Code/GraphMol/ChemTransforms/catch_tests.cpp +[ 52%] Building CXX object Code/GraphMol/ChemReactions/CMakeFiles/ChemReactions.dir/Enumerate/EnumerationPickler.cpp.o +cd /build/reproducible-path/rdkit-202503.1/obj-aarch64-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_BUILD_XYZ2MOL_SUPPORT -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 -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/ChemReactions/CMakeFiles/ChemReactions.dir/Enumerate/EnumerationPickler.cpp.o -MF CMakeFiles/ChemReactions.dir/Enumerate/EnumerationPickler.cpp.o.d -o CMakeFiles/ChemReactions.dir/Enumerate/EnumerationPickler.cpp.o -c /build/reproducible-path/rdkit-202503.1/Code/GraphMol/ChemReactions/Enumerate/EnumerationPickler.cpp [ 52%] Linking CXX executable atropisomersCatch cd /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers && /usr/bin/cmake -E cmake_link_script CMakeFiles/atropisomersCatch.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/atropisomersCatch.dir/link.d CMakeFiles/atropisomersCatch.dir/atropisomers_catch.cpp.o -o atropisomersCatch ../../RDGeneral/librdkitCatch.a ../../../lib/libRDKitFileParsers.so.1.2025.03.1 /usr/lib/libCatch2.a ../../../lib/libRDKitChemTransforms.so.1.2025.03.1 ../../../lib/libRDKitDepictor.so.1.2025.03.1 /usr/lib/aarch64-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/aarch64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl /usr/lib/aarch64-linux-gnu/libmaeparser.so @@ -5125,6 +5154,11 @@ make[4]: Entering directory '/build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu' [ 52%] Building CXX object Code/GraphMol/FilterCatalog/CMakeFiles/filterCatalogTest.dir/filtercatalogtest.cpp.o cd /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FilterCatalog && /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_BUILD_XYZ2MOL_SUPPORT -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 -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/GraphMol/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 +[ 52%] Linking CXX executable multithreadedSupplierCatchTest +cd /build/reproducible-path/rdkit-202503.1/obj-aarch64-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=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now -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/aarch64-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/aarch64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl /usr/lib/aarch64-linux-gnu/libmaeparser.so +make[4]: Leaving directory '/build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu' +[ 52%] Built target multithreadedSupplierCatchTest make -f Code/GraphMol/FragCatalog/CMakeFiles/testFragCatalog.dir/build.make Code/GraphMol/FragCatalog/CMakeFiles/testFragCatalog.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu' cd /build/reproducible-path/rdkit-202503.1/obj-aarch64-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-aarch64-linux-gnu /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FragCatalog /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FragCatalog/CMakeFiles/testFragCatalog.dir/DependInfo.cmake "--color=" @@ -5133,11 +5167,8 @@ make[4]: Entering directory '/build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu' [ 52%] Building CXX object Code/GraphMol/FragCatalog/CMakeFiles/testFragCatalog.dir/test1.cpp.o cd /build/reproducible-path/rdkit-202503.1/obj-aarch64-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 -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_BUILD_XYZ2MOL_SUPPORT -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 -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/GraphMol/FragCatalog/CMakeFiles/testFragCatalog.dir/test1.cpp.o -MF CMakeFiles/testFragCatalog.dir/test1.cpp.o.d -o CMakeFiles/testFragCatalog.dir/test1.cpp.o -c /build/reproducible-path/rdkit-202503.1/Code/GraphMol/FragCatalog/test1.cpp -[ 52%] Linking CXX executable multithreadedSupplierCatchTest -cd /build/reproducible-path/rdkit-202503.1/obj-aarch64-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=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now -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/aarch64-linux-gnu/libcoordgen.so 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Code/GraphMol/ChemReactions/CMakeFiles/ChemReactions.dir/Enumerate/EvenSamplePairs.cpp.o +cd /build/reproducible-path/rdkit-202503.1/obj-aarch64-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_BUILD_XYZ2MOL_SUPPORT -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=. 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/build/reproducible-path/rdkit-202503.1/Code/GraphMol/FragCatalog/Wrap/FragCatalog.cpp -[ 52%] Building CXX object Code/GraphMol/FragCatalog/Wrap/CMakeFiles/rdfragcatalog.dir/FragCatParams.cpp.o -cd /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FragCatalog/Wrap && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_NUMPY_DYN_LINK -DBOOST_NUMPY_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_BUILD_XYZ2MOL_SUPPORT -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -Drdfragcatalog_EXPORTS -I/build/reproducible-path/rdkit-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/aarch64-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 -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/FragCatalog/Wrap/CMakeFiles/rdfragcatalog.dir/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 -[ 53%] Linking CXX executable fileParsersTest1 -cd /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers && /usr/bin/cmake -E 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/build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/ChemReactions && /usr/bin/cmake -E cmake_symlink_library ../../../lib/libRDKitChemReactions.so.1.2025.03.1 ../../../lib/libRDKitChemReactions.so.1 ../../../lib/libRDKitChemReactions.so -make[4]: Leaving directory '/build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu' -[ 53%] Built target ChemReactions -[ 53%] Building CXX object Code/GraphMol/FragCatalog/Wrap/CMakeFiles/rdfragcatalog.dir/FragFPGenerator.cpp.o -cd /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FragCatalog/Wrap && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_NUMPY_DYN_LINK -DBOOST_NUMPY_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_BUILD_XYZ2MOL_SUPPORT -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -Drdfragcatalog_EXPORTS -I/build/reproducible-path/rdkit-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/aarch64-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 -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/FragCatalog/Wrap/CMakeFiles/rdfragcatalog.dir/FragFPGenerator.cpp.o -MF CMakeFiles/rdfragcatalog.dir/FragFPGenerator.cpp.o.d -o CMakeFiles/rdfragcatalog.dir/FragFPGenerator.cpp.o -c /build/reproducible-path/rdkit-202503.1/Code/GraphMol/FragCatalog/Wrap/FragFPGenerator.cpp -[ 53%] Linking CXX executable testFragCatalog -cd /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FragCatalog && /usr/bin/cmake -E cmake_link_script CMakeFiles/testFragCatalog.dir/link.txt --verbose=1 -/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/testFragCatalog.dir/link.d CMakeFiles/testFragCatalog.dir/test1.cpp.o -o testFragCatalog ../../../lib/libRDKitFragCatalog.so.1.2025.03.1 ../../../lib/libRDKitFileParsers.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/aarch64-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/aarch64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl /usr/lib/aarch64-linux-gnu/libmaeparser.so +[ 52%] Building CXX object Code/GraphMol/FragCatalog/Wrap/CMakeFiles/rdfragcatalog.dir/FragCatalog.cpp.o +cd /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FragCatalog/Wrap && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_NUMPY_DYN_LINK -DBOOST_NUMPY_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_BUILD_XYZ2MOL_SUPPORT -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -Drdfragcatalog_EXPORTS -I/build/reproducible-path/rdkit-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/aarch64-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 -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/FragCatalog/Wrap/CMakeFiles/rdfragcatalog.dir/FragCatalog.cpp.o -MF CMakeFiles/rdfragcatalog.dir/FragCatalog.cpp.o.d -o CMakeFiles/rdfragcatalog.dir/FragCatalog.cpp.o -c /build/reproducible-path/rdkit-202503.1/Code/GraphMol/FragCatalog/Wrap/FragCatalog.cpp +[ 52%] Linking CXX executable filterCatalogTest +cd /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FilterCatalog && /usr/bin/cmake -E cmake_link_script CMakeFiles/filterCatalogTest.dir/link.txt --verbose=1 +[ 53%] Linking CXX executable fileParsersTest1 +cd /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers && /usr/bin/cmake -E cmake_link_script CMakeFiles/fileParsersTest1.dir/link.txt --verbose=1 +/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/filterCatalogTest.dir/link.d CMakeFiles/filterCatalogTest.dir/filtercatalogtest.cpp.o -o filterCatalogTest ../../../lib/libRDKitFilterCatalog.so.1.2025.03.1 ../../../lib/libRDKitFileParsers.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/aarch64-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/aarch64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl /usr/lib/aarch64-linux-gnu/libmaeparser.so make[4]: Leaving directory '/build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu' -[ 53%] Built target testFragCatalog +[ 53%] Built target filterCatalogTest make -f Code/GraphMol/Fingerprints/CMakeFiles/testFingerprints.dir/build.make Code/GraphMol/Fingerprints/CMakeFiles/testFingerprints.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu' cd /build/reproducible-path/rdkit-202503.1/obj-aarch64-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-aarch64-linux-gnu /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/Fingerprints /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/Fingerprints/CMakeFiles/testFingerprints.dir/DependInfo.cmake "--color=" @@ -5186,11 +5202,9 @@ make[4]: Entering directory '/build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu' [ 53%] Building CXX object Code/GraphMol/Fingerprints/CMakeFiles/testFingerprints.dir/test1.cpp.o cd /build/reproducible-path/rdkit-202503.1/obj-aarch64-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_BUILD_XYZ2MOL_SUPPORT -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 -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/GraphMol/Fingerprints/CMakeFiles/testFingerprints.dir/test1.cpp.o -MF CMakeFiles/testFingerprints.dir/test1.cpp.o.d -o CMakeFiles/testFingerprints.dir/test1.cpp.o -c /build/reproducible-path/rdkit-202503.1/Code/GraphMol/Fingerprints/test1.cpp -[ 53%] Linking CXX executable filterCatalogTest -cd /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FilterCatalog && /usr/bin/cmake -E cmake_link_script CMakeFiles/filterCatalogTest.dir/link.txt --verbose=1 -/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/filterCatalogTest.dir/link.d CMakeFiles/filterCatalogTest.dir/filtercatalogtest.cpp.o -o filterCatalogTest ../../../lib/libRDKitFilterCatalog.so.1.2025.03.1 ../../../lib/libRDKitFileParsers.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/aarch64-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/aarch64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl /usr/lib/aarch64-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 -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/fileParsersTest1.dir/link.d CMakeFiles/fileParsersTest1.dir/test1.cpp.o -o fileParsersTest1 ../../../lib/libRDKitFileParsers.so.1.2025.03.1 ../../../lib/libRDKitChemTransforms.so.1.2025.03.1 ../../../lib/libRDKitDepictor.so.1.2025.03.1 /usr/lib/aarch64-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 ../../../lib/libRDKitRDGeneral.so.1.2025.03.1 /usr/lib/aarch64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl /usr/lib/aarch64-linux-gnu/libmaeparser.so make[4]: Leaving directory '/build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu' -[ 53%] Built target filterCatalogTest +[ 53%] Built target fileParsersTest1 make -f Code/GraphMol/Fingerprints/CMakeFiles/testMHFPFingerprint.dir/build.make Code/GraphMol/Fingerprints/CMakeFiles/testMHFPFingerprint.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu' cd /build/reproducible-path/rdkit-202503.1/obj-aarch64-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-aarch64-linux-gnu /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/Fingerprints /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/Fingerprints/CMakeFiles/testMHFPFingerprint.dir/DependInfo.cmake "--color=" @@ -5199,8 +5213,6 @@ make[4]: Entering directory '/build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu' [ 53%] Building CXX object Code/GraphMol/Fingerprints/CMakeFiles/testMHFPFingerprint.dir/testMHFPFingerprint.cpp.o cd /build/reproducible-path/rdkit-202503.1/obj-aarch64-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_BUILD_XYZ2MOL_SUPPORT -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 -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/GraphMol/Fingerprints/CMakeFiles/testMHFPFingerprint.dir/testMHFPFingerprint.cpp.o -MF CMakeFiles/testMHFPFingerprint.dir/testMHFPFingerprint.cpp.o.d -o CMakeFiles/testMHFPFingerprint.dir/testMHFPFingerprint.cpp.o -c /build/reproducible-path/rdkit-202503.1/Code/GraphMol/Fingerprints/testMHFPFingerprint.cpp -[ 53%] Building CXX object Code/GraphMol/Descriptors/CMakeFiles/Descriptors.dir/BCUT.cpp.o -cd /build/reproducible-path/rdkit-202503.1/obj-aarch64-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_BUILD_XYZ2MOL_SUPPORT -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 -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/Descriptors/CMakeFiles/Descriptors.dir/BCUT.cpp.o -MF CMakeFiles/Descriptors.dir/BCUT.cpp.o.d -o CMakeFiles/Descriptors.dir/BCUT.cpp.o -c /build/reproducible-path/rdkit-202503.1/Code/GraphMol/Descriptors/BCUT.cpp make -f Code/GraphMol/Fingerprints/CMakeFiles/testFingerprintGenerators.dir/build.make Code/GraphMol/Fingerprints/CMakeFiles/testFingerprintGenerators.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu' cd /build/reproducible-path/rdkit-202503.1/obj-aarch64-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-aarch64-linux-gnu /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/Fingerprints /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/Fingerprints/CMakeFiles/testFingerprintGenerators.dir/DependInfo.cmake "--color=" @@ -5209,8 +5221,12 @@ make[4]: Entering directory '/build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu' [ 53%] Building CXX object Code/GraphMol/Fingerprints/CMakeFiles/testFingerprintGenerators.dir/testFingerprintGenerators.cpp.o cd /build/reproducible-path/rdkit-202503.1/obj-aarch64-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_BUILD_XYZ2MOL_SUPPORT -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 -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/GraphMol/Fingerprints/CMakeFiles/testFingerprintGenerators.dir/testFingerprintGenerators.cpp.o -MF CMakeFiles/testFingerprintGenerators.dir/testFingerprintGenerators.cpp.o.d -o CMakeFiles/testFingerprintGenerators.dir/testFingerprintGenerators.cpp.o -c /build/reproducible-path/rdkit-202503.1/Code/GraphMol/Fingerprints/testFingerprintGenerators.cpp -[ 53%] Linking CXX executable substructTestCatch -cd /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/Substruct && /usr/bin/cmake -E cmake_link_script CMakeFiles/substructTestCatch.dir/link.txt --verbose=1 +[ 53%] Linking CXX shared library ../../../lib/libRDKitChemReactions.so +cd /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/ChemReactions && /usr/bin/cmake -E cmake_link_script CMakeFiles/ChemReactions.dir/link.txt --verbose=1 +/usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat 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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/aarch64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl /usr/lib/aarch64-linux-gnu/libmaeparser.so +cd /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/ChemReactions && /usr/bin/cmake -E cmake_symlink_library ../../../lib/libRDKitChemReactions.so.1.2025.03.1 ../../../lib/libRDKitChemReactions.so.1 ../../../lib/libRDKitChemReactions.so +make[4]: Leaving directory '/build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu' +[ 53%] Built target ChemReactions make -f Code/GraphMol/Fingerprints/CMakeFiles/fpTestCatch.dir/build.make Code/GraphMol/Fingerprints/CMakeFiles/fpTestCatch.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu' cd /build/reproducible-path/rdkit-202503.1/obj-aarch64-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-aarch64-linux-gnu /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/Fingerprints /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/Fingerprints/CMakeFiles/fpTestCatch.dir/DependInfo.cmake "--color=" @@ -5219,9 +5235,13 @@ make[4]: Entering directory '/build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu' [ 53%] Building CXX object Code/GraphMol/Fingerprints/CMakeFiles/fpTestCatch.dir/catch_tests.cpp.o cd /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/Fingerprints && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK 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../../../lib/libRDKitSmilesParse.so.1.2025.03.1 ../../../lib/libRDKitSubstructMatch.so.1.2025.03.1 ../../../lib/libRDKitGenericGroups.so.1.2025.03.1 ../../../lib/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 ../../../lib/libRDKitRDGeneral.so.1.2025.03.1 /usr/lib/aarch64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl /usr/lib/aarch64-linux-gnu/libmaeparser.so +[ 53%] Building CXX object Code/GraphMol/Descriptors/CMakeFiles/Descriptors.dir/BCUT.cpp.o +cd /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/Descriptors && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK 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Code/GraphMol/Descriptors/CMakeFiles/Descriptors.dir/BCUT.cpp.o -MF CMakeFiles/Descriptors.dir/BCUT.cpp.o.d -o CMakeFiles/Descriptors.dir/BCUT.cpp.o -c /build/reproducible-path/rdkit-202503.1/Code/GraphMol/Descriptors/BCUT.cpp +[ 53%] Linking CXX executable testSubstructMatch +cd /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/Substruct && /usr/bin/cmake -E cmake_link_script CMakeFiles/testSubstructMatch.dir/link.txt --verbose=1 +/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/testSubstructMatch.dir/link.d CMakeFiles/testSubstructMatch.dir/test1.cpp.o -o testSubstructMatch ../../../lib/libRDKitFileParsers.so.1.2025.03.1 ../../../lib/libRDKitChemTransforms.so.1.2025.03.1 ../../../lib/libRDKitDepictor.so.1.2025.03.1 /usr/lib/aarch64-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 ../../../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/aarch64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl /usr/lib/aarch64-linux-gnu/libmaeparser.so make[4]: Leaving directory '/build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu' -[ 53%] Built target substructTestCatch +[ 53%] Built target testSubstructMatch 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-aarch64-linux-gnu' cd /build/reproducible-path/rdkit-202503.1/obj-aarch64-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-aarch64-linux-gnu /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/Fingerprints /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/Fingerprints/CMakeFiles/fpGenTestCatch.dir/DependInfo.cmake "--color=" @@ -5230,45 +5250,83 @@ make[4]: Entering directory '/build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu' [ 53%] Building CXX object Code/GraphMol/Fingerprints/CMakeFiles/fpGenTestCatch.dir/fpgen_catch_tests.cpp.o cd /build/reproducible-path/rdkit-202503.1/obj-aarch64-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_BUILD_XYZ2MOL_SUPPORT -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202503.1/External -I/build/reproducible-path/rdkit-202503.1/Code -I/build/reproducible-path/rdkit-202503.1/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat 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&& /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_BUILD_XYZ2MOL_SUPPORT -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -Drdfragcatalog_EXPORTS -I/build/reproducible-path/rdkit-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/aarch64-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 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object Code/GraphMol/MolTransforms/CMakeFiles/testMolTransforms.dir/test1.cpp.o cd /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/MolTransforms && /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_BUILD_XYZ2MOL_SUPPORT -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 -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/GraphMol/MolTransforms/CMakeFiles/testMolTransforms.dir/test1.cpp.o -MF CMakeFiles/testMolTransforms.dir/test1.cpp.o.d -o CMakeFiles/testMolTransforms.dir/test1.cpp.o -c /build/reproducible-path/rdkit-202503.1/Code/GraphMol/MolTransforms/test1.cpp -[ 53%] Linking CXX executable testSubstructMatch -cd /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/Substruct && /usr/bin/cmake -E cmake_link_script CMakeFiles/testSubstructMatch.dir/link.txt --verbose=1 -/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now 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-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 -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/GraphMol/ForceFieldHelpers/CMakeFiles/forceFieldHelpersCatch.dir/catch_tests.cpp.o -MF CMakeFiles/forceFieldHelpersCatch.dir/catch_tests.cpp.o.d -o CMakeFiles/forceFieldHelpersCatch.dir/catch_tests.cpp.o -c /build/reproducible-path/rdkit-202503.1/Code/GraphMol/ForceFieldHelpers/catch_tests.cpp -[ 54%] Linking CXX shared module ../../../../rdkit/Chem/rdfragcatalog.so -cd /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FragCatalog/Wrap && /usr/bin/cmake -E cmake_link_script 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/usr/lib/aarch64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl +[ 54%] Linking CXX executable fpTestCatch +cd /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/Fingerprints && /usr/bin/cmake -E cmake_link_script CMakeFiles/fpTestCatch.dir/link.txt --verbose=1 +/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/fpTestCatch.dir/link.d CMakeFiles/fpTestCatch.dir/catch_tests.cpp.o -o fpTestCatch ../../RDGeneral/librdkitCatch.a ../../../lib/libRDKitFingerprints.so.1.2025.03.1 ../../../lib/libRDKitFileParsers.so.1.2025.03.1 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'/build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu' -[ 54%] Built target rdfragcatalog +[ 54%] Built target fpTestCatch make -f Code/GraphMol/ForceFieldHelpers/MMFF/CMakeFiles/testMMFFForceFieldHelpers.dir/build.make Code/GraphMol/ForceFieldHelpers/MMFF/CMakeFiles/testMMFFForceFieldHelpers.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu' cd /build/reproducible-path/rdkit-202503.1/obj-aarch64-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-aarch64-linux-gnu /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/ForceFieldHelpers/MMFF /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/ForceFieldHelpers/MMFF/CMakeFiles/testMMFFForceFieldHelpers.dir/DependInfo.cmake "--color=" @@ -5277,15 +5335,6 @@ make[4]: Entering directory '/build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu' [ 54%] Building CXX object Code/GraphMol/ForceFieldHelpers/MMFF/CMakeFiles/testMMFFForceFieldHelpers.dir/testMMFFHelpers.cpp.o cd /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/ForceFieldHelpers/MMFF && /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_BUILD_XYZ2MOL_SUPPORT -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 -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/GraphMol/ForceFieldHelpers/MMFF/CMakeFiles/testMMFFForceFieldHelpers.dir/testMMFFHelpers.cpp.o -MF CMakeFiles/testMMFFForceFieldHelpers.dir/testMMFFHelpers.cpp.o.d -o CMakeFiles/testMMFFForceFieldHelpers.dir/testMMFFHelpers.cpp.o -c /build/reproducible-path/rdkit-202503.1/Code/GraphMol/ForceFieldHelpers/MMFF/testMMFFHelpers.cpp -/build/reproducible-path/rdkit-202503.1/Code/GraphMol/Descriptors/BCUT.cpp: In function 'std::pair RDKit::Descriptors::{anonymous}::BCUT2D(std::unique_ptr >&, const std::vector&)': -/build/reproducible-path/rdkit-202503.1/Code/GraphMol/Descriptors/BCUT.cpp:70:71: note: parameter passing for argument of type 'std::pair' when C++17 is enabled changed to match C++14 in GCC 10.1 - 70 | const std::vector &atom_props) { - | ^ -[ 54%] Linking CXX executable chemTransformsTestCatch -cd /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/ChemTransforms && /usr/bin/cmake -E cmake_link_script CMakeFiles/chemTransformsTestCatch.dir/link.txt --verbose=1 -/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now -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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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-aarch64-linux-gnu' cd /build/reproducible-path/rdkit-202503.1/obj-aarch64-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-aarch64-linux-gnu /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/ForceFieldHelpers/MMFF /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/ForceFieldHelpers/MMFF/CMakeFiles/testMMFFForceFieldHelpersMultiThread.dir/DependInfo.cmake "--color=" @@ -5294,11 +5343,6 @@ make[4]: Entering directory '/build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu' [ 54%] Building CXX object Code/GraphMol/ForceFieldHelpers/MMFF/CMakeFiles/testMMFFForceFieldHelpersMultiThread.dir/testMultiThread.cpp.o cd /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/ForceFieldHelpers/MMFF && /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_BUILD_XYZ2MOL_SUPPORT -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 -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/GraphMol/ForceFieldHelpers/MMFF/CMakeFiles/testMMFFForceFieldHelpersMultiThread.dir/testMultiThread.cpp.o -MF CMakeFiles/testMMFFForceFieldHelpersMultiThread.dir/testMultiThread.cpp.o.d -o CMakeFiles/testMMFFForceFieldHelpersMultiThread.dir/testMultiThread.cpp.o -c /build/reproducible-path/rdkit-202503.1/Code/GraphMol/ForceFieldHelpers/MMFF/testMultiThread.cpp -[ 54%] Linking CXX executable testChemTransforms -cd /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/ChemTransforms && /usr/bin/cmake -E cmake_link_script CMakeFiles/testChemTransforms.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 -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/testChemTransforms.dir/link.d CMakeFiles/testChemTransforms.dir/testChemTransforms.cpp.o -o testChemTransforms ../../../lib/libRDKitFileParsers.so.1.2025.03.1 ../../../lib/libRDKitChemTransforms.so.1.2025.03.1 ../../../lib/libRDKitDepictor.so.1.2025.03.1 /usr/lib/aarch64-linux-gnu/libcoordgen.so ../../../lib/libRDKitMolAlign.so.1.2025.03.1 ../../../lib/libRDKitSubstructMatch.so.1.2025.03.1 ../../../lib/libRDKitSmilesParse.so.1.2025.03.1 ../../../lib/libRDKitMolTransforms.so.1.2025.03.1 ../../../lib/libRDKitEigenSolvers.so.1.2025.03.1 ../../../lib/libRDKitAlignment.so.1.2025.03.1 ../../../lib/libRDKitGenericGroups.so.1.2025.03.1 ../../../lib/libRDKitGraphMol.so.1.2025.03.1 ../../../lib/libRDKitRDGeometryLib.so.1.2025.03.1 ../../../lib/libRDKitDataStructs.so.1.2025.03.1 ../../../lib/libRDKitRDGeneral.so.1.2025.03.1 /usr/lib/aarch64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl /usr/lib/aarch64-linux-gnu/libmaeparser.so -make[4]: Leaving directory '/build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu' -[ 54%] Built target testChemTransforms 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-aarch64-linux-gnu' cd /build/reproducible-path/rdkit-202503.1/obj-aarch64-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-aarch64-linux-gnu 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../../../../rdkit/Chem/rdfragcatalog.so +cd /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FragCatalog/Wrap && /usr/bin/cmake -E cmake_link_script CMakeFiles/rdfragcatalog.dir/link.txt --verbose=1 +/usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -g -fwrapv -O2 -Wl,--dependency-file=CMakeFiles/rdfragcatalog.dir/link.d -Wl,-z,relro -Wl,-z,now -shared -o ../../../../rdkit/Chem/rdfragcatalog.so CMakeFiles/rdfragcatalog.dir/rdfragcatalog.cpp.o CMakeFiles/rdfragcatalog.dir/FragCatalog.cpp.o CMakeFiles/rdfragcatalog.dir/FragCatParams.cpp.o CMakeFiles/rdfragcatalog.dir/FragCatGenerator.cpp.o 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-DBOOST_NUMPY_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_MAX_ARITY=32 -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_BUILD_XYZ2MOL_SUPPORT -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DrdDistGeom_EXPORTS -I/build/reproducible-path/rdkit-202503.1/External -I/build/reproducible-path/rdkit-202503.1/Code -I/usr/lib/aarch64-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 -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 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-fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/Descriptors/CMakeFiles/Descriptors.dir/CoulombMat.cpp.o -MF CMakeFiles/Descriptors.dir/CoulombMat.cpp.o.d -o CMakeFiles/Descriptors.dir/CoulombMat.cpp.o -c /build/reproducible-path/rdkit-202503.1/Code/GraphMol/Descriptors/CoulombMat.cpp +[ 61%] Building CXX object Code/GraphMol/MolDraw2D/CMakeFiles/MolDraw2D.dir/MolDraw2DUtils.cpp.o +cd /build/reproducible-path/rdkit-202503.1/obj-aarch64-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 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-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 -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/MolDraw2D/CMakeFiles/MolDraw2D.dir/AtomSymbol.cpp.o -MF CMakeFiles/MolDraw2D.dir/AtomSymbol.cpp.o.d -o CMakeFiles/MolDraw2D.dir/AtomSymbol.cpp.o -c /build/reproducible-path/rdkit-202503.1/Code/GraphMol/MolDraw2D/AtomSymbol.cpp +[ 61%] Building CXX object Code/GraphMol/MolDraw2D/CMakeFiles/MolDraw2D.dir/DrawAnnotation.cpp.o +cd /build/reproducible-path/rdkit-202503.1/obj-aarch64-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_BUILD_XYZ2MOL_SUPPORT -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202503.1/External -I/usr/include/freetype2 -I/build/reproducible-path/rdkit-202503.1/Code -I/build/reproducible-path/rdkit-202503.1/External/boost-numeric-bindings -isystem /usr/include/eigen3 -isystem /usr/include/cairo -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/MolDraw2D/CMakeFiles/MolDraw2D.dir/DrawAnnotation.cpp.o -MF CMakeFiles/MolDraw2D.dir/DrawAnnotation.cpp.o.d -o CMakeFiles/MolDraw2D.dir/DrawAnnotation.cpp.o -c /build/reproducible-path/rdkit-202503.1/Code/GraphMol/MolDraw2D/DrawAnnotation.cpp make -f Code/GraphMol/MolEnumerator/CMakeFiles/MolEnumerator.dir/build.make Code/GraphMol/MolEnumerator/CMakeFiles/MolEnumerator.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu' cd /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202503.1 /build/reproducible-path/rdkit-202503.1/Code/GraphMol/MolEnumerator /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/MolEnumerator /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/MolEnumerator/CMakeFiles/MolEnumerator.dir/DependInfo.cmake "--color=" @@ -5592,112 +5627,75 @@ make[4]: Entering directory '/build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu' [ 61%] Building CXX object Code/GraphMol/MolEnumerator/CMakeFiles/MolEnumerator.dir/MolEnumerator.cpp.o cd /build/reproducible-path/rdkit-202503.1/obj-aarch64-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_BUILD_XYZ2MOL_SUPPORT -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 -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/MolEnumerator/CMakeFiles/MolEnumerator.dir/MolEnumerator.cpp.o -MF CMakeFiles/MolEnumerator.dir/MolEnumerator.cpp.o.d -o CMakeFiles/MolEnumerator.dir/MolEnumerator.cpp.o -c /build/reproducible-path/rdkit-202503.1/Code/GraphMol/MolEnumerator/MolEnumerator.cpp -[ 62%] Building CXX object Code/GraphMol/Descriptors/CMakeFiles/Descriptors.dir/CoulombMat.cpp.o -cd /build/reproducible-path/rdkit-202503.1/obj-aarch64-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_BUILD_XYZ2MOL_SUPPORT -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 -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/Descriptors/CMakeFiles/Descriptors.dir/CoulombMat.cpp.o -MF CMakeFiles/Descriptors.dir/CoulombMat.cpp.o.d -o CMakeFiles/Descriptors.dir/CoulombMat.cpp.o -c /build/reproducible-path/rdkit-202503.1/Code/GraphMol/Descriptors/CoulombMat.cpp -[ 62%] Building CXX object Code/GraphMol/RascalMCES/CMakeFiles/RascalMCES.dir/RascalCluster.cpp.o -cd /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/RascalMCES && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDKIT_RASCALMCES_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_BUILD_XYZ2MOL_SUPPORT -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DRascalMCES_EXPORTS -I/build/reproducible-path/rdkit-202503.1/External -I/build/reproducible-path/rdkit-202503.1/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/RascalMCES/CMakeFiles/RascalMCES.dir/RascalCluster.cpp.o -MF CMakeFiles/RascalMCES.dir/RascalCluster.cpp.o.d -o CMakeFiles/RascalMCES.dir/RascalCluster.cpp.o -c /build/reproducible-path/rdkit-202503.1/Code/GraphMol/RascalMCES/RascalCluster.cpp -[ 62%] Building CXX object Code/GraphMol/MolEnumerator/CMakeFiles/MolEnumerator.dir/PositionVariation.cpp.o -cd /build/reproducible-path/rdkit-202503.1/obj-aarch64-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_BUILD_XYZ2MOL_SUPPORT -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 -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/MolEnumerator/CMakeFiles/MolEnumerator.dir/PositionVariation.cpp.o -MF CMakeFiles/MolEnumerator.dir/PositionVariation.cpp.o.d -o CMakeFiles/MolEnumerator.dir/PositionVariation.cpp.o -c /build/reproducible-path/rdkit-202503.1/Code/GraphMol/MolEnumerator/PositionVariation.cpp -[ 62%] Building CXX object Code/GraphMol/MolDraw2D/CMakeFiles/MolDraw2D.dir/MolDraw2DUtils.cpp.o -cd /build/reproducible-path/rdkit-202503.1/obj-aarch64-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_BUILD_XYZ2MOL_SUPPORT -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202503.1/External -I/usr/include/freetype2 -I/build/reproducible-path/rdkit-202503.1/Code -I/build/reproducible-path/rdkit-202503.1/External/boost-numeric-bindings -isystem /usr/include/eigen3 -isystem /usr/include/cairo -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/MolDraw2D/CMakeFiles/MolDraw2D.dir/MolDraw2DUtils.cpp.o -MF CMakeFiles/MolDraw2D.dir/MolDraw2DUtils.cpp.o.d -o CMakeFiles/MolDraw2D.dir/MolDraw2DUtils.cpp.o -c /build/reproducible-path/rdkit-202503.1/Code/GraphMol/MolDraw2D/MolDraw2DUtils.cpp -[ 62%] Linking CXX shared library ../../../lib/libRDKitMMPA.so +[ 61%] Linking CXX shared library ../../../lib/libRDKitMMPA.so cd /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/MMPA && /usr/bin/cmake -E cmake_link_script CMakeFiles/MMPA.dir/link.txt --verbose=1 +[ 61%] Building CXX object Code/GraphMol/RascalMCES/CMakeFiles/RascalMCES.dir/RascalCluster.cpp.o +cd /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/RascalMCES && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDKIT_RASCALMCES_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_BUILD_XYZ2MOL_SUPPORT -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DRascalMCES_EXPORTS -I/build/reproducible-path/rdkit-202503.1/External -I/build/reproducible-path/rdkit-202503.1/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/RascalMCES/CMakeFiles/RascalMCES.dir/RascalCluster.cpp.o -MF CMakeFiles/RascalMCES.dir/RascalCluster.cpp.o.d -o CMakeFiles/RascalMCES.dir/RascalCluster.cpp.o -c /build/reproducible-path/rdkit-202503.1/Code/GraphMol/RascalMCES/RascalCluster.cpp /usr/bin/c++ -fPIC -g -O2 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-fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/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 +[ 62%] Building CXX object Code/GraphMol/MolDraw2D/CMakeFiles/MolDraw2D.dir/DrawMolMCH.cpp.o +cd /build/reproducible-path/rdkit-202503.1/obj-aarch64-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 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/build/reproducible-path/rdkit-202503.1/Code/GraphMol/FMCS/SubstructMatchCustom.cpp +[ 63%] Linking CXX executable molHashCatchTest +cd /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/MolHash && /usr/bin/cmake -E cmake_link_script CMakeFiles/molHashCatchTest.dir/link.txt --verbose=1 +/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/molHashCatchTest.dir/link.d CMakeFiles/molHashCatchTest.dir/catch_tests.cpp.o -o molHashCatchTest ../../RDGeneral/librdkitCatch.a ../../../lib/libRDKitFileParsers.so.1.2025.03.1 ../../../lib/libRDKitMolHash.so.1.2025.03.1 /usr/lib/libCatch2.a ../../../lib/libRDKitChemTransforms.so.1.2025.03.1 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'/build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu' -[ 62%] Building CXX object Code/GraphMol/Deprotect/CMakeFiles/Deprotect.dir/Deprotect.cpp.o +[ 63%] Building CXX object Code/GraphMol/Deprotect/CMakeFiles/Deprotect.dir/Deprotect.cpp.o cd /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/Deprotect && /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 -DDeprotect_EXPORTS -DRDKIT_DEPROTECT_BUILD -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_BUILD_XYZ2MOL_SUPPORT -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 -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/Deprotect/CMakeFiles/Deprotect.dir/Deprotect.cpp.o -MF CMakeFiles/Deprotect.dir/Deprotect.cpp.o.d -o CMakeFiles/Deprotect.dir/Deprotect.cpp.o -c /build/reproducible-path/rdkit-202503.1/Code/GraphMol/Deprotect/Deprotect.cpp -[ 62%] Building CXX object Code/GraphMol/MolDraw2D/CMakeFiles/MolDraw2D.dir/AtomSymbol.cpp.o -cd /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/MolDraw2D && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB 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-DRDK_BUILD_XYZ2MOL_SUPPORT -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 -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/MolEnumerator/CMakeFiles/MolEnumerator.dir/RepeatUnit.cpp.o -MF CMakeFiles/MolEnumerator.dir/RepeatUnit.cpp.o.d -o CMakeFiles/MolEnumerator.dir/RepeatUnit.cpp.o -c /build/reproducible-path/rdkit-202503.1/Code/GraphMol/MolEnumerator/RepeatUnit.cpp In file included from /usr/include/c++/14/bits/stl_algobase.h:64, from /usr/include/c++/14/string:51, from /build/reproducible-path/rdkit-202503.1/Code/GraphMol/MolDraw2D/DrawText.h:19, @@ -5709,58 +5707,61 @@ /usr/include/c++/14/bits/stl_pair.h:1132:5: note: parameter passing for argument of type 'std::pair' when C++17 is enabled changed to match C++14 in GCC 10.1 1132 | make_pair(_T1&& __x, _T2&& __y) | ^~~~~~~~~ -[ 65%] Linking CXX shared library ../../../lib/libRDKitMolEnumerator.so -cd /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/MolEnumerator && /usr/bin/cmake -E cmake_link_script CMakeFiles/MolEnumerator.dir/link.txt --verbose=1 -/usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,--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/aarch64-linux-gnu/libmaeparser.so ../../../lib/libRDKitChemTransforms.so.1.2025.03.1 ../../../lib/libRDKitDepictor.so.1.2025.03.1 /usr/lib/aarch64-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/aarch64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl -cd /build/reproducible-path/rdkit-202503.1/obj-aarch64-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 +[ 65%] Linking CXX executable trajectoryTest +cd /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/Trajectory && /usr/bin/cmake -E cmake_link_script CMakeFiles/trajectoryTest.dir/link.txt --verbose=1 +/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/trajectoryTest.dir/link.d CMakeFiles/trajectoryTest.dir/trajectoryTest.cpp.o -o trajectoryTest ../../../lib/libRDKitFileParsers.so.1.2025.03.1 ../../../lib/libRDKitForceFieldHelpers.so.1.2025.03.1 ../../../lib/libRDKitChemTransforms.so.1.2025.03.1 ../../../lib/libRDKitDepictor.so.1.2025.03.1 /usr/lib/aarch64-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/aarch64-linux-gnu/libmaeparser.so ../../../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 ../../../lib/libRDKitRDGeneral.so.1.2025.03.1 /usr/lib/aarch64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl make[4]: Leaving directory '/build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu' -[ 65%] Built target MolEnumerator -[ 65%] Building CXX object Code/GraphMol/MolDraw2D/CMakeFiles/MolDraw2D.dir/DrawTextSVG.cpp.o -cd 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-fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/MolDraw2D/CMakeFiles/MolDraw2D.dir/DrawTextSVG.cpp.o -MF CMakeFiles/MolDraw2D.dir/DrawTextSVG.cpp.o.d -o CMakeFiles/MolDraw2D.dir/DrawTextSVG.cpp.o -c /build/reproducible-path/rdkit-202503.1/Code/GraphMol/MolDraw2D/DrawTextSVG.cpp +[ 65%] Built target trajectoryTest +make -f Code/GraphMol/DetermineBonds/CMakeFiles/DetermineBonds.dir/build.make Code/GraphMol/DetermineBonds/CMakeFiles/DetermineBonds.dir/depend +make[4]: Entering directory '/build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu' +cd /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202503.1 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Code/GraphMol/DetermineBonds/CMakeFiles/DetermineBonds.dir/DetermineBonds.cpp.o -MF CMakeFiles/DetermineBonds.dir/DetermineBonds.cpp.o.d -o CMakeFiles/DetermineBonds.dir/DetermineBonds.cpp.o -c /build/reproducible-path/rdkit-202503.1/Code/GraphMol/DetermineBonds/DetermineBonds.cpp [ 65%] Building CXX object Code/GraphMol/MolDraw2D/CMakeFiles/MolDraw2D.dir/MolDraw2DJS.cpp.o cd /build/reproducible-path/rdkit-202503.1/obj-aarch64-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_BUILD_XYZ2MOL_SUPPORT -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202503.1/External -I/usr/include/freetype2 -I/build/reproducible-path/rdkit-202503.1/Code -I/build/reproducible-path/rdkit-202503.1/External/boost-numeric-bindings -isystem /usr/include/eigen3 -isystem /usr/include/cairo -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/MolDraw2D/CMakeFiles/MolDraw2D.dir/MolDraw2DJS.cpp.o -MF CMakeFiles/MolDraw2D.dir/MolDraw2DJS.cpp.o.d -o CMakeFiles/MolDraw2D.dir/MolDraw2DJS.cpp.o -c /build/reproducible-path/rdkit-202503.1/Code/GraphMol/MolDraw2D/MolDraw2DJS.cpp [ 65%] Building CXX object 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-ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/MolDraw2D/CMakeFiles/MolDraw2D.dir/DrawTextJS.cpp.o -MF CMakeFiles/MolDraw2D.dir/DrawTextJS.cpp.o.d -o CMakeFiles/MolDraw2D.dir/DrawTextJS.cpp.o -c /build/reproducible-path/rdkit-202503.1/Code/GraphMol/MolDraw2D/DrawTextJS.cpp -make -f Code/GraphMol/Wrap/CMakeFiles/rdmolops.dir/build.make Code/GraphMol/Wrap/CMakeFiles/rdmolops.dir/depend +[ 66%] Building CXX object Code/GraphMol/MolDraw2D/CMakeFiles/MolDraw2D.dir/MolDraw2DCairo.cpp.o +cd /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/MolDraw2D && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK 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-Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/MolDraw2D/CMakeFiles/MolDraw2D.dir/MolDraw2DCairo.cpp.o -MF CMakeFiles/MolDraw2D.dir/MolDraw2DCairo.cpp.o.d -o CMakeFiles/MolDraw2D.dir/MolDraw2DCairo.cpp.o -c /build/reproducible-path/rdkit-202503.1/Code/GraphMol/MolDraw2D/MolDraw2DCairo.cpp +make -f Code/GraphMol/MolInterchange/CMakeFiles/molInterchangeTest1.dir/build.make Code/GraphMol/MolInterchange/CMakeFiles/molInterchangeTest1.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu' -cd /build/reproducible-path/rdkit-202503.1/obj-aarch64-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-aarch64-linux-gnu /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/Wrap 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/build/reproducible-path/rdkit-202503.1/obj-aarch64-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-aarch64-linux-gnu' -[ 65%] Built target DetermineBonds -make -f Code/GraphMol/MolEnumerator/CMakeFiles/testMolEnumerator.dir/build.make Code/GraphMol/MolEnumerator/CMakeFiles/testMolEnumerator.dir/depend +[ 66%] Built target FMCS +make -f Code/GraphMol/MolInterchange/CMakeFiles/molInterchangeCatchTest.dir/build.make Code/GraphMol/MolInterchange/CMakeFiles/molInterchangeCatchTest.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu' -cd /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202503.1 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-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 -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/MolDraw2D/CMakeFiles/MolDraw2D.dir/DrawTextCairo.cpp.o -MF CMakeFiles/MolDraw2D.dir/DrawTextCairo.cpp.o.d -o CMakeFiles/MolDraw2D.dir/DrawTextCairo.cpp.o -c /build/reproducible-path/rdkit-202503.1/Code/GraphMol/MolDraw2D/DrawTextCairo.cpp +[ 66%] Building CXX object Code/GraphMol/MolDraw2D/CMakeFiles/MolDraw2D.dir/DrawTextFT.cpp.o +cd /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/MolDraw2D && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB 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/build/reproducible-path/rdkit-202503.1/obj-aarch64-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 make[4]: Leaving directory '/build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu' @@ -5773,12 +5774,14 @@ make[4]: Entering directory '/build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu' [ 66%] Building CXX object Code/GraphMol/Abbreviations/CMakeFiles/testAbbreviations.dir/catch_tests.cpp.o cd /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/Abbreviations && /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 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-fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -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/aarch64-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/aarch64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl /usr/lib/aarch64-linux-gnu/libmaeparser.so -cd /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/RascalMCES && /usr/bin/cmake -E cmake_symlink_library ../../../lib/libRDKitRascalMCES.so.1.2025.03.1 ../../../lib/libRDKitRascalMCES.so.1 ../../../lib/libRDKitRascalMCES.so -make[4]: Leaving directory '/build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu' -[ 66%] Built target RascalMCES -[ 66%] Building CXX object Code/GraphMol/MolDraw2D/CMakeFiles/MolDraw2D.dir/DrawTextCairo.cpp.o -cd /build/reproducible-path/rdkit-202503.1/obj-aarch64-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_BUILD_XYZ2MOL_SUPPORT -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202503.1/External -I/usr/include/freetype2 -I/build/reproducible-path/rdkit-202503.1/Code -I/build/reproducible-path/rdkit-202503.1/External/boost-numeric-bindings -isystem /usr/include/eigen3 -isystem /usr/include/cairo -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/MolDraw2D/CMakeFiles/MolDraw2D.dir/DrawTextCairo.cpp.o -MF CMakeFiles/MolDraw2D.dir/DrawTextCairo.cpp.o.d -o CMakeFiles/MolDraw2D.dir/DrawTextCairo.cpp.o -c /build/reproducible-path/rdkit-202503.1/Code/GraphMol/MolDraw2D/DrawTextCairo.cpp +[ 66%] Building CXX object Code/GraphMol/MolDraw2D/CMakeFiles/MolDraw2D.dir/DrawTextFTSVG.cpp.o +cd /build/reproducible-path/rdkit-202503.1/obj-aarch64-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 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-DRDK_USE_STRICT_ROTOR_DEFINITION -Drdmolops_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/aarch64-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 -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/Wrap/CMakeFiles/rdmolops.dir/MolOps.cpp.o -MF CMakeFiles/rdmolops.dir/MolOps.cpp.o.d -o CMakeFiles/rdmolops.dir/MolOps.cpp.o -c /build/reproducible-path/rdkit-202503.1/Code/GraphMol/Wrap/MolOps.cpp +[ 66%] Building CXX object Code/GraphMol/MolDraw2D/CMakeFiles/MolDraw2D.dir/DrawTextFTJS.cpp.o +cd /build/reproducible-path/rdkit-202503.1/obj-aarch64-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_BUILD_XYZ2MOL_SUPPORT -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202503.1/External -I/usr/include/freetype2 -I/build/reproducible-path/rdkit-202503.1/Code -I/build/reproducible-path/rdkit-202503.1/External/boost-numeric-bindings -isystem /usr/include/eigen3 -isystem /usr/include/cairo -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/MolDraw2D/CMakeFiles/MolDraw2D.dir/DrawTextFTJS.cpp.o -MF CMakeFiles/MolDraw2D.dir/DrawTextFTJS.cpp.o.d -o CMakeFiles/MolDraw2D.dir/DrawTextFTJS.cpp.o -c /build/reproducible-path/rdkit-202503.1/Code/GraphMol/MolDraw2D/DrawTextFTJS.cpp +[ 66%] Building CXX object Code/GraphMol/MolDraw2D/CMakeFiles/MolDraw2D.dir/DrawTextFTCairo.cpp.o +cd /build/reproducible-path/rdkit-202503.1/obj-aarch64-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_BUILD_XYZ2MOL_SUPPORT -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202503.1/External -I/usr/include/freetype2 -I/build/reproducible-path/rdkit-202503.1/Code -I/build/reproducible-path/rdkit-202503.1/External/boost-numeric-bindings -isystem /usr/include/eigen3 -isystem /usr/include/cairo -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/MolDraw2D/CMakeFiles/MolDraw2D.dir/DrawTextFTCairo.cpp.o -MF CMakeFiles/MolDraw2D.dir/DrawTextFTCairo.cpp.o.d -o CMakeFiles/MolDraw2D.dir/DrawTextFTCairo.cpp.o -c /build/reproducible-path/rdkit-202503.1/Code/GraphMol/MolDraw2D/DrawTextFTCairo.cpp make -f Code/GraphMol/MolProcessing/CMakeFiles/MolProcessing.dir/build.make Code/GraphMol/MolProcessing/CMakeFiles/MolProcessing.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu' cd /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202503.1 /build/reproducible-path/rdkit-202503.1/Code/GraphMol/MolProcessing /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/MolProcessing /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/MolProcessing/CMakeFiles/MolProcessing.dir/DependInfo.cmake "--color=" @@ -5787,6 +5790,8 @@ make[4]: Entering directory '/build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu' [ 67%] Building CXX object Code/GraphMol/MolProcessing/CMakeFiles/MolProcessing.dir/MolProcessing.cpp.o cd /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/MolProcessing && /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 -DMolProcessing_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_MOLPROCESSING_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_BUILD_XYZ2MOL_SUPPORT -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 -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/MolProcessing/CMakeFiles/MolProcessing.dir/MolProcessing.cpp.o -MF CMakeFiles/MolProcessing.dir/MolProcessing.cpp.o.d -o CMakeFiles/MolProcessing.dir/MolProcessing.cpp.o -c /build/reproducible-path/rdkit-202503.1/Code/GraphMol/MolProcessing/MolProcessing.cpp +[ 67%] Linking CXX shared library ../../../lib/libRDKitMolEnumerator.so +cd /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/MolEnumerator && /usr/bin/cmake -E cmake_link_script CMakeFiles/MolEnumerator.dir/link.txt --verbose=1 make -f Code/GraphMol/MolInteractionFields/CMakeFiles/testMIF.dir/build.make Code/GraphMol/MolInteractionFields/CMakeFiles/testMIF.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu' cd /build/reproducible-path/rdkit-202503.1/obj-aarch64-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-aarch64-linux-gnu /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/MolInteractionFields /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/MolInteractionFields/CMakeFiles/testMIF.dir/DependInfo.cmake "--color=" @@ -5795,11 +5800,10 @@ make[4]: Entering directory '/build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu' [ 67%] Building CXX object Code/GraphMol/MolInteractionFields/CMakeFiles/testMIF.dir/testMIF.cpp.o cd /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/MolInteractionFields && /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_BUILD_XYZ2MOL_SUPPORT -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 -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/GraphMol/MolInteractionFields/CMakeFiles/testMIF.dir/testMIF.cpp.o -MF CMakeFiles/testMIF.dir/testMIF.cpp.o.d -o CMakeFiles/testMIF.dir/testMIF.cpp.o -c /build/reproducible-path/rdkit-202503.1/Code/GraphMol/MolInteractionFields/testMIF.cpp -[ 67%] Linking CXX executable molInterchangeTest1 -cd /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/MolInterchange && /usr/bin/cmake -E cmake_link_script CMakeFiles/molInterchangeTest1.dir/link.txt --verbose=1 -/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/molInterchangeTest1.dir/link.d CMakeFiles/molInterchangeTest1.dir/test1.cpp.o -o molInterchangeTest1 ../../../lib/libRDKitMolInterchange.so.1.2025.03.1 ../../../lib/libRDKitFileParsers.so.1.2025.03.1 ../../../lib/libRDKitChemTransforms.so.1.2025.03.1 ../../../lib/libRDKitDepictor.so.1.2025.03.1 /usr/lib/aarch64-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/aarch64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl /usr/lib/aarch64-linux-gnu/libmaeparser.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 -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,--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/aarch64-linux-gnu/libmaeparser.so ../../../lib/libRDKitChemTransforms.so.1.2025.03.1 ../../../lib/libRDKitDepictor.so.1.2025.03.1 /usr/lib/aarch64-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/aarch64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl +cd /build/reproducible-path/rdkit-202503.1/obj-aarch64-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-aarch64-linux-gnu' -[ 67%] Built target molInterchangeTest1 +[ 67%] Built target MolEnumerator make -f Code/GraphMol/MarvinParse/CMakeFiles/MarvinParser.dir/build.make Code/GraphMol/MarvinParse/CMakeFiles/MarvinParser.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu' cd /build/reproducible-path/rdkit-202503.1/obj-aarch64-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-aarch64-linux-gnu /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/MarvinParse /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/MarvinParse/CMakeFiles/MarvinParser.dir/DependInfo.cmake "--color=" @@ -5808,13 +5812,12 @@ make[4]: Entering directory '/build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu' [ 68%] Building CXX object Code/GraphMol/MarvinParse/CMakeFiles/MarvinParser.dir/MarvinParser.cpp.o cd /build/reproducible-path/rdkit-202503.1/obj-aarch64-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 -DMarvinParser_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_MARVINPARSER_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_BUILD_XYZ2MOL_SUPPORT -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 -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/MarvinParse/CMakeFiles/MarvinParser.dir/MarvinParser.cpp.o -MF CMakeFiles/MarvinParser.dir/MarvinParser.cpp.o.d -o CMakeFiles/MarvinParser.dir/MarvinParser.cpp.o -c /build/reproducible-path/rdkit-202503.1/Code/GraphMol/MarvinParse/MarvinParser.cpp -[ 68%] Building CXX object Code/GraphMol/MarvinParse/CMakeFiles/MarvinParser.dir/MarvinWriter.cpp.o -cd /build/reproducible-path/rdkit-202503.1/obj-aarch64-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 -DMarvinParser_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_MARVINPARSER_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_BUILD_XYZ2MOL_SUPPORT -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 -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/MarvinParse/CMakeFiles/MarvinParser.dir/MarvinWriter.cpp.o -MF CMakeFiles/MarvinParser.dir/MarvinWriter.cpp.o.d -o CMakeFiles/MarvinParser.dir/MarvinWriter.cpp.o -c /build/reproducible-path/rdkit-202503.1/Code/GraphMol/MarvinParse/MarvinWriter.cpp -[ 68%] Linking CXX executable molInterchangeCatchTest -cd /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/MolInterchange && /usr/bin/cmake -E cmake_link_script CMakeFiles/molInterchangeCatchTest.dir/link.txt --verbose=1 -/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/molInterchangeCatchTest.dir/link.d CMakeFiles/molInterchangeCatchTest.dir/molinterchange_catch.cpp.o -o molInterchangeCatchTest ../../RDGeneral/librdkitCatch.a ../../../lib/libRDKitMolInterchange.so.1.2025.03.1 ../../../lib/libRDKitFileParsers.so.1.2025.03.1 /usr/lib/libCatch2.a ../../../lib/libRDKitChemTransforms.so.1.2025.03.1 ../../../lib/libRDKitDepictor.so.1.2025.03.1 /usr/lib/aarch64-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/aarch64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl /usr/lib/aarch64-linux-gnu/libmaeparser.so +[ 68%] Linking CXX shared library ../../../lib/libRDKitDetermineBonds.so +cd /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/DetermineBonds && /usr/bin/cmake -E cmake_link_script CMakeFiles/DetermineBonds.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 -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,--dependency-file=CMakeFiles/DetermineBonds.dir/link.d -Wl,-z,relro -Wl,-z,now -shared -Wl,-soname,libRDKitDetermineBonds.so.1 -o ../../../lib/libRDKitDetermineBonds.so.1.2025.03.1 CMakeFiles/DetermineBonds.dir/DetermineBonds.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/aarch64-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/aarch64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl /usr/lib/aarch64-linux-gnu/libmaeparser.so +cd /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/DetermineBonds && /usr/bin/cmake -E cmake_symlink_library ../../../lib/libRDKitDetermineBonds.so.1.2025.03.1 ../../../lib/libRDKitDetermineBonds.so.1 ../../../lib/libRDKitDetermineBonds.so make[4]: Leaving directory '/build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu' -[ 68%] Built target molInterchangeCatchTest +[ 68%] Built target DetermineBonds make -f Code/GraphMol/ChemReactions/CMakeFiles/testReaction.dir/build.make Code/GraphMol/ChemReactions/CMakeFiles/testReaction.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu' cd /build/reproducible-path/rdkit-202503.1/obj-aarch64-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-aarch64-linux-gnu /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/ChemReactions /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/ChemReactions/CMakeFiles/testReaction.dir/DependInfo.cmake "--color=" @@ -5823,14 +5826,6 @@ make[4]: Entering directory '/build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu' [ 68%] Building CXX object Code/GraphMol/ChemReactions/CMakeFiles/testReaction.dir/testReaction.cpp.o cd /build/reproducible-path/rdkit-202503.1/obj-aarch64-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 -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_BUILD_XYZ2MOL_SUPPORT -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 -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/GraphMol/ChemReactions/CMakeFiles/testReaction.dir/testReaction.cpp.o -MF CMakeFiles/testReaction.dir/testReaction.cpp.o.d -o CMakeFiles/testReaction.dir/testReaction.cpp.o -c /build/reproducible-path/rdkit-202503.1/Code/GraphMol/ChemReactions/testReaction.cpp -[ 68%] Building CXX object Code/GraphMol/MolDraw2D/CMakeFiles/MolDraw2D.dir/DrawTextFT.cpp.o -cd /build/reproducible-path/rdkit-202503.1/obj-aarch64-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_BUILD_XYZ2MOL_SUPPORT -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202503.1/External -I/usr/include/freetype2 -I/build/reproducible-path/rdkit-202503.1/Code -I/build/reproducible-path/rdkit-202503.1/External/boost-numeric-bindings -isystem /usr/include/eigen3 -isystem /usr/include/cairo -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/MolDraw2D/CMakeFiles/MolDraw2D.dir/DrawTextFT.cpp.o -MF CMakeFiles/MolDraw2D.dir/DrawTextFT.cpp.o.d -o CMakeFiles/MolDraw2D.dir/DrawTextFT.cpp.o -c /build/reproducible-path/rdkit-202503.1/Code/GraphMol/MolDraw2D/DrawTextFT.cpp -[ 68%] Linking CXX shared library ../../../lib/libRDKitMolProcessing.so -cd /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/MolProcessing && /usr/bin/cmake -E cmake_link_script CMakeFiles/MolProcessing.dir/link.txt --verbose=1 -/usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,--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/aarch64-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/aarch64-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/aarch64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_iostreams.so.1.83.0 -cd /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/MolProcessing && /usr/bin/cmake -E cmake_symlink_library ../../../lib/libRDKitMolProcessing.so.1.2025.03.1 ../../../lib/libRDKitMolProcessing.so.1 ../../../lib/libRDKitMolProcessing.so -make[4]: Leaving directory '/build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu' -[ 68%] Built target MolProcessing make -f Code/GraphMol/ChemReactions/CMakeFiles/testReactionFingerprints.dir/build.make Code/GraphMol/ChemReactions/CMakeFiles/testReactionFingerprints.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu' cd /build/reproducible-path/rdkit-202503.1/obj-aarch64-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-aarch64-linux-gnu /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/ChemReactions /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/ChemReactions/CMakeFiles/testReactionFingerprints.dir/DependInfo.cmake "--color=" @@ -5839,15 +5834,13 @@ make[4]: Entering directory '/build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu' [ 68%] Building CXX object Code/GraphMol/ChemReactions/CMakeFiles/testReactionFingerprints.dir/testReactionFingerprints.cpp.o cd /build/reproducible-path/rdkit-202503.1/obj-aarch64-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 -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_BUILD_XYZ2MOL_SUPPORT -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/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/aarch64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl make[4]: Leaving directory '/build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu' [ 72%] Built target testDescriptors @@ -6071,137 +6068,114 @@ make[4]: Entering directory '/build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu' [ 72%] Building CXX object Code/GraphMol/Descriptors/CMakeFiles/testAUTOCORR3D.dir/testAUTOCORR3D.cpp.o cd /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/Descriptors && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK 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Code/GraphMol/Descriptors/CMakeFiles/testAUTOCORR3D.dir/testAUTOCORR3D.cpp.o -MF CMakeFiles/testAUTOCORR3D.dir/testAUTOCORR3D.cpp.o.d -o CMakeFiles/testAUTOCORR3D.dir/testAUTOCORR3D.cpp.o -c /build/reproducible-path/rdkit-202503.1/Code/GraphMol/Descriptors/testAUTOCORR3D.cpp -[ 73%] Building CXX object Code/GraphMol/MolStandardize/CMakeFiles/MolStandardize.dir/FragmentCatalog/FragmentCatalogEntry.cpp.o -cd /build/reproducible-path/rdkit-202503.1/obj-aarch64-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_BUILD_XYZ2MOL_SUPPORT -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS 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../../../lib/libRDKitRDBoost.so.1.2025.03.1 /usr/lib/aarch64-linux-gnu/libmaeparser.so ../../../lib/libRDKitDepictor.so.1.2025.03.1 /usr/lib/aarch64-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/libRDKitSubstructMatch.so.1.2025.03.1 ../../../lib/libRDKitGenericGroups.so.1.2025.03.1 ../../../lib/libRDKitSubgraphs.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/aarch64-linux-gnu/libboost_numpy313.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_python313.so.1.83.0 ../../../lib/libRDKitRDGeneral.so.1.2025.03.1 /usr/lib/aarch64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl make[4]: Leaving directory '/build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu' -[ 75%] Built target testCoulombMat +[ 73%] Built target rdmolops make -f Code/GraphMol/MolDraw2D/CMakeFiles/moldraw2DTestCatch.dir/build.make Code/GraphMol/MolDraw2D/CMakeFiles/moldraw2DTestCatch.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu' cd /build/reproducible-path/rdkit-202503.1/obj-aarch64-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-aarch64-linux-gnu /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/MolDraw2D /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/MolDraw2D/CMakeFiles/moldraw2DTestCatch.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu' make -f Code/GraphMol/MolDraw2D/CMakeFiles/moldraw2DTestCatch.dir/build.make Code/GraphMol/MolDraw2D/CMakeFiles/moldraw2DTestCatch.dir/build make[4]: Entering directory '/build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu' -[ 75%] Building CXX object Code/GraphMol/MolDraw2D/CMakeFiles/moldraw2DTestCatch.dir/catch_tests.cpp.o +[ 73%] Building CXX object Code/GraphMol/MolDraw2D/CMakeFiles/moldraw2DTestCatch.dir/catch_tests.cpp.o cd /build/reproducible-path/rdkit-202503.1/obj-aarch64-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 -DRDK_BUILD_CAIRO_SUPPORT -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_FREETYPE_SUPPORT -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_BUILD_XYZ2MOL_SUPPORT -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202503.1/External -I/build/reproducible-path/rdkit-202503.1/Code -I/usr/include/freetype2 -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 -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/GraphMol/MolDraw2D/CMakeFiles/moldraw2DTestCatch.dir/catch_tests.cpp.o -MF CMakeFiles/moldraw2DTestCatch.dir/catch_tests.cpp.o.d -o CMakeFiles/moldraw2DTestCatch.dir/catch_tests.cpp.o -c /build/reproducible-path/rdkit-202503.1/Code/GraphMol/MolDraw2D/catch_tests.cpp -[ 75%] Building CXX object Code/GraphMol/MolStandardize/CMakeFiles/MolStandardize.dir/TautomerCatalog/TautomerCatalogUtils.cpp.o -cd /build/reproducible-path/rdkit-202503.1/obj-aarch64-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_BUILD_XYZ2MOL_SUPPORT -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 -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/MolStandardize/CMakeFiles/MolStandardize.dir/TautomerCatalog/TautomerCatalogUtils.cpp.o -MF CMakeFiles/MolStandardize.dir/TautomerCatalog/TautomerCatalogUtils.cpp.o.d -o CMakeFiles/MolStandardize.dir/TautomerCatalog/TautomerCatalogUtils.cpp.o -c /build/reproducible-path/rdkit-202503.1/Code/GraphMol/MolStandardize/TautomerCatalog/TautomerCatalogUtils.cpp -/build/reproducible-path/rdkit-202503.1/Code/GraphMol/Descriptors/Wrap/rdMolDescriptors.cpp: In function 'std::pair {anonymous}::{anonymous}::BCUT2D_list(const RDKit::ROMol&, boost::python::list)': -/build/reproducible-path/rdkit-202503.1/Code/GraphMol/Descriptors/Wrap/rdMolDescriptors.cpp:444:61: note: parameter passing for argument of type 'std::pair' when C++17 is enabled changed to match C++14 in GCC 10.1 - 444 | python::list atomprops) { - | ^ +[ 73%] Linking CXX executable testCoulombMat +cd /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/Descriptors && /usr/bin/cmake -E cmake_link_script CMakeFiles/testCoulombMat.dir/link.txt --verbose=1 +/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/testCoulombMat.dir/link.d CMakeFiles/testCoulombMat.dir/testCoulombMat.cpp.o -o testCoulombMat ../../../lib/libRDKitDescriptors.so.1.2025.03.1 ../../../lib/libRDKitDistGeomHelpers.so.1.2025.03.1 ../../../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/aarch64-linux-gnu/libcoordgen.so /usr/lib/aarch64-linux-gnu/libmaeparser.so ../../../lib/libRDKitSubgraphs.so.1.2025.03.1 ../../../lib/libRDKitMolAlign.so.1.2025.03.1 ../../../lib/libRDKitMolTransforms.so.1.2025.03.1 ../../../lib/libRDKitDistGeometry.so.1.2025.03.1 ../../../lib/libRDKitForceFieldHelpers.so.1.2025.03.1 ../../../lib/libRDKitSmilesParse.so.1.2025.03.1 ../../../lib/libRDKitSubstructMatch.so.1.2025.03.1 ../../../lib/libRDKitGenericGroups.so.1.2025.03.1 ../../../lib/libRDKitEigenSolvers.so.1.2025.03.1 ../../../lib/libRDKitForceField.so.1.2025.03.1 ../../../lib/libRDKitOptimizer.so.1.2025.03.1 ../../../lib/libRDKitTrajectory.so.1.2025.03.1 ../../../lib/libRDKitGraphMol.so.1.2025.03.1 ../../../lib/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/aarch64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl +make[4]: Leaving directory '/build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu' +[ 73%] Built target testCoulombMat 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-aarch64-linux-gnu' cd /build/reproducible-path/rdkit-202503.1/obj-aarch64-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-aarch64-linux-gnu /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/MolDraw2D /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/MolDraw2D/CMakeFiles/moldraw2DRxnTest1.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu' make -f Code/GraphMol/MolDraw2D/CMakeFiles/moldraw2DRxnTest1.dir/build.make Code/GraphMol/MolDraw2D/CMakeFiles/moldraw2DRxnTest1.dir/build make[4]: Entering directory '/build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu' -[ 75%] Building CXX object Code/GraphMol/MolDraw2D/CMakeFiles/moldraw2DRxnTest1.dir/rxn_test1.cpp.o +[ 73%] Building CXX object Code/GraphMol/MolDraw2D/CMakeFiles/moldraw2DRxnTest1.dir/rxn_test1.cpp.o cd /build/reproducible-path/rdkit-202503.1/obj-aarch64-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 -DRDK_BUILD_CAIRO_SUPPORT -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_FREETYPE_SUPPORT -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_BUILD_XYZ2MOL_SUPPORT -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202503.1/External -I/usr/include/freetype2 -I/build/reproducible-path/rdkit-202503.1/Code -I/build/reproducible-path/rdkit-202503.1/External/boost-numeric-bindings -isystem /usr/include/eigen3 -isystem /usr/include/cairo -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/GraphMol/MolDraw2D/CMakeFiles/moldraw2DRxnTest1.dir/rxn_test1.cpp.o -MF CMakeFiles/moldraw2DRxnTest1.dir/rxn_test1.cpp.o.d -o CMakeFiles/moldraw2DRxnTest1.dir/rxn_test1.cpp.o -c /build/reproducible-path/rdkit-202503.1/Code/GraphMol/MolDraw2D/rxn_test1.cpp +[ 73%] Building CXX object Code/GraphMol/MolStandardize/CMakeFiles/MolStandardize.dir/FragmentCatalog/FragmentCatalogParams.cpp.o +cd /build/reproducible-path/rdkit-202503.1/obj-aarch64-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_BUILD_XYZ2MOL_SUPPORT -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 -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/MolStandardize/CMakeFiles/MolStandardize.dir/FragmentCatalog/FragmentCatalogParams.cpp.o -MF CMakeFiles/MolStandardize.dir/FragmentCatalog/FragmentCatalogParams.cpp.o.d -o CMakeFiles/MolStandardize.dir/FragmentCatalog/FragmentCatalogParams.cpp.o -c /build/reproducible-path/rdkit-202503.1/Code/GraphMol/MolStandardize/FragmentCatalog/FragmentCatalogParams.cpp +/build/reproducible-path/rdkit-202503.1/Code/GraphMol/Descriptors/Wrap/rdMolDescriptors.cpp: In function 'std::pair {anonymous}::{anonymous}::BCUT2D_list(const RDKit::ROMol&, boost::python::list)': +/build/reproducible-path/rdkit-202503.1/Code/GraphMol/Descriptors/Wrap/rdMolDescriptors.cpp:444:61: note: parameter passing for argument of type 'std::pair' when C++17 is enabled changed to match C++14 in GCC 10.1 + 444 | python::list atomprops) { + | ^ make -f Code/GraphMol/MolDraw2D/Wrap/CMakeFiles/rdMolDraw2D.dir/build.make Code/GraphMol/MolDraw2D/Wrap/CMakeFiles/rdMolDraw2D.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu' cd /build/reproducible-path/rdkit-202503.1/obj-aarch64-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/Wrap /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/MolDraw2D/Wrap /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/MolDraw2D/Wrap/CMakeFiles/rdMolDraw2D.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu' make -f Code/GraphMol/MolDraw2D/Wrap/CMakeFiles/rdMolDraw2D.dir/build.make Code/GraphMol/MolDraw2D/Wrap/CMakeFiles/rdMolDraw2D.dir/build make[4]: Entering directory '/build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu' -[ 76%] Building CXX object Code/GraphMol/MolDraw2D/Wrap/CMakeFiles/rdMolDraw2D.dir/rdMolDraw2D.cpp.o +[ 74%] Building CXX object Code/GraphMol/MolDraw2D/Wrap/CMakeFiles/rdMolDraw2D.dir/rdMolDraw2D.cpp.o cd /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/MolDraw2D/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_CAIRO_SUPPORT -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_FREETYPE_SUPPORT -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_BUILD_XYZ2MOL_SUPPORT -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DrdMolDraw2D_EXPORTS -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 -I/usr/lib/aarch64-linux-gnu/python3-numpy/numpy/_core/include -isystem /usr/include/python3.13 -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 -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/MolDraw2D/Wrap/CMakeFiles/rdMolDraw2D.dir/rdMolDraw2D.cpp.o -MF CMakeFiles/rdMolDraw2D.dir/rdMolDraw2D.cpp.o.d -o CMakeFiles/rdMolDraw2D.dir/rdMolDraw2D.cpp.o -c /build/reproducible-path/rdkit-202503.1/Code/GraphMol/MolDraw2D/Wrap/rdMolDraw2D.cpp make -f Code/GraphMol/FMCS/CMakeFiles/testFMCS.dir/build.make Code/GraphMol/FMCS/CMakeFiles/testFMCS.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu' @@ -6209,8 +6183,6 @@ make[4]: Leaving directory '/build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu' make -f Code/GraphMol/FMCS/CMakeFiles/testFMCS.dir/build.make Code/GraphMol/FMCS/CMakeFiles/testFMCS.dir/build make[4]: Entering directory '/build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu' -[ 76%] Building CXX object Code/GraphMol/FMCS/CMakeFiles/testFMCS.dir/testFMCS_Unit.cpp.o -cd /build/reproducible-path/rdkit-202503.1/obj-aarch64-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 -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_BUILD_XYZ2MOL_SUPPORT -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 -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/GraphMol/FMCS/CMakeFiles/testFMCS.dir/testFMCS_Unit.cpp.o -MF CMakeFiles/testFMCS.dir/testFMCS_Unit.cpp.o.d -o CMakeFiles/testFMCS.dir/testFMCS_Unit.cpp.o -c /build/reproducible-path/rdkit-202503.1/Code/GraphMol/FMCS/testFMCS_Unit.cpp In file included from /usr/include/c++/14/bits/stl_algobase.h:64, from /usr/include/c++/14/bits/specfun.h:43, from /usr/include/c++/14/cmath:3906, @@ -6224,120 +6196,147 @@ /usr/include/c++/14/bits/stl_pair.h:1132:5: note: parameter passing for argument of type 'std::pair' when C++17 is enabled changed to match C++14 in GCC 10.1 1132 | make_pair(_T1&& __x, _T2&& __y) | ^~~~~~~~~ +[ 74%] Building CXX object Code/GraphMol/FMCS/CMakeFiles/testFMCS.dir/testFMCS_Unit.cpp.o +cd /build/reproducible-path/rdkit-202503.1/obj-aarch64-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 -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_BUILD_XYZ2MOL_SUPPORT -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 -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/GraphMol/FMCS/CMakeFiles/testFMCS.dir/testFMCS_Unit.cpp.o -MF CMakeFiles/testFMCS.dir/testFMCS_Unit.cpp.o.d -o CMakeFiles/testFMCS.dir/testFMCS_Unit.cpp.o -c /build/reproducible-path/rdkit-202503.1/Code/GraphMol/FMCS/testFMCS_Unit.cpp +[ 74%] Linking CXX shared library ../../../lib/libRDKitMarvinParser.so +cd /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/MarvinParse && /usr/bin/cmake -E cmake_link_script CMakeFiles/MarvinParser.dir/link.txt --verbose=1 +/usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security 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-I/build/reproducible-path/rdkit-202503.1/External -I/build/reproducible-path/rdkit-202503.1/Code -I/usr/lib/aarch64-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 -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/FMCS/Wrap/CMakeFiles/rdFMCS.dir/rdFMCS.cpp.o -MF CMakeFiles/rdFMCS.dir/rdFMCS.cpp.o.d -o CMakeFiles/rdFMCS.dir/rdFMCS.cpp.o -c /build/reproducible-path/rdkit-202503.1/Code/GraphMol/FMCS/Wrap/rdFMCS.cpp -[ 77%] Linking CXX executable descriptorsTestCatch -cd /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/Descriptors && /usr/bin/cmake -E cmake_link_script 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+cd /build/reproducible-path/rdkit-202503.1/obj-aarch64-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_BUILD_XYZ2MOL_SUPPORT -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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cmake_symlink_library ../../../lib/libRDKitMolStandardize.so.1.2025.03.1 ../../../lib/libRDKitMolStandardize.so.1 ../../../lib/libRDKitMolStandardize.so +[ 75%] Linking CXX shared library ../../../lib/libRDKitO3AAlign.so +cd /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/MolAlign && /usr/bin/cmake -E cmake_link_script CMakeFiles/O3AAlign.dir/link.txt --verbose=1 +/usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,--dependency-file=CMakeFiles/O3AAlign.dir/link.d -Wl,-z,relro -Wl,-z,now -shared -Wl,-soname,libRDKitO3AAlign.so.1 -o ../../../lib/libRDKitO3AAlign.so.1.2025.03.1 CMakeFiles/O3AAlign.dir/O3AAlignMolecules.cpp.o ../../../lib/libRDKitDescriptors.so.1.2025.03.1 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-Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/GraphMol/RascalMCES/CMakeFiles/testRascalMCES.dir/mces_catch.cpp.o -MF CMakeFiles/testRascalMCES.dir/mces_catch.cpp.o.d -o CMakeFiles/testRascalMCES.dir/mces_catch.cpp.o -c /build/reproducible-path/rdkit-202503.1/Code/GraphMol/RascalMCES/mces_catch.cpp -[ 77%] Linking CXX executable moldraw2DRxnTest1 -cd /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/MolDraw2D && /usr/bin/cmake -E cmake_link_script CMakeFiles/moldraw2DRxnTest1.dir/link.txt --verbose=1 -/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function 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CMakeFiles/MolStandardize.dir/AcidBaseCatalog/AcidBaseCatalogEntry.cpp.o.d -o CMakeFiles/MolStandardize.dir/AcidBaseCatalog/AcidBaseCatalogEntry.cpp.o -c /build/reproducible-path/rdkit-202503.1/Code/GraphMol/MolStandardize/AcidBaseCatalog/AcidBaseCatalogEntry.cpp +[ 75%] Linking CXX executable testMMPA +cd /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/MMPA && /usr/bin/cmake -E cmake_link_script CMakeFiles/testMMPA.dir/link.txt --verbose=1 +/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/testMMPA.dir/link.d CMakeFiles/testMMPA.dir/MMPA_UnitTest.cpp.o -o testMMPA ../../../lib/libRDKitMMPA.so.1.2025.03.1 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'/build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu' -[ 77%] Built target moldraw2DRxnTest1 +[ 75%] Built target testMMPA make -f Code/GraphMol/RascalMCES/CMakeFiles/testRascalCluster.dir/build.make Code/GraphMol/RascalMCES/CMakeFiles/testRascalCluster.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu' cd /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202503.1 /build/reproducible-path/rdkit-202503.1/Code/GraphMol/RascalMCES /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/RascalMCES /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/RascalMCES/CMakeFiles/testRascalCluster.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu' make -f 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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 -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/GraphMol/RascalMCES/CMakeFiles/testRascalCluster.dir/mces_cluster_catch.cpp.o -MF CMakeFiles/testRascalCluster.dir/mces_cluster_catch.cpp.o.d -o CMakeFiles/testRascalCluster.dir/mces_cluster_catch.cpp.o -c /build/reproducible-path/rdkit-202503.1/Code/GraphMol/RascalMCES/mces_cluster_catch.cpp -[ 77%] Linking CXX executable testMMPA -cd /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/MMPA && /usr/bin/cmake -E cmake_link_script CMakeFiles/testMMPA.dir/link.txt --verbose=1 -/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/testMMPA.dir/link.d CMakeFiles/testMMPA.dir/MMPA_UnitTest.cpp.o -o testMMPA ../../../lib/libRDKitMMPA.so.1.2025.03.1 ../../../lib/libRDKitFileParsers.so.1.2025.03.1 /usr/lib/aarch64-linux-gnu/libmaeparser.so ../../../lib/libRDKitChemTransforms.so.1.2025.03.1 ../../../lib/libRDKitDepictor.so.1.2025.03.1 /usr/lib/aarch64-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 ../../../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/aarch64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl +[ 75%] Linking CXX executable FMCStest +cd /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FMCS/Test && /usr/bin/cmake -E cmake_link_script CMakeFiles/FMCStest.dir/link.txt --verbose=1 +/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra 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/usr/lib/aarch64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl make[4]: Leaving directory '/build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu' -[ 77%] Built target testMMPA +[ 75%] Built target FMCStest make -f Code/GraphMol/RascalMCES/Wrap/CMakeFiles/rdRascalMCES.dir/build.make Code/GraphMol/RascalMCES/Wrap/CMakeFiles/rdRascalMCES.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu' cd /build/reproducible-path/rdkit-202503.1/obj-aarch64-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-aarch64-linux-gnu /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/RascalMCES/Wrap /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/RascalMCES/Wrap/CMakeFiles/rdRascalMCES.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu' make -f Code/GraphMol/RascalMCES/Wrap/CMakeFiles/rdRascalMCES.dir/build.make Code/GraphMol/RascalMCES/Wrap/CMakeFiles/rdRascalMCES.dir/build make[4]: Entering directory '/build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu' -[ 77%] Building CXX object Code/GraphMol/RascalMCES/Wrap/CMakeFiles/rdRascalMCES.dir/rdRascalMCES.cpp.o +[ 75%] Building CXX object Code/GraphMol/RascalMCES/Wrap/CMakeFiles/rdRascalMCES.dir/rdRascalMCES.cpp.o cd /build/reproducible-path/rdkit-202503.1/obj-aarch64-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_BUILD_XYZ2MOL_SUPPORT -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/aarch64-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 -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/RascalMCES/Wrap/CMakeFiles/rdRascalMCES.dir/rdRascalMCES.cpp.o -MF CMakeFiles/rdRascalMCES.dir/rdRascalMCES.cpp.o.d -o CMakeFiles/rdRascalMCES.dir/rdRascalMCES.cpp.o -c /build/reproducible-path/rdkit-202503.1/Code/GraphMol/RascalMCES/Wrap/rdRascalMCES.cpp -[ 77%] Linking CXX executable FMCStest -cd /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FMCS/Test && /usr/bin/cmake -E cmake_link_script CMakeFiles/FMCStest.dir/link.txt --verbose=1 -/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/FMCStest.dir/link.d CMakeFiles/FMCStest.dir/testFMCS.cpp.o -o FMCStest ../../../../lib/libRDKitFMCS.so.1.2025.03.1 ../../../../lib/libRDKitFileParsers.so.1.2025.03.1 /usr/lib/aarch64-linux-gnu/libmaeparser.so ../../../../lib/libRDKitChemTransforms.so.1.2025.03.1 ../../../../lib/libRDKitDepictor.so.1.2025.03.1 /usr/lib/aarch64-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/aarch64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl +[ 75%] Linking CXX shared module ../../../../rdkit/Chem/rdMMPA.so +cd /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/MMPA/Wrap && /usr/bin/cmake -E cmake_link_script CMakeFiles/rdMMPA.dir/link.txt --verbose=1 +[ 75%] Building CXX object Code/GraphMol/MolStandardize/CMakeFiles/MolStandardize.dir/AcidBaseCatalog/AcidBaseCatalogParams.cpp.o +cd /build/reproducible-path/rdkit-202503.1/obj-aarch64-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_BUILD_XYZ2MOL_SUPPORT -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 -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/MolStandardize/CMakeFiles/MolStandardize.dir/AcidBaseCatalog/AcidBaseCatalogParams.cpp.o -MF CMakeFiles/MolStandardize.dir/AcidBaseCatalog/AcidBaseCatalogParams.cpp.o.d -o CMakeFiles/MolStandardize.dir/AcidBaseCatalog/AcidBaseCatalogParams.cpp.o -c /build/reproducible-path/rdkit-202503.1/Code/GraphMol/MolStandardize/AcidBaseCatalog/AcidBaseCatalogParams.cpp +/usr/bin/c++ -fPIC -g -O2 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../../../../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/aarch64-linux-gnu/libboost_numpy313.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_python313.so.1.83.0 ../../../../lib/libRDKitRDGeneral.so.1.2025.03.1 /usr/lib/aarch64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl make[4]: Leaving directory '/build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu' -[ 77%] Built target FMCStest +[ 75%] Built target rdMMPA make -f Code/GraphMol/CIPLabeler/CMakeFiles/testCIPLabeler.dir/build.make 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../../../../lib/libRDKitSmilesParse.so.1.2025.03.1 ../../../../lib/libRDKitSubstructMatch.so.1.2025.03.1 ../../../../lib/libRDKitGenericGroups.so.1.2025.03.1 ../../../../lib/libRDKitGraphMol.so.1.2025.03.1 ../../../../lib/libRDKitRDGeometryLib.so.1.2025.03.1 ../../../../lib/libRDKitDataStructs.so.1.2025.03.1 /usr/lib/aarch64-linux-gnu/libboost_numpy313.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_python313.so.1.83.0 ../../../../lib/libRDKitRDGeneral.so.1.2025.03.1 /usr/lib/aarch64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl make[4]: Leaving directory '/build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu' -[ 77%] Built target rdMMPA +[ 75%] Built target rdFMCS make -f Code/GraphMol/Deprotect/CMakeFiles/deprotectTest.dir/build.make Code/GraphMol/Deprotect/CMakeFiles/deprotectTest.dir/depend make[4]: Entering directory 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Building CXX object Code/GraphMol/Deprotect/CMakeFiles/deprotectTest.dir/deprotectTest.cpp.o cd /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/Deprotect && /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_DEPROTECT_BUILD -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_BUILD_XYZ2MOL_SUPPORT -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 -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/GraphMol/Deprotect/CMakeFiles/deprotectTest.dir/deprotectTest.cpp.o -MF CMakeFiles/deprotectTest.dir/deprotectTest.cpp.o.d -o CMakeFiles/deprotectTest.dir/deprotectTest.cpp.o -c /build/reproducible-path/rdkit-202503.1/Code/GraphMol/Deprotect/deprotectTest.cpp -[ 77%] Linking CXX executable testRascalCluster +[ 75%] Building CXX object Code/GraphMol/MolStandardize/CMakeFiles/MolStandardize.dir/AcidBaseCatalog/AcidBaseCatalogUtils.cpp.o +cd /build/reproducible-path/rdkit-202503.1/obj-aarch64-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_BUILD_XYZ2MOL_SUPPORT -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 -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/MolStandardize/CMakeFiles/MolStandardize.dir/AcidBaseCatalog/AcidBaseCatalogUtils.cpp.o -MF CMakeFiles/MolStandardize.dir/AcidBaseCatalog/AcidBaseCatalogUtils.cpp.o.d -o CMakeFiles/MolStandardize.dir/AcidBaseCatalog/AcidBaseCatalogUtils.cpp.o -c /build/reproducible-path/rdkit-202503.1/Code/GraphMol/MolStandardize/AcidBaseCatalog/AcidBaseCatalogUtils.cpp +[ 75%] Linking CXX executable testRascalCluster cd /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/RascalMCES && /usr/bin/cmake -E cmake_link_script CMakeFiles/testRascalCluster.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/testRascalCluster.dir/link.d CMakeFiles/testRascalCluster.dir/mces_cluster_catch.cpp.o -o testRascalCluster 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Code/GraphMol/MolStandardize/CMakeFiles/MolStandardize.dir/TransformCatalog/TransformCatalogEntry.cpp.o +cd /build/reproducible-path/rdkit-202503.1/obj-aarch64-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_BUILD_XYZ2MOL_SUPPORT -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/MolStandardize/CMakeFiles/MolStandardize.dir/TransformCatalog/TransformCatalogParams.cpp.o -MF CMakeFiles/MolStandardize.dir/TransformCatalog/TransformCatalogParams.cpp.o.d -o CMakeFiles/MolStandardize.dir/TransformCatalog/TransformCatalogParams.cpp.o -c /build/reproducible-path/rdkit-202503.1/Code/GraphMol/MolStandardize/TransformCatalog/TransformCatalogParams.cpp +[ 77%] Linking CXX shared module ../../../../rdkit/Chem/rdMolDescriptors.so +cd /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/Descriptors/Wrap && /usr/bin/cmake -E cmake_link_script CMakeFiles/rdMolDescriptors.dir/link.txt --verbose=1 +[ 77%] Building CXX object Code/GraphMol/CIPLabeler/CMakeFiles/testCIPLabeler.dir/Mancude.cpp.o +cd /build/reproducible-path/rdkit-202503.1/obj-aarch64-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 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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 -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/GraphMol/CIPLabeler/CMakeFiles/testCIPLabeler.dir/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 /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 -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -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/aarch64-linux-gnu/libmaeparser.so ../../../../lib/libRDKitChemTransforms.so.1.2025.03.1 ../../../../lib/libRDKitDepictor.so.1.2025.03.1 /usr/lib/aarch64-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 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-Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/Wrap/CMakeFiles/rdchem.dir/Bond.cpp.o -MF CMakeFiles/rdchem.dir/Bond.cpp.o.d -o CMakeFiles/rdchem.dir/Bond.cpp.o -c /build/reproducible-path/rdkit-202503.1/Code/GraphMol/Wrap/Bond.cpp -[ 81%] Linking CXX executable molStandardizeTest -cd /build/reproducible-path/rdkit-202503.1/obj-aarch64-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 -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/molStandardizeTest.dir/link.d 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-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/aarch64-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 -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/Wrap/CMakeFiles/rdmolfiles.dir/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 +[ 78%] Linking CXX 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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/aarch64-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 -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/Wrap/CMakeFiles/rdchem.dir/Conformer.cpp.o -MF CMakeFiles/rdchem.dir/Conformer.cpp.o.d -o CMakeFiles/rdchem.dir/Conformer.cpp.o -c /build/reproducible-path/rdkit-202503.1/Code/GraphMol/Wrap/Conformer.cpp +[ 82%] Linking CXX shared library ../../../lib/libRDKitMolStandardize.so +cd /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/MolStandardize && /usr/bin/cmake 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/usr/lib/aarch64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl /usr/lib/aarch64-linux-gnu/libmaeparser.so +cd /build/reproducible-path/rdkit-202503.1/obj-aarch64-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-aarch64-linux-gnu' -[ 88%] Built target rdmolfiles +[ 82%] Built target MolStandardize +[ 82%] Building CXX object Code/GraphMol/Wrap/CMakeFiles/rdchem.dir/RingInfo.cpp.o +cd /build/reproducible-path/rdkit-202503.1/obj-aarch64-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 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Code/GraphMol/MarvinParse/CMakeFiles/testMrvToMol.dir/testMrvToMol.cpp.o cd /build/reproducible-path/rdkit-202503.1/obj-aarch64-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 -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_BUILD_XYZ2MOL_SUPPORT -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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-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 -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/GraphMol/MolAlign/CMakeFiles/testO3AAlign.dir/testO3AAlign.cpp.o -MF CMakeFiles/testO3AAlign.dir/testO3AAlign.cpp.o.d -o CMakeFiles/testO3AAlign.dir/testO3AAlign.cpp.o -c /build/reproducible-path/rdkit-202503.1/Code/GraphMol/MolAlign/testO3AAlign.cpp -[ 89%] Building CXX object Code/GraphMol/ChemReactions/Wrap/CMakeFiles/rdChemReactions.dir/rdChemReactions.cpp.o -cd /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/ChemReactions/Wrap && /usr/bin/c++ 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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 +[ 87%] Linking CXX executable testGenericGroups +cd /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/GenericGroups && /usr/bin/cmake -E cmake_link_script CMakeFiles/testGenericGroups.dir/link.txt --verbose=1 +/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/testGenericGroups.dir/link.d 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included from /usr/include/c++/14/bits/stl_algobase.h:64, - from /usr/include/c++/14/string:51, - from /build/reproducible-path/rdkit-202503.1/Code/RDGeneral/Invariant.h:17, - from /build/reproducible-path/rdkit-202503.1/Code/Numerics/Matrix.h:14, - from /build/reproducible-path/rdkit-202503.1/Code/Numerics/SquareMatrix.h:14, - from /build/reproducible-path/rdkit-202503.1/Code/Geometry/Transform3D.h:16, - from /build/reproducible-path/rdkit-202503.1/Code/GraphMol/MolAlign/AlignMolecules.h:14, - from /build/reproducible-path/rdkit-202503.1/Code/GraphMol/MolAlign/testO3AAlign.cpp:11: -/usr/include/c++/14/bits/stl_pair.h: In instantiation of 'constexpr std::pair::type>::__type, typename std::__strip_reference_wrapper::type>::__type> std::make_pair(_T1&&, _T2&&) [with _T1 = double&; _T2 = double&; typename __strip_reference_wrapper::type>::__type = double; typename decay<_Tp>::type = double; typename __strip_reference_wrapper::type>::__type = double; typename decay<_Tp2>::type = double]': -/build/reproducible-path/rdkit-202503.1/Code/GraphMol/MolAlign/testO3AAlign.cpp:643:37: required from here - 643 | oscores.push_back(std::make_pair(rmsd, score)); - | ~~~~~~~~~~~~~~^~~~~~~~~~~~~ -/usr/include/c++/14/bits/stl_pair.h:1132:5: note: parameter passing for argument of type 'std::pair' when C++17 is enabled changed to match C++14 in GCC 10.1 - 1132 | make_pair(_T1&& __x, _T2&& __y) - | ^~~~~~~~~ -/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 -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -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 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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 -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/GraphMol/MolStandardize/CMakeFiles/molValidateTest.dir/testValidate.cpp.o -MF CMakeFiles/molValidateTest.dir/testValidate.cpp.o.d -o CMakeFiles/molValidateTest.dir/testValidate.cpp.o -c /build/reproducible-path/rdkit-202503.1/Code/GraphMol/MolStandardize/testValidate.cpp +make -f Code/GraphMol/MolStandardize/CMakeFiles/molChargeTest.dir/build.make Code/GraphMol/MolStandardize/CMakeFiles/molChargeTest.dir/depend +make[4]: Entering directory 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CMakeFiles/molChargeTest.dir/testCharge.cpp.o -c /build/reproducible-path/rdkit-202503.1/Code/GraphMol/MolStandardize/testCharge.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, @@ -6891,122 +6753,249 @@ /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]); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -[ 91%] Linking CXX executable cxsmilesTest -cd /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/SmilesParse && /usr/bin/cmake -E cmake_link_script CMakeFiles/cxsmilesTest.dir/link.txt --verbose=1 -/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/cxsmilesTest.dir/link.d CMakeFiles/cxsmilesTest.dir/cxsmiles_test.cpp.o -o cxsmilesTest ../../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/aarch64-linux-gnu/libmaeparser.so ../../../lib/libRDKitChemTransforms.so.1.2025.03.1 ../../../lib/libRDKitDepictor.so.1.2025.03.1 /usr/lib/aarch64-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/aarch64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl +[ 87%] Linking CXX shared library ../../../lib/libRDKitTautomerQuery.so +cd /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/TautomerQuery && /usr/bin/cmake -E cmake_link_script CMakeFiles/TautomerQuery.dir/link.txt --verbose=1 +/usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security 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../../../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/aarch64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl +cd /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/TautomerQuery && /usr/bin/cmake -E cmake_symlink_library ../../../lib/libRDKitTautomerQuery.so.1.2025.03.1 ../../../lib/libRDKitTautomerQuery.so.1 ../../../lib/libRDKitTautomerQuery.so +make[4]: Leaving directory '/build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu' +[ 87%] Built target TautomerQuery +make -f Code/GraphMol/MolStandardize/CMakeFiles/molTautomerTest.dir/build.make Code/GraphMol/MolStandardize/CMakeFiles/molTautomerTest.dir/depend +make[4]: Entering directory '/build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu' +cd /build/reproducible-path/rdkit-202503.1/obj-aarch64-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-aarch64-linux-gnu /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/MolStandardize /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/MolStandardize/CMakeFiles/molTautomerTest.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu' -[ 91%] Built target cxsmilesTest +make 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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 -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/GraphMol/MolStandardize/CMakeFiles/molTautomerTest.dir/testTautomer.cpp.o -MF CMakeFiles/molTautomerTest.dir/testTautomer.cpp.o.d -o CMakeFiles/molTautomerTest.dir/testTautomer.cpp.o -c /build/reproducible-path/rdkit-202503.1/Code/GraphMol/MolStandardize/testTautomer.cpp +In file included from /usr/include/c++/14/bits/stl_algobase.h:64, + from /usr/include/c++/14/string:51, + from /build/reproducible-path/rdkit-202503.1/Code/RDGeneral/Invariant.h:17, + from /build/reproducible-path/rdkit-202503.1/Code/Numerics/Matrix.h:14, + from /build/reproducible-path/rdkit-202503.1/Code/Numerics/SquareMatrix.h:14, + from /build/reproducible-path/rdkit-202503.1/Code/Geometry/Transform3D.h:16, + from /build/reproducible-path/rdkit-202503.1/Code/GraphMol/MolAlign/AlignMolecules.h:14, + from /build/reproducible-path/rdkit-202503.1/Code/GraphMol/MolAlign/testO3AAlign.cpp:11: +/usr/include/c++/14/bits/stl_pair.h: In instantiation of 'constexpr std::pair::type>::__type, typename std::__strip_reference_wrapper::type>::__type> std::make_pair(_T1&&, _T2&&) [with _T1 = double&; _T2 = double&; typename __strip_reference_wrapper::type>::__type = double; typename decay<_Tp>::type = double; typename __strip_reference_wrapper::type>::__type = double; typename decay<_Tp2>::type = double]': +/build/reproducible-path/rdkit-202503.1/Code/GraphMol/MolAlign/testO3AAlign.cpp:643:37: required from here + 643 | oscores.push_back(std::make_pair(rmsd, score)); + | ~~~~~~~~~~~~~~^~~~~~~~~~~~~ +/usr/include/c++/14/bits/stl_pair.h:1132:5: note: parameter passing for argument of type 'std::pair' when C++17 is enabled changed to match C++14 in GCC 10.1 + 1132 | make_pair(_T1&& __x, _T2&& __y) + | ^~~~~~~~~ +make -f Code/GraphMol/MolStandardize/CMakeFiles/molStandardizeSmallTest.dir/build.make Code/GraphMol/MolStandardize/CMakeFiles/molStandardizeSmallTest.dir/depend +make[4]: Entering directory '/build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu' +cd /build/reproducible-path/rdkit-202503.1/obj-aarch64-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-aarch64-linux-gnu /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/MolStandardize 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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 -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/GraphMol/MolStandardize/CMakeFiles/molFragmentTest.dir/testFragment.cpp.o -MF CMakeFiles/molFragmentTest.dir/testFragment.cpp.o.d -o CMakeFiles/molFragmentTest.dir/testFragment.cpp.o -c /build/reproducible-path/rdkit-202503.1/Code/GraphMol/MolStandardize/testFragment.cpp +[ 87%] Linking CXX executable molNormalizeTest +cd /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/MolStandardize && /usr/bin/cmake -E cmake_link_script CMakeFiles/molNormalizeTest.dir/link.txt --verbose=1 +/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now -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/aarch64-linux-gnu/libmaeparser.so ../../../lib/libRDKitChemTransforms.so.1.2025.03.1 ../../../lib/libRDKitDepictor.so.1.2025.03.1 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/usr/lib/aarch64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl +cd /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/ScaffoldNetwork && /usr/bin/cmake -E cmake_symlink_library ../../../lib/libRDKitScaffoldNetwork.so.1.2025.03.1 ../../../lib/libRDKitScaffoldNetwork.so.1 ../../../lib/libRDKitScaffoldNetwork.so +make[4]: Leaving directory '/build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu' +[ 91%] Built target ScaffoldNetwork +[ 91%] Building CXX object Code/GraphMol/GeneralizedSubstruct/CMakeFiles/GeneralizedSubstruct.dir/TextIO.cpp.o +cd /build/reproducible-path/rdkit-202503.1/obj-aarch64-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 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CMakeFiles/GeneralizedSubstruct.dir/TextIO.cpp.o -c /build/reproducible-path/rdkit-202503.1/Code/GraphMol/GeneralizedSubstruct/TextIO.cpp +[ 91%] Building CXX object Code/GraphMol/MolStandardize/Wrap/CMakeFiles/rdMolStandardize.dir/Charge.cpp.o +cd /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/MolStandardize/Wrap && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_NUMPY_DYN_LINK -DBOOST_NUMPY_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_BUILD_XYZ2MOL_SUPPORT -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DrdMolStandardize_EXPORTS -I/build/reproducible-path/rdkit-202503.1/External -I/build/reproducible-path/rdkit-202503.1/Code -I/build/reproducible-path/rdkit-202503.1/External/boost-numeric-bindings -I/usr/lib/aarch64-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 -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/MolStandardize/Wrap/CMakeFiles/rdMolStandardize.dir/Charge.cpp.o -MF CMakeFiles/rdMolStandardize.dir/Charge.cpp.o.d -o CMakeFiles/rdMolStandardize.dir/Charge.cpp.o -c /build/reproducible-path/rdkit-202503.1/Code/GraphMol/MolStandardize/Wrap/Charge.cpp +[ 91%] Linking CXX executable molTautomerTest +cd 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'/build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu' -[ 92%] Built target tautomerQueryTestCatch -[ 92%] Building CXX object Code/GraphMol/RGroupDecomposition/CMakeFiles/RGroupDecomposition.dir/RGroupUtils.cpp.o +[ 91%] Built target tautomerQueryTestCatch +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-aarch64-linux-gnu' +cd /build/reproducible-path/rdkit-202503.1/obj-aarch64-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-aarch64-linux-gnu /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/ScaffoldNetwork/Wrap 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-DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_BUILD_XYZ2MOL_SUPPORT -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/aarch64-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 -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/ScaffoldNetwork/Wrap/CMakeFiles/rdScaffoldNetwork.dir/rdScaffoldNetwork.cpp.o -MF CMakeFiles/rdScaffoldNetwork.dir/rdScaffoldNetwork.cpp.o.d -o CMakeFiles/rdScaffoldNetwork.dir/rdScaffoldNetwork.cpp.o -c /build/reproducible-path/rdkit-202503.1/Code/GraphMol/ScaffoldNetwork/Wrap/rdScaffoldNetwork.cpp +[ 91%] Linking CXX shared module ../../../../rdkit/Chem/rdTautomerQuery.so +cd /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/TautomerQuery/Wrap && /usr/bin/cmake -E cmake_link_script CMakeFiles/rdTautomerQuery.dir/link.txt --verbose=1 +/usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -g -fwrapv -O2 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object Code/GraphMol/RGroupDecomposition/CMakeFiles/RGroupDecomposition.dir/RGroupScore.cpp.o cd /build/reproducible-path/rdkit-202503.1/obj-aarch64-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_BUILD_XYZ2MOL_SUPPORT -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 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Code/GraphMol/RGroupDecomposition/CMakeFiles/RGroupDecomposition.dir/RGroupFingerprintScore.cpp.o -cd /build/reproducible-path/rdkit-202503.1/obj-aarch64-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_BUILD_XYZ2MOL_SUPPORT -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 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../../../../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/aarch64-linux-gnu/libboost_numpy313.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_python313.so.1.83.0 ../../../../lib/libRDKitRDGeneral.so.1.2025.03.1 /usr/lib/aarch64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl +[ 92%] Building CXX object Code/GraphMol/MolStandardize/Wrap/CMakeFiles/rdMolStandardize.dir/Normalize.cpp.o +cd 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-ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/MolStandardize/Wrap/CMakeFiles/rdMolStandardize.dir/Normalize.cpp.o -MF CMakeFiles/rdMolStandardize.dir/Normalize.cpp.o.d -o CMakeFiles/rdMolStandardize.dir/Normalize.cpp.o -c /build/reproducible-path/rdkit-202503.1/Code/GraphMol/MolStandardize/Wrap/Normalize.cpp +[ 92%] Building CXX object Code/GraphMol/MolStandardize/Wrap/CMakeFiles/rdMolStandardize.dir/Metal.cpp.o +cd /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/MolStandardize/Wrap && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_NUMPY_DYN_LINK -DBOOST_NUMPY_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB 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-Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/MolStandardize/Wrap/CMakeFiles/rdMolStandardize.dir/Metal.cpp.o -MF CMakeFiles/rdMolStandardize.dir/Metal.cpp.o.d -o CMakeFiles/rdMolStandardize.dir/Metal.cpp.o -c /build/reproducible-path/rdkit-202503.1/Code/GraphMol/MolStandardize/Wrap/Metal.cpp +[ 93%] Linking CXX executable molStandardizeCatchTest +cd /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/MolStandardize && /usr/bin/cmake -E cmake_link_script CMakeFiles/molStandardizeCatchTest.dir/link.txt --verbose=1 +/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/molStandardizeCatchTest.dir/link.d CMakeFiles/molStandardizeCatchTest.dir/catch_tests.cpp.o -o molStandardizeCatchTest ../../RDGeneral/librdkitCatch.a ../../../lib/libRDKitMolStandardize.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/aarch64-linux-gnu/libmaeparser.so ../../../lib/libRDKitChemTransforms.so.1.2025.03.1 ../../../lib/libRDKitDepictor.so.1.2025.03.1 /usr/lib/aarch64-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/aarch64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl make[4]: Leaving directory '/build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu' -[ 93%] Built target rdTautomerQuery -[ 93%] Building CXX object Code/GraphMol/RGroupDecomposition/CMakeFiles/RGroupDecomposition.dir/RGroupGa.cpp.o -cd /build/reproducible-path/rdkit-202503.1/obj-aarch64-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_BUILD_XYZ2MOL_SUPPORT -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 -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/RGroupDecomposition/CMakeFiles/RGroupDecomposition.dir/RGroupGa.cpp.o -MF CMakeFiles/RGroupDecomposition.dir/RGroupGa.cpp.o.d -o CMakeFiles/RGroupDecomposition.dir/RGroupGa.cpp.o -c /build/reproducible-path/rdkit-202503.1/Code/GraphMol/RGroupDecomposition/RGroupGa.cpp +[ 93%] Built target molStandardizeCatchTest +[ 93%] Building CXX object Code/GraphMol/MolStandardize/Wrap/CMakeFiles/rdMolStandardize.dir/Tautomer.cpp.o +cd /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/MolStandardize/Wrap && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_NUMPY_DYN_LINK -DBOOST_NUMPY_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_BUILD_XYZ2MOL_SUPPORT -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DrdMolStandardize_EXPORTS -I/build/reproducible-path/rdkit-202503.1/External -I/build/reproducible-path/rdkit-202503.1/Code -I/build/reproducible-path/rdkit-202503.1/External/boost-numeric-bindings -I/usr/lib/aarch64-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 -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/MolStandardize/Wrap/CMakeFiles/rdMolStandardize.dir/Tautomer.cpp.o -MF CMakeFiles/rdMolStandardize.dir/Tautomer.cpp.o.d -o CMakeFiles/rdMolStandardize.dir/Tautomer.cpp.o -c /build/reproducible-path/rdkit-202503.1/Code/GraphMol/MolStandardize/Wrap/Tautomer.cpp [ 93%] Linking CXX shared library ../../../lib/libRDKitGeneralizedSubstruct.so cd /build/reproducible-path/rdkit-202503.1/obj-aarch64-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 -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,--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/aarch64-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/aarch64-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/aarch64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl cd /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/GeneralizedSubstruct && /usr/bin/cmake -E cmake_symlink_library ../../../lib/libRDKitGeneralizedSubstruct.so.1.2025.03.1 ../../../lib/libRDKitGeneralizedSubstruct.so.1 ../../../lib/libRDKitGeneralizedSubstruct.so make[4]: Leaving directory '/build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu' [ 93%] Built target GeneralizedSubstruct -[ 93%] Building CXX object Code/GraphMol/RGroupDecomposition/CMakeFiles/RGroupDecomposition.dir/RGroupDecompJSONParsers.cpp.o -cd /build/reproducible-path/rdkit-202503.1/obj-aarch64-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_BUILD_XYZ2MOL_SUPPORT -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 -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/RGroupDecomposition/CMakeFiles/RGroupDecomposition.dir/RGroupDecompJSONParsers.cpp.o -MF CMakeFiles/RGroupDecomposition.dir/RGroupDecompJSONParsers.cpp.o.d -o CMakeFiles/RGroupDecomposition.dir/RGroupDecompJSONParsers.cpp.o -c /build/reproducible-path/rdkit-202503.1/Code/GraphMol/RGroupDecomposition/RGroupDecompJSONParsers.cpp -In file included from /usr/include/boost/python/override.hpp:13, - from /usr/include/boost/python/wrapper.hpp:8, - from /usr/include/boost/python/object/value_holder.hpp:15, - from /usr/include/boost/python/object/class_metadata.hpp:14, - from /usr/include/boost/python/class.hpp:23, - from /usr/include/boost/python/suite/indexing/indexing_suite.hpp:9, - from /usr/include/boost/python/suite/indexing/map_indexing_suite.hpp:9, - from /build/reproducible-path/rdkit-202503.1/Code/GraphMol/MolStandardize/Wrap/Tautomer.cpp:11: -In member function 'boost::python::converter::extract_rvalue::result_type boost::python::converter::extract_rvalue::operator()() const [with T = long int]', - inlined from 'boost::python::extract::operator result_type() const [with T = long int]' at /usr/include/boost/python/extract.hpp:136:23, - inlined from 'static void boost::python::detail::slice_helper::base_get_slice_data(Container&, PySliceObject*, Index&, Index&) [with Container = std::vector; DerivedPolicies = boost::python::detail::final_vector_derived_policies, false>; ProxyHandler = boost::python::detail::proxy_helper, boost::python::detail::final_vector_derived_policies, false>, boost::python::detail::container_element, long unsigned int, boost::python::detail::final_vector_derived_policies, false> >, long unsigned int>; Data = RDKit::MolStandardize::TautomerScoringFunctions::SubstructTerm; Index = long unsigned int]' at /usr/include/boost/python/suite/indexing/detail/indexing_suite_detail.hpp:617:27: -/usr/include/boost/python/extract.hpp:185:11: warning: '*(long int*)((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))' may be used uninitialized [-Wmaybe-uninitialized] - 185 | ); - | ^ -In file included from /usr/include/boost/python/suite/indexing/indexing_suite.hpp:12: -/usr/include/boost/python/suite/indexing/detail/indexing_suite_detail.hpp: In static member function 'static void boost::python::detail::slice_helper::base_get_slice_data(Container&, PySliceObject*, Index&, Index&) [with Container = std::vector; DerivedPolicies = boost::python::detail::final_vector_derived_policies, false>; ProxyHandler = boost::python::detail::proxy_helper, boost::python::detail::final_vector_derived_policies, false>, boost::python::detail::container_element, long unsigned int, boost::python::detail::final_vector_derived_policies, false> >, long unsigned int>; Data = RDKit::MolStandardize::TautomerScoringFunctions::SubstructTerm; Index = long unsigned int]': -/usr/include/boost/python/suite/indexing/detail/indexing_suite_detail.hpp:617:27: note: '' declared here - 617 | long to = extract( slice->stop); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ -In member function 'boost::python::converter::extract_rvalue::result_type boost::python::converter::extract_rvalue::operator()() const [with T = long int]', - inlined from 'boost::python::extract::operator result_type() const [with T = long int]' at /usr/include/boost/python/extract.hpp:136:23, - inlined from 'static void boost::python::detail::slice_helper::base_get_slice_data(Container&, PySliceObject*, Index&, Index&) [with Container = std::vector; DerivedPolicies = boost::python::detail::final_vector_derived_policies, false>; ProxyHandler = boost::python::detail::proxy_helper, boost::python::detail::final_vector_derived_policies, false>, boost::python::detail::container_element, long unsigned int, boost::python::detail::final_vector_derived_policies, false> >, long unsigned int>; Data = RDKit::MolStandardize::TautomerScoringFunctions::SubstructTerm; Index = long unsigned int]' at /usr/include/boost/python/suite/indexing/detail/indexing_suite_detail.hpp:603:29: -/usr/include/boost/python/extract.hpp:185:11: warning: '*(long int*)((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))' may be used uninitialized [-Wmaybe-uninitialized] - 185 | ); - | ^ -/usr/include/boost/python/suite/indexing/detail/indexing_suite_detail.hpp: In static member function 'static void boost::python::detail::slice_helper::base_get_slice_data(Container&, PySliceObject*, Index&, Index&) [with Container = std::vector; DerivedPolicies = boost::python::detail::final_vector_derived_policies, false>; ProxyHandler = boost::python::detail::proxy_helper, boost::python::detail::final_vector_derived_policies, false>, boost::python::detail::container_element, long unsigned int, boost::python::detail::final_vector_derived_policies, false> >, long unsigned int>; Data = RDKit::MolStandardize::TautomerScoringFunctions::SubstructTerm; Index = long unsigned int]': -/usr/include/boost/python/suite/indexing/detail/indexing_suite_detail.hpp:603:29: note: '' declared here - 603 | long from = extract( slice->start); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ make -f Code/GraphMol/SynthonSpaceSearch/CMakeFiles/SynthonSpaceSearch.dir/build.make Code/GraphMol/SynthonSpaceSearch/CMakeFiles/SynthonSpaceSearch.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu' cd /build/reproducible-path/rdkit-202503.1/obj-aarch64-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-aarch64-linux-gnu /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/SynthonSpaceSearch /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/SynthonSpaceSearch/CMakeFiles/SynthonSpaceSearch.dir/DependInfo.cmake "--color=" @@ -7015,26 +7004,50 @@ make[4]: Entering directory '/build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu' [ 93%] Building CXX object Code/GraphMol/SynthonSpaceSearch/CMakeFiles/SynthonSpaceSearch.dir/SynthonSpaceSearch_details.cpp.o cd /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/SynthonSpaceSearch && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDKIT_SYNTHONSPACESEARCH_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_BUILD_XYZ2MOL_SUPPORT -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DSynthonSpaceSearch_EXPORTS -I/build/reproducible-path/rdkit-202503.1/External -I/build/reproducible-path/rdkit-202503.1/Code -I/build/reproducible-path/rdkit-202503.1/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/SynthonSpaceSearch/CMakeFiles/SynthonSpaceSearch.dir/SynthonSpaceSearch_details.cpp.o -MF CMakeFiles/SynthonSpaceSearch.dir/SynthonSpaceSearch_details.cpp.o.d -o CMakeFiles/SynthonSpaceSearch.dir/SynthonSpaceSearch_details.cpp.o -c /build/reproducible-path/rdkit-202503.1/Code/GraphMol/SynthonSpaceSearch/SynthonSpaceSearch_details.cpp +[ 93%] Building CXX object Code/GraphMol/RGroupDecomposition/CMakeFiles/RGroupDecomposition.dir/RGroupFingerprintScore.cpp.o +cd /build/reproducible-path/rdkit-202503.1/obj-aarch64-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_BUILD_XYZ2MOL_SUPPORT -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 -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/RGroupDecomposition/CMakeFiles/RGroupDecomposition.dir/RGroupFingerprintScore.cpp.o -MF CMakeFiles/RGroupDecomposition.dir/RGroupFingerprintScore.cpp.o.d -o CMakeFiles/RGroupDecomposition.dir/RGroupFingerprintScore.cpp.o -c /build/reproducible-path/rdkit-202503.1/Code/GraphMol/RGroupDecomposition/RGroupFingerprintScore.cpp +[ 93%] Building CXX object Code/GraphMol/RGroupDecomposition/CMakeFiles/RGroupDecomposition.dir/RGroupGa.cpp.o +cd /build/reproducible-path/rdkit-202503.1/obj-aarch64-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_BUILD_XYZ2MOL_SUPPORT -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 -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/RGroupDecomposition/CMakeFiles/RGroupDecomposition.dir/RGroupGa.cpp.o -MF CMakeFiles/RGroupDecomposition.dir/RGroupGa.cpp.o.d -o CMakeFiles/RGroupDecomposition.dir/RGroupGa.cpp.o -c /build/reproducible-path/rdkit-202503.1/Code/GraphMol/RGroupDecomposition/RGroupGa.cpp +[ 93%] Building CXX object Code/GraphMol/RGroupDecomposition/CMakeFiles/RGroupDecomposition.dir/RGroupDecompJSONParsers.cpp.o +cd /build/reproducible-path/rdkit-202503.1/obj-aarch64-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_BUILD_XYZ2MOL_SUPPORT -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 -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/RGroupDecomposition/CMakeFiles/RGroupDecomposition.dir/RGroupDecompJSONParsers.cpp.o -MF CMakeFiles/RGroupDecomposition.dir/RGroupDecompJSONParsers.cpp.o.d -o CMakeFiles/RGroupDecomposition.dir/RGroupDecompJSONParsers.cpp.o -c /build/reproducible-path/rdkit-202503.1/Code/GraphMol/RGroupDecomposition/RGroupDecompJSONParsers.cpp +[ 94%] Building CXX object Code/GraphMol/SynthonSpaceSearch/CMakeFiles/SynthonSpaceSearch.dir/SynthonSpace.cpp.o +cd /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/SynthonSpaceSearch && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDKIT_SYNTHONSPACESEARCH_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_BUILD_XYZ2MOL_SUPPORT -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DSynthonSpaceSearch_EXPORTS -I/build/reproducible-path/rdkit-202503.1/External -I/build/reproducible-path/rdkit-202503.1/Code -I/build/reproducible-path/rdkit-202503.1/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/SynthonSpaceSearch/CMakeFiles/SynthonSpaceSearch.dir/SynthonSpace.cpp.o -MF CMakeFiles/SynthonSpaceSearch.dir/SynthonSpace.cpp.o.d -o CMakeFiles/SynthonSpaceSearch.dir/SynthonSpace.cpp.o -c /build/reproducible-path/rdkit-202503.1/Code/GraphMol/SynthonSpaceSearch/SynthonSpace.cpp +[ 94%] Linking CXX shared module ../../../../rdkit/Chem/Scaffolds/rdScaffoldNetwork.so +cd /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/ScaffoldNetwork/Wrap && /usr/bin/cmake -E cmake_link_script CMakeFiles/rdScaffoldNetwork.dir/link.txt --verbose=1 +/usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -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 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/usr/lib/aarch64-linux-gnu/libboost_python313.so.1.83.0 ../../../../lib/libRDKitRDGeneral.so.1.2025.03.1 /usr/lib/aarch64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl +make[4]: Leaving directory '/build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu' +[ 94%] Built target rdScaffoldNetwork +[ 94%] Building CXX object Code/GraphMol/SynthonSpaceSearch/CMakeFiles/SynthonSpaceSearch.dir/SynthonSet.cpp.o +cd /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/SynthonSpaceSearch && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDKIT_SYNTHONSPACESEARCH_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS 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/build/reproducible-path/rdkit-202503.1/obj-aarch64-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-aarch64-linux-gnu /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/GeneralizedSubstruct/Wrap /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/GeneralizedSubstruct/Wrap/CMakeFiles/rdGeneralizedSubstruct.dir/DependInfo.cmake "--color=" @@ -7043,9 +7056,14 @@ make[4]: Entering directory '/build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu' [ 95%] Building CXX object Code/GraphMol/GeneralizedSubstruct/Wrap/CMakeFiles/rdGeneralizedSubstruct.dir/rdGeneralizedSubstruct.cpp.o cd /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/GeneralizedSubstruct/Wrap && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB 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-Wl,--dependency-file=CMakeFiles/rdMolStandardize.dir/link.d -Wl,-z,relro -Wl,-z,now -shared -o ../../../../rdkit/Chem/MolStandardize/rdMolStandardize.so CMakeFiles/rdMolStandardize.dir/rdMolStandardize.cpp.o CMakeFiles/rdMolStandardize.dir/Validate.cpp.o CMakeFiles/rdMolStandardize.dir/Charge.cpp.o CMakeFiles/rdMolStandardize.dir/Fragment.cpp.o CMakeFiles/rdMolStandardize.dir/Normalize.cpp.o CMakeFiles/rdMolStandardize.dir/Metal.cpp.o CMakeFiles/rdMolStandardize.dir/Tautomer.cpp.o CMakeFiles/rdMolStandardize.dir/Pipeline.cpp.o ../../../../lib/libRDKitMolStandardize.so.1.2025.03.1 ../../../../lib/libRDKitRDBoost.so.1.2025.03.1 ../../../../lib/libRDKitChemReactions.so.1.2025.03.1 ../../../../lib/libRDKitFilterCatalog.so.1.2025.03.1 ../../../../lib/libRDKitCatalogs.so.1.2025.03.1 ../../../../lib/libRDKitFingerprints.so.1.2025.03.1 ../../../../lib/libRDKitSubgraphs.so.1.2025.03.1 ../../../../lib/libRDKitFileParsers.so.1.2025.03.1 /usr/lib/aarch64-linux-gnu/libmaeparser.so 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../../../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/aarch64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl +cd /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/RGroupDecomposition && /usr/bin/cmake -E cmake_symlink_library ../../../lib/libRDKitRGroupDecomposition.so.1.2025.03.1 ../../../lib/libRDKitRGroupDecomposition.so.1 ../../../lib/libRDKitRGroupDecomposition.so make[4]: Leaving directory '/build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu' -[ 95%] Built target rdMolStandardize +[ 95%] Built target RGroupDecomposition 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-aarch64-linux-gnu' cd /build/reproducible-path/rdkit-202503.1/obj-aarch64-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-aarch64-linux-gnu /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/PgSQL/rdkit /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/PgSQL/rdkit/CMakeFiles/rdkit.dir/DependInfo.cmake "--color=" @@ -7054,25 +7072,24 @@ make[4]: Entering directory '/build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu' [ 95%] Building CXX object Code/PgSQL/rdkit/CMakeFiles/rdkit.dir/adapter.cpp.o cd /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/PgSQL/rdkit && /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 -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_BUILD_XYZ2MOL_SUPPORT -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 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/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 +[ 95%] Building CXX object Code/GraphMol/SynthonSpaceSearch/CMakeFiles/SynthonSpaceSearch.dir/SynthonSpaceFingerprintSearcher.cpp.o +cd /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/SynthonSpaceSearch && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDKIT_SYNTHONSPACESEARCH_BUILD 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CMakeFiles/SynthonSpaceSearch.dir/SynthonSpaceFingerprintSearcher.cpp.o.d -o CMakeFiles/SynthonSpaceSearch.dir/SynthonSpaceFingerprintSearcher.cpp.o -c /build/reproducible-path/rdkit-202503.1/Code/GraphMol/SynthonSpaceSearch/SynthonSpaceFingerprintSearcher.cpp [ 95%] Building C object Code/PgSQL/rdkit/CMakeFiles/rdkit.dir/bfp_op.c.o cd /build/reproducible-path/rdkit-202503.1/obj-aarch64-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_BUILD_XYZ2MOL_SUPPORT -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 -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -fPIC -fPIC -MD -MT Code/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 [ 95%] Building C object Code/PgSQL/rdkit/CMakeFiles/rdkit.dir/cache.c.o cd /build/reproducible-path/rdkit-202503.1/obj-aarch64-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_BUILD_XYZ2MOL_SUPPORT -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 -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -fPIC -fPIC -MD -MT Code/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 -[ 95%] Building CXX object Code/GraphMol/SubstructLibrary/CMakeFiles/SubstructLibrary.dir/PatternFactory.cpp.o -cd /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/SubstructLibrary && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB 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[-Wunused-parameter] 1637 | unsigned int bitFlags) { | ~~~~~~~~~~~~~^~~~~~~~ -[ 95%] Linking CXX shared library ../../../lib/libRDKitRGroupDecomposition.so -cd /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/RGroupDecomposition && /usr/bin/cmake -E cmake_link_script CMakeFiles/RGroupDecomposition.dir/link.txt --verbose=1 -/usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,--dependency-file=CMakeFiles/RGroupDecomposition.dir/link.d -Wl,-z,relro -Wl,-z,now -shared -Wl,-soname,libRDKitRGroupDecomposition.so.1 -o ../../../lib/libRDKitRGroupDecomposition.so.1.2025.03.1 CMakeFiles/RGroupDecomposition.dir/RGroupDecomp.cpp.o 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/usr/lib/aarch64-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/aarch64-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/aarch64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl -cd /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/RGroupDecomposition && /usr/bin/cmake -E cmake_symlink_library ../../../lib/libRDKitRGroupDecomposition.so.1.2025.03.1 ../../../lib/libRDKitRGroupDecomposition.so.1 ../../../lib/libRDKitRGroupDecomposition.so -make[4]: Leaving directory '/build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu' -[ 95%] Built target RGroupDecomposition -[ 95%] Building CXX object Code/GraphMol/SynthonSpaceSearch/CMakeFiles/SynthonSpaceSearch.dir/SynthonSpaceFingerprintSearcher.cpp.o -cd /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/SynthonSpaceSearch && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDKIT_SYNTHONSPACESEARCH_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_BUILD_XYZ2MOL_SUPPORT -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DSynthonSpaceSearch_EXPORTS -I/build/reproducible-path/rdkit-202503.1/External -I/build/reproducible-path/rdkit-202503.1/Code -I/build/reproducible-path/rdkit-202503.1/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/SynthonSpaceSearch/CMakeFiles/SynthonSpaceSearch.dir/SynthonSpaceFingerprintSearcher.cpp.o -MF CMakeFiles/SynthonSpaceSearch.dir/SynthonSpaceFingerprintSearcher.cpp.o.d -o CMakeFiles/SynthonSpaceSearch.dir/SynthonSpaceFingerprintSearcher.cpp.o -c /build/reproducible-path/rdkit-202503.1/Code/GraphMol/SynthonSpaceSearch/SynthonSpaceFingerprintSearcher.cpp -[ 95%] Building C object Code/PgSQL/rdkit/CMakeFiles/rdkit.dir/guc.c.o -cd /build/reproducible-path/rdkit-202503.1/obj-aarch64-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_BUILD_XYZ2MOL_SUPPORT -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 -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -fPIC -fPIC -MD -MT Code/PgSQL/rdkit/CMakeFiles/rdkit.dir/guc.c.o -MF CMakeFiles/rdkit.dir/guc.c.o.d -o CMakeFiles/rdkit.dir/guc.c.o -c /build/reproducible-path/rdkit-202503.1/Code/PgSQL/rdkit/guc.c [ 95%] Building CXX object Code/GraphMol/SynthonSpaceSearch/CMakeFiles/SynthonSpaceSearch.dir/SynthonSpaceRascalSearcher.cpp.o cd /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/SynthonSpaceSearch && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDKIT_SYNTHONSPACESEARCH_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_BUILD_XYZ2MOL_SUPPORT -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DSynthonSpaceSearch_EXPORTS -I/build/reproducible-path/rdkit-202503.1/External -I/build/reproducible-path/rdkit-202503.1/Code -I/build/reproducible-path/rdkit-202503.1/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/SynthonSpaceSearch/CMakeFiles/SynthonSpaceSearch.dir/SynthonSpaceRascalSearcher.cpp.o -MF CMakeFiles/SynthonSpaceSearch.dir/SynthonSpaceRascalSearcher.cpp.o.d -o CMakeFiles/SynthonSpaceSearch.dir/SynthonSpaceRascalSearcher.cpp.o -c /build/reproducible-path/rdkit-202503.1/Code/GraphMol/SynthonSpaceSearch/SynthonSpaceRascalSearcher.cpp -[ 95%] Building C object Code/PgSQL/rdkit/CMakeFiles/rdkit.dir/low_gist.c.o -cd /build/reproducible-path/rdkit-202503.1/obj-aarch64-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_BUILD_XYZ2MOL_SUPPORT -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 -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -fPIC -fPIC -MD -MT Code/PgSQL/rdkit/CMakeFiles/rdkit.dir/low_gist.c.o -MF CMakeFiles/rdkit.dir/low_gist.c.o.d -o CMakeFiles/rdkit.dir/low_gist.c.o -c /build/reproducible-path/rdkit-202503.1/Code/PgSQL/rdkit/low_gist.c -[ 95%] Building CXX object Code/GraphMol/SynthonSpaceSearch/CMakeFiles/SynthonSpaceSearch.dir/SynthonSpaceHitSet.cpp.o -cd /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/SynthonSpaceSearch && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDKIT_SYNTHONSPACESEARCH_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_BUILD_XYZ2MOL_SUPPORT -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DSynthonSpaceSearch_EXPORTS -I/build/reproducible-path/rdkit-202503.1/External -I/build/reproducible-path/rdkit-202503.1/Code -I/build/reproducible-path/rdkit-202503.1/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/SynthonSpaceSearch/CMakeFiles/SynthonSpaceSearch.dir/SynthonSpaceHitSet.cpp.o -MF CMakeFiles/SynthonSpaceSearch.dir/SynthonSpaceHitSet.cpp.o.d -o CMakeFiles/SynthonSpaceSearch.dir/SynthonSpaceHitSet.cpp.o -c /build/reproducible-path/rdkit-202503.1/Code/GraphMol/SynthonSpaceSearch/SynthonSpaceHitSet.cpp -[ 95%] Building CXX object Code/GraphMol/SynthonSpaceSearch/CMakeFiles/SynthonSpaceSearch.dir/SearchResults.cpp.o -cd /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/SynthonSpaceSearch && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDKIT_SYNTHONSPACESEARCH_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_BUILD_XYZ2MOL_SUPPORT -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DSynthonSpaceSearch_EXPORTS -I/build/reproducible-path/rdkit-202503.1/External -I/build/reproducible-path/rdkit-202503.1/Code -I/build/reproducible-path/rdkit-202503.1/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/SynthonSpaceSearch/CMakeFiles/SynthonSpaceSearch.dir/SearchResults.cpp.o -MF CMakeFiles/SynthonSpaceSearch.dir/SearchResults.cpp.o.d -o CMakeFiles/SynthonSpaceSearch.dir/SearchResults.cpp.o -c /build/reproducible-path/rdkit-202503.1/Code/GraphMol/SynthonSpaceSearch/SearchResults.cpp -[ 95%] Linking CXX shared module ../../../../rdkit/Chem/rdGeneralizedSubstruct.so -cd /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/GeneralizedSubstruct/Wrap && /usr/bin/cmake -E cmake_link_script CMakeFiles/rdGeneralizedSubstruct.dir/link.txt --verbose=1 -/usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -g -fwrapv -O2 -Wl,--dependency-file=CMakeFiles/rdGeneralizedSubstruct.dir/link.d -Wl,-z,relro -Wl,-z,now -shared -o ../../../../rdkit/Chem/rdGeneralizedSubstruct.so CMakeFiles/rdGeneralizedSubstruct.dir/rdGeneralizedSubstruct.cpp.o ../../../../lib/libRDKitGeneralizedSubstruct.so.1.2025.03.1 ../../../../lib/libRDKitRDBoost.so.1.2025.03.1 ../../../../lib/libRDKitMolEnumerator.so.1.2025.03.1 ../../../../lib/libRDKitTautomerQuery.so.1.2025.03.1 ../../../../lib/libRDKitMolStandardize.so.1.2025.03.1 ../../../../lib/libRDKitChemReactions.so.1.2025.03.1 ../../../../lib/libRDKitFileParsers.so.1.2025.03.1 /usr/lib/aarch64-linux-gnu/libmaeparser.so ../../../../lib/libRDKitFilterCatalog.so.1.2025.03.1 ../../../../lib/libRDKitCatalogs.so.1.2025.03.1 ../../../../lib/libRDKitChemTransforms.so.1.2025.03.1 ../../../../lib/libRDKitDepictor.so.1.2025.03.1 /usr/lib/aarch64-linux-gnu/libcoordgen.so ../../../../lib/libRDKitMolAlign.so.1.2025.03.1 ../../../../lib/libRDKitMolTransforms.so.1.2025.03.1 ../../../../lib/libRDKitEigenSolvers.so.1.2025.03.1 ../../../../lib/libRDKitAlignment.so.1.2025.03.1 ../../../../lib/libRDKitFingerprints.so.1.2025.03.1 ../../../../lib/libRDKitSubstructMatch.so.1.2025.03.1 ../../../../lib/libRDKitGenericGroups.so.1.2025.03.1 ../../../../lib/libRDKitSmilesParse.so.1.2025.03.1 ../../../../lib/libRDKitSubgraphs.so.1.2025.03.1 ../../../../lib/libRDKitGraphMol.so.1.2025.03.1 ../../../../lib/libRDKitRDGeometryLib.so.1.2025.03.1 ../../../../lib/libRDKitDataStructs.so.1.2025.03.1 /usr/lib/aarch64-linux-gnu/libboost_numpy313.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_python313.so.1.83.0 ../../../../lib/libRDKitRDGeneral.so.1.2025.03.1 /usr/lib/aarch64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl -make[4]: Leaving directory '/build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu' -[ 95%] Built target rdGeneralizedSubstruct -make -f Code/GraphMol/RGroupDecomposition/CMakeFiles/testRGroupDecomp.dir/build.make Code/GraphMol/RGroupDecomposition/CMakeFiles/testRGroupDecomp.dir/depend -make[4]: Entering directory '/build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu' -cd /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202503.1 /build/reproducible-path/rdkit-202503.1/Code/GraphMol/RGroupDecomposition /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/RGroupDecomposition /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/RGroupDecomposition/CMakeFiles/testRGroupDecomp.dir/DependInfo.cmake "--color=" -make[4]: Leaving directory '/build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu' -make -f Code/GraphMol/RGroupDecomposition/CMakeFiles/testRGroupDecomp.dir/build.make Code/GraphMol/RGroupDecomposition/CMakeFiles/testRGroupDecomp.dir/build -make[4]: Entering directory '/build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu' -[ 95%] Building CXX object Code/GraphMol/RGroupDecomposition/CMakeFiles/testRGroupDecomp.dir/testRGroupDecomp.cpp.o -cd /build/reproducible-path/rdkit-202503.1/obj-aarch64-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 -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_BUILD_XYZ2MOL_SUPPORT -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 -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/GraphMol/RGroupDecomposition/CMakeFiles/testRGroupDecomp.dir/testRGroupDecomp.cpp.o -MF CMakeFiles/testRGroupDecomp.dir/testRGroupDecomp.cpp.o.d -o CMakeFiles/testRGroupDecomp.dir/testRGroupDecomp.cpp.o -c /build/reproducible-path/rdkit-202503.1/Code/GraphMol/RGroupDecomposition/testRGroupDecomp.cpp +In file included from /usr/include/boost/python/override.hpp:13, + from /usr/include/boost/python/wrapper.hpp:8, + from /usr/include/boost/python/object/value_holder.hpp:15, + from /usr/include/boost/python/object/class_metadata.hpp:14, + from /usr/include/boost/python/class.hpp:23, + from /usr/include/boost/python/suite/indexing/indexing_suite.hpp:9, + from /usr/include/boost/python/suite/indexing/map_indexing_suite.hpp:9, + from /build/reproducible-path/rdkit-202503.1/Code/GraphMol/MolStandardize/Wrap/Tautomer.cpp:11: +In member function 'boost::python::converter::extract_rvalue::result_type boost::python::converter::extract_rvalue::operator()() const [with T = long int]', + inlined from 'boost::python::extract::operator result_type() const [with T = long int]' at /usr/include/boost/python/extract.hpp:136:23, + inlined from 'static void boost::python::detail::slice_helper::base_get_slice_data(Container&, PySliceObject*, Index&, Index&) [with Container = std::vector; DerivedPolicies = boost::python::detail::final_vector_derived_policies, false>; ProxyHandler = boost::python::detail::proxy_helper, boost::python::detail::final_vector_derived_policies, false>, boost::python::detail::container_element, long unsigned int, boost::python::detail::final_vector_derived_policies, false> >, long unsigned int>; Data = RDKit::MolStandardize::TautomerScoringFunctions::SubstructTerm; Index = long unsigned int]' at /usr/include/boost/python/suite/indexing/detail/indexing_suite_detail.hpp:617:27: +/usr/include/boost/python/extract.hpp:185:11: warning: '*(long int*)((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))' may be used uninitialized [-Wmaybe-uninitialized] + 185 | ); + | ^ +In file included from /usr/include/boost/python/suite/indexing/indexing_suite.hpp:12: +/usr/include/boost/python/suite/indexing/detail/indexing_suite_detail.hpp: In static member function 'static void boost::python::detail::slice_helper::base_get_slice_data(Container&, PySliceObject*, Index&, Index&) [with Container = std::vector; DerivedPolicies = boost::python::detail::final_vector_derived_policies, false>; ProxyHandler = boost::python::detail::proxy_helper, boost::python::detail::final_vector_derived_policies, false>, boost::python::detail::container_element, long unsigned int, boost::python::detail::final_vector_derived_policies, false> >, long unsigned int>; Data = RDKit::MolStandardize::TautomerScoringFunctions::SubstructTerm; Index = long unsigned int]': +/usr/include/boost/python/suite/indexing/detail/indexing_suite_detail.hpp:617:27: note: '' declared here + 617 | long to = extract( slice->stop); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ +In member function 'boost::python::converter::extract_rvalue::result_type boost::python::converter::extract_rvalue::operator()() const [with T = long int]', + inlined from 'boost::python::extract::operator result_type() const [with T = long int]' at /usr/include/boost/python/extract.hpp:136:23, + inlined from 'static void boost::python::detail::slice_helper::base_get_slice_data(Container&, PySliceObject*, Index&, Index&) [with Container = std::vector; DerivedPolicies = boost::python::detail::final_vector_derived_policies, false>; ProxyHandler = boost::python::detail::proxy_helper, boost::python::detail::final_vector_derived_policies, false>, boost::python::detail::container_element, long unsigned int, boost::python::detail::final_vector_derived_policies, false> >, long unsigned int>; Data = RDKit::MolStandardize::TautomerScoringFunctions::SubstructTerm; Index = long unsigned int]' at /usr/include/boost/python/suite/indexing/detail/indexing_suite_detail.hpp:603:29: +/usr/include/boost/python/extract.hpp:185:11: warning: '*(long int*)((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))' may be used uninitialized [-Wmaybe-uninitialized] + 185 | ); + | ^ +/usr/include/boost/python/suite/indexing/detail/indexing_suite_detail.hpp: In static member function 'static void boost::python::detail::slice_helper::base_get_slice_data(Container&, PySliceObject*, Index&, Index&) [with Container = std::vector; DerivedPolicies = boost::python::detail::final_vector_derived_policies, false>; ProxyHandler = boost::python::detail::proxy_helper, boost::python::detail::final_vector_derived_policies, false>, boost::python::detail::container_element, long unsigned int, boost::python::detail::final_vector_derived_policies, false> >, long unsigned int>; Data = RDKit::MolStandardize::TautomerScoringFunctions::SubstructTerm; Index = long unsigned int]': +/usr/include/boost/python/suite/indexing/detail/indexing_suite_detail.hpp:603:29: note: '' declared here + 603 | long from = extract( slice->start); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ [ 95%] Linking CXX executable generalizedSubstructCatch cd /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/GeneralizedSubstruct && /usr/bin/cmake -E cmake_link_script CMakeFiles/generalizedSubstructCatch.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now -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/aarch64-linux-gnu/libmaeparser.so ../../../lib/libRDKitChemTransforms.so.1.2025.03.1 ../../../lib/libRDKitDepictor.so.1.2025.03.1 /usr/lib/aarch64-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/aarch64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl @@ -7127,63 +7144,67 @@ make[4]: Entering directory '/build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu' [ 95%] Building CXX object Code/GraphMol/RGroupDecomposition/CMakeFiles/testRGroupDecompInternals.dir/testRGroupInternals.cpp.o cd /build/reproducible-path/rdkit-202503.1/obj-aarch64-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 -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_BUILD_XYZ2MOL_SUPPORT -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 -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/GraphMol/RGroupDecomposition/CMakeFiles/testRGroupDecompInternals.dir/testRGroupInternals.cpp.o -MF CMakeFiles/testRGroupDecompInternals.dir/testRGroupInternals.cpp.o.d -o CMakeFiles/testRGroupDecompInternals.dir/testRGroupInternals.cpp.o -c /build/reproducible-path/rdkit-202503.1/Code/GraphMol/RGroupDecomposition/testRGroupInternals.cpp -[ 95%] Building C object Code/PgSQL/rdkit/CMakeFiles/rdkit.dir/mol_op.c.o -cd /build/reproducible-path/rdkit-202503.1/obj-aarch64-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_BUILD_XYZ2MOL_SUPPORT -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 -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -fPIC -fPIC -MD -MT Code/PgSQL/rdkit/CMakeFiles/rdkit.dir/mol_op.c.o -MF CMakeFiles/rdkit.dir/mol_op.c.o.d -o CMakeFiles/rdkit.dir/mol_op.c.o -c /build/reproducible-path/rdkit-202503.1/Code/PgSQL/rdkit/mol_op.c -[ 95%] Building C object Code/PgSQL/rdkit/CMakeFiles/rdkit.dir/rdkit_gist.c.o -cd /build/reproducible-path/rdkit-202503.1/obj-aarch64-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_BUILD_XYZ2MOL_SUPPORT -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 -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -fPIC -fPIC -MD -MT Code/PgSQL/rdkit/CMakeFiles/rdkit.dir/rdkit_gist.c.o -MF CMakeFiles/rdkit.dir/rdkit_gist.c.o.d -o CMakeFiles/rdkit.dir/rdkit_gist.c.o -c /build/reproducible-path/rdkit-202503.1/Code/PgSQL/rdkit/rdkit_gist.c -[ 96%] Building C object Code/PgSQL/rdkit/CMakeFiles/rdkit.dir/bfp_gist.c.o -cd /build/reproducible-path/rdkit-202503.1/obj-aarch64-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_BUILD_XYZ2MOL_SUPPORT -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 -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -fPIC -fPIC -MD -MT Code/PgSQL/rdkit/CMakeFiles/rdkit.dir/bfp_gist.c.o -MF CMakeFiles/rdkit.dir/bfp_gist.c.o.d -o CMakeFiles/rdkit.dir/bfp_gist.c.o -c /build/reproducible-path/rdkit-202503.1/Code/PgSQL/rdkit/bfp_gist.c -[ 96%] Building C object Code/PgSQL/rdkit/CMakeFiles/rdkit.dir/bfp_gin.c.o -cd /build/reproducible-path/rdkit-202503.1/obj-aarch64-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_BUILD_XYZ2MOL_SUPPORT -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 -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function 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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 -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/SynthonSpaceSearch/CMakeFiles/SynthonSpaceSearch.dir/SynthonSpaceHitSet.cpp.o -MF CMakeFiles/SynthonSpaceSearch.dir/SynthonSpaceHitSet.cpp.o.d -o CMakeFiles/SynthonSpaceSearch.dir/SynthonSpaceHitSet.cpp.o -c /build/reproducible-path/rdkit-202503.1/Code/GraphMol/SynthonSpaceSearch/SynthonSpaceHitSet.cpp +[ 95%] Linking CXX shared module ../../../../rdkit/Chem/rdGeneralizedSubstruct.so +cd /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/GeneralizedSubstruct/Wrap && /usr/bin/cmake -E cmake_link_script CMakeFiles/rdGeneralizedSubstruct.dir/link.txt --verbose=1 +/usr/bin/c++ -fPIC -g -O2 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CMakeFiles/SynthonSpaceSearch.dir/MemoryMappedFileReader.cpp.o.d -o CMakeFiles/SynthonSpaceSearch.dir/MemoryMappedFileReader.cpp.o -c /build/reproducible-path/rdkit-202503.1/Code/GraphMol/SynthonSpaceSearch/MemoryMappedFileReader.cpp +[ 96%] Building C object Code/PgSQL/rdkit/CMakeFiles/rdkit.dir/rxn_op.c.o +cd /build/reproducible-path/rdkit-202503.1/obj-aarch64-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_BUILD_XYZ2MOL_SUPPORT -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 -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -fPIC -fPIC -MD -MT Code/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 +make -f Code/GraphMol/SubstructLibrary/CMakeFiles/substructLibraryTest.dir/build.make Code/GraphMol/SubstructLibrary/CMakeFiles/substructLibraryTest.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu' cd /build/reproducible-path/rdkit-202503.1/obj-aarch64-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-aarch64-linux-gnu /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/SubstructLibrary /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/SubstructLibrary/CMakeFiles/substructLibraryTest.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu' @@ -7191,6 +7212,10 @@ make[4]: Entering directory '/build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu' [ 96%] Building CXX object Code/GraphMol/SubstructLibrary/CMakeFiles/substructLibraryTest.dir/substructLibraryTest.cpp.o cd /build/reproducible-path/rdkit-202503.1/obj-aarch64-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_BUILD_XYZ2MOL_SUPPORT -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 -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/GraphMol/SubstructLibrary/CMakeFiles/substructLibraryTest.dir/substructLibraryTest.cpp.o -MF CMakeFiles/substructLibraryTest.dir/substructLibraryTest.cpp.o.d -o CMakeFiles/substructLibraryTest.dir/substructLibraryTest.cpp.o -c /build/reproducible-path/rdkit-202503.1/Code/GraphMol/SubstructLibrary/substructLibraryTest.cpp +[ 96%] Building C object Code/PgSQL/rdkit/CMakeFiles/rdkit.dir/sfp_op.c.o +cd /build/reproducible-path/rdkit-202503.1/obj-aarch64-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 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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/aarch64-linux-gnu/libpq.so ../../../lib/libRDKitRDInchiLib.so.1.2025.03.1 /usr/lib/aarch64-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/aarch64-linux-gnu/libcairo.so /usr/lib/aarch64-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/aarch64-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/aarch64-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/aarch64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_iostreams.so.1.83.0 make[4]: Leaving directory '/build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu' +cd /build/reproducible-path/rdkit-202503.1/obj-aarch64-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-aarch64-linux-gnu/Code/PgSQL/rdkit/sql make -f Code/GraphMol/SubstructLibrary/Wrap/CMakeFiles/rdSubstructLibrary.dir/build.make Code/GraphMol/SubstructLibrary/Wrap/CMakeFiles/rdSubstructLibrary.dir/build make[4]: Entering directory '/build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu' +cd /build/reproducible-path/rdkit-202503.1/obj-aarch64-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-aarch64-linux-gnu/Code/PgSQL/rdkit/data [ 97%] Building CXX object Code/GraphMol/SubstructLibrary/Wrap/CMakeFiles/rdSubstructLibrary.dir/rdSubstructLibrary.cpp.o cd /build/reproducible-path/rdkit-202503.1/obj-aarch64-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_BUILD_XYZ2MOL_SUPPORT -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/aarch64-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 -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/SubstructLibrary/Wrap/CMakeFiles/rdSubstructLibrary.dir/rdSubstructLibrary.cpp.o -MF CMakeFiles/rdSubstructLibrary.dir/rdSubstructLibrary.cpp.o.d -o CMakeFiles/rdSubstructLibrary.dir/rdSubstructLibrary.cpp.o -c /build/reproducible-path/rdkit-202503.1/Code/GraphMol/SubstructLibrary/Wrap/rdSubstructLibrary.cpp +cd /build/reproducible-path/rdkit-202503.1/obj-aarch64-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-aarch64-linux-gnu/Code/PgSQL/rdkit/expected +make[4]: Leaving directory '/build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu' +[ 97%] Built target rdkit [ 97%] Building CXX object Code/GraphMol/SubstructLibrary/Wrap/CMakeFiles/rdSubstructLibrary.dir/SubstructLibraryWrap.cpp.o cd /build/reproducible-path/rdkit-202503.1/obj-aarch64-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_BUILD_XYZ2MOL_SUPPORT -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/aarch64-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 -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/SubstructLibrary/Wrap/CMakeFiles/rdSubstructLibrary.dir/SubstructLibraryWrap.cpp.o -MF CMakeFiles/rdSubstructLibrary.dir/SubstructLibraryWrap.cpp.o.d -o CMakeFiles/rdSubstructLibrary.dir/SubstructLibraryWrap.cpp.o -c /build/reproducible-path/rdkit-202503.1/Code/GraphMol/SubstructLibrary/Wrap/SubstructLibraryWrap.cpp +[ 97%] Linking CXX executable testRGroupDecompInternals +cd /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/RGroupDecomposition && /usr/bin/cmake -E cmake_link_script CMakeFiles/testRGroupDecompInternals.dir/link.txt --verbose=1 +/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now -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/aarch64-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/aarch64-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/aarch64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl +make[4]: Leaving directory '/build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu' +[ 97%] Built target testRGroupDecompInternals [ 98%] Linking CXX shared library ../../../lib/libRDKitSynthonSpaceSearch.so cd /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/SynthonSpaceSearch && /usr/bin/cmake -E cmake_link_script CMakeFiles/SynthonSpaceSearch.dir/link.txt --verbose=1 /usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,--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/aarch64-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/aarch64-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/aarch64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl @@ -7217,48 +7253,43 @@ [ 98%] Built target SynthonSpaceSearch 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/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-aarch64-linux-gnu' cd /build/reproducible-path/rdkit-202503.1/obj-aarch64-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-aarch64-linux-gnu /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/SynthonSpaceSearch /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/SynthonSpaceSearch/CMakeFiles/testSynthonSpaceSubstructureSearch.dir/DependInfo.cmake "--color=" -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-aarch64-linux-gnu' cd /build/reproducible-path/rdkit-202503.1/obj-aarch64-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-aarch64-linux-gnu /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/SynthonSpaceSearch /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/SynthonSpaceSearch/CMakeFiles/testSynthonSpaceRascalSearch.dir/DependInfo.cmake "--color=" make[4]: Entering directory '/build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu' cd /build/reproducible-path/rdkit-202503.1/obj-aarch64-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-aarch64-linux-gnu /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/SynthonSpaceSearch/Wrap /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/SynthonSpaceSearch/Wrap/CMakeFiles/rdSynthonSpaceSearch.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/rdkit-202503.1/obj-aarch64-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-aarch64-linux-gnu' make[4]: Leaving directory '/build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu' -make -f Code/GraphMol/SynthonSpaceSearch/CMakeFiles/testSynthonSpaceSubstructureSearch.dir/build.make Code/GraphMol/SynthonSpaceSearch/CMakeFiles/testSynthonSpaceSubstructureSearch.dir/build +make -f Code/GraphMol/SynthonSpaceSearch/CMakeFiles/testSynthonSpaceRascalSearch.dir/build.make Code/GraphMol/SynthonSpaceSearch/CMakeFiles/testSynthonSpaceRascalSearch.dir/build +make[4]: Entering directory '/build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu' make[4]: Leaving directory '/build/reproducible-path/rdkit-202503.1/obj-aarch64-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-aarch64-linux-gnu' -make[4]: Entering directory '/build/reproducible-path/rdkit-202503.1/obj-aarch64-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-aarch64-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_BUILD_XYZ2MOL_SUPPORT -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 -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/GraphMol/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 -[ 98%] Building CXX object Code/GraphMol/SynthonSpaceSearch/Wrap/CMakeFiles/rdSynthonSpaceSearch.dir/rdSynthonSpaceSearch.cpp.o -cd /build/reproducible-path/rdkit-202503.1/obj-aarch64-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 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-D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/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%] Building CXX object Code/GraphMol/SynthonSpaceSearch/CMakeFiles/testSynthonSpaceSubstructureSearch.dir/substructure_search_catch_tests.cpp.o +[ 98%] Building CXX object Code/GraphMol/SynthonSpaceSearch/Wrap/CMakeFiles/rdSynthonSpaceSearch.dir/rdSynthonSpaceSearch.cpp.o cd /build/reproducible-path/rdkit-202503.1/obj-aarch64-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 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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 -[ 98%] Linking CXX executable testRGroupDecompInternals -cd /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/RGroupDecomposition && /usr/bin/cmake -E cmake_link_script CMakeFiles/testRGroupDecompInternals.dir/link.txt --verbose=1 -/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now -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/aarch64-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/aarch64-linux-gnu/libmaeparser.so ../../../lib/libRDKitFilterCatalog.so.1.2025.03.1 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-c /build/reproducible-path/rdkit-202503.1/Code/GraphMol/SynthonSpaceSearch/rascal_search_catch_tests.cpp [ 98%] Linking CXX executable gaExample cd /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/RGroupDecomposition && /usr/bin/cmake -E cmake_link_script CMakeFiles/gaExample.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now -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/aarch64-linux-gnu/libboost_program_options.so.1.83.0 ../../../lib/libRDKitFMCS.so.1.2025.03.1 ../../../lib/libRDKitga.so.1.2025.03.1 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/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 -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now -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/aarch64-linux-gnu/libmaeparser.so ../../../lib/libRDKitChemTransforms.so.1.2025.03.1 ../../../lib/libRDKitDepictor.so.1.2025.03.1 /usr/lib/aarch64-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/aarch64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl make[4]: Leaving directory '/build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu' [ 99%] Built target substructLibraryCatchTest -[ 99%] Linking CXX executable substructLibraryTest -cd /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/SubstructLibrary && /usr/bin/cmake -E cmake_link_script CMakeFiles/substructLibraryTest.dir/link.txt --verbose=1 -/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now -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/aarch64-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/aarch64-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/aarch64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl -make[4]: Leaving directory '/build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu' -[ 99%] Built target substructLibraryTest [ 99%] Linking CXX shared module ../../../../rdkit/Chem/rdRGroupDecomposition.so cd /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/RGroupDecomposition/Wrap && /usr/bin/cmake -E cmake_link_script CMakeFiles/rdRGroupDecomposition.dir/link.txt --verbose=1 /usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -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/aarch64-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/aarch64-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/aarch64-linux-gnu/libboost_numpy313.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_python313.so.1.83.0 ../../../../lib/libRDKitRDGeneral.so.1.2025.03.1 /usr/lib/aarch64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl @@ -7276,8 +7307,13 @@ [100%] Built target testSynthonSpaceRascalSearch [100%] Linking CXX executable testSynthonSpaceSubstructureSearch cd /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/SynthonSpaceSearch && /usr/bin/cmake -E cmake_link_script CMakeFiles/testSynthonSpaceSubstructureSearch.dir/link.txt --verbose=1 +[100%] Linking CXX executable testRGroupDecomp +cd /build/reproducible-path/rdkit-202503.1/obj-aarch64-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-aarch64-linux-gnu/Code/GraphMol/SynthonSpaceSearch/./Code/GraphMol/SynthonSpaceSearch/substructure_search_catch_tests.cpp:334:(.text+0x1904): 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 -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now -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/aarch64-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/aarch64-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/aarch64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl +make[4]: Leaving directory '/build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu' +[100%] 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 -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now -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/aarch64-linux-gnu/libmaeparser.so ../../../lib/libRDKitChemTransforms.so.1.2025.03.1 ../../../lib/libRDKitDepictor.so.1.2025.03.1 /usr/lib/aarch64-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/aarch64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl make[4]: Leaving directory '/build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu' [100%] Built target testSynthonSpaceSubstructureSearch @@ -7286,11 +7322,6 @@ /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 -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -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/aarch64-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/aarch64-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/aarch64-linux-gnu/libboost_numpy313.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_python313.so.1.83.0 ../../../../lib/libRDKitRDGeneral.so.1.2025.03.1 /usr/lib/aarch64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl make[4]: Leaving directory '/build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu' [100%] Built target rdSynthonSpaceSearch -[100%] Linking CXX executable testRGroupDecomp -cd /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/RGroupDecomposition && /usr/bin/cmake -E cmake_link_script CMakeFiles/testRGroupDecomp.dir/link.txt --verbose=1 -/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now -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/aarch64-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/aarch64-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/aarch64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl -make[4]: Leaving directory '/build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu' -[100%] Built target testRGroupDecomp [100%] Linking CXX shared module ../../../../rdkit/Chem/rdSubstructLibrary.so cd /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/SubstructLibrary/Wrap && /usr/bin/cmake -E cmake_link_script CMakeFiles/rdSubstructLibrary.dir/link.txt --verbose=1 /usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -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/aarch64-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/aarch64-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/aarch64-linux-gnu/libboost_numpy313.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_python313.so.1.83.0 ../../../../lib/libRDKitRDGeneral.so.1.2025.03.1 /usr/lib/aarch64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl @@ -12959,7 +12990,7 @@ 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 @@ -15176,47 +15207,34 @@ 12: Test command: /usr/bin/python3 "/build/reproducible-path/rdkit-202503.1/Code/DataStructs/Wrap/testBV.py" 12: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/DataStructs/Wrap 12: Test timeout computed to be: 1500 -3: [00:36:12] Testing Github940: property dictionaries leaking memory -3: [00:36:12] done +3: [09:33:07] Testing Github940: property dictionaries leaking memory +3: [09:33:07] done 3: Testing RDValue 3: Testing RDAny 3: dict set int vect 3: dict get int vect -3: static boost any:0.000227 s -3: dynamic boost any:0.001011 s -3: static RDAny:0.000126 s -3: dynamic RDAny:0.001023 s -3: static RDValue:0 s -3: dynamic RDValue:0.000155 s -3: deleted! -3: [00:36:12] ------------------------------------- -3: [00:36:12] Testing String Pickle Roundtrips. -3: [00:36:12] done -3: [00:36:12] ------------------------------------- -3: [00:36:12] Testing conversion of vect to string. -3: [00:36:12] done -3: [00:36:12] ------------------------------------- -3: [00:36:12] Testing returning const references. -3: [00:36:12] any cast -3: [00:36:12] done: 0.000802 300000 -3: [00:36:12] copy -3: [00:36:12] done: 0.000834 300000 -3: [00:36:12] ref -3: [00:36:12] done: 0.000818 300000 -3: [00:36:12] dict -3: [00:36:12] done: 0.001949 300000 -3: [00:36:12] ref with hasVal -3: [00:36:12] done: 0.001325 300000 -3: [00:36:12] done -3: [00:36:12] ------------------------------------- -3: [00:36:12] Testing dict update. -3: [00:36:12] done -3: deleted! -3: deleted! -3: deleted! -3: deleted! -3: deleted! +3: static boost any:0.000685 s +3: dynamic boost any:0.002995 s +3: static RDAny:0.000365 s +3: dynamic RDAny:0.002865 s +3: static RDValue:1e-06 s +3: dynamic RDValue:0.00045 s 3: deleted! +3: [09:33:07] ------------------------------------- +3: [09:33:07] Testing String Pickle Roundtrips. +3: [09:33:07] done +3: [09:33:07] ------------------------------------- +3: [09:33:07] Testing conversion of vect to string. +3: [09:33:07] done +3: [09:33:07] ------------------------------------- +3: [09:33:07] Testing returning const references. +3: [09:33:07] any cast +3: [09:33:07] done: 0.002475 300000 +3: [09:33:07] copy +3: [09:33:07] done: 0.002456 300000 +3: [09:33:07] ref +3: [09:33:07] done: 0.002359 300000 +3: [09:33:07] dict 4: -- running tests -- 4: min: -2147483648 -2147483648 4: min: 0 0 @@ -15229,34 +15247,30 @@ 4: == unsigned int 4: == bool 4: == std::string -5: [00:36:12] +5: [09:33:07] 5: ----------------------------------------- -5: [00:36:12] Finished: testPushAndPop() -5: [00:36:12] +5: [09:33:07] Finished: testPushAndPop() +5: [09:33:07] 5: ----------------------------------------- -5: [00:36:12] +5: [09:33:07] 5: ----------------------------------------- -6: Randomness seeded to: 1946061671 -6: =============================================================================== -6: All tests passed (32 assertions in 2 test cases) -6: -8: [00:36:12] pass -8: [00:36:12] v3 4 -8: [00:36:12] v4 5 -8: [00:36:12] SPARSE ----------------------------------- -8: [00:36:12] Set 10: 0 -8: [00:36:12] Set 11: 0 -8: [00:36:12] Set 14: 0 -8: [00:36:12] Set 10: 1 -8: [00:36:12] Get 14: 1 -8: [00:36:12] Num: 20 -8: [00:36:12] NumOn: 3 -8: [00:36:12] NumOff: 17 +8: [09:33:07] pass +8: [09:33:07] v3 4 +8: [09:33:07] v4 5 +8: [09:33:07] SPARSE ----------------------------------- +8: [09:33:07] Set 10: 0 +8: [09:33:07] Set 11: 0 +8: [09:33:07] Set 14: 0 +8: [09:33:07] Set 10: 1 +8: [09:33:07] Get 14: 1 +8: [09:33:07] Num: 20 +8: [09:33:07] NumOn: 3 +8: [09:33:07] NumOff: 17 8: 10, 11, 14, -8: [00:36:12] t2[19]: 0 -8: [00:36:12] t2[14]: 1 -8: [00:36:12] t2[19]: 0 -8: [00:36:12] t2[14]: 0 +8: [09:33:07] t2[19]: 0 +8: [09:33:07] t2[14]: 1 +8: [09:33:07] t2[19]: 0 +8: [09:33:07] t2[14]: 0 8: t1: 10, 11, 14, 8: t2: 10, 11, 15, 17, 8: t1|t2: 10, 11, 14, 15, 17, @@ -15264,20 +15278,29 @@ 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: [00:36:12] Explicit ---------------------------------- -8: [00:36:12] Set 10: 0 -8: [00:36:12] Set 11: 0 -8: [00:36:12] Set 14: 0 -8: [00:36:12] Set 10: 1 -8: [00:36:12] Get 14: 1 -8: [00:36:12] Num: 20 -8: [00:36:12] NumOn: 3 -8: [00:36:12] NumOff: 17 + 1/238 Test #4: testRDValue ............................ Passed 0.03 sec +test 13 + Start 13: pyDiscreteValueVect + +13: Test command: /usr/bin/python3 "/build/reproducible-path/rdkit-202503.1/Code/DataStructs/Wrap/testDiscreteValueVect.py" +13: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/DataStructs/Wrap +13: Test timeout computed to be: 1500 +3: [09:33:07] done: 0.005744 300000 +3: [09:33:07] ref with hasVal +8: [09:33:07] Explicit ---------------------------------- +8: [09:33:07] Set 10: 0 +8: [09:33:07] Set 11: 0 +8: [09:33:07] Set 14: 0 +8: [09:33:07] Set 10: 1 +8: [09:33:07] Get 14: 1 +8: [09:33:07] Num: 20 +8: [09:33:07] NumOn: 3 +8: [09:33:07] NumOff: 17 8: 10, 11, 14, -8: [00:36:12] t2[19]: 0 -8: [00:36:12] t2[14]: 1 -8: [00:36:12] t2[19]: 0 -8: [00:36:12] t2[14]: 0 +8: [09:33:07] t2[19]: 0 +8: [09:33:07] t2[14]: 1 +8: [09:33:07] t2[19]: 0 +8: [09:33:07] t2[14]: 0 8: t1: 10, 11, 14, 8: t2: 10, 11, 15, 17, 8: t1|t2: 10, 11, 14, 15, 17, @@ -15285,70 +15308,53 @@ 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: [00:36:12] Done -8: [00:36:12] Test DiscreteValue Vectors 1 ---------------------------- -8: [00:36:12] Expected failure: Value out of range -8: [00:36:12] Expected failure: Value out of range -8: [00:36:12] Expected failure: Value out of range -8: [00:36:12] Expected failure: Value out of range -8: [00:36:12] Expected failure: Value out of range -8: [00:36:12] Test DiscreteValue Vectors 2 ------------------------------ -8: [00:36:12] Test DiscreteValue Vectors 3 --------------------------- -8: [00:36:12] Test DiscreteValue Operations ----------------------------- -8: [00:36:12] Test DiscreteValue Operations 2 -------------------------- -8: [00:36:12] Test SparseIntVect ------------------------------------ -8: [00:36:12] Test SparseIntVect Serialization -------------------------- -8: [00:36:12] Test BitVect Serialization ------------------------------- -8: [00:36:12] Test BitVect to FPS ------------------------------- -8: [00:36:12] Test BitVect to binary string ------------------------------- -8: [00:36:12] Test Similarity Measures BitVect ------------------------------- -8: [00:36:12] Test Similarity Measures SparseBitVect ------------------------------- -8: [00:36:12] Test BitVect with all ones ------------------------------- -8: [00:36:12] Test Explicit BitVects: Concatenation Operation ------------------------------- -8: [00:36:12] Test bitmap operations ------------------------------- -8: [00:36:12] Test bitmaps as properties ------------------------------- -8: [00:36:12] Test #3944: SparseIntVect copy constructor and assignment operators not clearing existing data------------------------------- -8: [00:36:12] Test RealValue Vectors 1: Constructors and Accessing Values ------------------------------- -8: [00:36:12] Test RealValue Vectors 2: L1Norm ------------------------------- -8: [00:36:12] Test RealValue Vectors 3: Pickles ------------------------------- -8: [00:36:12] Test RealValue Vectors 4: Vector Operations ------------------------------- - 1/238 Test #3: testDict ............................... Passed 0.06 sec - 2/238 Test #4: testRDValue ............................ Passed 0.06 sec - 3/238 Test #6: dictTestsCatch ......................... Passed 0.05 sec - 4/238 Test #8: testDataStructs ........................ Passed 0.03 sec - 5/238 Test #9: testFPB ................................ Passed 0.03 sec -11: Randomness seeded to: 3617309401 -11: =============================================================================== -11: All tests passed (3 assertions in 1 test case) -11: - 6/238 Test #11: catchDataStructs ....................... Passed 0.02 sec -7: [00:36:12] should not be silent -7: [00:36:12] should not be silent -7: Randomness seeded to: 997489908 -7: [00:36:12] should not be silent -7: [00:36:12] should not be silent -7: [00:36:12] should not be silent -7: [00:36:12] should not be silent -7: [00:36:12] should not be silent -7: [00:36:12] should not be silent -7: [00:36:12] should not be silent -7: [00:36:12] should not be silent -7: =============================================================================== -7: All tests passed (26 assertions in 3 test cases) -7: - 7/238 Test #7: logTestsCatch .......................... Passed 0.04 sec -test 13 - Start 13: pyDiscreteValueVect - -13: Test command: /usr/bin/python3 "/build/reproducible-path/rdkit-202503.1/Code/DataStructs/Wrap/testDiscreteValueVect.py" -13: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/DataStructs/Wrap -13: Test timeout computed to be: 1500 +8: [09:33:07] Done +8: [09:33:07] Test DiscreteValue Vectors 1 ---------------------------- +3: [09:33:07] done: 0.00385 300000 +3: [09:33:07] done +3: [09:33:07] ------------------------------------- +3: [09:33:07] Testing dict update. +3: [09:33:07] done +3: deleted! +3: deleted! +3: deleted! +3: deleted! +3: deleted! +3: deleted! + 2/238 Test #3: testDict ............................... Passed 0.04 sec +8: [09:33:07] Expected failure: Value out of range +8: [09:33:07] Expected failure: Value out of range +8: [09:33:07] Expected failure: Value out of range +8: [09:33:07] Expected failure: Value out of range +8: [09:33:07] Expected failure: Value out of range +8: [09:33:07] Test DiscreteValue Vectors 2 ------------------------------ +8: [09:33:07] Test DiscreteValue Vectors 3 --------------------------- +8: [09:33:07] Test DiscreteValue Operations ----------------------------- +6: Randomness seeded to: 2001032618 +6: =============================================================================== +6: All tests passed (32 assertions in 2 test cases) +6: test 14 Start 14: pyRealValueVect 14: Test command: /usr/bin/python3 "/build/reproducible-path/rdkit-202503.1/Code/DataStructs/Wrap/testRealValueVect.py" 14: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/DataStructs/Wrap 14: Test timeout computed to be: 1500 +8: [09:33:07] Test DiscreteValue Operations 2 -------------------------- +8: [09:33:07] Test SparseIntVect ------------------------------------ +7: [09:33:07] should not be silent +7: [09:33:07] should not be silent +7: Randomness seeded to: 1110130160 +7: [09:33:07] should not be silent +7: [09:33:07] should not be silent +7: [09:33:07] should not be silent +7: [09:33:07] should not be silent +7: [09:33:07] should not be silent +7: [09:33:07] should not be silent +7: [09:33:07] should not be silent + 3/238 Test #6: dictTestsCatch ......................... Passed 0.04 sec + 4/238 Test #9: testFPB ................................ Passed 0.03 sec +7: [09:33:07] should not be silent test 15 Start 15: pySparseIntVect @@ -15361,18 +15367,43 @@ 16: Test command: /usr/bin/python3 "/build/reproducible-path/rdkit-202503.1/Code/DataStructs/Wrap/testFPB.py" 16: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/DataStructs/Wrap 16: Test timeout computed to be: 1500 +7: =============================================================================== +7: All tests passed (26 assertions in 3 test cases) +7: +8: [09:33:07] Test SparseIntVect Serialization -------------------------- +8: [09:33:07] Test BitVect Serialization ------------------------------- +8: [09:33:07] Test BitVect to FPS ------------------------------- +8: [09:33:07] Test BitVect to binary string ------------------------------- +8: [09:33:07] Test Similarity Measures BitVect ------------------------------- +8: [09:33:07] Test Similarity Measures SparseBitVect ------------------------------- +8: [09:33:07] Test BitVect with all ones ------------------------------- +8: [09:33:07] Test Explicit BitVects: Concatenation Operation ------------------------------- +8: [09:33:07] Test bitmap operations ------------------------------- +8: [09:33:07] Test bitmaps as properties ------------------------------- +8: [09:33:07] Test #3944: SparseIntVect copy constructor and assignment operators not clearing existing data------------------------------- +8: [09:33:07] Test RealValue Vectors 1: Constructors and Accessing Values ------------------------------- +8: [09:33:07] Test RealValue Vectors 2: L1Norm ------------------------------- +8: [09:33:07] Test RealValue Vectors 3: Pickles ------------------------------- +8: [09:33:07] Test RealValue Vectors 4: Vector Operations ------------------------------- + 5/238 Test #8: testDataStructs ........................ Passed 0.04 sec test 17 Start 17: testTransforms 17: Test command: /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/Geometry/testTransforms 17: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/Geometry 17: Test timeout computed to be: 1500 + 6/238 Test #7: logTestsCatch .......................... Passed 0.05 sec test 18 Start 18: testGrid 18: Test command: /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/Geometry/testGrid 18: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/Geometry 18: Test timeout computed to be: 1500 +11: Randomness seeded to: 1054287591 +11: =============================================================================== +11: All tests passed (3 assertions in 1 test case) +11: + 7/238 Test #11: catchDataStructs ....................... Passed 0.04 sec test 19 Start 19: testRealValueGrid @@ -15394,8 +15425,8 @@ 17: testPointOps2D 17: **************************************** 17: test12D -17: ref1: 0.945282 3.54842 ref2: 4.88225 3.48198 -17: pt1: 3.38794 4.36761 pt2: 3.34956 1.33699 +17: ref1: 4.3826 1.37558 ref2: 2.68034 4.62361 +17: pt1: 0.27898 0.413618 pt2: 3.11714 0.457395 17: **************************************** 17: test23D 17: **************************************** @@ -15410,13 +15441,128 @@ 17: **************************************** 17: testFromQuaternion 17: **************************************** - 9/238 Test #17: testTransforms ......................... Passed 0.02 sec + 9/238 Test #17: testTransforms ......................... Passed 0.03 sec test 21 Start 21: testPyGeometry 21: Test command: /usr/bin/python3 "/build/reproducible-path/rdkit-202503.1/Code/Geometry/Wrap/testGeometry.py" 21: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/Geometry/Wrap 21: Test timeout computed to be: 1500 +18: *********************************************************** +18: Testing Grid +18: --------------------------------- +18: testUniformGrid1 +18: +18: --------------------------------- +18: testUniformGrid2 +18: +18: --------------------------------- +18: testUniformGridPickling +18: +18: --------------------------------- +18: testGridOps +18: +18: --------------------------------- +18: testUniformGridIndexing +18: + 10/238 Test #18: testGrid ............................... Passed 0.05 sec +test 22 + Start 22: testMatrices + +22: Test command: /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/Numerics/testMatrices +22: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/Numerics +22: 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: + 11/238 Test #19: testRealValueGrid ...................... Passed 0.05 sec +test 23 + Start 23: testConrec + +23: Test command: /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/Numerics/testConrec +23: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/Numerics +23: Test timeout computed to be: 1500 +22: [09:33:07] ----------------------------------------- +22: [09:33:07] Testing RDNumerics: vectors and matrices Code +22: [09:33:07] --------------------------------------- +22: [09:33:07] test1Vector +22: [09:33:07] --------------------------------------- +22: [09:33:07] test2Matrix +22: [09:33:07] --------------------------------------- +22: [09:33:07] test3SquareMatrix +22: [09:33:07] --------------------------------------- +22: [09:33:07] test4SymmMatrix + 12/238 Test #22: testMatrices ........................... Passed 0.01 sec +test 24 + Start 24: testAlignment + +24: Test command: /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/Numerics/Alignment/testAlignment +24: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/Numerics/Alignment +24: Test timeout computed to be: 1500 +20: Randomness seeded to: 1562077783 +20: =============================================================================== +20: All tests passed (50 assertions in 5 test cases) +20: + 13/238 Test #20: geometryTestsCatch ..................... Passed 0.05 sec +test 25 + Start 25: pyAlignment + +25: Test command: /usr/bin/python3 "/build/reproducible-path/rdkit-202503.1/Code/Numerics/Alignment/Wrap/testAlignment.py" +25: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/Numerics/Alignment/Wrap +25: Test timeout computed to be: 1500 +24: ----------------------------------------- +24: Testing Alignment Code +24: --------------------------------------- +24: testBasic +24: --------------------------------------- +24: testTriangle +24: --------------------------------------- +24: testFourPts +24: --------------------------------------- +24: testReflection +24: --------------------------------------- + 14/238 Test #24: testAlignment .......................... Passed 0.01 sec +test 26 + Start 26: testOptimizer + +26: Test command: /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/Numerics/Optimizer/testOptimizer +26: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/Numerics/Optimizer +26: Test timeout computed to be: 1500 +26: ------------------------------------- +26: Testing linear search. +26: done +26: ------------------------------------- +26: Testing BFGS optimization. +26: done + 15/238 Test #26: testOptimizer .......................... Passed 0.01 sec +test 27 + Start 27: ForceFieldsCatch + +27: Test command: /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/ForceField/ForceFieldsCatch +27: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/ForceField +27: Test timeout computed to be: 1500 +23: Randomness seeded to: 4119840600 +23: =============================================================================== +23: All tests passed (76 assertions in 3 test cases) +23: + 16/238 Test #23: testConrec ............................. Passed 0.03 sec +test 28 + Start 28: testUFFForceField + +28: Test command: /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/ForceField/UFF/testUFFForceField +28: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/ForceField/UFF +28: Test timeout computed to be: 1500 1: core 1: RDKit 2D 1: @@ -15471,55 +15617,8 @@ 1: 7 1 1 0 1: M END 1: -20: Randomness seeded to: 1062788118 -20: =============================================================================== -20: All tests passed (50 assertions in 5 test cases) -20: -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: - 10/238 Test #18: testGrid ............................... Passed 0.03 sec - 11/238 Test #20: geometryTestsCatch ..................... Passed 0.02 sec -test 22 - Start 22: testMatrices - -22: Test command: /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/Numerics/testMatrices -22: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/Numerics -22: Test timeout computed to be: 1500 -test 23 - Start 23: testConrec - -23: Test command: /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/Numerics/testConrec -23: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/Numerics -23: Test timeout computed to be: 1500 +28: ------------------------------------- +28: Unit tests for force field basics. 1: core 1: RDKit 2D 1: @@ -15546,6 +15645,12 @@ 1: 10 1 1 0 1: M END 1: +28: done +28: ------------------------------------- +28: Unit tests for basics of UFF bond-stretch terms. +28: done +28: ------------------------------------- +28: Unit tests for UFF bond-stretch terms. 1: core+sidechain 1: RDKit 2D 1: @@ -15606,6 +15711,7 @@ 1: 12 1 1 0 1: M END 1: +28: done 1: core 1: RDKit 2D 1: @@ -15632,6 +15738,11 @@ 1: 10 1 1 0 1: M END 1: +28: ------------------------------------- +28: Unit tests for basics of UFF angle terms. +28: done +28: ------------------------------------- +28: Unit tests for UFF angle-bend terms. 1: core+sidechain 1: RDKit 2D 1: @@ -15670,6 +15781,20 @@ 1: 16 1 1 0 1: M END 1: +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 1: templated 1: RDKit 2D 1: @@ -15708,6 +15833,15 @@ 1: 16 1 1 0 1: M END 1: +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 1: core 1: RDKit 2D 1: @@ -15733,6 +15867,15 @@ 1: 9 5 1 0 1: M END 1: +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: core+sidechain 1: RDKit 2D 1: @@ -15840,8 +15983,6 @@ 1: 4 5 1 0 1: M END 1: -22: [00:36:12] ----------------------------------------- - 12/238 Test #19: testRealValueGrid ...................... Passed 0.04 sec 1: core+sidechain 1: RDKit 2D 1: @@ -15880,28 +16021,6 @@ 1: 5 7 1 0 1: M END 1: -22: [00:36:12] Testing RDNumerics: vectors and matrices Code -22: [00:36:12] --------------------------------------- -22: [00:36:12] test1Vector -test 24 - Start 24: testAlignment - -24: Test command: /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/Numerics/Alignment/testAlignment -24: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/Numerics/Alignment -24: Test timeout computed to be: 1500 -22: [00:36:12] --------------------------------------- -22: [00:36:12] test2Matrix -22: [00:36:12] --------------------------------------- -22: [00:36:12] test3SquareMatrix -22: [00:36:12] --------------------------------------- -22: [00:36:12] test4SymmMatrix - 13/238 Test #22: testMatrices ........................... Passed 0.01 sec -test 25 - Start 25: pyAlignment - -25: Test command: /usr/bin/python3 "/build/reproducible-path/rdkit-202503.1/Code/Numerics/Alignment/Wrap/testAlignment.py" -25: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/Numerics/Alignment/Wrap -25: Test timeout computed to be: 1500 1: test1 1: RDKit 2D 1: @@ -15932,28 +16051,6 @@ 1: 8 1 1 0 1: M END 1: -24: ----------------------------------------- -24: Testing Alignment Code -24: --------------------------------------- -24: testBasic -24: --------------------------------------- -24: testTriangle -24: --------------------------------------- -24: testFourPts -24: --------------------------------------- -24: testReflection -24: --------------------------------------- - 14/238 Test #24: testAlignment .......................... Passed 0.01 sec -test 26 - Start 26: testOptimizer - -26: Test command: /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/Numerics/Optimizer/testOptimizer -26: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/Numerics/Optimizer -26: Test timeout computed to be: 1500 -23: Randomness seeded to: 2422866796 -23: =============================================================================== -23: All tests passed (76 assertions in 3 test cases) -23: 1: test2 1: RDKit 2D 1: @@ -15969,77 +16066,11 @@ 1: 2 5 1 0 1: M END 1: - 15/238 Test #23: testConrec ............................. Passed 0.02 sec -test 27 - Start 27: ForceFieldsCatch - -27: Test command: /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/ForceField/ForceFieldsCatch -27: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/ForceField -27: Test timeout computed to be: 1500 -26: ------------------------------------- -26: Testing linear search. -26: done -26: ------------------------------------- -26: Testing BFGS optimization. -26: done - 16/238 Test #26: testOptimizer .......................... Passed 0.01 sec -test 28 - Start 28: testUFFForceField - -28: Test command: /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/ForceField/UFF/testUFFForceField -28: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/ForceField/UFF -28: Test timeout computed to be: 1500 -27: Randomness seeded to: 70019623 +27: Randomness seeded to: 3614998050 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. - 17/238 Test #27: ForceFieldsCatch ....................... Passed 0.04 sec + 17/238 Test #27: ForceFieldsCatch ....................... Passed 0.06 sec test 29 Start 29: testMMFFForceField @@ -16054,8 +16085,6 @@ 28: done 28: ------------------------------------- 28: Unit test for UFF butane scan. -29: -29: Computing MMFF94 energies for /build/reproducible-path/rdkit-202503.1/Code/ForceField/MMFF/test_data/MMFF94_dative.sdf... 1: cyclosporine a 1: RDKit 2D 1: @@ -16416,26 +16445,23 @@ 1: 30 11 1 0 1: M END 1: -28: done - 18/238 Test #28: testUFFForceField ...................... Passed 0.28 sec +29: +29: Computing MMFF94 energies for /build/reproducible-path/rdkit-202503.1/Code/ForceField/MMFF/test_data/MMFF94_dative.sdf... + 18/238 Test #1: testCoordGen ........................... Passed 0.34 sec test 30 Start 30: pyForceFieldConstraints 30: Test command: /usr/bin/python3 "/build/reproducible-path/rdkit-202503.1/Code/ForceField/Wrap/testConstraints.py" 30: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/ForceField/Wrap 30: Test timeout computed to be: 1500 - 19/238 Test #1: testCoordGen ........................... Passed 0.47 sec +28: done + 19/238 Test #28: testUFFForceField ...................... Passed 0.19 sec test 31 Start 31: testDistGeom 31: Test command: /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/DistGeom/testDistGeom 31: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/DistGeom 31: Test timeout computed to be: 1500 -14: ...... -14: ---------------------------------------------------------------------- -14: Ran 6 tests in 0.006s -14: -14: OK 31: *********************************************************** 31: test1 31: *********************************************************** @@ -16447,244 +16473,237 @@ 31: 1 1 1 0 31: *********************************************************** 31: - 20/238 Test #31: testDistGeom ........................... Passed 0.02 sec + 20/238 Test #31: testDistGeom ........................... Passed 0.01 sec test 32 Start 32: pyDistGeom 32: Test command: /usr/bin/python3 "/build/reproducible-path/rdkit-202503.1/Code/DistGeom/Wrap/rough_test.py" 32: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/DistGeom/Wrap 32: Test timeout computed to be: 1500 +14: ...... +14: ---------------------------------------------------------------------- +14: Ran 6 tests in 0.005s +14: +14: OK 15: ......... 15: ---------------------------------------------------------------------- -15: Ran 9 tests in 0.015s +15: Ran 9 tests in 0.012s 15: 15: OK 13: ...... 13: ---------------------------------------------------------------------- -13: Ran 6 tests in 0.018s +13: Ran 6 tests in 0.007s 13: 13: OK 16: ......... 16: ---------------------------------------------------------------------- -16: Ran 9 tests in 0.036s +16: Ran 9 tests in 0.021s 16: 16: OK 25: ..... 25: ---------------------------------------------------------------------- -25: Ran 5 tests in 0.012s +25: Ran 5 tests in 0.008s 25: 25: OK 25: Testing Alignment Wrapper code: - 21/238 Test #14: pyRealValueVect ........................ Passed 0.47 sec + 21/238 Test #15: pySparseIntVect ........................ Passed 0.38 sec test 33 Start 33: graphmolcpTest 33: Test command: /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/graphmolcpTest 33: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol 33: Test timeout computed to be: 1500 -21: .................... -21: ---------------------------------------------------------------------- -21: Ran 20 tests in 0.050s -21: -21: OK -21: Testing Geometry wrapper -33: -33: -33: -33: COPY - 22/238 Test #15: pySparseIntVect ........................ Passed 0.48 sec + 22/238 Test #14: pyRealValueVect ........................ Passed 0.38 sec test 34 Start 34: graphmolqueryTest 34: Test command: /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/graphmolqueryTest 34: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol 34: Test timeout computed to be: 1500 - 23/238 Test #33: graphmolcpTest ......................... Passed 0.02 sec + 23/238 Test #13: pyDiscreteValueVect .................... Passed 0.39 sec test 35 Start 35: graphmolMolOpsTest 35: Test command: /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/graphmolMolOpsTest 35: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol 35: Test timeout computed to be: 1500 -34: [00:36:13] ---------------------- Test1 -34: [00:36:13] Done! -34: [00:36:13] ---------------------- Test2 -34: [00:36:13] Done! -34: [00:36:13] ---------------------- Test3 -34: [00:36:13] Done! -34: [00:36:13] ---------------------- Test4 -34: [00:36:13] Done! -34: [00:36:13] ---------------------- Test5 -34: [00:36:13] Done! -34: [00:36:13] -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-aarch64-linux-gnu//lib/libRDKitRDGeneral.so.1 -34: 1# Invar::operator<<(std::ostream&, Invar::Invariant const&) in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu//lib/libRDKitRDGeneral.so.1 -34: 2# RDKit::QueryAtom::expandQuery(Queries::Query*, Queries::CompositeQueryType, bool) in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu//lib/libRDKitGraphMol.so.1 -34: 3# 0x0000AAAACD863610 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/graphmolqueryTest -34: 4# 0x0000AAAACD860A88 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/graphmolqueryTest -34: 5# 0x0000FFFF80FD229C in /lib/aarch64-linux-gnu/libc.so.6 -34: 6# __libc_start_main in /lib/aarch64-linux-gnu/libc.so.6 -34: 7# 0x0000AAAACD860B70 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/graphmolqueryTest -34: ---------- -34: **** -34: -34: [00:36:13] Done! -34: [00:36:13] ---------------------- Test issue 2892580 -34: [00:36:13] Done! -34: [00:36:13] ---------------------- Test github issue 53: query molecules not matching [R] -34: [00:36:13] Done! -34: [00:36:13] ---------------------- Test queries using qualifiers instead of == -34: [00:36:13] Done! -34: [00:36:13] ---------------------- Test Github issue 165: radicals not used in atom-atom matching -34: [00:36:13] Done! -34: [00:36:13] ---------------------- Test extra atom queries -34: [00:36:13] Done! -34: [00:36:13] ---------------------- Test extra bond queries -34: [00:36:13] Done! -34: [00:36:13] ---------------------- Test num heteroatom neighbor queries -34: [00:36:13] Done! -34: [00:36:13] ---------------------- Test atom type queries -34: [00:36:13] Done! -34: [00:36:13] ---------------------- Test Github #2471: dummy atom queries are flagged as complex -34: [00:36:13] Done! -34: [00:36:13] ---------------------- Testing hasBondTypeQuery() and hasComplexBondTypeQuery() -34: [00:36:13] Done! - 24/238 Test #34: graphmolqueryTest ...................... Passed 0.04 sec +21: .................... +21: ---------------------------------------------------------------------- +21: Ran 20 tests in 0.033s +21: +21: OK +21: Testing Geometry wrapper +33: +33: +33: +33: COPY + 24/238 Test #16: pyFPB .................................. Passed 0.39 sec test 36 Start 36: graphmoltestChirality 36: Test command: /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/graphmoltestChirality 36: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol 36: Test timeout computed to be: 1500 - 25/238 Test #13: pyDiscreteValueVect .................... Passed 0.53 sec +34: [09:33:07] ---------------------- Test1 +34: [09:33:07] Done! + 25/238 Test #33: graphmolcpTest ......................... Passed 0.02 sec test 37 Start 37: graphmoltestPickler 37: Test command: /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/graphmoltestPickler 37: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol 37: Test timeout computed to be: 1500 -35: 1 1 2 -35: 1 1 1 -35: 2 1 0.75 - 26/238 Test #21: testPyGeometry ......................... Passed 0.50 sec +34: [09:33:07] ---------------------- Test2 +34: [09:33:07] Done! +34: [09:33:07] ---------------------- Test3 +34: [09:33:07] Done! +34: [09:33:07] ---------------------- Test4 +34: [09:33:07] Done! +34: [09:33:07] ---------------------- Test5 +34: [09:33:07] Done! +34: [09:33:07] +34: +34: **** + 26/238 Test #25: pyAlignment ............................ Passed 0.32 sec test 38 Start 38: graphmoltestPicklerGlobalSetting 38: Test command: /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/graphmoltestPicklerGlobalSetting 38: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol 38: Test timeout computed to be: 1500 -35: path: 2 -35: [00:36:13] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 10 ignored -35: [00:36:13] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 10 ignored - 27/238 Test #16: pyFPB .................................. Passed 0.54 sec - 28/238 Test #25: pyAlignment ............................ Passed 0.48 sec +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-aarch64-linux-gnu//lib/libRDKitRDGeneral.so.1 +34: 1# Invar::operator<<(std::ostream&, Invar::Invariant const&) in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu//lib/libRDKitRDGeneral.so.1 +34: 2# RDKit::QueryAtom::expandQuery(Queries::Query*, Queries::CompositeQueryType, bool) in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu//lib/libRDKitGraphMol.so.1 +34: 3# 0x0000AAAADB163610 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/graphmolqueryTest +34: 4# 0x0000AAAADB160A88 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/graphmolqueryTest +34: 5# 0x0000FFFFA766229C in /lib/aarch64-linux-gnu/libc.so.6 +34: 6# __libc_start_main in /lib/aarch64-linux-gnu/libc.so.6 +34: 7# 0x0000AAAADB160B70 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/graphmolqueryTest +34: ---------- +34: **** +34: +34: [09:33:07] Done! +34: [09:33:07] ---------------------- Test issue 2892580 +34: [09:33:07] Done! +34: [09:33:07] ---------------------- Test github issue 53: query molecules not matching [R] +34: [09:33:07] Done! +34: [09:33:07] ---------------------- Test queries using qualifiers instead of == +34: [09:33:07] Done! +34: [09:33:07] ---------------------- Test Github issue 165: radicals not used in atom-atom matching +34: [09:33:07] Done! +34: [09:33:07] ---------------------- Test extra atom queries +34: [09:33:07] Done! +34: [09:33:07] ---------------------- Test extra bond queries +34: [09:33:07] Done! +34: [09:33:07] ---------------------- Test num heteroatom neighbor queries +37: [09:33:07] ------------------------------------- +37: [09:33:07] Testing String Pickle Roundtrips. +34: [09:33:07] Done! +34: [09:33:07] ---------------------- Test atom type queries +34: [09:33:07] Done! +34: [09:33:07] ---------------------- Test Github #2471: dummy atom queries are flagged as complex +34: [09:33:07] Done! +34: [09:33:07] ---------------------- Testing hasBondTypeQuery() and hasComplexBondTypeQuery() +34: [09:33:07] Done! + 27/238 Test #34: graphmolqueryTest ...................... Passed 0.03 sec test 39 Start 39: graphmolIterTest 39: Test command: /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/graphmolIterTest 39: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol 39: Test timeout computed to be: 1500 +35: 1 1 2 +35: 1 1 1 +35: 2 1 0.75 +36: -------------------------- +36: -------------------------- +36: C/C=C/C(C)Cl +38: [09:33:07] done +35: path: 2 + 28/238 Test #21: testPyGeometry ......................... Passed 0.38 sec test 40 Start 40: hanoiTest 40: Test command: /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/hanoiTest 40: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol 40: Test timeout computed to be: 1500 -35: [00:36:13] Explicit valence for atom # 0 B, 5, is greater than permitted -35: [00:36:13] Explicit valence for atom # 1 C, 5, is greater than permitted -35: [00:36:13] Explicit valence for atom # 1 C, 5, is greater than permitted -35: [00:36:13] Explicit valence for atom # 1 C, 5, is greater than permitted -35: [00:36:13] Explicit valence for atom # 1 Si, 7, is greater than permitted -37: [00:36:13] ------------------------------------- -37: [00:36:13] Testing String Pickle Roundtrips. -2: .... -2: ---------------------------------------------------------------------- -2: Ran 4 tests in 0.047s -2: -2: OK -36: -------------------------- -36: -------------------------- -36: C/C=C/C(C)Cl -38: [00:36:13] done - 29/238 Test #38: graphmoltestPicklerGlobalSetting ....... Passed 0.03 sec -40: [00:36:13] Testing the hanoi sort -40: [00:36:13] populating vectors + 29/238 Test #38: graphmoltestPicklerGlobalSetting ....... Passed 0.02 sec test 41 Start 41: graphmolMemTest1 41: Test command: /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/graphmolMemTest1 41: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol 41: Test timeout computed to be: 1500 - 30/238 Test #39: graphmolIterTest ....................... Passed 0.03 sec +35: [09:33:07] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 10 ignored +35: [09:33:07] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 10 ignored + 30/238 Test #39: graphmolIterTest ....................... Passed 0.02 sec test 42 Start 42: resMolSupplierTest 42: Test command: /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/resMolSupplierTest 42: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol 42: Test timeout computed to be: 1500 -36: [00:36:13] Conflicting single bond directions around double bond at index 2. -36: [00:36:13] BondStereo set to STEREONONE and single bond directions set to NONE. -36: [00:36:13] Conflicting single bond directions around double bond at index 4. -36: [00:36:13] BondStereo set to STEREONONE and single bond directions set to NONE. -36: [00:36:13] Conflicting single bond directions around double bond at index 15. -36: [00:36:13] BondStereo set to STEREONONE and single bond directions set to NONE. -36: [00:36:13] Conflicting single bond directions around double bond at index 2. -36: [00:36:13] BondStereo set to STEREONONE and single bond directions set to NONE. -36: [00:36:13] Conflicting single bond directions around double bond at index 1. -36: [00:36:13] BondStereo set to STEREONONE and single bond directions set to NONE. - 31/238 Test #41: graphmolMemTest1 ....................... Passed 0.02 sec +35: [09:33:07] Explicit valence for atom # 0 B, 5, is greater than permitted +35: [09:33:07] Explicit valence for atom # 1 C, 5, is greater than permitted +40: [09:33:07] Testing the hanoi sort +40: [09:33:07] populating vectors +35: [09:33:07] Explicit valence for atom # 1 C, 5, is greater than permitted +35: [09:33:07] Explicit valence for atom # 1 C, 5, is greater than permitted +35: [09:33:07] Explicit valence for atom # 1 Si, 7, is greater than permitted + 31/238 Test #41: graphmolMemTest1 ....................... Passed 0.01 sec test 43 Start 43: molBundleTest 43: Test command: /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/molBundleTest 43: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol 43: Test timeout computed to be: 1500 -36: -------------------------------------------------- -37: [00:36:13] done -37: [00:36:13] ------------------------------------- -37: [00:36:13] Testing reading existing pickle file (v2). - 32/238 Test #36: graphmoltestChirality .................. Passed 0.08 sec +37: [09:33:07] done +37: [09:33:07] ------------------------------------- +37: [09:33:07] Testing reading existing pickle file (v2). +36: [09:33:07] Conflicting single bond directions around double bond at index 2. +36: [09:33:07] BondStereo set to STEREONONE and single bond directions set to NONE. +36: [09:33:07] Conflicting single bond directions around double bond at index 4. +36: [09:33:07] BondStereo set to STEREONONE and single bond directions set to NONE. +36: [09:33:07] Conflicting single bond directions around double bond at index 15. +36: [09:33:07] BondStereo set to STEREONONE and single bond directions set to NONE. +36: [09:33:07] Conflicting single bond directions around double bond at index 2. +36: [09:33:07] BondStereo set to STEREONONE and single bond directions set to NONE. +36: [09:33:07] Conflicting single bond directions around double bond at index 1. +36: [09:33:07] BondStereo set to STEREONONE and single bond directions set to NONE. +32: ...... +32: ---------------------------------------------------------------------- +32: Ran 6 tests in 0.003s +32: +32: OK + 32/238 Test #43: molBundleTest .......................... Passed 0.02 sec test 44 Start 44: testSGroup 44: Test command: /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/testSGroup 44: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol 44: Test timeout computed to be: 1500 -35: smi: Cc1ccc(S(=O)(=O)/N=C2\CC(=N\C(C)(C)C)/C2=N\C(C)(C)C)cc1 - 33/238 Test #43: molBundleTest .......................... Passed 0.03 sec +36: -------------------------------------------------- + 33/238 Test #36: graphmoltestChirality .................. Passed 0.07 sec test 45 Start 45: test-valgrind 45: Test command: /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/test-valgrind 45: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol 45: Test timeout computed to be: 1500 - 34/238 Test #2: pyCoordGen ............................. Passed 0.70 sec -test 46 - Start 46: graphmolTestsCatch - -46: Test command: /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch -46: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol -46: Test timeout computed to be: 1500 - 35/238 Test #45: test-valgrind .......................... Passed 0.02 sec -test 47 - Start 47: graphmolOrganometallicsCatch - -47: Test command: /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/graphmolOrganometallicsCatch -47: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol -47: Test timeout computed to be: 1500 -35: [00:36:13] non-ring atom 0 marked aromatic -35: [00:36:13] non-ring atom 0 marked aromatic -37: [00:36:13] done -37: [00:36:13] ------------------------------------- -37: [00:36:13] Testing combining molecules using pickles. +2: .... +2: ---------------------------------------------------------------------- +2: Ran 4 tests in 0.016s +2: +2: OK +37: [09:33:07] done +37: [09:33:07] ------------------------------------- +37: [09:33:07] 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 @@ -16701,105 +16720,68 @@ 37: 4 4->5 order: 1 37: 5 5->6 order: 1 37: 6 6->3 order: 1 -37: [00:36:13] done -37: [00:36:13] ------------------------------------- -37: [00:36:13] Testing Issue164: Roundtrip Pickle Failure. -35: [00:36:13] Conflicting single bond directions around double bond at index 17. -35: [00:36:13] BondStereo set to STEREONONE and single bond directions set to NONE. -32: ...... -32: ---------------------------------------------------------------------- -32: Ran 6 tests in 0.005s -32: -32: OK -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 -37: [00:36:13] done -37: [00:36:13] ------------------------------------- -37: [00:36:13] Testing Issue219: Pickle Failure with Conformations. -37: [00:36:13] done -37: [00:36:13] ------------------------------------- -37: [00:36:13] Testing Issue220: Pickle problems with bond stereochemistry. -37: [00:36:13] done -37: [00:36:13] ------------------------------------- -37: [00:36:13] Testing query serialization. -37: [00:36:13] C=[$(C=O)] -37: [00:36:13] S(=O)(=O)-[C&H2][F,Br,I,Cl] S(=O)(=O)-[C&H2][F,Br,I,Cl] -37: [00:36:13] done -37: [00:36:13] ------------------------------------- -37: [00:36:13] Testing radical handling in pickles. -37: [00:36:13] done -37: [00:36:13] done -37: [00:36:13] ------------------------------------- -37: [00:36:13] Testing sf.net issue 2788233. -37: [00:36:13] done -37: [00:36:13] ------------------------------------- -37: [00:36:13] Testing sf.net issue 3202580. +37: [09:33:07] done +37: [09:33:07] ------------------------------------- +37: [09:33:07] Testing Issue164: Roundtrip Pickle Failure. +35: smi: Cc1ccc(S(=O)(=O)/N=C2\CC(=N\C(C)(C)C)/C2=N\C(C)(C)C)cc1 + 34/238 Test #45: test-valgrind .......................... Passed 0.02 sec +test 46 + Start 46: graphmolTestsCatch + +46: Test command: /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch +46: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol +46: Test timeout computed to be: 1500 +37: [09:33:07] done +37: [09:33:07] ------------------------------------- +37: [09:33:07] Testing Issue219: Pickle Failure with Conformations. +37: [09:33:07] done +37: [09:33:07] ------------------------------------- +37: [09:33:07] Testing Issue220: Pickle problems with bond stereochemistry. +37: [09:33:07] done +37: [09:33:07] ------------------------------------- +37: [09:33:07] Testing query serialization. + 35/238 Test #32: pyDistGeom ............................. Passed 0.18 sec +test 47 + Start 47: graphmolOrganometallicsCatch + +47: Test command: /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/graphmolOrganometallicsCatch +47: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol +47: Test timeout computed to be: 1500 +37: [09:33:07] C=[$(C=O)] +37: [09:33:07] S(=O)(=O)-[C&H2][F,Br,I,Cl] S(=O)(=O)-[C&H2][F,Br,I,Cl] +37: [09:33:07] done +37: [09:33:07] ------------------------------------- +37: [09:33:07] Testing radical handling in pickles. +37: [09:33:07] done +37: [09:33:07] done +37: [09:33:07] ------------------------------------- +37: [09:33:07] Testing sf.net issue 2788233. +37: [09:33:07] done +37: [09:33:07] ------------------------------------- +37: [09:33:07] Testing sf.net issue 3202580. 37: mass! 13.0034 -37: [00:36:13] done -37: [00:36:13] ------------------------------------- -37: [00:36:13] Testing sf.net issue 3316407. -37: [00:36:13] done -37: [00:36:13] ------------------------------------- -37: [00:36:13] Testing sf.net issue 3496759. +37: [09:33:07] done +37: [09:33:07] ------------------------------------- +37: [09:33:07] Testing sf.net issue 3316407. +37: [09:33:07] done +37: [09:33:07] ------------------------------------- +37: [09:33:07] Testing sf.net issue 3496759. +35: [09:33:07] non-ring atom 0 marked aromatic 37: smi match: *C *C -46: Randomness seeded to: 1746242754 -46: [00:36:13] WARNING: not removing hydrogen atom without neighbors -46: [00:36:13] WARNING: could not find number of expected rings. Switching to an approximate ring finding algorithm. 37: smi match: **=* **=* -46: [00:36:13] WARNING: could not find number of expected rings. Switching to an approximate ring finding algorithm. +35: [09:33:07] non-ring atom 0 marked aromatic 37: smi match: [N-]=[N+]=NC=O [N-]=[N+]=NC=O -46: [00:36:13] WARNING: could not find number of expected rings. Switching to an approximate ring finding algorithm. 37: smi match: *OS(=O)OC *OS(=O)OC 37: smi match: *S(=O)(=O)OC *S(=O)(=O)OC - 36/238 Test #44: testSGroup ............................. Passed 0.06 sec -test 48 - Start 48: graphmolSGroupCatch - -48: Test command: /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/graphmolSGroupCatch -48: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol -48: Test timeout computed to be: 1500 -46: [00:36:13] WARNING: could not find number of expected rings. Switching to an approximate ring finding algorithm. -46: [00:36:13] WARNING: could not find number of expected rings. Switching to an approximate ring finding algorithm. 37: smi match: O=COC=O O=COC=O 37: smi match: OO OO 37: smi match: O=COc1c(F)c(F)c(F)c(F)c1F O=COc1c(F)c(F)c(F)c(F)c1F 37: smi match: O=COc1ccc(N(=O)=O)cc1 O=COc1ccc(N(=O)=O)cc1 37: smi match: nnnOC=O nnnOC=O -46: [00:36:13] Explicit valence for atom # 1 N, 5, is greater than permitted -46: [00:36:13] Explicit valence for atom # 1 N, 6, is greater than permitted -46: [00:36:13] Explicit valence for atom # 1 N, 5, is greater than permitted -46: [00:36:13] Explicit valence for atom # 1 N, 5, is greater than permitted -46: [00:36:13] Explicit valence for atom # 2 O, 3, is greater than permitted -46: [00:36:13] Explicit valence for atom # 2 O, 3, is greater than permitted -46: [00:36:13] non-ring atom 2 marked aromatic -46: [00:36:13] non-ring atom 2 marked aromatic -46: [00:36:13] Can't kekulize mol. Unkekulized atoms: 0 1 2 3 4 -46: [00:36:13] Can't kekulize mol. Unkekulized atoms: 0 1 2 3 4 -46: [00:36:13] Can't kekulize mol. Unkekulized atoms: 1 2 3 -46: [00:36:13] Can't kekulize mol. Unkekulized atoms: 1 2 3 -46: [00:36:13] Can't kekulize mol. Unkekulized atoms: 0 1 2 -46: [00:36:13] Can't kekulize mol. Unkekulized atoms: 0 1 2 -46: [00:36:13] Explicit valence for atom # 1 O, 3, is greater than permitted -46: [00:36:13] Explicit valence for atom # 4 F, 2, is greater than permitted -46: [00:36:13] Can't kekulize mol. Unkekulized atoms: 6 7 8 -46: [00:36:13] Explicit valence for atom # 1 C, 5, is greater than permitted -46: [00:36:13] WARNING: not removing hydrogen atom with dummy atom neighbors -46: [00:36:13] WARNING: not removing hydrogen atom with dummy atom neighbors -46: [00:36:13] WARNING: not removing hydrogen atom with wedged bond -46: [00:36:13] WARNING: not removing hydrogen atom without neighbors -46: [00:36:13] WARNING: not removing hydrogen atom without neighbors 37: smi match: *=C=N *=C=N 37: smi match: OS(=O)(=O)C(F)(F)F OS(=O)(=O)C(F)(F)F 37: smi match: SP(S)=S SP(S)=S -35: done 37: smi match: NP(N)(N)=O NP(N)(N)=O -35: starting sanitization 37: smi match: cN=[N+]=[N-] cN=[N+]=[N-] 37: smi match: *CC=O *CC=O 37: smi match: NNC=O NNC=O @@ -16834,15 +16816,11 @@ 37: smi match: O=C1CCN1 O=C1CCN1 37: smi match: O=C1C~CC(=O)C~C1 O=C1C~CC(=O)C~C1 37: smi match: C=CC=CC=CC=C C=CC=CC=CC=C -35: done 37: smi match: C1CCC(OC2CCC3CCCCC3C2)OC1 C1CCC(OC2CCC3CCCCC3C2)OC1 37: smi match: O=C1NCC2CCCCC21 O=C1NCC2CCCCC21 37: smi match: O=C1CCCC(=O)N1 O=C1CCCC(=O)N1 37: smi match: C1CCC(C2CCCO2)OC1 C1CCC(C2CCCO2)OC1 -46: [00:36:13] WARNING: not removing hydrogen atom without neighbors -46: [00:36:13] WARNING: not removing hydrogen atom without neighbors 37: smi match: [OH]C1Cc2c([OH])cc([OH])cc2OC1c1ccc([OH])c([OH])c1 [OH]C1Cc2c([OH])cc([OH])cc2OC1c1ccc([OH])c([OH])c1 -46: [00:36:13] Unreasonable formal charge on atom # 0. 37: smi match: C1CC2CCC(O1)O2 C1CC2CCC(O1)O2 37: smi match: cN(=O)~O cN(=O)~O 37: smi match: *[CH2]N1C(=O)CCC1=O *[CH2]N1C(=O)CCC1=O @@ -16853,13 +16831,10 @@ 37: smi match: * * 37: smi match: *C=C *C=C 37: smi match: N#CS N#CS -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 37: smi match: *C=S *C=S 37: smi match: *N *N +35: [09:33:07] Conflicting single bond directions around double bond at index 17. +35: [09:33:07] BondStereo set to STEREONONE and single bond directions set to NONE. 37: smi match: *C(=C)C=O *C(=C)C=O 37: smi match: *C#C *C#C 37: smi match: N#CCO N#CCO @@ -16869,10 +16844,6 @@ 37: smi match: C=C(C=O)C=O C=C(C=O)C=O 37: smi match: N=CC=O N=CC=O 37: smi match: *C(C=O)C=O *C(C=O)C=O -47: Randomness seeded to: 1772385647 -47: =============================================================================== -47: All tests passed (62 assertions in 6 test cases) -47: 37: smi match: *C(C=O)=C(*)C=O *C(C=O)=C(*)C=O 37: smi match: O=CC=CC=O O=CC=CC=O 37: smi match: O=CN(O)C=O O=CN(O)C=O @@ -16884,6 +16855,7 @@ 37: smi match: O=CS O=CS 37: smi match: O=CSC=S O=CSC=S 37: smi match: S=CS S=CS +35: starting ring finding 37: smi match: C=O C=O 37: smi match: *C=N *C=N 37: smi match: CCCCCCC CCCCCCC @@ -16894,6 +16866,10 @@ 37: smi match: C=CCO C=CCO 37: smi match: C=CC=N C=CC=N 37: smi match: C=CC=O C=CC=O +35: done +35: starting ring finding +35: done +35: starting ring finding 37: smi match: C=CC(=O)C=C C=CC(=O)C=C 37: smi match: C=CC=S C=CC=S 37: smi match: C=CC(=S)S C=CC(=S)S @@ -16905,6 +16881,7 @@ 37: smi match: C=CO C=CO 37: smi match: C=COC=O C=COC=O 37: smi match: C=CS C=CS +35: done 37: smi match: C=C[SH](=O)=O C=C[SH](=O)=O 37: smi match: C=NCO C=NCO 37: smi match: C=NC=O C=NC=O @@ -16914,437 +16891,16 @@ 37: smi match: C=NOC=O C=NOC=O 37: smi match: C=N=O C=N=O 37: smi match: N#CS N#CS +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 37: smi match: *CN=O *CN=O 37: smi match: NCN NCN -46: [00:36:13] -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-aarch64-linux-gnu//lib/libRDKitRDGeneral.so.1 -46: 1# Invar::operator<<(std::ostream&, Invar::Invariant const&) in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu//lib/libRDKitRDGeneral.so.1 -46: 2# RDKit::ROMol::getAtomDegree(RDKit::Atom const*) const in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu//lib/libRDKitGraphMol.so.1 -46: 3# 0x0000AAAABDFCB824 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch -46: 4# 0x0000AAAABE017A8C in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch -46: 5# 0x0000AAAABE018440 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch -46: 6# 0x0000AAAABE018874 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch -46: 7# 0x0000AAAABDFECC58 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch -46: 8# 0x0000AAAABDFED1A4 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch -46: 9# 0x0000AAAABDF6DE10 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch -46: 10# 0x0000FFFF8A5C229C in /lib/aarch64-linux-gnu/libc.so.6 -46: 11# __libc_start_main in /lib/aarch64-linux-gnu/libc.so.6 -46: 12# 0x0000AAAABDF6DEF0 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch -46: ---------- -46: **** -46: -46: [00:36:13] -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-aarch64-linux-gnu//lib/libRDKitRDGeneral.so.1 -46: 1# Invar::operator<<(std::ostream&, Invar::Invariant const&) in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu//lib/libRDKitRDGeneral.so.1 -46: 2# RDKit::ROMol::getAtomDegree(RDKit::Atom const*) const in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu//lib/libRDKitGraphMol.so.1 -46: 3# 0x0000AAAABDFCB898 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch -46: 4# 0x0000AAAABE017A8C in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch -46: 5# 0x0000AAAABE018440 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch -46: 6# 0x0000AAAABE018874 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch -46: 7# 0x0000AAAABDFECC58 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch -46: 8# 0x0000AAAABDFED1A4 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch -46: 9# 0x0000AAAABDF6DE10 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch -46: 10# 0x0000FFFF8A5C229C in /lib/aarch64-linux-gnu/libc.so.6 -46: 11# __libc_start_main in /lib/aarch64-linux-gnu/libc.so.6 -46: 12# 0x0000AAAABDF6DEF0 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch -46: ---------- -46: **** -46: -46: [00:36:13] -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-aarch64-linux-gnu//lib/libRDKitRDGeneral.so.1 -46: 1# Invar::operator<<(std::ostream&, Invar::Invariant const&) in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu//lib/libRDKitRDGeneral.so.1 -46: 2# RDKit::ROMol::getAtomDegree(RDKit::Atom const*) const in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu//lib/libRDKitGraphMol.so.1 -46: 3# 0x0000AAAABDFCB918 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch -46: 4# 0x0000AAAABE017A8C in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch -46: 5# 0x0000AAAABE018440 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch -46: 6# 0x0000AAAABE018874 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch -46: 7# 0x0000AAAABDFECC58 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch -46: 8# 0x0000AAAABDFED1A4 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch -46: 9# 0x0000AAAABDF6DE10 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch -46: 10# 0x0000FFFF8A5C229C in /lib/aarch64-linux-gnu/libc.so.6 -46: 11# __libc_start_main in /lib/aarch64-linux-gnu/libc.so.6 -46: 12# 0x0000AAAABDF6DEF0 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch -46: ---------- -46: **** -46: -46: [00:36:13] -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-aarch64-linux-gnu//lib/libRDKitRDGeneral.so.1 -46: 1# Invar::operator<<(std::ostream&, Invar::Invariant const&) in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu//lib/libRDKitRDGeneral.so.1 -46: 2# RDKit::ROMol::getAtomNeighbors(RDKit::Atom const*) const in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu//lib/libRDKitGraphMol.so.1 -46: 3# 0x0000AAAABDFCB9E0 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch -46: 4# 0x0000AAAABE017A8C in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch -46: 5# 0x0000AAAABE018440 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch -46: 6# 0x0000AAAABE018874 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch -46: 7# 0x0000AAAABDFECC58 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch -46: 8# 0x0000AAAABDFED1A4 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch -46: 9# 0x0000AAAABDF6DE10 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch -46: 10# 0x0000FFFF8A5C229C in /lib/aarch64-linux-gnu/libc.so.6 -46: 11# __libc_start_main in /lib/aarch64-linux-gnu/libc.so.6 -46: 12# 0x0000AAAABDF6DEF0 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch -46: ---------- -46: **** -46: -46: [00:36:13] -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-aarch64-linux-gnu//lib/libRDKitRDGeneral.so.1 -46: 1# Invar::operator<<(std::ostream&, Invar::Invariant const&) in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu//lib/libRDKitRDGeneral.so.1 -46: 2# RDKit::ROMol::getAtomNeighbors(RDKit::Atom const*) const in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu//lib/libRDKitGraphMol.so.1 -46: 3# 0x0000AAAABDFCBA58 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch -46: 4# 0x0000AAAABE017A8C in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch -46: 5# 0x0000AAAABE018440 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch -46: 6# 0x0000AAAABE018874 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch -46: 7# 0x0000AAAABDFECC58 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch -46: 8# 0x0000AAAABDFED1A4 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch -46: 9# 0x0000AAAABDF6DE10 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch -46: 10# 0x0000FFFF8A5C229C in /lib/aarch64-linux-gnu/libc.so.6 -46: 11# __libc_start_main in /lib/aarch64-linux-gnu/libc.so.6 -46: 12# 0x0000AAAABDF6DEF0 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch -46: ---------- -46: **** -46: -46: [00:36:13] -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-aarch64-linux-gnu//lib/libRDKitRDGeneral.so.1 -46: 1# Invar::operator<<(std::ostream&, Invar::Invariant const&) in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu//lib/libRDKitRDGeneral.so.1 -46: 2# RDKit::ROMol::getAtomNeighbors(RDKit::Atom const*) const in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu//lib/libRDKitGraphMol.so.1 -46: 3# 0x0000AAAABDFCBADC in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch -46: 4# 0x0000AAAABE017A8C in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch -46: 5# 0x0000AAAABE018440 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch -46: 6# 0x0000AAAABE018874 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch -46: 7# 0x0000AAAABDFECC58 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch -46: 8# 0x0000AAAABDFED1A4 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch -46: 9# 0x0000AAAABDF6DE10 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch -46: 10# 0x0000FFFF8A5C229C in /lib/aarch64-linux-gnu/libc.so.6 -46: 11# __libc_start_main in /lib/aarch64-linux-gnu/libc.so.6 -46: 12# 0x0000AAAABDF6DEF0 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch -46: ---------- -46: **** -46: -46: [00:36:13] -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-aarch64-linux-gnu//lib/libRDKitRDGeneral.so.1 -46: 1# Invar::operator<<(std::ostream&, Invar::Invariant const&) in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu//lib/libRDKitRDGeneral.so.1 -46: 2# RDKit::ROMol::getAtomBonds(RDKit::Atom const*) const in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu//lib/libRDKitGraphMol.so.1 -46: 3# 0x0000AAAABDFCC1F0 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch -46: 4# 0x0000AAAABE017A8C in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch -46: 5# 0x0000AAAABE018440 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch -46: 6# 0x0000AAAABE018874 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch -46: 7# 0x0000AAAABDFECC58 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch -46: 8# 0x0000AAAABDFED1A4 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch -46: 9# 0x0000AAAABDF6DE10 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch -46: 10# 0x0000FFFF8A5C229C in /lib/aarch64-linux-gnu/libc.so.6 -46: 11# __libc_start_main in /lib/aarch64-linux-gnu/libc.so.6 -46: 12# 0x0000AAAABDF6DEF0 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch -46: ---------- -46: **** -46: -46: [00:36:13] -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-aarch64-linux-gnu//lib/libRDKitRDGeneral.so.1 -46: 1# Invar::operator<<(std::ostream&, Invar::Invariant const&) in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu//lib/libRDKitRDGeneral.so.1 -46: 2# RDKit::ROMol::getAtomBonds(RDKit::Atom const*) const in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu//lib/libRDKitGraphMol.so.1 -46: 3# 0x0000AAAABDFCBC0C in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch -46: 4# 0x0000AAAABE017A8C in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch -46: 5# 0x0000AAAABE018440 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch -46: 6# 0x0000AAAABE018874 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch -46: 7# 0x0000AAAABDFECC58 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch -46: 8# 0x0000AAAABDFED1A4 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch -46: 9# 0x0000AAAABDF6DE10 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch -46: 10# 0x0000FFFF8A5C229C in /lib/aarch64-linux-gnu/libc.so.6 -46: 11# __libc_start_main in /lib/aarch64-linux-gnu/libc.so.6 -46: 12# 0x0000AAAABDF6DEF0 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch -46: ---------- -46: **** -46: -46: [00:36:13] -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-aarch64-linux-gnu//lib/libRDKitRDGeneral.so.1 -46: 1# Invar::operator<<(std::ostream&, Invar::Invariant const&) in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu//lib/libRDKitRDGeneral.so.1 -46: 2# RDKit::ROMol::getAtomBonds(RDKit::Atom const*) const in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu//lib/libRDKitGraphMol.so.1 -46: 3# 0x0000AAAABDFCBC90 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch -46: 4# 0x0000AAAABE017A8C in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch -46: 5# 0x0000AAAABE018440 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch -46: 6# 0x0000AAAABE018874 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch -46: 7# 0x0000AAAABDFECC58 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch -46: 8# 0x0000AAAABDFED1A4 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch -46: 9# 0x0000AAAABDF6DE10 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch -46: 10# 0x0000FFFF8A5C229C in /lib/aarch64-linux-gnu/libc.so.6 -46: 11# __libc_start_main in /lib/aarch64-linux-gnu/libc.so.6 -46: 12# 0x0000AAAABDF6DEF0 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch -46: ---------- -46: **** -46: -46: [00:36:13] -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-aarch64-linux-gnu//lib/libRDKitRDGeneral.so.1 -46: 1# Invar::operator<<(std::ostream&, Invar::Invariant const&) in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu//lib/libRDKitRDGeneral.so.1 -46: 2# RDKit::ROMol::addAtom(RDKit::Atom*, bool, bool) in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu//lib/libRDKitGraphMol.so.1 -46: 3# 0x0000AAAABDFCC1D4 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch -46: 4# 0x0000AAAABE017A8C in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch -46: 5# 0x0000AAAABE018440 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch -46: 6# 0x0000AAAABE018874 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch -46: 7# 0x0000AAAABDFECC58 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch -46: 8# 0x0000AAAABDFED1A4 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch -46: 9# 0x0000AAAABDF6DE10 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch -46: 10# 0x0000FFFF8A5C229C in /lib/aarch64-linux-gnu/libc.so.6 -46: 11# __libc_start_main in /lib/aarch64-linux-gnu/libc.so.6 -46: 12# 0x0000AAAABDF6DEF0 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch -46: ---------- -46: **** -46: -46: [00:36:13] -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-aarch64-linux-gnu//lib/libRDKitRDGeneral.so.1 -46: 1# Invar::operator<<(std::ostream&, Invar::Invariant const&) in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu//lib/libRDKitRDGeneral.so.1 -46: 2# RDKit::ROMol::addAtom(RDKit::Atom*, bool, bool) in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu//lib/libRDKitGraphMol.so.1 -46: 3# 0x0000AAAABDFCBE80 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch -46: 4# 0x0000AAAABE017A8C in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch -46: 5# 0x0000AAAABE018440 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch -46: 6# 0x0000AAAABE018874 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch -46: 7# 0x0000AAAABDFECC58 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch -46: 8# 0x0000AAAABDFED1A4 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch -46: 9# 0x0000AAAABDF6DE10 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch -46: 10# 0x0000FFFF8A5C229C in /lib/aarch64-linux-gnu/libc.so.6 -46: 11# __libc_start_main in /lib/aarch64-linux-gnu/libc.so.6 -46: 12# 0x0000AAAABDF6DEF0 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch -46: ---------- -46: **** -46: -46: [00:36:13] -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-aarch64-linux-gnu//lib/libRDKitRDGeneral.so.1 -46: 1# Invar::operator<<(std::ostream&, Invar::Invariant const&) in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu//lib/libRDKitRDGeneral.so.1 -46: 2# RDKit::ROMol::addBond(RDKit::Bond*, bool) in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu//lib/libRDKitGraphMol.so.1 -46: 3# 0x0000AAAABDFCC1B4 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch -46: 4# 0x0000AAAABE017A8C in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch -46: 5# 0x0000AAAABE018440 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch -46: 6# 0x0000AAAABE018874 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch -46: 7# 0x0000AAAABDFECC58 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch -46: 8# 0x0000AAAABDFED1A4 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch -46: 9# 0x0000AAAABDF6DE10 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch -46: 10# 0x0000FFFF8A5C229C in /lib/aarch64-linux-gnu/libc.so.6 -46: 11# __libc_start_main in /lib/aarch64-linux-gnu/libc.so.6 -46: 12# 0x0000AAAABDF6DEF0 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch -46: ---------- -46: **** -46: -46: [00:36:13] WARNING: could not find number of expected rings. Switching to an approximate ring finding algorithm. -46: [00:36:13] WARNING: could not find number of expected rings. Switching to an approximate ring finding algorithm. -46: [00:36:13] WARNING: not removing hydrogen atom without neighbors -46: [00:36:13] Explicit valence for atom # 1 F greater than permitted -46: [00:36:13] -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-aarch64-linux-gnu//lib/libRDKitRDGeneral.so.1 -46: 1# Invar::operator<<(std::ostream&, Invar::Invariant const&) in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu//lib/libRDKitRDGeneral.so.1 -46: 2# RDKit::Atom::setQuery(Queries::Query*) in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu//lib/libRDKitGraphMol.so.1 -46: 3# 0x0000AAAABDF7A58C in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch -46: 4# 0x0000AAAABE017A8C in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch -46: 5# 0x0000AAAABE018440 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch -46: 6# 0x0000AAAABE018874 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch -46: 7# 0x0000AAAABDFECC58 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch -46: 8# 0x0000AAAABDFED1A4 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch -46: 9# 0x0000AAAABDF6DE10 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch -46: 10# 0x0000FFFF8A5C229C in /lib/aarch64-linux-gnu/libc.so.6 -46: 11# __libc_start_main in /lib/aarch64-linux-gnu/libc.so.6 -46: 12# 0x0000AAAABDF6DEF0 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch -46: ---------- -46: **** -46: -46: [00:36:13] -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-aarch64-linux-gnu//lib/libRDKitRDGeneral.so.1 -46: 1# Invar::operator<<(std::ostream&, Invar::Invariant const&) in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu//lib/libRDKitRDGeneral.so.1 -46: 2# RDKit::Atom::expandQuery(Queries::Query*, Queries::CompositeQueryType, bool) in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu//lib/libRDKitGraphMol.so.1 -46: 3# 0x0000AAAABDF7A618 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch -46: 4# 0x0000AAAABE017A8C in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch -46: 5# 0x0000AAAABE018440 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch -46: 6# 0x0000AAAABE018874 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch -46: 7# 0x0000AAAABDFECC58 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch -46: 8# 0x0000AAAABDFED1A4 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch -46: 9# 0x0000AAAABDF6DE10 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch -46: 10# 0x0000FFFF8A5C229C in /lib/aarch64-linux-gnu/libc.so.6 -46: 11# __libc_start_main in /lib/aarch64-linux-gnu/libc.so.6 -46: 12# 0x0000AAAABDF6DEF0 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch -46: ---------- -46: **** -46: -46: [00:36:13] -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-aarch64-linux-gnu//lib/libRDKitRDGeneral.so.1 -46: 1# Invar::operator<<(std::ostream&, Invar::Invariant const&) in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu//lib/libRDKitRDGeneral.so.1 -46: 2# RDKit::Bond::setQuery(Queries::Query*) in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu//lib/libRDKitGraphMol.so.1 -46: 3# 0x0000AAAABDF7A1DC in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch -46: 4# 0x0000AAAABE017A8C in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch -46: 5# 0x0000AAAABE018440 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch -46: 6# 0x0000AAAABE018874 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch -46: 7# 0x0000AAAABDFECC58 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch -46: 8# 0x0000AAAABDFED1A4 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch -46: 9# 0x0000AAAABDF6DE10 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch -46: 10# 0x0000FFFF8A5C229C in /lib/aarch64-linux-gnu/libc.so.6 -46: 11# __libc_start_main in /lib/aarch64-linux-gnu/libc.so.6 -46: 12# 0x0000AAAABDF6DEF0 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch -46: ---------- -46: **** -46: 37: smi match: ON=CCN=O ON=CCN=O -46: [00:36:13] -46: -46: **** 37: smi match: NC(S)=N[SH](=O)=O NC(S)=N[SH](=O)=O -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-aarch64-linux-gnu//lib/libRDKitRDGeneral.so.1 -46: 1# Invar::operator<<(std::ostream&, Invar::Invariant const&) in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu//lib/libRDKitRDGeneral.so.1 -46: 2# RDKit::Bond::expandQuery(Queries::Query*, Queries::CompositeQueryType, bool) in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu//lib/libRDKitGraphMol.so.1 -46: 3# 0x0000AAAABDF7A268 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch -46: 4# 0x0000AAAABE017A8C in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch -46: 5# 0x0000AAAABE018440 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch -46: 6# 0x0000AAAABE018874 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch -46: 7# 0x0000AAAABDFECC58 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch -46: 8# 0x0000AAAABDFED1A4 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch -46: 9# 0x0000AAAABDF6DE10 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch -46: 10# 0x0000FFFF8A5C229C in /lib/aarch64-linux-gnu/libc.so.6 -46: 11# __libc_start_main in /lib/aarch64-linux-gnu/libc.so.6 -46: 12# 0x0000AAAABDF6DEF0 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch -46: ---------- -46: **** -46: 37: smi match: N=C(N)S N=C(N)S 37: smi match: NC(=O)Oc1ccccc1 NC(=O)Oc1ccccc1 37: smi match: NC=S NC=S -46: [00:36:13] Can't kekulize mol. Unkekulized atoms: 0 1 2 3 4 -46: [00:36:13] Can't kekulize mol. Unkekulized atoms: 0 1 2 3 4 37: smi match: NC(N)=S NC(N)=S -46: [00:36:13] Can't kekulize mol. Unkekulized atoms: 6 7 8 9 10 -46: [00:36:13] Can't kekulize mol. Unkekulized atoms: 6 7 8 9 10 - 37/238 Test #47: graphmolOrganometallicsCatch ........... Passed 0.06 sec -test 49 - Start 49: graphmolAdjustQueryCatch - -49: Test command: /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/graphmolAdjustQueryCatch -49: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol -49: Test timeout computed to be: 1500 -46: [00:36:13] Can't kekulize mol. Unkekulized atoms: 0 1 2 3 4 -46: [00:36:13] Unusual charge on atom 0 number of radical electrons set to zero -46: [00:36:13] Unusual charge on atom 0 number of radical electrons set to zero -46: [00:36:13] Unusual charge on atom 0 number of radical electrons set to zero -46: [00:36:13] non-ring atom 0 marked aromatic -46: [00:36:13] non-ring atom 0 marked aromatic -46: [00:36:13] Explicit valence for atom # 1 C, 5, is greater than permitted -46: [00:36:13] Explicit valence for atom # 9 C, 5, is greater than permitted 37: smi match: C=CN C=CN 37: smi match: NOC=O NOC=O 37: smi match: C1CN1 C1CN1 @@ -17366,6 +16922,7 @@ 37: smi match: OS(=O)=O OS(=O)=O 37: smi match: N#CS N#CS 37: smi match: C=C(S)S C=C(S)S + 36/238 Test #2: pyCoordGen ............................. Passed 0.56 sec 37: smi match: N=C(N)S N=C(N)S 37: smi match: N=C(S)S N=C(S)S 37: smi match: NC(=S)S NC(=S)S @@ -17376,6 +16933,12 @@ 37: smi match: NCN NCN 37: smi match: cC(c)(O)O cC(c)(O)O 37: smi match: *C(c)O *C(c)O +test 48 + Start 48: graphmolSGroupCatch + +48: Test command: /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/graphmolSGroupCatch +48: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol +48: Test timeout computed to be: 1500 37: smi match: C=CS(c)(=O)=O C=CS(c)(=O)=O 37: smi match: cS(=O)(=O)O cS(=O)(=O)O 37: smi match: *c1ccccn1=O *c1ccccn1=O @@ -17401,31 +16964,6 @@ 37: smi match: N=C(=N)S N=C(=N)S 37: smi match: O=N=O O=N=O 37: smi match: O=NO O=NO -48: Randomness seeded to: 4088529163 -48: =============================================================================== -48: All tests passed (136 assertions in 8 test cases) -48: -35: [00:36:13] WARNING: not removing hydrogen atom with dummy atom neighbors -35: ------------------------------- -35: [00:36:13] Explicit valence for atom # 0 N, 4, is greater than permitted - 38/238 Test #48: graphmolSGroupCatch .................... Passed 0.04 sec -46: [00:36:13] Explicit valence for atom # 3 N, 4, is greater than permitted -46: [00:36:13] Explicit valence for atom # 15 C, 5, is greater than permitted -46: [00:36:13] Explicit valence for atom # 11 C, 5, is greater than permitted -test 50 - Start 50: chiralityTestsCatch - -50: Test command: /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/chiralityTestsCatch -50: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol -50: Test timeout computed to be: 1500 -46: [00:36:13] Explicit valence for atom # 9 C, 5, is greater than permitted -46: [00:36:13] Explicit valence for atom # 9 C, 5, is greater than permitted -46: [00:36:13] Explicit valence for atom # 9 C, 6, is greater than permitted -46: [00:36:13] Can't kekulize mol. Unkekulized atoms: 0 1 2 3 4 -46: [00:36:13] Can't kekulize mol. Unkekulized atoms: 7 -46: [00:36:13] Can't kekulize mol. Unkekulized atoms: 3 -46: [00:36:13] Can't kekulize mol. Unkekulized atoms: 3 7 -46: [00:36:13] Can't kekulize mol. Unkekulized atoms: 3 7 37: smi match: ONO ONO 37: smi match: C1SCS1 C1SCS1 37: smi match: N=C=S N=C=S @@ -17441,7 +16979,6 @@ 37: smi match: NN=O NN=O 37: smi match: NC(=O)S NC(=O)S 37: smi match: N#CS N#CS -46: [00:36:13] WARNING: could not find number of expected rings. Switching to an approximate ring finding algorithm. 37: smi match: NC(=O)C(N)=O NC(=O)C(N)=O 37: smi match: c=N c=N 37: smi match: C1COCO1 C1COCO1 @@ -17450,9 +16987,18 @@ 37: smi match: O=CNOC=O O=CNOC=O 37: smi match: O=C1C=CC(=O)C=C1 O=C1C=CC(=O)C=C1 37: smi match: ONO ONO +35: done +35: starting sanitization + 37/238 Test #44: testSGroup ............................. Passed 0.06 sec 37: smi match: ON(~O)~O ON(~O)~O 37: smi match: OC1COC(O)C1 OC1COC(O)C1 37: smi match: OC1CCOC1O OC1CCOC1O +test 49 + Start 49: graphmolAdjustQueryCatch + +49: Test command: /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/graphmolAdjustQueryCatch +49: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol +49: Test timeout computed to be: 1500 37: smi match: OC1CCOC(O)C1 OC1CCOC(O)C1 37: smi match: N=[N+]=N N=[N+]=N 37: smi match: N#CN N#CN @@ -17481,23 +17027,6 @@ 37: smi match: *C(*)C=C *C(*)C=C 37: smi match: *CC=C *CC=C 37: smi match: CN=C=O CN=C=O -35: [00:36:13] Can't kekulize mol. Unkekulized atoms: 0 1 2 3 4 -35: [00:36:13] Can't kekulize mol. Unkekulized atoms: 6 7 8 9 10 -35: [00:36:13] Can't kekulize mol. Unkekulized atoms: 0 1 2 3 4 -35: [00:36:13] WARNING: merging explicit H queries involved in ORs is not supported. This query will not be merged -35: [00:36:13] WARNING: merging explicit H queries involved in ORs is not supported. This query will not be merged -35: [00:36:13] WARNING: merging explicit H queries involved in ORs is not supported. This query will not be merged -35: [00:36:13] WARNING: merging explicit H queries involved in ORs is not supported. This query will not be merged -35: [00:36:13] WARNING: merging explicit H queries involved in ORs is not supported. This query will not be merged -35: - 39/238 Test #32: pyDistGeom ............................. Passed 0.30 sec -test 51 - Start 51: canonTestsCatch - -51: Test command: /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/canonTestsCatch -51: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol -51: Test timeout computed to be: 1500 -46: [00:36:13] WARNING: could not find number of expected rings. Switching to an approximate ring finding algorithm. 37: smi match: CN=C=S CN=C=S 37: smi match: *C=O *C=O 37: smi match: N=N N=N @@ -17514,6 +17043,12 @@ 37: smi match: C#CC#N C#CC#N 37: smi match: C#CC=O C#CC=O 37: smi match: C#CC(=O)OCC C#CC(=O)OCC +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 37: smi match: C#CC=O C#CC=O 37: smi match: *C(=O)C#C *C(=O)C#C 37: smi match: C=CC=O C=CC=O @@ -17525,7 +17060,6 @@ 37: smi match: *C(*)(*)C=O *C(*)(*)C=O 37: smi match: *C(*)C=O *C(*)C=O 37: smi match: *CC=O *CC=O -35: [00:36:13] WARNING: not removing hydrogen atom with dummy atom neighbors 37: smi match: *C(*)(*)[SH](=O)=O *C(*)(*)[SH](=O)=O 37: smi match: *C(*)(*)[SH](=O)=O *C(*)(*)[SH](=O)=O 37: smi match: *C(*)[SH](=O)=O *C(*)[SH](=O)=O @@ -17535,6 +17069,7 @@ 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 +30: ...[09:33:07] Molecule does not have explicit Hs. Consider calling AddHs() 37: smi match: O~O O~O 37: smi match: N~[SiH4] N~[SiH4] 37: smi match: *P *P @@ -17558,7 +17093,12 @@ 37: smi match: O=CON1C(=O)CCC1=O O=CON1C(=O)CCC1=O 37: smi match: O=COn1ccnc1 O=COn1ccnc1 37: smi match: O=COc1c(F)c(F)c(F)c(F)c1F O=COc1c(F)c(F)c(F)c(F)c1F +46: Randomness seeded to: 1676605826 +46: [09:33:07] WARNING: not removing hydrogen atom without neighbors 37: smi match: CC(C)(C)S CC(C)(C)S +46: [09:33:07] WARNING: could not find number of expected rings. Switching to an approximate ring finding algorithm. +46: [09:33:07] WARNING: could not find number of expected rings. Switching to an approximate ring finding algorithm. +46: [09:33:07] WARNING: could not find number of expected rings. Switching to an approximate ring finding algorithm. 37: smi match: [CH2][CH]~[CH]~[CH]~[CH]~[CH]~[CH]~[CH]~[CH]~[CH]~[CH]~C [CH2][CH]~[CH]~[CH]~[CH]~[CH]~[CH]~[CH]~[CH]~[CH]~[CH]~C 37: smi match: [CH]=O [CH]=O 37: smi match: C~[CH2]~[CH2]~[CH2]~[CH2]~[CH2]~C C~[CH2]~[CH2]~[CH2]~[CH2]~[CH2]~C @@ -17568,6 +17108,8 @@ 37: smi match: * * 37: smi match: C[nH3+] C[nH3+] 37: smi match: cC(=N)[NH2] cC(=N)[NH2] +46: [09:33:07] WARNING: could not find number of expected rings. Switching to an approximate ring finding algorithm. +46: [09:33:07] WARNING: could not find number of expected rings. Switching to an approximate ring finding algorithm. 37: smi match: O=CN[OH] O=CN[OH] 37: smi match: NN NN 37: smi match: * * @@ -17578,8 +17120,10 @@ 37: smi match: *N=C(*)* *N=C(*)* 37: smi match: *C(*)(*)C=O *C(*)(*)C=O 37: smi match: CSC=O CSC=O +35: [09:33:07] WARNING: not removing hydrogen atom with dummy atom neighbors 37: smi match: * * 37: smi match: O=CCl O=CCl +46: [09:33:07] Explicit valence for atom # 1 N, 5, is greater than permitted 37: smi match: *** *** 37: smi match: *C=O *C=O 37: smi match: C[OH] C[OH] @@ -17594,6 +17138,24 @@ 37: smi match: cCC(=O)[OH] cCC(=O)[OH] 37: smi match: *C(*)(*)C(=O)[OH] *C(*)(*)C(=O)[OH] 37: smi match: CC(=O)C(=O)[OH] CC(=O)C(=O)[OH] +46: [09:33:07] Explicit valence for atom # 1 N, 6, is greater than permitted +46: [09:33:07] Explicit valence for atom # 1 N, 5, is greater than permitted +46: [09:33:07] Explicit valence for atom # 1 N, 5, is greater than permitted +46: [09:33:07] Explicit valence for atom # 2 O, 3, is greater than permitted +46: [09:33:07] Explicit valence for atom # 2 O, 3, is greater than permitted +46: [09:33:07] non-ring atom 2 marked aromatic +46: [09:33:07] non-ring atom 2 marked aromatic +46: [09:33:07] Can't kekulize mol. Unkekulized atoms: 0 1 2 3 4 +46: [09:33:07] Can't kekulize mol. Unkekulized atoms: 0 1 2 3 4 +46: [09:33:07] Can't kekulize mol. Unkekulized atoms: 1 2 3 +46: [09:33:07] Can't kekulize mol. Unkekulized atoms: 1 2 3 +46: [09:33:07] Can't kekulize mol. Unkekulized atoms: 0 1 2 +46: [09:33:07] Can't kekulize mol. Unkekulized atoms: 0 1 2 +46: [09:33:07] Explicit valence for atom # 1 O, 3, is greater than permitted +46: [09:33:07] Explicit valence for atom # 4 F, 2, is greater than permitted +46: [09:33:07] Can't kekulize mol. Unkekulized atoms: 6 7 8 +35: ------------------------------- +35: [09:33:07] Explicit valence for atom # 0 N, 4, is greater than permitted 37: smi match: C=CC(=O)[OH] C=CC(=O)[OH] 37: smi match: N#CC(=O)[OH] N#CC(=O)[OH] 37: smi match: O=C([OH])CN(~O)~O O=C([OH])CN(~O)~O @@ -17603,9 +17165,15 @@ 37: smi match: *=CC#N *=CC#N 37: smi match: *C[OH] *C[OH] 37: smi match: ** ** +46: [09:33:07] Explicit valence for atom # 1 C, 5, is greater than permitted 37: smi match: *C[OH] *C[OH] 37: smi match: *C(*)=O *C(*)=O +46: [09:33:07] WARNING: not removing hydrogen atom with dummy atom neighbors +46: [09:33:07] WARNING: not removing hydrogen atom with dummy atom neighbors 37: smi match: * * +46: [09:33:07] WARNING: not removing hydrogen atom with wedged bond +46: [09:33:07] WARNING: not removing hydrogen atom without neighbors +46: [09:33:07] WARNING: not removing hydrogen atom without neighbors 37: smi match: *CC(=O)[OH] *CC(=O)[OH] 37: smi match: CC(=O)OC(C)=O CC(=O)OC(C)=O 37: smi match: *c *c @@ -17615,18 +17183,6 @@ 37: smi match: *c *c 37: smi match: **:*cF **:*cF 37: smi match: cB([OH])[OH] cB([OH])[OH] -50: Randomness seeded to: 243569070 -50: [00:36:13] unable to set wavy bonds for double bonds: 3 -46: [00:36:13] Explicit valence for atom # 1 O, 3, is greater than permitted -46: [00:36:13] WARNING: merging explicit H queries involved in ORs is not supported. This query will not be merged -46: [00:36:13] WARNING: merging explicit H queries involved in ORs is not supported. This query will not be merged -46: [00:36:13] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -46: [00:36:13] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -30: ...[00:36:13] Molecule does not have explicit Hs. Consider calling AddHs() -49: Randomness seeded to: 1137126708 -49: =============================================================================== -49: All tests passed (292 assertions in 12 test cases) -49: 37: smi match: N~N~N N~N~N 37: smi match: *N=N* *N=N* 37: smi match: *CC[OH] *CC[OH] @@ -17637,26 +17193,28 @@ 37: smi match: CC(=O)CC(=O)[OH] CC(=O)CC(=O)[OH] 37: smi match: *OC(=O)CC(C)=O *OC(=O)CC(C)=O 37: smi match: *OC(*)=O *OC(*)=O +46: [09:33:07] WARNING: not removing hydrogen atom without neighbors +46: [09:33:07] WARNING: not removing hydrogen atom without neighbors 37: smi match: *C(=O)[OH] *C(=O)[OH] +35: [09:33:07] Can't kekulize mol. Unkekulized atoms: 0 1 2 3 4 37: smi match: O=C[OH] O=C[OH] 37: smi match: *OC(=O)O* *OC(=O)O* 37: smi match: * * +35: [09:33:07] Can't kekulize mol. Unkekulized atoms: 6 7 8 9 10 +35: [09:33:07] Can't kekulize mol. Unkekulized atoms: 0 1 2 3 4 37: smi match: *OC(=O)Cl *OC(=O)Cl +35: [09:33:07] WARNING: merging explicit H queries involved in ORs is not supported. This query will not be merged 37: smi match: *C#N *C#N +35: [09:33:07] WARNING: merging explicit H queries involved in ORs is not supported. This query will not be merged +35: [09:33:07] WARNING: merging explicit H queries involved in ORs is not supported. This query will not be merged +35: [09:33:07] WARNING: merging explicit H queries involved in ORs is not supported. This query will not be merged +35: [09:33:07] WARNING: merging explicit H queries involved in ORs is not supported. This query will not be merged +35: +46: [09:33:07] Unreasonable formal charge on atom # 0. 37: smi match: NCC(=O)NCC=O NCC(=O)NCC=O 37: smi match: SS SS 37: smi match: * * 37: smi match: *=* *=* -46: [00:36:13] Invalid value for molAttachPoint: 4 on atom 1. Not expanding this atttachment point. -46: [00:36:13] Invalid value for _fromAttachPoint: -1 on atom 0. Not collapsing this atom -46: [00:36:13] Invalid value for _fromAttachPoint: 4 on atom 0. Not collapsing this atom - 40/238 Test #49: graphmolAdjustQueryCatch ............... Passed 0.07 sec -test 52 - Start 52: moliteratorTestsCatch - -52: Test command: /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/moliteratorTestsCatch -52: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol -52: Test timeout computed to be: 1500 37: smi match: *=* *=* 37: smi match: *=* *=* 37: smi match: *=* *=* @@ -17670,14 +17228,15 @@ 37: smi match: C=N[NH2] C=N[NH2] 37: smi match: C=NC=O C=NC=O 37: smi match: * * -46: [00:36:13] non-ring atom 0 marked aromatic -50: [00:36:13] WARNING: not removing hydrogen atom with neighbor that has non-tetrahedral stereochemistry -50: [00:36:13] WARNING: not removing hydrogen atom with neighbor that has non-tetrahedral stereochemistry 37: smi match: C#NC C#NC 37: smi match: CN=C=O CN=C=O 37: smi match: CN=C=S CN=C=S 37: smi match: *OC(*)(*)O* *OC(*)(*)O* 37: smi match: *C(*)=O *C(*)=O +47: Randomness seeded to: 3734187997 +47: =============================================================================== +47: All tests passed (62 assertions in 6 test cases) +47: 37: smi match: C~C~C~C~C~C~C C~C~C~C~C~C~C 37: smi match: *~*=O *~*=O 37: smi match: *~*=O *~*=O @@ -17689,15 +17248,20 @@ 37: smi match: OC(=O)C(O)=O OC(=O)C(O)=O 37: smi match: C=NO C=NO 37: smi match: O~O O~O -46: [00:36:13] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored -46: [00:36:13] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored 37: smi match: c[OH] c[OH] 37: smi match: O=P(~[OH])~O O=P(~[OH])~O 37: smi match: CO~P(=O)~O CO~P(=O)~O + 38/238 Test #47: graphmolOrganometallicsCatch ........... Passed 0.06 sec 37: smi match: O=P(~[OH])(~O)~O O=P(~[OH])(~O)~O 37: smi match: CO~P(=O)(~O)~O CO~P(=O)(~O)~O 37: smi match: O=P(~O)~O O=P(~O)~O 37: smi match: O=P(~O)(~O)~O O=P(~O)(~O)~O +test 50 + Start 50: chiralityTestsCatch + +50: Test command: /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/chiralityTestsCatch +50: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol +50: Test timeout computed to be: 1500 37: smi match: C[NH2] C[NH2] 37: smi match: O~*1~**~*(~O)~**~1 O~*1~**~*(~O)~**~1 37: smi match: * * @@ -17712,121 +17276,592 @@ 37: smi match: *c1nnc(=N)s1 *c1nnc(=N)s1 37: smi match: *C(*)=S *C(*)=S 37: smi match: *OC(*)=S *OC(*)=S +46: [09:33:07] +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-aarch64-linux-gnu//lib/libRDKitRDGeneral.so.1 +46: 1# Invar::operator<<(std::ostream&, Invar::Invariant const&) in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu//lib/libRDKitRDGeneral.so.1 +46: 2# RDKit::ROMol::getAtomDegree(RDKit::Atom const*) const in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu//lib/libRDKitGraphMol.so.1 +46: 3# 0x0000AAAACE08B824 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch +46: 4# 0x0000AAAACE0D7A8C in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch +46: 5# 0x0000AAAACE0D8440 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch +46: 6# 0x0000AAAACE0D8874 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch +46: 7# 0x0000AAAACE0ACC58 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch +46: 8# 0x0000AAAACE0AD1A4 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch +46: 9# 0x0000AAAACE02DE10 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch +46: 10# 0x0000FFFFB2C5229C in /lib/aarch64-linux-gnu/libc.so.6 +46: 11# __libc_start_main in /lib/aarch64-linux-gnu/libc.so.6 +46: 12# 0x0000AAAACE02DEF0 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch +46: ---------- +46: **** +46: +46: [09:33:07] +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-aarch64-linux-gnu//lib/libRDKitRDGeneral.so.1 +46: 1# Invar::operator<<(std::ostream&, Invar::Invariant const&) in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu//lib/libRDKitRDGeneral.so.1 +46: 2# RDKit::ROMol::getAtomDegree(RDKit::Atom const*) const in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu//lib/libRDKitGraphMol.so.1 +46: 3# 0x0000AAAACE08B898 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch +46: 4# 0x0000AAAACE0D7A8C in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch +46: 5# 0x0000AAAACE0D8440 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch +46: 6# 0x0000AAAACE0D8874 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch +46: 7# 0x0000AAAACE0ACC58 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch +46: 8# 0x0000AAAACE0AD1A4 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch +46: 9# 0x0000AAAACE02DE10 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch +46: 10# 0x0000FFFFB2C5229C in /lib/aarch64-linux-gnu/libc.so.6 +46: 11# __libc_start_main in /lib/aarch64-linux-gnu/libc.so.6 +46: 12# 0x0000AAAACE02DEF0 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch +46: ---------- +46: **** +46: +46: [09:33:07] +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-aarch64-linux-gnu//lib/libRDKitRDGeneral.so.1 +46: 1# Invar::operator<<(std::ostream&, Invar::Invariant const&) in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu//lib/libRDKitRDGeneral.so.1 +46: 2# RDKit::ROMol::getAtomDegree(RDKit::Atom const*) const in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu//lib/libRDKitGraphMol.so.1 +46: 3# 0x0000AAAACE08B918 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch +46: 4# 0x0000AAAACE0D7A8C in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch +46: 5# 0x0000AAAACE0D8440 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch +46: 6# 0x0000AAAACE0D8874 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch +46: 7# 0x0000AAAACE0ACC58 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch +46: 8# 0x0000AAAACE0AD1A4 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch +46: 9# 0x0000AAAACE02DE10 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch +46: 10# 0x0000FFFFB2C5229C in /lib/aarch64-linux-gnu/libc.so.6 +46: 11# __libc_start_main in /lib/aarch64-linux-gnu/libc.so.6 +46: 12# 0x0000AAAACE02DEF0 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch +46: ---------- +46: **** +46: +46: [09:33:07] +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-aarch64-linux-gnu//lib/libRDKitRDGeneral.so.1 +46: 1# Invar::operator<<(std::ostream&, Invar::Invariant const&) in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu//lib/libRDKitRDGeneral.so.1 +46: 2# RDKit::ROMol::getAtomNeighbors(RDKit::Atom const*) const in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu//lib/libRDKitGraphMol.so.1 +46: 3# 0x0000AAAACE08B9E0 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch +46: 4# 0x0000AAAACE0D7A8C in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch +46: 5# 0x0000AAAACE0D8440 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch +46: 6# 0x0000AAAACE0D8874 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch +46: 7# 0x0000AAAACE0ACC58 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch +46: 8# 0x0000AAAACE0AD1A4 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch +46: 9# 0x0000AAAACE02DE10 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch +46: 10# 0x0000FFFFB2C5229C in /lib/aarch64-linux-gnu/libc.so.6 +46: 11# __libc_start_main in /lib/aarch64-linux-gnu/libc.so.6 +46: 12# 0x0000AAAACE02DEF0 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch +46: ---------- +46: **** +46: +46: [09:33:07] +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-aarch64-linux-gnu//lib/libRDKitRDGeneral.so.1 +46: 1# Invar::operator<<(std::ostream&, Invar::Invariant const&) in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu//lib/libRDKitRDGeneral.so.1 +46: 2# RDKit::ROMol::getAtomNeighbors(RDKit::Atom const*) const in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu//lib/libRDKitGraphMol.so.1 +46: 3# 0x0000AAAACE08BA58 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch +46: 4# 0x0000AAAACE0D7A8C in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch +46: 5# 0x0000AAAACE0D8440 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch +46: 6# 0x0000AAAACE0D8874 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch +46: 7# 0x0000AAAACE0ACC58 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch +46: 8# 0x0000AAAACE0AD1A4 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch +46: 9# 0x0000AAAACE02DE10 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch +46: 10# 0x0000FFFFB2C5229C in /lib/aarch64-linux-gnu/libc.so.6 +46: 11# __libc_start_main in /lib/aarch64-linux-gnu/libc.so.6 +46: 12# 0x0000AAAACE02DEF0 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch +46: ---------- +46: **** +46: +46: [09:33:07] +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-aarch64-linux-gnu//lib/libRDKitRDGeneral.so.1 +46: 1# Invar::operator<<(std::ostream&, Invar::Invariant const&) in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu//lib/libRDKitRDGeneral.so.1 +46: 2# RDKit::ROMol::getAtomNeighbors(RDKit::Atom const*) const in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu//lib/libRDKitGraphMol.so.1 +46: 3# 0x0000AAAACE08BADC in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch +46: 4# 0x0000AAAACE0D7A8C in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch +46: 5# 0x0000AAAACE0D8440 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch +46: 6# 0x0000AAAACE0D8874 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch +46: 7# 0x0000AAAACE0ACC58 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch +46: 8# 0x0000AAAACE0AD1A4 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch +46: 9# 0x0000AAAACE02DE10 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch +46: 10# 0x0000FFFFB2C5229C in /lib/aarch64-linux-gnu/libc.so.6 +46: 11# __libc_start_main in /lib/aarch64-linux-gnu/libc.so.6 +46: 12# 0x0000AAAACE02DEF0 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch +46: ---------- +46: **** +46: +46: [09:33:07] +46: +46: **** +35: [09:33:07] WARNING: not removing hydrogen atom with dummy atom neighbors 37: smi match: * * 37: smi match: C[SH] C[SH] 37: smi match: c[SH] c[SH] 37: smi match: NC(N)=S NC(N)=S +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-aarch64-linux-gnu//lib/libRDKitRDGeneral.so.1 +46: 1# Invar::operator<<(std::ostream&, Invar::Invariant const&) in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu//lib/libRDKitRDGeneral.so.1 +46: 2# RDKit::ROMol::getAtomBonds(RDKit::Atom const*) const in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu//lib/libRDKitGraphMol.so.1 +46: 3# 0x0000AAAACE08C1F0 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch +46: 4# 0x0000AAAACE0D7A8C in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch +46: 5# 0x0000AAAACE0D8440 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch +46: 6# 0x0000AAAACE0D8874 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch +46: 7# 0x0000AAAACE0ACC58 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch +46: 8# 0x0000AAAACE0AD1A4 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch +46: 9# 0x0000AAAACE02DE10 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch +46: 10# 0x0000FFFFB2C5229C in /lib/aarch64-linux-gnu/libc.so.6 +46: 11# __libc_start_main in /lib/aarch64-linux-gnu/libc.so.6 +46: 12# 0x0000AAAACE02DEF0 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch +46: ---------- +46: **** +46: +46: [09:33:07] +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-aarch64-linux-gnu//lib/libRDKitRDGeneral.so.1 +46: 1# Invar::operator<<(std::ostream&, Invar::Invariant const&) in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu//lib/libRDKitRDGeneral.so.1 +46: 2# RDKit::ROMol::getAtomBonds(RDKit::Atom const*) const in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu//lib/libRDKitGraphMol.so.1 +46: 3# 0x0000AAAACE08BC0C in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch +46: 4# 0x0000AAAACE0D7A8C in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch +46: 5# 0x0000AAAACE0D8440 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch +46: 6# 0x0000AAAACE0D8874 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch +46: 7# 0x0000AAAACE0ACC58 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch +46: 8# 0x0000AAAACE0AD1A4 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch +46: 9# 0x0000AAAACE02DE10 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch +46: 10# 0x0000FFFFB2C5229C in /lib/aarch64-linux-gnu/libc.so.6 +46: 11# __libc_start_main in /lib/aarch64-linux-gnu/libc.so.6 +46: 12# 0x0000AAAACE02DEF0 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch +46: ---------- +46: **** +46: +46: [09:33:07] +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-aarch64-linux-gnu//lib/libRDKitRDGeneral.so.1 +46: 1# Invar::operator<<(std::ostream&, Invar::Invariant const&) in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu//lib/libRDKitRDGeneral.so.1 +46: 2# RDKit::ROMol::getAtomBonds(RDKit::Atom const*) const in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu//lib/libRDKitGraphMol.so.1 +46: 3# 0x0000AAAACE08BC90 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch +46: 4# 0x0000AAAACE0D7A8C in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch +46: 5# 0x0000AAAACE0D8440 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch +46: 6# 0x0000AAAACE0D8874 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch +46: 7# 0x0000AAAACE0ACC58 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch +46: 8# 0x0000AAAACE0AD1A4 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch +46: 9# 0x0000AAAACE02DE10 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch +46: 10# 0x0000FFFFB2C5229C in /lib/aarch64-linux-gnu/libc.so.6 +46: 11# __libc_start_main in /lib/aarch64-linux-gnu/libc.so.6 +46: 12# 0x0000AAAACE02DEF0 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch +46: ---------- +46: **** +46: 37: smi match: * * -40: [00:36:13] sorting (hanoi sort) vectors 37: smi match: ***** ***** 37: smi match: NC(N)=O NC(N)=O -37: [00:36:13] done -37: [00:36:13] ------------------------------------- -37: [00:36:13] Testing sf.net issue 280. -37: [00:36:13] done -37: [00:36:13] ------------------------------------- -37: [00:36:13] Testing sf.net issue 285. -37: [00:36:13] done -37: [00:36:13] done -37: [00:36:13] done -37: [00:36:13] done -37: [00:36:13] done -37: [00:36:13] done -37: [00:36:13] done -37: [00:36:13] ------------------------------------- -37: [00:36:13] Testing Github2441: Add RDProps interface to Conformers. -37: [00:36:13] done -37: [00:36:13] ------------------------------------- -37: [00:36:13] Testing Issue2510: Pickle Confs as double. -37: [00:36:13] done -37: [00:36:13] ------------------------------------- -37: [00:36:13] Testing Github #2465: Negative atom-map numbers cause depickling to fail. -37: [00:36:13] done -37: [00:36:13] ------------------------------------- -37: [00:36:13] Testing loading pickled mols with conformers -37: [00:36:13] done -37: [00:36:13] ------------------------------------- -37: [00:36:13] Testing conformer reading/writing options -37: [00:36:13] done -37: [00:36:13] ------------------------------------- -37: [00:36:13] Testing property reading options -46: [00:36:13] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -52: Randomness seeded to: 1759666385 -52: =============================================================================== -52: All tests passed (14 assertions in 4 test cases) -52: - 41/238 Test #52: moliteratorTestsCatch .................. Passed 0.03 sec +37: [09:33:07] done +37: [09:33:07] ------------------------------------- +37: [09:33:07] Testing sf.net issue 280. +46: [09:33:07] +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-aarch64-linux-gnu//lib/libRDKitRDGeneral.so.1 +46: 1# Invar::operator<<(std::ostream&, Invar::Invariant const&) in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu//lib/libRDKitRDGeneral.so.1 +46: 2# RDKit::ROMol::addAtom(RDKit::Atom*, bool, bool) in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu//lib/libRDKitGraphMol.so.1 +46: 3# 0x0000AAAACE08C1D4 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch +46: 4# 0x0000AAAACE0D7A8C in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch +46: 5# 0x0000AAAACE0D8440 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch +46: 6# 0x0000AAAACE0D8874 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch +46: 7# 0x0000AAAACE0ACC58 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch +46: 8# 0x0000AAAACE0AD1A4 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch +46: 9# 0x0000AAAACE02DE10 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch +46: 10# 0x0000FFFFB2C5229C in /lib/aarch64-linux-gnu/libc.so.6 +46: 11# __libc_start_main in /lib/aarch64-linux-gnu/libc.so.6 +46: 12# 0x0000AAAACE02DEF0 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch +46: ---------- +46: **** +46: +46: [09:33:07] +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-aarch64-linux-gnu//lib/libRDKitRDGeneral.so.1 +46: 1# Invar::operator<<(std::ostream&, Invar::Invariant const&) in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu//lib/libRDKitRDGeneral.so.1 +46: 2# RDKit::ROMol::addAtom(RDKit::Atom*, bool, bool) in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu//lib/libRDKitGraphMol.so.1 +46: 3# 0x0000AAAACE08BE80 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch +46: 4# 0x0000AAAACE0D7A8C in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch +46: 5# 0x0000AAAACE0D8440 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch +46: 6# 0x0000AAAACE0D8874 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch +46: 7# 0x0000AAAACE0ACC58 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch +46: 8# 0x0000AAAACE0AD1A4 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch +46: 9# 0x0000AAAACE02DE10 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch +46: 10# 0x0000FFFFB2C5229C in /lib/aarch64-linux-gnu/libc.so.6 +46: 11# __libc_start_main in /lib/aarch64-linux-gnu/libc.so.6 +46: 12# 0x0000AAAACE02DEF0 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch +46: ---------- +46: **** +46: +46: [09:33:07] +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-aarch64-linux-gnu//lib/libRDKitRDGeneral.so.1 +46: 1# Invar::operator<<(std::ostream&, Invar::Invariant const&) in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu//lib/libRDKitRDGeneral.so.1 +46: 2# RDKit::ROMol::addBond(RDKit::Bond*, bool) in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu//lib/libRDKitGraphMol.so.1 +46: 3# 0x0000AAAACE08C1B4 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch +46: 4# 0x0000AAAACE0D7A8C in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch +46: 5# 0x0000AAAACE0D8440 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch +46: 6# 0x0000AAAACE0D8874 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch +46: 7# 0x0000AAAACE0ACC58 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch +46: 8# 0x0000AAAACE0AD1A4 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch +46: 9# 0x0000AAAACE02DE10 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch +46: 10# 0x0000FFFFB2C5229C in /lib/aarch64-linux-gnu/libc.so.6 +46: 11# __libc_start_main in /lib/aarch64-linux-gnu/libc.so.6 +46: 12# 0x0000AAAACE02DEF0 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch +46: ---------- +46: **** +46: +46: [09:33:07] WARNING: could not find number of expected rings. Switching to an approximate ring finding algorithm. +46: [09:33:07] WARNING: could not find number of expected rings. Switching to an approximate ring finding algorithm. +46: [09:33:07] WARNING: not removing hydrogen atom without neighbors +46: [09:33:07] Explicit valence for atom # 1 F greater than permitted +46: [09:33:07] +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-aarch64-linux-gnu//lib/libRDKitRDGeneral.so.1 +46: 1# Invar::operator<<(std::ostream&, Invar::Invariant const&) in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu//lib/libRDKitRDGeneral.so.1 +46: 2# RDKit::Atom::setQuery(Queries::Query*) in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu//lib/libRDKitGraphMol.so.1 +46: 3# 0x0000AAAACE03A58C in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch +46: 4# 0x0000AAAACE0D7A8C in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch +46: 5# 0x0000AAAACE0D8440 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch +46: 6# 0x0000AAAACE0D8874 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch +46: 7# 0x0000AAAACE0ACC58 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch +46: 8# 0x0000AAAACE0AD1A4 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch +46: 9# 0x0000AAAACE02DE10 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch +46: 10# 0x0000FFFFB2C5229C in /lib/aarch64-linux-gnu/libc.so.6 +46: 11# __libc_start_main in /lib/aarch64-linux-gnu/libc.so.6 +46: 12# 0x0000AAAACE02DEF0 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch +46: ---------- +46: **** +46: +46: [09:33:07] +46: +46: **** +37: [09:33:07] done +37: [09:33:07] ------------------------------------- +37: [09:33:07] Testing sf.net issue 285. +37: [09:33:07] done +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-aarch64-linux-gnu//lib/libRDKitRDGeneral.so.1 +46: 1# Invar::operator<<(std::ostream&, Invar::Invariant const&) in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu//lib/libRDKitRDGeneral.so.1 +46: 2# RDKit::Atom::expandQuery(Queries::Query*, Queries::CompositeQueryType, bool) in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu//lib/libRDKitGraphMol.so.1 +46: 3# 0x0000AAAACE03A618 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch +46: 4# 0x0000AAAACE0D7A8C in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch +46: 5# 0x0000AAAACE0D8440 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch +46: 6# 0x0000AAAACE0D8874 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch +46: 7# 0x0000AAAACE0ACC58 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch +46: 8# 0x0000AAAACE0AD1A4 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch +46: 9# 0x0000AAAACE02DE10 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch +46: 10# 0x0000FFFFB2C5229C in /lib/aarch64-linux-gnu/libc.so.6 +46: 11# __libc_start_main in /lib/aarch64-linux-gnu/libc.so.6 +46: 12# 0x0000AAAACE02DEF0 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch +46: ---------- +46: **** +46: +46: [09:33:07] +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-aarch64-linux-gnu//lib/libRDKitRDGeneral.so.1 +46: 1# Invar::operator<<(std::ostream&, Invar::Invariant const&) in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu//lib/libRDKitRDGeneral.so.1 +46: 2# RDKit::Bond::setQuery(Queries::Query*) in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu//lib/libRDKitGraphMol.so.1 +46: 3# 0x0000AAAACE03A1DC in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch +46: 4# 0x0000AAAACE0D7A8C in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch +46: 5# 0x0000AAAACE0D8440 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch +46: 6# 0x0000AAAACE0D8874 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch +46: 7# 0x0000AAAACE0ACC58 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch +46: 8# 0x0000AAAACE0AD1A4 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch +46: 9# 0x0000AAAACE02DE10 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch +46: 10# 0x0000FFFFB2C5229C in /lib/aarch64-linux-gnu/libc.so.6 +46: 11# __libc_start_main in /lib/aarch64-linux-gnu/libc.so.6 +46: 12# 0x0000AAAACE02DEF0 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch +46: ---------- +46: **** +46: +46: [09:33:07] +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-aarch64-linux-gnu//lib/libRDKitRDGeneral.so.1 +46: 1# Invar::operator<<(std::ostream&, Invar::Invariant const&) in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu//lib/libRDKitRDGeneral.so.1 +46: 2# RDKit::Bond::expandQuery(Queries::Query*, Queries::CompositeQueryType, bool) in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu//lib/libRDKitGraphMol.so.1 +46: 3# 0x0000AAAACE03A268 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch +46: 4# 0x0000AAAACE0D7A8C in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch +46: 5# 0x0000AAAACE0D8440 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch +46: 6# 0x0000AAAACE0D8874 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch +46: 7# 0x0000AAAACE0ACC58 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch +46: 8# 0x0000AAAACE0AD1A4 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch +46: 9# 0x0000AAAACE02DE10 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch +46: 10# 0x0000FFFFB2C5229C in /lib/aarch64-linux-gnu/libc.so.6 +46: 11# __libc_start_main in /lib/aarch64-linux-gnu/libc.so.6 +46: 12# 0x0000AAAACE02DEF0 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch +46: ---------- +46: **** +46: +37: [09:33:07] done +37: [09:33:07] done +37: [09:33:07] done +37: [09:33:07] done +37: [09:33:07] done +37: [09:33:07] done +37: [09:33:07] ------------------------------------- +37: [09:33:07] Testing Github2441: Add RDProps interface to Conformers. +37: [09:33:07] done +37: [09:33:07] ------------------------------------- +37: [09:33:07] Testing Issue2510: Pickle Confs as double. +37: [09:33:07] done +37: [09:33:07] ------------------------------------- +37: [09:33:07] Testing Github #2465: Negative atom-map numbers cause depickling to fail. +37: [09:33:07] done +37: [09:33:07] ------------------------------------- +37: [09:33:07] Testing loading pickled mols with conformers +46: [09:33:07] Can't kekulize mol. Unkekulized atoms: 0 1 2 3 4 +46: [09:33:07] Can't kekulize mol. Unkekulized atoms: 0 1 2 3 4 +46: [09:33:07] Can't kekulize mol. Unkekulized atoms: 6 7 8 9 10 +46: [09:33:07] Can't kekulize mol. Unkekulized atoms: 6 7 8 9 10 +37: [09:33:07] done +37: [09:33:07] ------------------------------------- +37: [09:33:07] Testing conformer reading/writing options +37: [09:33:07] done +37: [09:33:07] ------------------------------------- +37: [09:33:07] Testing property reading options +46: [09:33:07] Can't kekulize mol. Unkekulized atoms: 0 1 2 3 4 +37: [09:33:07] done +37: [09:33:07] ------------------------------------- +37: [09:33:07] Testing property reading options +37: [09:33:07] done +37: [09:33:07] ------------------------------------- +37: [09:33:07] Testing boost::serialization integration +37: [09:33:07] done +37: [09:33:07] ------------------------------------- +37: [09:33:07] Testing github issue 6036 +40: [09:33:07] sorting (hanoi sort) vectors +48: Randomness seeded to: 2573053506 +48: =============================================================================== +48: All tests passed (136 assertions in 8 test cases) +48: +46: [09:33:07] Unusual charge on atom 0 number of radical electrons set to zero +46: [09:33:07] Unusual charge on atom 0 number of radical electrons set to zero +46: [09:33:07] Unusual charge on atom 0 number of radical electrons set to zero + 39/238 Test #37: graphmoltestPickler .................... Passed 0.16 sec + 40/238 Test #48: graphmolSGroupCatch .................... Passed 0.05 sec +test 51 + Start 51: canonTestsCatch + +51: Test command: /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/canonTestsCatch +51: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol +51: Test timeout computed to be: 1500 +test 52 + Start 52: moliteratorTestsCatch + +52: Test command: /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/moliteratorTestsCatch +52: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol +52: Test timeout computed to be: 1500 +46: [09:33:07] non-ring atom 0 marked aromatic +46: [09:33:07] non-ring atom 0 marked aromatic +46: [09:33:07] Explicit valence for atom # 1 C, 5, is greater than permitted +46: [09:33:07] Explicit valence for atom # 9 C, 5, is greater than permitted +46: [09:33:07] Explicit valence for atom # 3 N, 4, is greater than permitted +46: [09:33:07] Explicit valence for atom # 15 C, 5, is greater than permitted +46: [09:33:07] Explicit valence for atom # 11 C, 5, is greater than permitted +46: [09:33:07] Explicit valence for atom # 9 C, 5, is greater than permitted +46: [09:33:07] Explicit valence for atom # 9 C, 5, is greater than permitted +46: [09:33:07] Explicit valence for atom # 9 C, 6, is greater than permitted +46: [09:33:07] Can't kekulize mol. Unkekulized atoms: 0 1 2 3 4 +46: [09:33:07] Can't kekulize mol. Unkekulized atoms: 7 +46: [09:33:07] Can't kekulize mol. Unkekulized atoms: 3 +46: [09:33:07] Can't kekulize mol. Unkekulized atoms: 3 7 +46: [09:33:07] Can't kekulize mol. Unkekulized atoms: 3 7 +46: [09:33:07] WARNING: could not find number of expected rings. Switching to an approximate ring finding algorithm. +46: [09:33:07] WARNING: could not find number of expected rings. Switching to an approximate ring finding algorithm. +49: Randomness seeded to: 190038616 +49: =============================================================================== +49: All tests passed (292 assertions in 12 test cases) +49: + 41/238 Test #49: graphmolAdjustQueryCatch ............... Passed 0.07 sec test 53 Start 53: queryTestsCatch 53: Test command: /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/queryTestsCatch 53: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol 53: Test timeout computed to be: 1500 -50: [00:36:13] Warning: ambiguous stereochemistry - zero-length (or near zero-length) bond - at atom 1 ignored. -50: [00:36:13] Warning: ambiguous stereochemistry - zero-length (or near zero-length) bond - at atom 1 ignored. -37: [00:36:13] done -37: [00:36:13] ------------------------------------- -37: [00:36:13] Testing property reading options -37: [00:36:13] done -37: [00:36:13] ------------------------------------- -37: [00:36:13] Testing boost::serialization integration -37: [00:36:13] done -37: [00:36:13] ------------------------------------- -37: [00:36:13] Testing github issue 6036 - 42/238 Test #37: graphmoltestPickler .................... Passed 0.26 sec +52: Randomness seeded to: 3384251566 +52: =============================================================================== +52: All tests passed (14 assertions in 4 test cases) +52: +46: [09:33:07] Explicit valence for atom # 1 O, 3, is greater than permitted + 42/238 Test #52: moliteratorTestsCatch .................. Passed 0.03 sec test 54 Start 54: molbundleTestsCatch 54: Test command: /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/molbundleTestsCatch 54: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol 54: Test timeout computed to be: 1500 -50: [00:36:13] Warning: ambiguous stereochemistry - overlapping neighbors - at atom 2 ignored -46: [00:36:13] 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: -46: [00:36:13] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -53: Randomness seeded to: 843846603 +46: [09:33:07] WARNING: merging explicit H queries involved in ORs is not supported. This query will not be merged +46: [09:33:07] WARNING: merging explicit H queries involved in ORs is not supported. This query will not be merged +46: [09:33:07] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +46: [09:33:07] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +46: [09:33:07] Invalid value for molAttachPoint: 4 on atom 1. Not expanding this atttachment point. +46: [09:33:07] Invalid value for _fromAttachPoint: -1 on atom 0. Not collapsing this atom +46: [09:33:07] Invalid value for _fromAttachPoint: 4 on atom 0. Not collapsing this atom +46: [09:33:07] non-ring atom 0 marked aromatic +46: [09:33:07] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored +46: [09:33:07] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored +50: Randomness seeded to: 3575665081 +50: [09:33:07] unable to set wavy bonds for double bonds: 3 +46: [09:33:07] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +46: [09:33:07] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +46: [09:33:07] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +50: [09:33:07] WARNING: not removing hydrogen atom with neighbor that has non-tetrahedral stereochemistry +50: [09:33:07] WARNING: not removing hydrogen atom with neighbor that has non-tetrahedral stereochemistry +46: [09:33:07] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 2 ignored +46: [09:33:07] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 2 ignored +54: Randomness seeded to: 258402751 +54: =============================================================================== +54: All tests passed (6 assertions in 1 test case) +54: +53: Randomness seeded to: 3606885805 53: =============================================================================== 53: All tests passed (10 assertions in 1 test case) 53: - 43/238 Test #50: chiralityTestsCatch .................... Passed 0.11 sec + 43/238 Test #53: queryTestsCatch ........................ Passed 0.05 sec test 55 Start 55: pickleTestsCatch 55: Test command: /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/pickleTestsCatch 55: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol 55: Test timeout computed to be: 1500 -46: [00:36:13] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 2 ignored -46: [00:36:13] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 2 ignored -54: Randomness seeded to: 3305625312 -54: =============================================================================== -54: All tests passed (6 assertions in 1 test case) -54: - 44/238 Test #53: queryTestsCatch ........................ Passed 0.03 sec +46: [09:33:07] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. + 44/238 Test #54: molbundleTestsCatch .................... Passed 0.04 sec test 56 Start 56: tableTestsCatch 56: Test command: /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/tableTestsCatch 56: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol 56: Test timeout computed to be: 1500 - 45/238 Test #54: molbundleTestsCatch .................... Passed 0.03 sec +46: [09:33:07] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored +46: [09:33:07] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored +46: [09:33:08] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored +46: [09:33:08] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored +50: [09:33:08] Warning: ambiguous stereochemistry - zero-length (or near zero-length) bond - at atom 1 ignored. +50: [09:33:08] Warning: ambiguous stereochemistry - zero-length (or near zero-length) bond - at atom 1 ignored. +46: [09:33:08] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +50: [09:33:08] Warning: ambiguous stereochemistry - overlapping neighbors - at atom 2 ignored +50: =============================================================================== +50: All tests passed (2295 assertions in 80 test cases) +50: + 45/238 Test #50: chiralityTestsCatch .................... Passed 0.11 sec test 57 Start 57: molopsTestsCatch 57: Test command: /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/molopsTestsCatch 57: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol 57: Test timeout computed to be: 1500 -46: [00:36:13] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -46: [00:36:13] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored -46: [00:36:13] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored -46: [00:36:13] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored -46: [00:36:13] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored -55: Randomness seeded to: 220565314 +55: Randomness seeded to: 2153493103 55: =============================================================================== 55: All tests passed (45 assertions in 4 test cases) 55: -46: [00:36:13] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +56: Randomness seeded to: 155139902 +56: =============================================================================== +56: All tests passed (7 assertions in 2 test cases) +56: 46/238 Test #55: pickleTestsCatch ....................... Passed 0.03 sec test 58 Start 58: smiTest1 @@ -17834,10 +17869,6 @@ 58: Test command: /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/SmilesParse/smiTest1 58: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/SmilesParse 58: Test timeout computed to be: 1500 -56: Randomness seeded to: 4114299760 -56: =============================================================================== -56: All tests passed (7 assertions in 2 test cases) -56: 47/238 Test #56: tableTestsCatch ........................ Passed 0.04 sec test 59 Start 59: smiTest2 @@ -17845,117 +17876,120 @@ 59: Test command: /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/SmilesParse/smiTest2 59: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/SmilesParse 59: Test timeout computed to be: 1500 -59: [00:36:13] SMILES Parse Error: Failed parsing SMILES 'CO' for input: 'CO' -59: [00:36:13] SMILES Parse Error: Failed parsing SMILES 'C-O' for input: 'C-O' -59: [00:36:13] SMILES Parse Error: syntax error while parsing: - -59: [00:36:13] SMILES Parse Error: check for mistakes around position 1: -59: [00:36:13] - -59: [00:36:13] ^ -59: [00:36:13] SMILES Parse Error: Failed parsing SMILES '-' for input: '-' -59: [00:36:13] SMILES Parse Error: Failed parsing SMILES '[Bg]' for input: '[Bg]' -59: [00:36:13] SMILES Parse Error: Failed parsing SMILES 'C' for input: 'C' -59: [00:36:13] SMILES Parse Error: Failed parsing SMILES 'C-O' for input: 'C-O' -59: [00:36:13] SMILES Parse Error: Failed parsing SMILES '*' for input: '*' -59: [00:36:13] SMARTS Parse Error: Failed parsing SMARTS 'CO' for input: 'CO' -59: [00:36:13] SMARTS Parse Error: Failed parsing SMARTS 'C-O' for input: 'C-O' -59: [00:36:13] SMARTS Parse Error: Failed parsing SMARTS '-' for input: '-' -59: [00:36:13] SMARTS Parse Error: Failed parsing SMARTS '[Bg]' for input: '[Bg]' -59: [00:36:13] SMARTS Parse Error: Failed parsing SMARTS 'C' for input: 'C' -59: [00:36:13] SMARTS Parse Error: Failed parsing SMARTS '-O' for input: '-O' -59: [00:36:13] SMARTS Parse Error: Failed parsing SMARTS '*' for input: '*' - 48/238 Test #59: smiTest2 ............................... Passed 0.01 sec +46: [09:33:08] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +46: [09:33:08] Explicit valence for atom # 0 Al, 6, is greater than permitted +46: [09:33:08] Explicit valence for atom # 0 Al, 6, is greater than permitted +46: [09:33:08] Explicit valence for atom # 1 Si, 6, is greater than permitted +46: [09:33:08] Explicit valence for atom # 1 Si, 6, is greater than permitted +46: [09:33:08] Explicit valence for atom # 0 P, 6, is greater than permitted +46: [09:33:08] Explicit valence for atom # 0 P, 6, is greater than permitted +46: [09:33:08] Explicit valence for atom # 0 P, 7, is greater than permitted +46: [09:33:08] Explicit valence for atom # 0 P, 7, is greater than permitted +46: [09:33:08] Explicit valence for atom # 1 As, 6, is greater than permitted +46: [09:33:08] Explicit valence for atom # 1 As, 6, is greater than permitted +46: [09:33:08] Explicit valence for atom # 1 As, 7, is greater than permitted +46: [09:33:08] Explicit valence for atom # 1 As, 7, is greater than permitted +46: [09:33:08] Explicit valence for atom # 0 Sb, 6, is greater than permitted +46: [09:33:08] Explicit valence for atom # 0 Sb, 6, is greater than permitted +46: [09:33:08] Explicit valence for atom # 0 Sb, 7, is greater than permitted +46: [09:33:08] Explicit valence for atom # 0 Sb, 7, is greater than permitted +46: [09:33:08] Explicit valence for atom # 1 Bi, 6, is greater than permitted +46: [09:33:08] Explicit valence for atom # 1 Bi, 6, is greater than permitted +46: [09:33:08] Explicit valence for atom # 1 Bi, 8, is greater than permitted +46: [09:33:08] Explicit valence for atom # 1 Bi, 8, is greater than permitted +46: =============================================================================== +46: All tests passed (4479 assertions in 107 test cases) +46: +59: [09:33:08] SMILES Parse Error: Failed parsing SMILES 'CO' for input: 'CO' +59: [09:33:08] SMILES Parse Error: Failed parsing SMILES 'C-O' for input: 'C-O' + 48/238 Test #46: graphmolTestsCatch ..................... Passed 0.20 sec test 60 Start 60: cxsmilesTest 60: Test command: /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/SmilesParse/cxsmilesTest 60: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/SmilesParse 60: Test timeout computed to be: 1500 -57: Randomness seeded to: 2226035200 -57: =============================================================================== -57: All tests passed (230 assertions in 7 test cases) -57: - 49/238 Test #57: molopsTestsCatch ....................... Passed 0.05 sec +59: [09:33:08] SMILES Parse Error: syntax error while parsing: - +59: [09:33:08] SMILES Parse Error: check for mistakes around position 1: +59: [09:33:08] - +59: [09:33:08] ^ +59: [09:33:08] SMILES Parse Error: Failed parsing SMILES '-' for input: '-' +59: [09:33:08] SMILES Parse Error: Failed parsing SMILES '[Bg]' for input: '[Bg]' +59: [09:33:08] SMILES Parse Error: Failed parsing SMILES 'C' for input: 'C' +59: [09:33:08] SMILES Parse Error: Failed parsing SMILES 'C-O' for input: 'C-O' +59: [09:33:08] SMILES Parse Error: Failed parsing SMILES '*' for input: '*' +59: [09:33:08] SMARTS Parse Error: Failed parsing SMARTS 'CO' for input: 'CO' +59: [09:33:08] SMARTS Parse Error: Failed parsing SMARTS 'C-O' for input: 'C-O' +59: [09:33:08] SMARTS Parse Error: Failed parsing SMARTS '-' for input: '-' +59: [09:33:08] SMARTS Parse Error: Failed parsing SMARTS '[Bg]' for input: '[Bg]' +59: [09:33:08] SMARTS Parse Error: Failed parsing SMARTS 'C' for input: 'C' +59: [09:33:08] SMARTS Parse Error: Failed parsing SMARTS '-O' for input: '-O' +59: [09:33:08] SMARTS Parse Error: Failed parsing SMARTS '*' for input: '*' + 49/238 Test #59: smiTest2 ............................... Passed 0.01 sec test 61 Start 61: smaTest1 61: Test command: /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/SmilesParse/smaTest1 61: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/SmilesParse 61: Test timeout computed to be: 1500 -58: [00:36:13] WARNING: not removing hydrogen atom without neighbors -58: [00:36:13] WARNING: not removing hydrogen atom without neighbors -58: [00:36:13] WARNING: not removing hydrogen atom without neighbors -58: [00:36:13] WARNING: not removing hydrogen atom without neighbors -58: [00:36:13] WARNING: not removing hydrogen atom without neighbors -58: [00:36:13] WARNING: not removing hydrogen atom without neighbors -58: [00:36:13] WARNING: not removing hydrogen atom without neighbors -58: [00:36:13] WARNING: not removing hydrogen atom without neighbors -58: [00:36:13] WARNING: not removing hydrogen atom without neighbors -58: [00:36:13] WARNING: not removing hydrogen atom without neighbors -58: [00:36:13] WARNING: not removing hydrogen atom without neighbors -58: [00:36:13] Invalid chiral specification on atom 0 -58: [00:36:13] Invalid chiral specification on atom 0 -58: [00:36:13] Invalid chiral specification on atom 0 -58: [00:36:13] Invalid chiral specification on atom 0 -58: [00:36:13] Invalid chiral specification on atom 0 -46: [00:36:13] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -58: [00:36:13] SMILES Parse Error: unclosed ring for input: 'C1.C11.C' -58: [00:36:13] SMILES Parse Error: unclosed ring for input: 'C1C.CC11CCC' -46: [00:36:13] Explicit valence for atom # 0 Al, 6, is greater than permitted -46: [00:36:13] Explicit valence for atom # 0 Al, 6, is greater than permitted -46: [00:36:13] Explicit valence for atom # 1 Si, 6, is greater than permitted -46: [00:36:13] Explicit valence for atom # 1 Si, 6, is greater than permitted -46: [00:36:13] Explicit valence for atom # 0 P, 6, is greater than permitted -46: [00:36:13] Explicit valence for atom # 0 P, 6, is greater than permitted -46: [00:36:13] Explicit valence for atom # 0 P, 7, is greater than permitted -46: [00:36:13] Explicit valence for atom # 0 P, 7, is greater than permitted -46: [00:36:13] Explicit valence for atom # 1 As, 6, is greater than permitted -46: [00:36:13] Explicit valence for atom # 1 As, 6, is greater than permitted -46: [00:36:13] Explicit valence for atom # 1 As, 7, is greater than permitted -46: [00:36:13] Explicit valence for atom # 1 As, 7, is greater than permitted -46: [00:36:13] Explicit valence for atom # 0 Sb, 6, is greater than permitted -46: [00:36:13] Explicit valence for atom # 0 Sb, 6, is greater than permitted -46: [00:36:13] Explicit valence for atom # 0 Sb, 7, is greater than permitted -46: [00:36:13] Explicit valence for atom # 0 Sb, 7, is greater than permitted -46: [00:36:13] Explicit valence for atom # 1 Bi, 6, is greater than permitted -46: [00:36:13] Explicit valence for atom # 1 Bi, 6, is greater than permitted -46: [00:36:13] Explicit valence for atom # 1 Bi, 8, is greater than permitted -46: [00:36:13] Explicit valence for atom # 1 Bi, 8, is greater than permitted -46: =============================================================================== -46: All tests passed (4479 assertions in 107 test cases) -46: - 50/238 Test #46: graphmolTestsCatch ..................... Passed 0.29 sec +58: [09:33:08] WARNING: not removing hydrogen atom without neighbors +58: [09:33:08] WARNING: not removing hydrogen atom without neighbors +57: Randomness seeded to: 4071487927 +57: =============================================================================== +57: All tests passed (230 assertions in 7 test cases) +57: +58: [09:33:08] WARNING: not removing hydrogen atom without neighbors +58: [09:33:08] WARNING: not removing hydrogen atom without neighbors +58: [09:33:08] WARNING: not removing hydrogen atom without neighbors +58: [09:33:08] WARNING: not removing hydrogen atom without neighbors +58: [09:33:08] WARNING: not removing hydrogen atom without neighbors +58: [09:33:08] WARNING: not removing hydrogen atom without neighbors +58: [09:33:08] WARNING: not removing hydrogen atom without neighbors +58: [09:33:08] WARNING: not removing hydrogen atom without neighbors + 50/238 Test #57: molopsTestsCatch ....................... Passed 0.04 sec test 62 Start 62: smiTestCatch 62: Test command: /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/SmilesParse/smiTestCatch 62: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/SmilesParse 62: Test timeout computed to be: 1500 -62: Randomness seeded to: 3419307683 -62: [00:36:13] SMILES Parse Error: unclosed ring for input: 'c1ccccc' -62: [00:36:13] Can't kekulize mol. Unkekulized atoms: 0 1 2 3 4 -62: [00:36:13] SMARTS Parse Error: unclosed ring for input: 'c1ccccc' -62: [00:36:13] SMARTS Parse Error: unclosed ring for input: 'C1C' -62: [00:36:13] Can't kekulize mol. Unkekulized atoms: 0 1 2 3 4 -62: [00:36:13] SMARTS Parse Error: syntax error while parsing: C)foo -62: [00:36:13] SMARTS Parse Error: Failed parsing SMARTS 'C)foo' for input: 'C)foo' -62: [00:36:13] SMARTS Parse Error: syntax error while parsing: CCC |$foo;;bar$| -62: [00:36:13] SMARTS Parse Error: Failed parsing SMARTS 'CCC |$foo;;bar$|' for input: 'CCC |$foo;;bar$|' -62: [00:36:13] unrecognized CXSMILES CONNECT value: 'EU'. Assuming 'eu' -61: [00:36:13] SMARTS Parse Error: syntax error while parsing: [C:10H3]CC -61: [00:36:13] SMARTS Parse Error: Failed parsing SMARTS '[C:10H3]CC' for input: '[C:10H3]CC' -61: [00:36:13] SMARTS Parse Error: syntax error while parsing: [C:10:3]ON -61: [00:36:13] SMARTS Parse Error: Failed parsing SMARTS '[C:10:3]ON' for input: '[C:10:3]ON' -61: [00:36:13] WARNING: merging explicit H queries involved in ORs is not supported. This query will not be merged -61: [00:36:13] WARNING: merging explicit H queries involved in ORs is not supported. This query will not be merged -58: --C1CCC2(CC1)CCCCC2CCC1CCCC1 - 51/238 Test #61: smaTest1 ............................... Passed 0.14 sec +58: [09:33:08] WARNING: not removing hydrogen atom without neighbors +58: [09:33:08] Invalid chiral specification on atom 0 +58: [09:33:08] Invalid chiral specification on atom 0 +58: [09:33:08] Invalid chiral specification on atom 0 +58: [09:33:08] Invalid chiral specification on atom 0 +58: [09:33:08] Invalid chiral specification on atom 0 +58: [09:33:08] SMILES Parse Error: unclosed ring for input: 'C1.C11.C' +58: [09:33:08] SMILES Parse Error: unclosed ring for input: 'C1C.CC11CCC' +35: [09:33:08] Maximum BFS search size exceeded. +35: This is likely due to a highly symmetric fused ring system. +62: Randomness seeded to: 280927544 +62: [09:33:08] SMILES Parse Error: unclosed ring for input: 'c1ccccc' +62: [09:33:08] Can't kekulize mol. Unkekulized atoms: 0 1 2 3 4 +62: [09:33:08] SMARTS Parse Error: unclosed ring for input: 'c1ccccc' +62: [09:33:08] SMARTS Parse Error: unclosed ring for input: 'C1C' +30: ......[09:33:08] Molecule does not have explicit Hs. Consider calling AddHs() +61: [09:33:08] SMARTS Parse Error: syntax error while parsing: [C:10H3]CC +61: [09:33:08] SMARTS Parse Error: Failed parsing SMARTS '[C:10H3]CC' for input: '[C:10H3]CC' +61: [09:33:08] SMARTS Parse Error: syntax error while parsing: [C:10:3]ON +61: [09:33:08] SMARTS Parse Error: Failed parsing SMARTS '[C:10:3]ON' for input: '[C:10:3]ON' +62: [09:33:08] Can't kekulize mol. Unkekulized atoms: 0 1 2 3 4 +62: [09:33:08] SMARTS Parse Error: syntax error while parsing: C)foo +62: [09:33:08] SMARTS Parse Error: Failed parsing SMARTS 'C)foo' for input: 'C)foo' +62: [09:33:08] SMARTS Parse Error: syntax error while parsing: CCC |$foo;;bar$| +62: [09:33:08] SMARTS Parse Error: Failed parsing SMARTS 'CCC |$foo;;bar$|' for input: 'CCC |$foo;;bar$|' +61: [09:33:08] WARNING: merging explicit H queries involved in ORs is not supported. This query will not be merged +61: [09:33:08] WARNING: merging explicit H queries involved in ORs is not supported. This query will not be merged +62: [09:33:08] unrecognized CXSMILES CONNECT value: 'EU'. Assuming 'eu' + 51/238 Test #61: smaTest1 ............................... Passed 0.08 sec test 63 Start 63: nontetrahedralCatch 63: Test command: /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/SmilesParse/nontetrahedralCatch 63: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/SmilesParse 63: Test timeout computed to be: 1500 -60: Randomness seeded to: 2132382008 +58: --C1CCC2(CC1)CCCCC2CCC1CCCC1 +60: Randomness seeded to: 3330260581 60: Test 60: 60: ShortAtropisomerNoCoords.cxsmi @@ -18016,49 +18050,47 @@ 60: 60: BMS-986142_atrop5.cxsmi 60: -62: [00:36:13] w block attempts to set wedging on bond 0 more than once. -62: [00:36:13] improperly formatted w block -60: [00:36:13] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored -60: [00:36:13] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored -30: ......[00:36:13] Molecule does not have explicit Hs. Consider calling AddHs() 58: smi: ClC1CCCCC1 58: smi: ClC1CCCCC1 58: smi: ClC1CCCCC1Br -60: [00:36:13] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored -60: [00:36:13] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored 58: smi: c1ccccc1 58: smi: c1ccncc1 58: smi: c1cc[nH]c1 58: smi: c1cc[nH]c1 58: smi: c1cc[pH]c1 -60: [00:36:13] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored -60: [00:36:13] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored -60: [00:36:13] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored -58: [00:36:13] WARNING: could not find number of expected rings. Switching to an approximate ring finding algorithm. -60: [00:36:13] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored -58: [00:36:13] WARNING: could not find number of expected rings. Switching to an approximate ring finding algorithm. -60: [00:36:13] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored -62: [00:36:13] atom 3 is not associated with bond 1(1-2) in w block -60: [00:36:13] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored +60: [09:33:08] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored +60: [09:33:08] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored +60: [09:33:08] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored +60: [09:33:08] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored +58: [09:33:08] WARNING: could not find number of expected rings. Switching to an approximate ring finding algorithm. +58: [09:33:08] WARNING: could not find number of expected rings. Switching to an approximate ring finding algorithm. +60: [09:33:08] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored +60: [09:33:08] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored +60: [09:33:08] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored +60: [09:33:08] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored +60: [09:33:08] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored +60: [09:33:08] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored 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: [00:36:13] SMILES Parse Error: syntax error while parsing: c%()ccccc%() -58: [00:36:13] SMILES Parse Error: check for mistakes around position 4: -58: [00:36:13] c%()ccccc%() -58: [00:36:13] ~~~^ -58: [00:36:13] SMILES Parse Error: Failed parsing SMILES 'c%()ccccc%()' for input: 'c%()ccccc%()' -58: [00:36:13] SMILES Parse Error: syntax error while parsing: c%(100000)ccccc%(100000) -58: [00:36:13] SMILES Parse Error: check for mistakes around position 9: -58: [00:36:13] c%(100000)ccccc%(100000) -58: [00:36:13] ~~~~~~~~^ -58: [00:36:13] SMILES Parse Error: Failed parsing SMILES 'c%(100000)ccccc%(100000)' for input: 'c%(100000)ccccc%(100000)' -58: [00:36:13] SMILES Parse Error: duplicated ring closure 1 bonds atom 2 to itself for input: 'C1CC111' -58: [00:36:13] SMILES Parse Error: ring closure 1 duplicates bond between atom 0 and atom 1 for input: 'C1C1' -58: [00:36:13] SMILES Parse Error: syntax error while parsing: COc(c1)cccc1C# -58: [00:36:13] SMILES Parse Error: check for mistakes around position 14: +63: Randomness seeded to: 2915030677 +63: [09:33:08] WARNING: not removing hydrogen atom with neighbor that has non-tetrahedral stereochemistry +63: [09:33:08] WARNING: not removing hydrogen atom with neighbor that has non-tetrahedral stereochemistry +62: [09:33:08] w block attempts to set wedging on bond 0 more than once. +58: [09:33:08] SMILES Parse Error: syntax error while parsing: c%()ccccc%() +58: [09:33:08] SMILES Parse Error: check for mistakes around position 4: +58: [09:33:08] c%()ccccc%() +58: [09:33:08] ~~~^ +58: [09:33:08] SMILES Parse Error: Failed parsing SMILES 'c%()ccccc%()' for input: 'c%()ccccc%()' +58: [09:33:08] SMILES Parse Error: syntax error while parsing: c%(100000)ccccc%(100000) +58: [09:33:08] SMILES Parse Error: check for mistakes around position 9: +58: [09:33:08] c%(100000)ccccc%(100000) +58: [09:33:08] ~~~~~~~~^ +58: [09:33:08] SMILES Parse Error: Failed parsing SMILES 'c%(100000)ccccc%(100000)' for input: 'c%(100000)ccccc%(100000)' +58: [09:33:08] SMILES Parse Error: duplicated ring closure 1 bonds atom 2 to itself for input: 'C1CC111' +58: [09:33:08] SMILES Parse Error: ring closure 1 duplicates bond between atom 0 and atom 1 for input: 'C1C1' 60: Test 60: 60: BMS-986142_atrop6.cxsmi @@ -18067,50 +18099,66 @@ 60: 60: BMS-986142_atropBad1.cxsmi 60: -58: [00:36:13] COc(c1)cccc1C# -58: [00:36:13] ~~~~~~~~~~~~~^ -58: [00:36:13] SMILES Parse Error: Failed parsing SMILES 'COc(c1)cccc1C#' for input: 'COc(c1)cccc1C#' -58: [00:36:13] SMARTS Parse Error: syntax error while parsing: COc(c1)cccc1C# -58: [00:36:13] SMARTS Parse Error: Failed parsing SMARTS 'COc(c1)cccc1C#' for input: 'COc(c1)cccc1C#' -60: [00:36:13] The 2 defining bonds for an atropisomer are co-planar - atoms are: 6 7 -58: [00:36:13] SMILES Parse Error: syntax error while parsing: COc(c1)cccc1C# -58: [00:36:13] SMILES Parse Error: check for mistakes around position 14: -58: [00:36:13] COc(c1)cccc1C# -58: [00:36:13] ~~~~~~~~~~~~~^ -58: [00:36:13] SMILES Parse Error: Failed parsing SMILES 'COc(c1)cccc1C#' for input: 'COc(c1)cccc1C#' -58: [00:36:13] SMARTS Parse Error: syntax error while parsing: COc(c1)cccc1C# -58: [00:36:13] SMARTS Parse Error: Failed parsing SMARTS 'COc(c1)cccc1C#' for input: 'COc(c1)cccc1C#' -58: [00:36:13] SMILES Parse Error: syntax error while parsing: COc(c1)cccc1C# -58: [00:36:13] SMILES Parse Error: check for mistakes around position 14: -58: [00:36:13] COc(c1)cccc1C# -58: [00:36:13] ~~~~~~~~~~~~~^ -58: [00:36:13] SMILES Parse Error: Failed parsing SMILES 'COc(c1)cccc1C#' for input: 'COc(c1)cccc1C#' -58: [00:36:13] SMARTS Parse Error: syntax error while parsing: COc(c1)cccc1C# -60: [00:36:13] The 2 defining bonds for an atropisomer are co-planar - atoms are: 6 7 -58: [00:36:13] SMARTS Parse Error: Failed parsing SMARTS 'COc(c1)cccc1C#' for input: 'COc(c1)cccc1C#' +60: [09:33:08] The 2 defining bonds for an atropisomer are co-planar - atoms are: 6 7 +60: [09:33:08] The 2 defining bonds for an atropisomer are co-planar - atoms are: 6 7 +62: [09:33:08] improperly formatted w block +62: [09:33:08] atom 3 is not associated with bond 1(1-2) in w block +60: [09:33:08] The 2 defining bonds for an atropisomer are co-planar - atoms are: 6 7 +63: [09:33:08] WARNING: not removing hydrogen atom with neighbor that has non-tetrahedral stereochemistry +63: [09:33:08] WARNING: not removing hydrogen atom with neighbor that has non-tetrahedral stereochemistry +60: [09:33:08] The 2 defining bonds for an atropisomer are co-planar - atoms are: 6 7 +58: [09:33:08] SMILES Parse Error: syntax error while parsing: COc(c1)cccc1C# +58: [09:33:08] SMILES Parse Error: check for mistakes around position 14: +58: [09:33:08] COc(c1)cccc1C# +58: [09:33:08] ~~~~~~~~~~~~~^ +58: [09:33:08] SMILES Parse Error: Failed parsing SMILES 'COc(c1)cccc1C#' for input: 'COc(c1)cccc1C#' +58: [09:33:08] SMARTS Parse Error: syntax error while parsing: COc(c1)cccc1C# +58: [09:33:08] SMARTS Parse Error: Failed parsing SMARTS 'COc(c1)cccc1C#' for input: 'COc(c1)cccc1C#' +58: [09:33:08] SMILES Parse Error: syntax error while parsing: COc(c1)cccc1C# +58: [09:33:08] SMILES Parse Error: check for mistakes around position 14: +58: [09:33:08] COc(c1)cccc1C# +58: [09:33:08] ~~~~~~~~~~~~~^ +58: [09:33:08] SMILES Parse Error: Failed parsing SMILES 'COc(c1)cccc1C#' for input: 'COc(c1)cccc1C#' +58: [09:33:08] SMARTS Parse Error: syntax error while parsing: COc(c1)cccc1C# +58: [09:33:08] SMARTS Parse Error: Failed parsing SMARTS 'COc(c1)cccc1C#' for input: 'COc(c1)cccc1C#' +58: [09:33:08] SMILES Parse Error: syntax error while parsing: COc(c1)cccc1C# +58: [09:33:08] SMILES Parse Error: check for mistakes around position 14: +58: [09:33:08] COc(c1)cccc1C# +58: [09:33:08] ~~~~~~~~~~~~~^ +58: [09:33:08] SMILES Parse Error: Failed parsing SMILES 'COc(c1)cccc1C#' for input: 'COc(c1)cccc1C#' +58: [09:33:08] SMARTS Parse Error: syntax error while parsing: COc(c1)cccc1C# +58: [09:33:08] 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 -60: [00:36:13] The 2 defining bonds for an atropisomer are co-planar - atoms are: 6 7 -63: Randomness seeded to: 4196027718 -58: [00:36:13] SMILES Parse Error: extra close parentheses while parsing: C) -58: [00:36:13] SMILES Parse Error: check for mistakes around position 2: -58: [00:36:13] C) -58: [00:36:13] ~^ -58: [00:36:13] SMILES Parse Error: Failed parsing SMILES 'C)' for input: 'C)' -63: [00:36:13] WARNING: not removing hydrogen atom with neighbor that has non-tetrahedral stereochemistry -60: [00:36:13] The 2 defining bonds for an atropisomer are co-planar - atoms are: 6 7 - 52/238 Test #58: smiTest1 ............................... Passed 0.21 sec -62: [00:36:13] -62: -62: **** -35: [00:36:13] Maximum BFS search size exceeded. -35: This is likely due to a highly symmetric fused ring system. +60: [09:33:08] The 2 defining bonds for an atropisomer are co-planar - atoms are: 6 7 +58: [09:33:08] SMILES Parse Error: extra close parentheses while parsing: C) +58: [09:33:08] SMILES Parse Error: check for mistakes around position 2: +58: [09:33:08] C) +58: [09:33:08] ~^ +58: [09:33:08] SMILES Parse Error: Failed parsing SMILES 'C)' for input: 'C)' +63: [09:33:08] WARNING: not removing hydrogen atom with neighbor that has non-tetrahedral stereochemistry +63: [09:33:08] WARNING: not removing hydrogen atom with neighbor that has non-tetrahedral stereochemistry +60: Test +60: +60: BMS-986142_atropBad2.cxsmi +60: +60: [09:33:08] The bonds on one end of an atropisomer are both UP or both DOWN - atoms are: 6 7 + 52/238 Test #58: smiTest1 ............................... Passed 0.16 sec test 64 Start 64: v2smiTestCatch 64: Test command: /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/SmilesParse/v2smiTestCatch 64: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/SmilesParse 64: Test timeout computed to be: 1500 +63: [09:33:08] WARNING: not removing hydrogen atom with neighbor that has non-tetrahedral stereochemistry +63: [09:33:08] WARNING: not removing hydrogen atom with neighbor that has non-tetrahedral stereochemistry +60: [09:33:08] The bonds on one end of an atropisomer are both UP or both DOWN - atoms are: 6 7 +60: [09:33:08] The bonds on one end of an atropisomer are both UP or both DOWN - atoms are: 6 7 +60: [09:33:08] The bonds on one end of an atropisomer are both UP or both DOWN - atoms are: 6 7 +60: [09:33:08] The bonds on one end of an atropisomer are both UP or both DOWN - atoms are: 6 7 +62: [09:33:08] +62: +62: **** 62: Range Error 62: idx 62: Violation occurred on line 209 in file ./Code/GraphMol/ROMol.cpp @@ -18124,35 +18172,31 @@ 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-aarch64-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-aarch64-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-aarch64-linux-gnu//lib/libRDKitSmilesParse.so.1 -62: 7# 0x0000AAAAC743980C in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/SmilesParse/smiTestCatch -62: 8# 0x0000AAAAC748D10C in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/SmilesParse/smiTestCatch -62: 9# 0x0000AAAAC748DAC0 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/SmilesParse/smiTestCatch -62: 10# 0x0000AAAAC748DEF4 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/SmilesParse/smiTestCatch -62: 11# 0x0000AAAAC74602B8 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/SmilesParse/smiTestCatch -62: 12# 0x0000AAAAC7460804 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/SmilesParse/smiTestCatch -62: 13# 0x0000AAAAC73F5550 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/SmilesParse/smiTestCatch -62: 14# 0x0000FFFFA2C1229C in /lib/aarch64-linux-gnu/libc.so.6 +62: 7# 0x0000AAAAD4C6980C in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/SmilesParse/smiTestCatch +62: 8# 0x0000AAAAD4CBD10C in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/SmilesParse/smiTestCatch +62: 9# 0x0000AAAAD4CBDAC0 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/SmilesParse/smiTestCatch +62: 10# 0x0000AAAAD4CBDEF4 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/SmilesParse/smiTestCatch +62: 11# 0x0000AAAAD4C902B8 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/SmilesParse/smiTestCatch +62: 12# 0x0000AAAAD4C90804 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/SmilesParse/smiTestCatch +62: 13# 0x0000AAAAD4C25550 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/SmilesParse/smiTestCatch +62: 14# 0x0000FFFF8C2D229C in /lib/aarch64-linux-gnu/libc.so.6 62: 15# __libc_start_main in /lib/aarch64-linux-gnu/libc.so.6 -62: 16# 0x0000AAAAC73F5630 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/SmilesParse/smiTestCatch +62: 16# 0x0000AAAAD4C25630 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/SmilesParse/smiTestCatch 62: ---------- 62: **** 62: -60: [00:36:13] The 2 defining bonds for an atropisomer are co-planar - atoms are: 6 7 -60: Test -60: -60: BMS-986142_atropBad2.cxsmi -60: -60: [00:36:13] The bonds on one end of an atropisomer are both UP or both DOWN - atoms are: 6 7 -60: [00:36:13] The bonds on one end of an atropisomer are both UP or both DOWN - atoms are: 6 7 -60: [00:36:13] The bonds on one end of an atropisomer are both UP or both DOWN - atoms are: 6 7 -63: [00:36:13] WARNING: not removing hydrogen atom with neighbor that has non-tetrahedral stereochemistry -60: [00:36:13] The bonds on one end of an atropisomer are both UP or both DOWN - atoms are: 6 7 -60: [00:36:13] The bonds on one end of an atropisomer are both UP or both DOWN - atoms are: 6 7 -63: [00:36:13] WARNING: not removing hydrogen atom with neighbor that has non-tetrahedral stereochemistry -63: [00:36:13] WARNING: not removing hydrogen atom with neighbor that has non-tetrahedral stereochemistry -63: [00:36:13] WARNING: not removing hydrogen atom with neighbor that has non-tetrahedral stereochemistry -63: [00:36:13] WARNING: not removing hydrogen atom with neighbor that has non-tetrahedral stereochemistry -62: [00:36:13] +63: [09:33:08] ignoring non-tetrahedral stereo specification since setAllowNontetrahedralChirality() is false. +63: =============================================================================== +63: All tests passed (308 assertions in 9 test cases) +63: + 53/238 Test #63: nontetrahedralCatch .................... Passed 0.08 sec +test 65 + Start 65: testDepictor + +65: Test command: /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/Depictor/testDepictor +65: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/Depictor +65: Test timeout computed to be: 1500 +62: [09:33:08] 62: 62: **** 62: Range Error @@ -18168,62 +18212,38 @@ 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-aarch64-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-aarch64-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-aarch64-linux-gnu//lib/libRDKitSmilesParse.so.1 -62: 7# 0x0000AAAAC743980C in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/SmilesParse/smiTestCatch -62: 8# 0x0000AAAAC748D10C in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/SmilesParse/smiTestCatch -62: 9# 0x0000AAAAC748DAC0 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/SmilesParse/smiTestCatch -62: 10# 0x0000AAAAC748DEF4 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/SmilesParse/smiTestCatch -62: 11# 0x0000AAAAC74602B8 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/SmilesParse/smiTestCatch -62: 12# 0x0000AAAAC7460804 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/SmilesParse/smiTestCatch -62: 13# 0x0000AAAAC73F5550 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/SmilesParse/smiTestCatch -62: 14# 0x0000FFFFA2C1229C in /lib/aarch64-linux-gnu/libc.so.6 +62: 7# 0x0000AAAAD4C6980C in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/SmilesParse/smiTestCatch +62: 8# 0x0000AAAAD4CBD10C in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/SmilesParse/smiTestCatch +62: 9# 0x0000AAAAD4CBDAC0 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/SmilesParse/smiTestCatch +62: 10# 0x0000AAAAD4CBDEF4 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/SmilesParse/smiTestCatch +62: 11# 0x0000AAAAD4C902B8 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/SmilesParse/smiTestCatch +62: 12# 0x0000AAAAD4C90804 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/SmilesParse/smiTestCatch +62: 13# 0x0000AAAAD4C25550 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/SmilesParse/smiTestCatch +62: 14# 0x0000FFFF8C2D229C in /lib/aarch64-linux-gnu/libc.so.6 62: 15# __libc_start_main in /lib/aarch64-linux-gnu/libc.so.6 -62: 16# 0x0000AAAAC73F5630 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/SmilesParse/smiTestCatch +62: 16# 0x0000AAAAD4C25630 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/SmilesParse/smiTestCatch 62: ---------- 62: **** 62: -62: [00:36:13] SMARTS Parse Error: unclosed ring for input: 'C1.C2.C3.C4.C5' -62: [00:36:13] SMILES Parse Error: unclosed ring for input: 'C1.C2.C3.C4.C5' -62: [00:36:13] SMARTS Parse Error: syntax error while parsing: C1C)foo -62: [00:36:13] SMARTS Parse Error: Failed parsing SMARTS 'C1C)foo' for input: 'C1C)foo' -62: [00:36:13] SMILES Parse Error: extra close parentheses while parsing: C1C)foo -62: [00:36:13] SMILES Parse Error: check for mistakes around position 4: -62: [00:36:13] C1C)foo -62: [00:36:13] ~~~^ -62: [00:36:13] SMILES Parse Error: Failed parsing SMILES 'C1C)foo' for input: 'C1C)foo' +62: [09:33:08] SMARTS Parse Error: unclosed ring for input: 'C1.C2.C3.C4.C5' +62: [09:33:08] SMILES Parse Error: unclosed ring for input: 'C1.C2.C3.C4.C5' +62: [09:33:08] SMARTS Parse Error: syntax error while parsing: C1C)foo +62: [09:33:08] SMARTS Parse Error: Failed parsing SMARTS 'C1C)foo' for input: 'C1C)foo' +62: [09:33:08] SMILES Parse Error: extra close parentheses while parsing: C1C)foo +62: [09:33:08] SMILES Parse Error: check for mistakes around position 4: +62: [09:33:08] C1C)foo +62: [09:33:08] ~~~^ +62: [09:33:08] SMILES Parse Error: Failed parsing SMILES 'C1C)foo' for input: 'C1C)foo' 62: =============================================================================== 62: All tests passed (1588 assertions in 69 test cases) 62: - 53/238 Test #62: smiTestCatch ........................... Passed 0.16 sec -test 65 - Start 65: testDepictor - -65: Test command: /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/Depictor/testDepictor -65: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/Depictor -65: Test timeout computed to be: 1500 -64: Randomness seeded to: 34376161 -64: =============================================================================== -64: All tests passed (14 assertions in 2 test cases) -64: - 54/238 Test #64: v2smiTestCatch ......................... Passed 0.03 sec -63: [00:36:13] WARNING: not removing hydrogen atom with neighbor that has non-tetrahedral stereochemistry -63: [00:36:13] WARNING: not removing hydrogen atom with neighbor that has non-tetrahedral stereochemistry + 54/238 Test #62: smiTestCatch ........................... Passed 0.16 sec test 66 Start 66: depictorCatch 66: Test command: /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/Depictor/depictorCatch 66: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/Depictor 66: Test timeout computed to be: 1500 -63: [00:36:13] ignoring non-tetrahedral stereo specification since setAllowNontetrahedralChirality() is false. -63: =============================================================================== -63: All tests passed (308 assertions in 9 test cases) -63: - 55/238 Test #63: nontetrahedralCatch .................... Passed 0.07 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-aarch64-linux-gnu/Code/GraphMol/Depictor/Wrap -67: Test timeout computed to be: 1500 60: Test 60: 60: JDQ443_3d.cxsmi @@ -18248,11 +18268,22 @@ 60: 60: JDQ443_atropBad1.cxsmi 60: -60: [00:36:13] The 2 defining bonds for an atropisomer are co-planar - atoms are: 2 3 -60: [00:36:13] The 2 defining bonds for an atropisomer are co-planar - atoms are: 2 3 -60: [00:36:13] The 2 defining bonds for an atropisomer are co-planar - atoms are: 2 3 -60: [00:36:13] The 2 defining bonds for an atropisomer are co-planar - atoms are: 2 3 -60: [00:36:13] The 2 defining bonds for an atropisomer are co-planar - atoms are: 2 3 +60: [09:33:08] The 2 defining bonds for an atropisomer are co-planar - atoms are: 2 3 +60: [09:33:08] The 2 defining bonds for an atropisomer are co-planar - atoms are: 2 3 +60: [09:33:08] The 2 defining bonds for an atropisomer are co-planar - atoms are: 2 3 +60: [09:33:08] The 2 defining bonds for an atropisomer are co-planar - atoms are: 2 3 +60: [09:33:08] The 2 defining bonds for an atropisomer are co-planar - atoms are: 2 3 +64: Randomness seeded to: 1351923367 +64: =============================================================================== +64: All tests passed (14 assertions in 2 test cases) +64: + 55/238 Test #64: v2smiTestCatch ......................... Passed 0.06 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-aarch64-linux-gnu/Code/GraphMol/Depictor/Wrap +67: Test timeout computed to be: 1500 60: Test 60: 60: RP-6306_atrop1.cxsmi @@ -18273,16 +18304,16 @@ 60: 60: RP-6306_atrop5.cxsmi 60: -60: [00:36:13] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored -60: [00:36:13] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored -60: [00:36:13] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored -60: [00:36:13] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored -60: [00:36:13] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored -60: [00:36:13] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored -60: [00:36:13] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored -60: [00:36:13] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored -60: [00:36:13] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored -60: [00:36:13] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored +60: [09:33:08] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored +60: [09:33:08] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored +60: [09:33:08] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored +60: [09:33:08] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored +60: [09:33:08] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored +60: [09:33:08] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored +60: [09:33:08] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored +60: [09:33:08] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored +60: [09:33:08] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored +60: [09:33:08] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored 60: Test 60: 60: RP-6306_atrop6.cxsmi @@ -18291,20 +18322,29 @@ 60: 60: RP-6306_atropBad1.cxsmi 60: -60: [00:36:13] The 2 defining bonds for an atropisomer are co-planar - atoms are: 4 5 -60: [00:36:13] The 2 defining bonds for an atropisomer are co-planar - atoms are: 4 5 -60: [00:36:13] The 2 defining bonds for an atropisomer are co-planar - atoms are: 4 5 -60: [00:36:13] The 2 defining bonds for an atropisomer are co-planar - atoms are: 4 5 -60: [00:36:13] The 2 defining bonds for an atropisomer are co-planar - atoms are: 4 5 +60: [09:33:08] The 2 defining bonds for an atropisomer are co-planar - atoms are: 4 5 +60: [09:33:08] The 2 defining bonds for an atropisomer are co-planar - atoms are: 4 5 +60: [09:33:08] The 2 defining bonds for an atropisomer are co-planar - atoms are: 4 5 +60: [09:33:08] The 2 defining bonds for an atropisomer are co-planar - atoms are: 4 5 +60: [09:33:08] The 2 defining bonds for an atropisomer are co-planar - atoms are: 4 5 60: Test 60: 60: RP-6306_atropBad2.cxsmi 60: -60: [00:36:13] The bonds on one end of an atropisomer are both UP or both DOWN - atoms are: 4 5 -60: [00:36:13] The bonds on one end of an atropisomer are both UP or both DOWN - atoms are: 4 5 -60: [00:36:13] The bonds on one end of an atropisomer are both UP or both DOWN - atoms are: 4 5 -60: [00:36:13] The bonds on one end of an atropisomer are both UP or both DOWN - atoms are: 4 5 -60: [00:36:13] The bonds on one end of an atropisomer are both UP or both DOWN - atoms are: 4 5 +60: [09:33:08] The bonds on one end of an atropisomer are both UP or both DOWN - atoms are: 4 5 +35: [09:33:08] Maximum BFS search size exceeded. +35: This is likely due to a highly symmetric fused ring system. +60: [09:33:08] The bonds on one end of an atropisomer are both UP or both DOWN - atoms are: 4 5 +60: [09:33:08] The bonds on one end of an atropisomer are both UP or both DOWN - atoms are: 4 5 +60: [09:33:08] The bonds on one end of an atropisomer are both UP or both DOWN - atoms are: 4 5 +60: [09:33:08] The bonds on one end of an atropisomer are both UP or both DOWN - atoms are: 4 5 +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: [09:33:08] ----------------------- +35: Testing isRingFused 60: Test 60: 60: RP-6306_3d.cxsmi @@ -18329,50 +18369,57 @@ 60: 60: Sotorasib_atrop5.cxsmi 60: -60: [00:36:13] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 13 ignored -60: [00:36:13] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 13 ignored -60: [00:36:13] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 13 ignored -60: [00:36:13] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 13 ignored -60: [00:36:13] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 13 ignored -60: [00:36:13] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 13 ignored -60: [00:36:13] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 13 ignored -60: [00:36:13] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 13 ignored -60: [00:36:13] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 13 ignored -60: [00:36:13] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 13 ignored +60: [09:33:08] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 13 ignored +60: [09:33:08] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 13 ignored +60: [09:33:08] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 13 ignored +60: [09:33:08] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 13 ignored +60: [09:33:08] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 13 ignored +60: [09:33:08] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 13 ignored + 56/238 Test #35: graphmolMolOpsTest ..................... Passed 0.57 sec +test 68 + Start 68: testMrvToMol + +68: Test command: /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/MarvinParse/testMrvToMol +68: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/MarvinParse +68: Test timeout computed to be: 1500 +60: [09:33:08] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 13 ignored +60: [09:33:08] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 13 ignored +60: [09:33:08] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 13 ignored +60: [09:33:08] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 13 ignored 60: Test 60: 60: Sotorasib_atropBad1.cxsmi 60: -60: [00:36:13] The 2 defining bonds for an atropisomer are co-planar - atoms are: 13 14 -60: [00:36:13] The 2 defining bonds for an atropisomer are co-planar - atoms are: 13 14 -60: [00:36:13] The 2 defining bonds for an atropisomer are co-planar - atoms are: 13 14 -60: [00:36:13] The 2 defining bonds for an atropisomer are co-planar - atoms are: 13 14 -60: [00:36:13] The 2 defining bonds for an atropisomer are co-planar - atoms are: 13 14 +60: [09:33:08] The 2 defining bonds for an atropisomer are co-planar - atoms are: 13 14 +60: [09:33:08] The 2 defining bonds for an atropisomer are co-planar - atoms are: 13 14 +60: [09:33:08] The 2 defining bonds for an atropisomer are co-planar - atoms are: 13 14 +30: ... +30: ---------------------------------------------------------------------- +30: Ran 12 tests in 0.496s +30: +30: OK +60: [09:33:08] The 2 defining bonds for an atropisomer are co-planar - atoms are: 13 14 +60: [09:33:08] The 2 defining bonds for an atropisomer are co-planar - atoms are: 13 14 60: Test 60: 60: Sotorasib_atropBad2.cxsmi 60: -60: [00:36:13] The bonds on one end of an atropisomer are both UP or both DOWN - atoms are: 13 14 -66: Randomness seeded to: 4096941462 +60: [09:33:08] The bonds on one end of an atropisomer are both UP or both DOWN - atoms are: 13 14 +60: [09:33:08] The bonds on one end of an atropisomer are both UP or both DOWN - atoms are: 13 14 +60: [09:33:08] The bonds on one end of an atropisomer are both UP or both DOWN - atoms are: 13 14 +60: [09:33:08] The bonds on one end of an atropisomer are both UP or both DOWN - atoms are: 13 14 +60: [09:33:08] The bonds on one end of an atropisomer are both UP or both DOWN - atoms are: 13 14 +66: Randomness seeded to: 3131871076 66: =============================================================================== 66: All tests passed (580 assertions in 18 test cases) 66: -60: [00:36:13] The bonds on one end of an atropisomer are both UP or both DOWN - atoms are: 13 14 -60: [00:36:13] The bonds on one end of an atropisomer are both UP or both DOWN - atoms are: 13 14 -60: [00:36:13] The bonds on one end of an atropisomer are both UP or both DOWN - atoms are: 13 14 - 56/238 Test #66: depictorCatch .......................... Passed 0.13 sec -60: [00:36:13] The bonds on one end of an atropisomer are both UP or both DOWN - atoms are: 13 14 -test 68 - Start 68: testMrvToMol + 57/238 Test #66: depictorCatch .......................... Passed 0.12 sec +test 69 + Start 69: fileParsersTest1 -68: Test command: /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/MarvinParse/testMrvToMol -68: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/MarvinParse -68: Test timeout computed to be: 1500 -30: ... -30: ---------------------------------------------------------------------- -30: Ran 12 tests in 0.578s -30: -30: OK +69: Test command: /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersTest1 +69: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers +69: Test timeout computed to be: 1500 60: Test 60: 60: Sotorasib_3d.cxsmi @@ -18397,11 +18444,11 @@ 60: 60: ZM374979_atropBad1.cxsmi 60: -60: [00:36:13] The 2 defining bonds for an atropisomer are co-planar - atoms are: 0 31 -60: [00:36:13] The 2 defining bonds for an atropisomer are co-planar - atoms are: 0 31 -60: [00:36:13] The 2 defining bonds for an atropisomer are co-planar - atoms are: 0 31 -60: [00:36:13] The 2 defining bonds for an atropisomer are co-planar - atoms are: 0 31 -60: [00:36:13] The 2 defining bonds for an atropisomer are co-planar - atoms are: 0 31 +60: [09:33:08] The 2 defining bonds for an atropisomer are co-planar - atoms are: 0 31 +60: [09:33:08] The 2 defining bonds for an atropisomer are co-planar - atoms are: 0 31 +60: [09:33:08] The 2 defining bonds for an atropisomer are co-planar - atoms are: 0 31 +60: [09:33:08] The 2 defining bonds for an atropisomer are co-planar - atoms are: 0 31 +60: [09:33:08] The 2 defining bonds for an atropisomer are co-planar - atoms are: 0 31 68: Using new chirality perception 68: Test 68: @@ -18411,14 +18458,16 @@ 68: 68: 145323811.mol 68: -68: [00:36:13] unsupported number of radical electrons 5 - 57/238 Test #30: pyForceFieldConstraints ................ Passed 0.94 sec -test 69 - Start 69: fileParsersTest1 +68: [09:33:08] unsupported number of radical electrons 5 + 58/238 Test #30: pyForceFieldConstraints ................ Passed 0.74 sec +test 70 + Start 70: testAtropisomers -69: Test command: /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersTest1 -69: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers -69: Test timeout computed to be: 1500 +70: Test command: /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/testAtropisomers +70: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers +70: Test timeout computed to be: 1500 +69: *************************************** +69: *************************************** 60: Test 60: 60: Mrtx1719_3d.cxsmi @@ -18443,11 +18492,14 @@ 60: 60: Mrtx1719_atropBad1.cxsmi 60: -60: [00:36:14] The 2 defining bonds for an atropisomer are co-planar - atoms are: 11 12 -60: [00:36:14] The 2 defining bonds for an atropisomer are co-planar - atoms are: 11 12 -60: [00:36:14] The 2 defining bonds for an atropisomer are co-planar - atoms are: 11 12 -60: [00:36:14] The 2 defining bonds for an atropisomer are co-planar - atoms are: 11 12 -60: [00:36:14] The 2 defining bonds for an atropisomer are co-planar - atoms are: 11 12 +60: [09:33:08] The 2 defining bonds for an atropisomer are co-planar - atoms are: 11 12 +69: [09:33:08] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +69: [09:33:08] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +60: [09:33:08] The 2 defining bonds for an atropisomer are co-planar - atoms are: 11 12 +60: [09:33:08] The 2 defining bonds for an atropisomer are co-planar - atoms are: 11 12 +60: [09:33:08] The 2 defining bonds for an atropisomer are co-planar - atoms are: 11 12 +60: [09:33:08] The 2 defining bonds for an atropisomer are co-planar - atoms are: 11 12 +70: [09:33:08] ---- Running with POSIX locale ----- 68: Test 68: 68: NewChiralTest.sdf @@ -18480,72 +18532,97 @@ 68: 68: ProblemShort.mol 68: -68: [00:36:14] For a MultipleSgroup expansion, the matching orphaned bond was not found +68: [09:33:08] For a MultipleSgroup expansion, the matching orphaned bond was not found 68: The multiple sgroup will be ignored -69: *************************************** -69: *************************************** -69: [00:36:14] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -69: [00:36:14] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -35: [00:36:14] Maximum BFS search size exceeded. -35: This is likely due to a highly symmetric fused ring system. -65: [00:36:14] Warning: stereochemistry around double bond may be incorrect in depiction. -69: [00:36:14] bond with order 0 found on line 7. This is not part of the MDL specification. -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 -69: [00:36:14] Skipping unrecognized collection type at line 26: MDLV30/HILITE BONDS=(1 7) -69: [00:36:14] Skipping unrecognized collection type at line 27: MDLV30/HILITE ATOMS=(1 7) -69: [00:36:14] Warning: molecule is tagged as 3D, but all Z coords are zero and 2D stereo markers have been found, marking the mol as 2D. -35: [00:36:14] ----------------------- -35: Testing isRingFused - 58/238 Test #35: graphmolMolOpsTest ..................... Passed 0.92 sec -test 70 - Start 70: testAtropisomers - -70: Test command: /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/testAtropisomers -70: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers -70: Test timeout computed to be: 1500 +69: [09:33:08] bond with order 0 found on line 7. This is not part of the MDL specification. +70: [09:33:08] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +70: [09:33:08] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +70: [09:33:08] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +70: [09:33:08] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +70: [09:33:08] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +70: [09:33:08] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +65: [09:33:08] Warning: stereochemistry around double bond may be incorrect in depiction. +70: [09:33:08] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored +70: [09:33:08] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored +70: [09:33:08] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored +70: [09:33:08] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored +69: [09:33:08] Skipping unrecognized collection type at line 26: MDLV30/HILITE BONDS=(1 7) +69: [09:33:08] Skipping unrecognized collection type at line 27: MDLV30/HILITE ATOMS=(1 7) +70: [09:33:08] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored +70: [09:33:08] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored +69: [09:33:08] Warning: molecule is tagged as 3D, but all Z coords are zero and 2D stereo markers have been found, marking the mol as 2D. +70: [09:33:08] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored +70: [09:33:08] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored +70: [09:33:08] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored +70: [09:33:08] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored +70: [09:33:08] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored +70: [09:33:08] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored +70: [09:33:08] The bonds on one end of an atropisomer are both UP or both DOWN - atoms are: 7 29 +70: [09:33:08] The bonds on one end of an atropisomer are both UP or both DOWN - atoms are: 7 29 +70: [09:33:08] The bonds on one end of an atropisomer are both UP or both DOWN - atoms are: 7 29 +70: [09:33:08] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 69: generating smiles +70: [09:33:08] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 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 -70: [00:36:14] ---- Running with POSIX locale ----- +70: [09:33:08] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 69: check isomorphism -70: [00:36:14] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -70: [00:36:14] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -70: [00:36:14] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. - 59/238 Test #65: testDepictor ........................... Passed 0.39 sec -70: [00:36:14] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +70: [09:33:08] The 2 defining bonds for an atropisomer are co-planar - atoms are: 17 21 +70: [09:33:08] The 2 defining bonds for an atropisomer are co-planar - atoms are: 17 21 +70: [09:33:08] The 2 defining bonds for an atropisomer are co-planar - atoms are: 17 21 +70: [09:33:08] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 2 ignored +70: [09:33:08] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 2 ignored +70: [09:33:08] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 2 ignored +70: [09:33:08] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 2 ignored +70: [09:33:08] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 2 ignored +70: [09:33:08] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 2 ignored +70: [09:33:08] The bonds on one end of an atropisomer are both UP or both DOWN - atoms are: 2 8 +70: [09:33:08] The bonds on one end of an atropisomer are both UP or both DOWN - atoms are: 2 8 +70: [09:33:08] The bonds on one end of an atropisomer are both UP or both DOWN - atoms are: 2 8 +70: [09:33:08] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 2 ignored +70: [09:33:08] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 2 ignored +70: [09:33:08] The 2 defining bonds for an atropisomer are co-planar - atoms are: 2 8 +70: [09:33:08] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 2 ignored +70: [09:33:08] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 2 ignored +70: [09:33:08] The 2 defining bonds for an atropisomer are co-planar - atoms are: 2 8 +70: [09:33:08] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 2 ignored +70: [09:33:08] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 2 ignored +70: [09:33:08] The 2 defining bonds for an atropisomer are co-planar - atoms are: 2 8 + 59/238 Test #65: testDepictor ........................... Passed 0.27 sec +70: [09:33:08] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. test 71 Start 71: testSquiggleDoubleBonds 71: Test command: /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/testSquiggleDoubleBonds 71: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers 71: Test timeout computed to be: 1500 -70: [00:36:14] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -70: [00:36:14] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -70: [00:36:14] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored -70: [00:36:14] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored -70: [00:36:14] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored -70: [00:36:14] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored -70: [00:36:14] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored -70: [00:36:14] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored -70: [00:36:14] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored -70: [00:36:14] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored -70: [00:36:14] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored -70: [00:36:14] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored -70: [00:36:14] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored -70: [00:36:14] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored -70: [00:36:14] The bonds on one end of an atropisomer are both UP or both DOWN - atoms are: 7 29 -70: [00:36:14] The bonds on one end of an atropisomer are both UP or both DOWN - atoms are: 7 29 -71: Randomness seeded to: 1498705124 +70: [09:33:08] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +70: [09:33:08] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +70: [09:33:08] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored +70: [09:33:08] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored +70: [09:33:08] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored +70: [09:33:08] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored +70: [09:33:08] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored +70: [09:33:08] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored +70: [09:33:08] The 2 defining bonds for an atropisomer are co-planar - atoms are: 7 20 +70: [09:33:08] The 2 defining bonds for an atropisomer are co-planar - atoms are: 7 20 +70: [09:33:08] The 2 defining bonds for an atropisomer are co-planar - atoms are: 7 20 +70: [09:33:08] The bonds on one end of an atropisomer are both UP or both DOWN - atoms are: 7 20 +70: [09:33:08] The bonds on one end of an atropisomer are both UP or both DOWN - atoms are: 7 20 +70: [09:33:08] The bonds on one end of an atropisomer are both UP or both DOWN - atoms are: 7 20 +70: [09:33:08] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +70: [09:33:08] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +70: [09:33:08] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +70: [09:33:08] The 2 defining bonds for an atropisomer are co-planar - atoms are: 0 31 +70: [09:33:08] The 2 defining bonds for an atropisomer are co-planar - atoms are: 0 31 +70: [09:33:08] The 2 defining bonds for an atropisomer are co-planar - atoms are: 0 31 +70: [09:33:08] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +70: [09:33:08] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +70: [09:33:08] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +71: Randomness seeded to: 1835628300 71: =============================================================================== 71: All tests passed (15 assertions in 3 test cases) 71: -70: [00:36:14] The bonds on one end of an atropisomer are both UP or both DOWN - atoms are: 7 29 -70: [00:36:14] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -70: [00:36:14] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 60/238 Test #71: testSquiggleDoubleBonds ................ Passed 0.04 sec test 72 Start 72: testMolSupplier @@ -18553,127 +18630,58 @@ 72: Test command: /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/testMolSupplier 72: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers 72: Test timeout computed to be: 1500 -70: [00:36:14] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -70: [00:36:14] The 2 defining bonds for an atropisomer are co-planar - atoms are: 17 21 -70: [00:36:14] The 2 defining bonds for an atropisomer are co-planar - atoms are: 17 21 -70: [00:36:14] The 2 defining bonds for an atropisomer are co-planar - atoms are: 17 21 -72: [00:36:14] +70: [09:33:08] The 2 defining bonds for an atropisomer are co-planar - atoms are: 15 16 +70: [09:33:08] The 2 defining bonds for an atropisomer are co-planar - atoms are: 15 16 +70: [09:33:08] The 2 defining bonds for an atropisomer are co-planar - atoms are: 15 16 +72: [09:33:08] 72: ----------------------------------------- -70: [00:36:14] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 2 ignored -70: [00:36:14] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 2 ignored -70: [00:36:14] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 2 ignored -70: [00:36:14] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 2 ignored -70: [00:36:14] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 2 ignored -70: [00:36:14] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 2 ignored -70: [00:36:14] The bonds on one end of an atropisomer are both UP or both DOWN - atoms are: 2 8 -70: [00:36:14] The bonds on one end of an atropisomer are both UP or both DOWN - atoms are: 2 8 -70: [00:36:14] The bonds on one end of an atropisomer are both UP or both DOWN - atoms are: 2 8 -70: [00:36:14] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 2 ignored -70: [00:36:14] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 2 ignored -70: [00:36:14] The 2 defining bonds for an atropisomer are co-planar - atoms are: 2 8 -70: [00:36:14] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 2 ignored -70: [00:36:14] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 2 ignored -70: [00:36:14] The 2 defining bonds for an atropisomer are co-planar - atoms are: 2 8 -70: [00:36:14] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 2 ignored -70: [00:36:14] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 2 ignored -70: [00:36:14] The 2 defining bonds for an atropisomer are co-planar - atoms are: 2 8 -70: [00:36:14] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -70: [00:36:14] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -70: [00:36:14] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -72: [00:36:14] Ignoring invalid chirality label: '2_bad_chirality' -70: [00:36:14] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored -70: [00:36:14] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored -70: [00:36:14] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored -70: [00:36:14] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored -70: [00:36:14] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored -70: [00:36:14] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored -70: [00:36:14] The 2 defining bonds for an atropisomer are co-planar - atoms are: 7 20 -70: [00:36:14] The 2 defining bonds for an atropisomer are co-planar - atoms are: 7 20 -70: [00:36:14] The 2 defining bonds for an atropisomer are co-planar - atoms are: 7 20 -70: [00:36:14] The bonds on one end of an atropisomer are both UP or both DOWN - atoms are: 7 20 -70: [00:36:14] The bonds on one end of an atropisomer are both UP or both DOWN - atoms are: 7 20 -70: [00:36:14] The bonds on one end of an atropisomer are both UP or both DOWN - atoms are: 7 20 -70: [00:36:14] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -70: [00:36:14] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -70: [00:36:14] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -70: [00:36:14] The 2 defining bonds for an atropisomer are co-planar - atoms are: 0 31 -70: [00:36:14] The 2 defining bonds for an atropisomer are co-planar - atoms are: 0 31 -70: [00:36:14] The 2 defining bonds for an atropisomer are co-planar - atoms are: 0 31 -70: [00:36:14] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -70: [00:36:14] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -70: [00:36:14] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -70: [00:36:14] The 2 defining bonds for an atropisomer are co-planar - atoms are: 15 16 -70: [00:36:14] The 2 defining bonds for an atropisomer are co-planar - atoms are: 15 16 -70: [00:36:14] The 2 defining bonds for an atropisomer are co-planar - atoms are: 15 16 -72: [00:36:14] Finished: testMolSup() -72: [00:36:14] ----------------------------------------- -72: -72: [00:36:14] ----------------------------------------- -72: [00:36:14] Finished: testRandMolSup() -72: [00:36:14] ----------------------------------------- -72: -72: [00:36:14] ----------------------------------------- -72: [00:36:14] Finished: testSmilesSup() -72: [00:36:14] ----------------------------------------- -72: -72: [00:36:14] ----------------------------------------- -72: [00:36:14] ------------------------------------------------------ -72: [00:36:14] SMILES Parse Error: syntax error while parsing: fail -72: [00:36:14] SMILES Parse Error: check for mistakes around position 1: -72: [00:36:14] fail -72: [00:36:14] ^ -72: [00:36:14] SMILES Parse Error: Failed parsing SMILES 'fail' for input: 'fail' -72: [00:36:14] ERROR: Smiles parse error on line 3 -72: [00:36:14] ERROR: Cannot create molecule from : 'fail' -72: [00:36:14] ------------------------------------------------------ -72: [00:36:14] ------------------------------------------------------ -72: [00:36:14] >>> This may result in an infinite loop. It should finish almost immediately: -72: [00:36:14] <<< done. -72: [00:36:14] Finished: testSmilesSupFromText() -72: [00:36:14] ----------------------------------------- -72: -72: [00:36:14] ----------------------------------------- -72: [00:36:14] Finished: testSmilesWriter() -72: [00:36:14] ----------------------------------------- -72: -72: [00:36:14] ----------------------------------------- -72: [00:36:14] Finished: testSDWriter() -72: [00:36:14] ----------------------------------------- -72: -72: [00:36:14] ----------------------------------------- -72: [00:36:14] Finished: testSDSupplierEnding() -72: [00:36:14] ----------------------------------------- -72: -72: [00:36:14] ----------------------------------------- -72: [00:36:14] Finished: testSuppliersEmptyFile() -72: [00:36:14] ----------------------------------------- -72: -72: [00:36:14] ----------------------------------------- -72: [00:36:14] Finished: testCisTrans() -72: [00:36:14] ----------------------------------------- -72: -72: [00:36:14] ----------------------------------------- -72: [00:36:14] Finished: testStereoRound() -72: [00:36:14] ----------------------------------------- -72: -72: [00:36:14] ----------------------------------------- -72: [00:36:14] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -72: [00:36:14] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -72: [00:36:14] Finished: testIssue226() -72: [00:36:14] ----------------------------------------- +72: [09:33:08] Ignoring invalid chirality label: '2_bad_chirality' +67: ..............[09:33:08] SMILES Parse Error: syntax error while parsing: invalidsmiles +67: [09:33:08] SMILES Parse Error: check for mistakes around position 1: +67: [09:33:08] invalidsmiles +67: [09:33:08] ^ +67: [09:33:08] SMILES Parse Error: Failed parsing SMILES 'invalidsmiles' for input: 'invalidsmiles' +29: Checking against /build/reproducible-path/rdkit-202503.1/Code/ForceField/MMFF/test_data/MMFF94_reference.log... +72: [09:33:08] Finished: testMolSup() +72: [09:33:08] ----------------------------------------- 72: -72: [00:36:14] ----------------------------------------- -72: [00:36:14] Finished: testTDTSupplier1() -72: [00:36:14] ----------------------------------------- +72: [09:33:08] ----------------------------------------- +72: [09:33:08] Finished: testRandMolSup() +72: [09:33:08] ----------------------------------------- 72: -72: [00:36:14] ----------------------------------------- -72: [00:36:14] Finished: testTDTSupplier2() -72: [00:36:14] ----------------------------------------- +72: [09:33:08] ----------------------------------------- +70: [09:33:08] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +70: [09:33:08] 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 + 61/238 Test #70: testAtropisomers ....................... Passed 0.27 sec +test 73 + Start 73: testGeneralFileReader + +73: Test command: /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/testGeneralFileReader +73: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers +73: Test timeout computed to be: 1500 +72: [09:33:08] Finished: testSmilesSup() +72: [09:33:08] ----------------------------------------- 72: -72: [00:36:14] ----------------------------------------- -72: [00:36:14] Finished: testTDTSupplier3() -72: [00:36:14] ----------------------------------------- +72: [09:33:08] ----------------------------------------- +72: [09:33:08] ------------------------------------------------------ +72: [09:33:08] SMILES Parse Error: syntax error while parsing: fail +72: [09:33:08] SMILES Parse Error: check for mistakes around position 1: +72: [09:33:08] fail +72: [09:33:08] ^ +72: [09:33:08] SMILES Parse Error: Failed parsing SMILES 'fail' for input: 'fail' +72: [09:33:08] ERROR: Smiles parse error on line 3 +72: [09:33:08] ERROR: Cannot create molecule from : 'fail' +72: [09:33:08] ------------------------------------------------------ +72: [09:33:08] ------------------------------------------------------ +72: [09:33:08] >>> This may result in an infinite loop. It should finish almost immediately: +72: [09:33:08] <<< done. +72: [09:33:08] Finished: testSmilesSupFromText() +72: [09:33:08] ----------------------------------------- 72: +72: [09:33:08] ----------------------------------------- 68: Test 68: 68: badWedgeError.sdf @@ -18986,89 +18994,35 @@ 68: 68: MulticenterSgroup.mrv 68: -68: [00:36:14] Can't kekulize mol. Unkekulized atoms: 6 7 8 9 10 -68: [00:36:14] Can't kekulize mol. Unkekulized atoms: 6 7 8 9 10 -72: [00:36:14] ----------------------------------------- -72: [00:36:14] Finished: testSDSupplierFromText() -72: [00:36:14] ----------------------------------------- -72: -72: [00:36:14] ----------------------------------------- -72: [00:36:14] ERROR: Problems encountered parsing data fields -72: [00:36:14] ERROR: moving to the beginning of the next molecule -72: [00:36:14] ERROR: Problems encountered parsing data fields -72: [00:36:14] ERROR: moving to the beginning of the next molecule -72: [00:36:14] Spurious data before the first property will be ignored -72: [00:36:14] Property will be truncated after the first blank line -72: [00:36:14] Property will be truncated after the first blank line -72: [00:36:14] Property will be truncated after the first blank line -72: [00:36:14] Finished: testSDSupplierStrLax1() -72: [00:36:14] ----------------------------------------- -72: -72: [00:36:14] ----------------------------------------- -72: [00:36:14] ERROR: Problems encountered parsing data fields -72: [00:36:14] ERROR: moving to the beginning of the next molecule -72: [00:36:14] Property will be truncated after the first blank line -72: [00:36:14] Finished: testSDSupplierStrLax2() -72: [00:36:14] ----------------------------------------- -72: -72: [00:36:14] ----------------------------------------- -72: [00:36:14] ERROR: Problems encountered parsing data fields -72: [00:36:14] ERROR: moving to the beginning of the next molecule -72: [00:36:14] ERROR: Problems encountered parsing data fields -72: [00:36:14] ERROR: moving to the beginning of the next molecule -72: [00:36:14] Spurious data before the first property will be ignored -72: [00:36:14] Property will be truncated after the first blank line -72: [00:36:14] Property will be truncated after the first blank line -72: [00:36:14] Property will be truncated after the first blank line -72: [00:36:14] Finished: testSDSupplierFromTextStrLax1() -72: [00:36:14] ----------------------------------------- +68: [09:33:08] Can't kekulize mol. Unkekulized atoms: 6 7 8 9 10 +68: [09:33:08] Can't kekulize mol. Unkekulized atoms: 6 7 8 9 10 +72: [09:33:08] Finished: testSmilesWriter() +72: [09:33:08] ----------------------------------------- 72: -72: [00:36:14] ----------------------------------------- -72: [00:36:14] ERROR: Problems encountered parsing data fields -72: [00:36:14] ERROR: moving to the beginning of the next molecule -72: [00:36:14] Property will be truncated after the first blank line -72: [00:36:14] Finished: testSDSupplierFromTextStrLax2() -72: [00:36:14] ----------------------------------------- +72: [09:33:08] ----------------------------------------- +72: [09:33:08] Finished: testSDWriter() +72: [09:33:08] ----------------------------------------- 72: -72: [00:36:14] ----------------------------------------- -72: [00:36:14] Finished: testIssue265() -72: [00:36:14] ----------------------------------------- +72: [09:33:08] ----------------------------------------- +72: [09:33:08] Finished: testSDSupplierEnding() +72: [09:33:08] ----------------------------------------- 72: -72: [00:36:14] ----------------------------------------- -72: [00:36:14] ERROR: End of data field name not found -72: [00:36:14] ERROR: moving to the beginning of the next molecule -72: [00:36:14] Explicit valence for atom # 0 F, 2, is greater than permitted -72: [00:36:14] ERROR: Could not sanitize molecule ending on line 16 -72: [00:36:14] ERROR: Explicit valence for atom # 0 F, 2, is greater than permitted -72: [00:36:14] ERROR: Atom line too short: ' 1 2 1 0 0 0 0' on line 12 -72: [00:36:14] ERROR: moving to the beginning of the next molecule -72: [00:36:14] ERROR: Bond line too short: 'M END' on line 18 -72: [00:36:14] ERROR: moving to the beginning of the next molecule -72: [00:36:14] Finished: testSDErrorHandling() -72: [00:36:14] ----------------------------------------- +72: [09:33:08] ----------------------------------------- +72: [09:33:08] Finished: testSuppliersEmptyFile() +72: [09:33:08] ----------------------------------------- 72: -72: [00:36:14] ----------------------------------------- -72: [00:36:14] Finished: testIssue381() -72: [00:36:14] ----------------------------------------- +72: [09:33:08] ----------------------------------------- +72: [09:33:08] Finished: testCisTrans() +72: [09:33:08] ----------------------------------------- 72: -72: [00:36:14] ----------------------------------------- -72: [00:36:14] Finished: testSetStreamIndices() -72: [00:36:14] ----------------------------------------- -72: -72: [00:36:14] ----------------------------------------- -72: [00:36:14] Finished: testMixIterAndRandom() -72: [00:36:14] ----------------------------------------- -72: -72: [00:36:14] ----------------------------------------- -72: build: -72: [00:36:14] Finished: testRemoveHs() -72: [00:36:14] ----------------------------------------- -72: -72: [00:36:14] ----------------------------------------- -72: [00:36:14] Finished: testGetItemText() -72: [00:36:14] ----------------------------------------- -72: -72: [00:36:14] ----------------------------------------- +72: [09:33:08] ----------------------------------------- +73: [09:33:08] +73: ----------------------------------------- +73: [09:33:08] Finished: testDetermineFormat() +73: [09:33:08] ----------------------------------------- +73: +73: [09:33:08] +73: ----------------------------------------- 68: Test 68: 68: GenericSgroup.mrv @@ -19101,7 +19055,17 @@ 68: 68: MarvinBadMissingMolID.mrv 68: -68: [00:36:14] +72: [09:33:08] Finished: testStereoRound() +72: [09:33:08] ----------------------------------------- +72: +72: [09:33:08] ----------------------------------------- +72: [09:33:08] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +72: [09:33:08] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +72: [09:33:08] Finished: testIssue226() +72: [09:33:08] ----------------------------------------- +72: +72: [09:33:08] ----------------------------------------- +68: [09:33:08] 68: 68: **** 68: Test Assert @@ -19112,15 +19076,20 @@ 68: Stacktrace: 68: 0# Invar::Invariant::toString[abi:cxx11]() const in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu//lib/libRDKitRDGeneral.so.1 68: 1# Invar::operator<<(std::ostream&, Invar::Invariant const&) in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu//lib/libRDKitRDGeneral.so.1 -68: 2# 0x0000AAAADBE6E0DC in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/MarvinParse/testMrvToMol -68: 3# 0x0000AAAADBE75D7C in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/MarvinParse/testMrvToMol -68: 4# 0x0000AAAADBE64918 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/MarvinParse/testMrvToMol -68: 5# 0x0000FFFF89B2229C in /lib/aarch64-linux-gnu/libc.so.6 +68: 2# 0x0000AAAAB6F8E0DC in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/MarvinParse/testMrvToMol +68: 3# 0x0000AAAAB6F95D7C in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/MarvinParse/testMrvToMol +68: 4# 0x0000AAAAB6F84918 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/MarvinParse/testMrvToMol +68: 5# 0x0000FFFFA339229C in /lib/aarch64-linux-gnu/libc.so.6 68: 6# __libc_start_main in /lib/aarch64-linux-gnu/libc.so.6 -68: 7# 0x0000AAAADBE64B70 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/MarvinParse/testMrvToMol +68: 7# 0x0000AAAAB6F84B70 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/MarvinParse/testMrvToMol 68: ---------- 68: **** 68: +67: ..... +67: ---------------------------------------------------------------------- +67: Ran 19 tests in 0.237s +67: +67: OK 68: Test 68: 68: MarvinBadMissingAtomID.mrv @@ -19130,11 +19099,6 @@ 68: 68: MarvinBadX2.mrv 68: -67: ..............[00:36:14] SMILES Parse Error: syntax error while parsing: invalidsmiles -67: [00:36:14] SMILES Parse Error: check for mistakes around position 1: -67: [00:36:14] invalidsmiles -67: [00:36:14] ^ -67: [00:36:14] SMILES Parse Error: Failed parsing SMILES 'invalidsmiles' for input: 'invalidsmiles' 68: The values x2 and y2 must be large floats in MRV file 68: Test 68: @@ -19146,13 +19110,10 @@ 68: MarvinBadStereoGroupsAbs.mrv 68: 68: Unrecognized group definition -72: [00:36:14] Finished: testForwardSDSupplier() -72: [00:36:14] ----------------------------------------- -72: -72: [00:36:14] ----------------------------------------- -72: [00:36:14] Finished: testMissingCRSDSupplier() -72: [00:36:14] ----------------------------------------- +72: [09:33:08] Finished: testTDTSupplier1() +72: [09:33:08] ----------------------------------------- 72: +72: [09:33:08] ----------------------------------------- 68: Test 68: 68: MarvinBadElementType.mrv @@ -19170,22 +19131,16 @@ 68: MarvinBadMissingBondOrder.mrv 68: 68: bond must have one of: order, queryType, or convention in MRV File -72: [00:36:14] ----------------------------------------- +72: [09:33:08] Finished: testTDTSupplier2() +72: [09:33:08] ----------------------------------------- +72: 68: Test 68: 68: MarvinBadMissingSruMolID.mrv 68: -72: [00:36:14] Finished: testIssue3482695() -72: [00:36:14] ----------------------------------------- -72: -72: [00:36:14] ----------------------------------------- -72: [00:36:14] ERROR: Cannot convert 'foo' to unsigned int on line 557 -72: [00:36:14] ERROR: moving to the beginning of the next molecule 68: Expected a molID in MRV file -72: [00:36:14] Finished: testIssue3525673() -72: [00:36:14] ----------------------------------------- -72: -72: [00:36:14] ----------------------------------------- +72: [09:33:08] ----------------------------------------- +72: [09:33:08] Finished: testTDTSupplier3() 68: Test 68: 68: MarvinBadMissingSruID.mrv @@ -19207,10 +19162,6 @@ 68: MarvinBadSruAtomRef.mrv 68: 68: AtomRef specification for an SRU, Copolymer, or Modification group definition was not found in any parent -72: [00:36:14] Finished: testBlankLinesInProps() -72: [00:36:14] ----------------------------------------- -72: -72: [00:36:14] ----------------------------------------- 68: Test 68: 68: MarvinBadSruID.mrv @@ -19223,19 +19174,26 @@ 68: 68: MarvinBadSruAtomRef.mrv 68: -72: [00:36:14] Finished: testSkipLines() -72: [00:36:14] ----------------------------------------- +68: AtomRef specification for an SRU, Copolymer, or Modification group definition was not found in any parent +72: [09:33:08] ----------------------------------------- 72: -72: [00:36:14] ----------------------------------------- -72: [00:36:14] Finished: testGitHub23() -72: [00:36:14] ----------------------------------------- +72: [09:33:08] ----------------------------------------- +72: [09:33:08] Finished: testSDSupplierFromText() +72: [09:33:08] ----------------------------------------- 72: -72: [00:36:14] ----------------------------------------- -72: [00:36:14] Finished: testGitHub88() -72: [00:36:14] ----------------------------------------- +72: [09:33:08] ----------------------------------------- +72: [09:33:08] ERROR: Problems encountered parsing data fields +72: [09:33:08] ERROR: moving to the beginning of the next molecule +72: [09:33:08] ERROR: Problems encountered parsing data fields +72: [09:33:08] ERROR: moving to the beginning of the next molecule +72: [09:33:08] Spurious data before the first property will be ignored +72: [09:33:08] Property will be truncated after the first blank line +72: [09:33:08] Property will be truncated after the first blank line +72: [09:33:08] Property will be truncated after the first blank line +72: [09:33:08] Finished: testSDSupplierStrLax1() +72: [09:33:08] ----------------------------------------- 72: -72: [00:36:14] ----------------------------------------- -68: AtomRef specification for an SRU, Copolymer, or Modification group definition was not found in any parent +72: [09:33:08] ----------------------------------------- 68: Test 68: 68: MarvinBadSruAtomRef.mrv @@ -19246,17 +19204,46 @@ 68: MarvinBadSruConnect.mrv 68: 68: Expected a connect string of "hh, ht, eu" for a SruSgroup definition in MRV file +72: [09:33:08] ERROR: Problems encountered parsing data fields +72: [09:33:08] ERROR: moving to the beginning of the next molecule +72: [09:33:08] Property will be truncated after the first blank line +72: [09:33:08] Finished: testSDSupplierStrLax2() +72: [09:33:08] ----------------------------------------- +72: +72: [09:33:08] ----------------------------------------- +72: [09:33:08] ERROR: Problems encountered parsing data fields +72: [09:33:08] ERROR: moving to the beginning of the next molecule +72: [09:33:08] ERROR: Problems encountered parsing data fields +72: [09:33:08] ERROR: moving to the beginning of the next molecule +72: [09:33:08] Spurious data before the first property will be ignored +72: [09:33:08] Property will be truncated after the first blank line +72: [09:33:08] Property will be truncated after the first blank line +72: [09:33:08] Property will be truncated after the first blank line +72: [09:33:08] Finished: testSDSupplierFromTextStrLax1() +72: [09:33:08] ----------------------------------------- +72: +72: [09:33:08] ----------------------------------------- +72: [09:33:08] ERROR: Problems encountered parsing data fields +72: [09:33:08] ERROR: moving to the beginning of the next molecule +72: [09:33:08] Property will be truncated after the first blank line +72: [09:33:08] Finished: testSDSupplierFromTextStrLax2() +72: [09:33:08] ----------------------------------------- +72: +72: [09:33:08] ----------------------------------------- 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 -70: [00:36:14] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 68: Test 68: 68: MarvinBadSupAttachBond.mrv 68: 68: Bond specification for an AttachmentPoint definition must be in the bond array in MRV file +72: [09:33:08] Finished: testIssue265() +72: [09:33:08] ----------------------------------------- +72: +72: [09:33:08] ----------------------------------------- 68: Test 68: 68: MarvinBadSupAttachOrder.mrv @@ -19271,104 +19258,176 @@ 68: 68: MarvinBadSupAttachAtom.mrv 68: -70: [00:36:14] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +72: [09:33:08] ERROR: End of data field name not found +72: [09:33:08] ERROR: moving to the beginning of the next molecule 68: Atom specification for an AttachmentPoint definition must be in the parent's atom array in MRV file -72: [00:36:14] Finished: testGitHub2285() -72: [00:36:14] ----------------------------------------- -72: -72: [00:36:14] ----------------------------------------- -72: [00:36:14] SMILES Parse Error: unclosed ring for input: 'c1ccccc' -72: [00:36:14] ERROR: Smiles parse error on line 1 -72: [00:36:14] ERROR: Cannot create molecule from : 'c1ccccc' +72: [09:33:08] Explicit valence for atom # 0 F, 2, is greater than permitted +72: [09:33:08] ERROR: Could not sanitize molecule ending on line 16 +72: [09:33:08] ERROR: Explicit valence for atom # 0 F, 2, is greater than permitted 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 -72: [00:36:14] SMILES Parse Error: extra open parentheses while parsing: C(C -72: [00:36:14] SMILES Parse Error: check for mistakes around position 2: -72: [00:36:14] C(C -72: [00:36:14] ~^ -72: [00:36:14] SMILES Parse Error: Failed parsing SMILES 'C(C' for input: 'C(C' 68: Test 68: 68: MarvinBadSupMissingAttachBond.mrv 68: 68: No attachment point found for bond to the condensed atom in a superatomSgroup -72: [00:36:14] ERROR: Smiles parse error on line 3 -72: [00:36:14] ERROR: Cannot create molecule from : 'C(C' -72: [00:36:14] Explicit valence for atom # 1 C, 5, is greater than permitted -72: [00:36:14] ERROR: Could not sanitize molecule on line 5 68: Test 68: 68: MarvinBadSupMissingAttachOrder.mrv 68: 68: Expected atom, order and bond, for an AttachmentPoint definition in MRV file -72: [00:36:14] ERROR: Explicit valence for atom # 1 C, 5, is greater than permitted -72: [00:36:14] Explicit valence for atom # 1 F, 2, is greater than permitted -72: [00:36:14] ERROR: Could not sanitize molecule ending on line 21 -72: [00:36:14] ERROR: Explicit valence for atom # 1 F, 2, is greater than permitted -72: [00:36:14] Explicit valence for atom # 1 F, 2, is greater than permitted -72: [00:36:14] ERROR: Could not sanitize molecule ending on line 21 -72: [00:36:14] ERROR: Explicit valence for atom # 1 F, 2, is greater than permitted -72: [00:36:14] Explicit valence for atom # 1 F, 2, is greater than permitted -72: [00:36:14] ERROR: Could not sanitize molecule ending on line 21 -72: [00:36:14] ERROR: Explicit valence for atom # 1 F, 2, is greater than permitted -72: [00:36:14] ERROR: Atom line too short: ' -9.6' on line 28 -72: [00:36:14] ERROR: moving to the beginning of the next molecule -72: [00:36:14] Explicit valence for atom # 1 F, 2, is greater than permitted -72: [00:36:14] ERROR: Could not sanitize molecule ending on line 21 -72: [00:36:14] ERROR: Explicit valence for atom # 1 F, 2, is greater than permitted -72: [00:36:14] ERROR: Atom line too short: ' -9.6' on line 28 -72: [00:36:14] ERROR: moving to the beginning of the next molecule -72: [00:36:14] Finished: testGitHub2479() -72: [00:36:14] ----------------------------------------- +72: [09:33:08] ERROR: Atom line too short: ' 1 2 1 0 0 0 0' on line 12 +72: [09:33:08] ERROR: moving to the beginning of the next molecule +72: [09:33:08] ERROR: Bond line too short: 'M END' on line 18 +72: [09:33:08] ERROR: moving to the beginning of the next molecule +72: [09:33:08] Finished: testSDErrorHandling() +72: [09:33:08] ----------------------------------------- 72: -72: [00:36:14] ----------------------------------------- -70: Atropisomers- 1 hits 3 misses -70: Final results: -70: Found atropisomers in TestMultInSDF.sdf - 1 hits 4 misses -72: [00:36:14] Ignoring invalid chirality label: '7_S_8_9_6_10' -72: [00:36:14] Finished: testGitHub2881() -72: [00:36:14] ----------------------------------------- +72: [09:33:08] ----------------------------------------- +72: [09:33:08] Finished: testIssue381() +72: [09:33:08] ----------------------------------------- 72: -72: [00:36:14] ----------------------------------------- - 61/238 Test #70: testAtropisomers ....................... Passed 0.38 sec -72: [00:36:14] Finished: testGitHub3517() -72: [00:36:14] ----------------------------------------- +72: [09:33:08] ----------------------------------------- +73: [09:33:08] Finished: testSdf() +73: [09:33:08] ----------------------------------------- +73: +73: [09:33:08] +73: ----------------------------------------- +72: [09:33:08] Finished: testSetStreamIndices() +72: [09:33:08] ----------------------------------------- 72: -test 73 - Start 73: testGeneralFileReader - -73: Test command: /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/testGeneralFileReader -73: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers -73: Test timeout computed to be: 1500 - 62/238 Test #72: testMolSupplier ........................ Passed 0.29 sec +72: [09:33:08] ----------------------------------------- +72: [09:33:08] Finished: testMixIterAndRandom() +72: [09:33:08] ----------------------------------------- +72: +72: [09:33:08] ----------------------------------------- +72: build: +73: [09:33:08] Finished: testSmi() +73: [09:33:08] ----------------------------------------- +73: +73: [09:33:08] +73: ----------------------------------------- +72: [09:33:08] Finished: testRemoveHs() +72: [09:33:08] ----------------------------------------- +72: +72: [09:33:08] ----------------------------------------- +72: [09:33:08] Finished: testGetItemText() +72: [09:33:08] ----------------------------------------- +72: +72: [09:33:08] ----------------------------------------- +72: [09:33:08] Finished: testForwardSDSupplier() +72: [09:33:08] ----------------------------------------- +72: +72: [09:33:08] ----------------------------------------- +72: [09:33:08] Finished: testMissingCRSDSupplier() +72: [09:33:08] ----------------------------------------- +72: +72: [09:33:08] ----------------------------------------- +72: [09:33:08] Finished: testIssue3482695() +72: [09:33:08] ----------------------------------------- +72: +72: [09:33:08] ----------------------------------------- +72: [09:33:08] ERROR: Cannot convert 'foo' to unsigned int on line 557 +72: [09:33:08] ERROR: moving to the beginning of the next molecule +72: [09:33:08] Finished: testIssue3525673() +72: [09:33:08] ----------------------------------------- +72: +72: [09:33:08] ----------------------------------------- +72: [09:33:08] Finished: testBlankLinesInProps() +72: [09:33:08] ----------------------------------------- +72: +72: [09:33:08] ----------------------------------------- +72: [09:33:08] Finished: testSkipLines() +72: [09:33:08] ----------------------------------------- +72: +72: [09:33:08] ----------------------------------------- +72: [09:33:08] Finished: testGitHub23() +72: [09:33:08] ----------------------------------------- +72: +72: [09:33:08] ----------------------------------------- +72: [09:33:08] Finished: testGitHub88() +72: [09:33:08] ----------------------------------------- +72: +72: [09:33:08] ----------------------------------------- + 62/238 Test #67: pyDepictor ............................. Passed 0.46 sec test 74 Start 74: testMultithreadedMolSupplier 74: Test command: /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/testMultithreadedMolSupplier 74: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers 74: Test timeout computed to be: 1500 -73: [00:36:14] -73: ----------------------------------------- -73: [00:36:14] Finished: testDetermineFormat() -73: [00:36:14] ----------------------------------------- -73: -73: [00:36:14] -73: ----------------------------------------- -74: [00:36:14] +72: [09:33:08] Finished: testGitHub2285() +72: [09:33:08] ----------------------------------------- +72: +72: [09:33:08] ----------------------------------------- +72: [09:33:08] SMILES Parse Error: unclosed ring for input: 'c1ccccc' +72: [09:33:08] ERROR: Smiles parse error on line 1 +72: [09:33:08] ERROR: Cannot create molecule from : 'c1ccccc' +72: [09:33:08] SMILES Parse Error: extra open parentheses while parsing: C(C +72: [09:33:08] SMILES Parse Error: check for mistakes around position 2: +72: [09:33:08] C(C +72: [09:33:08] ~^ +72: [09:33:08] SMILES Parse Error: Failed parsing SMILES 'C(C' for input: 'C(C' +72: [09:33:08] ERROR: Smiles parse error on line 3 +72: [09:33:08] ERROR: Cannot create molecule from : 'C(C' +72: [09:33:08] Explicit valence for atom # 1 C, 5, is greater than permitted +72: [09:33:08] ERROR: Could not sanitize molecule on line 5 +72: [09:33:08] ERROR: Explicit valence for atom # 1 C, 5, is greater than permitted +72: [09:33:08] Explicit valence for atom # 1 F, 2, is greater than permitted +72: [09:33:08] ERROR: Could not sanitize molecule ending on line 21 +72: [09:33:08] ERROR: Explicit valence for atom # 1 F, 2, is greater than permitted +72: [09:33:08] Explicit valence for atom # 1 F, 2, is greater than permitted +72: [09:33:08] ERROR: Could not sanitize molecule ending on line 21 +72: [09:33:08] ERROR: Explicit valence for atom # 1 F, 2, is greater than permitted +72: [09:33:08] Explicit valence for atom # 1 F, 2, is greater than permitted +72: [09:33:08] ERROR: Could not sanitize molecule ending on line 21 +72: [09:33:08] ERROR: Explicit valence for atom # 1 F, 2, is greater than permitted +72: [09:33:08] ERROR: Atom line too short: ' -9.6' on line 28 +72: [09:33:08] ERROR: moving to the beginning of the next molecule +72: [09:33:08] Explicit valence for atom # 1 F, 2, is greater than permitted +72: [09:33:08] ERROR: Could not sanitize molecule ending on line 21 +72: [09:33:08] ERROR: Explicit valence for atom # 1 F, 2, is greater than permitted +72: [09:33:08] ERROR: Atom line too short: ' -9.6' on line 28 +72: [09:33:08] ERROR: moving to the beginning of the next molecule +72: [09:33:08] Finished: testGitHub2479() +72: [09:33:08] ----------------------------------------- +72: +72: [09:33:08] ----------------------------------------- +72: [09:33:08] Ignoring invalid chirality label: '7_S_8_9_6_10' +72: [09:33:08] Finished: testGitHub2881() +72: [09:33:08] ----------------------------------------- +72: +72: [09:33:08] ----------------------------------------- +72: [09:33:08] Finished: testGitHub3517() +72: [09:33:08] ----------------------------------------- +72: + 63/238 Test #72: testMolSupplier ........................ Passed 0.20 sec +test 75 + Start 75: testMolWriter + +75: Test command: /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/testMolWriter +75: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers +75: Test timeout computed to be: 1500 +74: [09:33:08] 74: ----------------------------------------- -73: [00:36:14] Finished: testSdf() -73: [00:36:14] ----------------------------------------- +73: [09:33:08] Finished: testMae() +73: [09:33:08] ----------------------------------------- 73: -73: [00:36:14] +73: [09:33:08] 73: ----------------------------------------- -73: [00:36:14] Finished: testSmi() -73: [00:36:14] ----------------------------------------- +73: [09:33:08] Finished: testTdt() +73: [09:33:08] ----------------------------------------- 73: -73: [00:36:14] -73: ----------------------------------------- + 64/238 Test #73: testGeneralFileReader .................. Passed 0.09 sec +test 76 + Start 76: testTplParser + +76: Test command: /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/testTplParser +76: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers +76: Test timeout computed to be: 1500 68: Test 68: 68: marvin03.mrv @@ -19433,13 +19492,8 @@ 68: 68: BMS-986142_atrop5.mrv 68: -68: [00:36:14] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored -68: [00:36:14] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored -67: ..... -67: ---------------------------------------------------------------------- -67: Ran 19 tests in 0.459s -67: -67: OK +68: [09:33:08] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored +68: [09:33:08] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored 68: Test 68: 68: BMS-986142_atrop6.mrv @@ -19452,13 +19506,20 @@ 68: 68: BMS-986142_atrop8.mrv 68: -68: [00:36:14] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored -68: [00:36:14] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored +68: [09:33:08] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored +68: [09:33:08] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored 68: Test 68: 68: BMS-986142_atropBad2.mrv 68: -68: [00:36:14] The bonds on one end of an atropisomer are both UP or both DOWN - atoms are: 7 29 +68: [09:33:08] The bonds on one end of an atropisomer are both UP or both DOWN - atoms are: 7 29 + 65/238 Test #76: testTplParser .......................... Passed 0.02 sec +test 77 + Start 77: testMol2ToMol + +77: Test command: /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/testMol2ToMol +77: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers +77: Test timeout computed to be: 1500 68: Test 68: 68: JDQ443_3d.mrv @@ -19479,15 +19540,44 @@ 68: 68: JDQ443_atropBad1.mrv 68: -68: [00:36:14] The 2 defining bonds for an atropisomer are co-planar - atoms are: 17 21 -73: [00:36:14] Finished: testMae() -73: [00:36:14] ----------------------------------------- -73: -73: [00:36:14] -73: ----------------------------------------- -73: [00:36:14] Finished: testTdt() -73: [00:36:14] ----------------------------------------- -73: +68: [09:33:08] The 2 defining bonds for an atropisomer are co-planar - atoms are: 17 21 +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: + 66/238 Test #60: cxsmilesTest ........................... Passed 0.74 sec +test 78 + Start 78: testSequence + +78: Test command: /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/testSequence +78: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers +78: Test timeout computed to be: 1500 + 67/238 Test #77: testMol2ToMol .......................... Passed 0.03 sec +test 79 + Start 79: testExtendedStereoParsing + +79: Test command: /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/testExtendedStereoParsing +79: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers +79: Test timeout computed to be: 1500 68: Test 68: 68: RP-6306_atrop1.mrv @@ -19508,126 +19598,20 @@ 68: 68: RP-6306_atrop5.mrv 68: -68: [00:36:14] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 2 ignored -68: [00:36:14] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 2 ignored - 63/238 Test #73: testGeneralFileReader .................. Passed 0.14 sec -test 75 - Start 75: testMolWriter - -75: Test command: /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/testMolWriter -75: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers -75: Test timeout computed to be: 1500 +68: [09:33:08] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 2 ignored +68: [09:33:08] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 2 ignored 68: Test 68: 68: RP-6306_atropBad1.mrv 68: -68: [00:36:14] The bonds on one end of an atropisomer are both UP or both DOWN - atoms are: 2 8 +68: [09:33:08] 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: -68: [00:36:14] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 2 ignored -68: [00:36:14] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 2 ignored -68: [00:36:14] The 2 defining bonds for an atropisomer are co-planar - atoms are: 2 8 - 64/238 Test #67: pyDepictor ............................. Passed 0.87 sec -test 76 - Start 76: testTplParser - -76: Test command: /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/testTplParser -76: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers -76: Test timeout computed to be: 1500 -68: Test -68: -68: RP-6306_3d.mrv -68: -68: Test -68: -68: Sotorasib_atrop1.mrv -68: -68: Test -68: -68: Sotorasib_atrop2.mrv -68: -68: Test -68: -68: Sotorasib_atrop3.mrv -68: -68: Test -68: -68: Sotorasib_atrop4.mrv -68: -68: Test -68: -68: Sotorasib_atrop5.mrv -68: -68: [00:36:14] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored -68: [00:36:14] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored -68: Test -68: -68: Sotorasib_atropBad1.mrv -68: -68: [00:36:14] The 2 defining bonds for an atropisomer are co-planar - atoms are: 7 20 -68: Test -68: -68: Sotorasib_atropBad2.mrv -68: -68: [00:36:14] The bonds on one end of an atropisomer are both UP or both DOWN - atoms are: 7 20 - 65/238 Test #76: testTplParser .......................... Passed 0.04 sec -test 77 - Start 77: testMol2ToMol - -77: Test command: /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/testMol2ToMol -77: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers -77: Test timeout computed to be: 1500 -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: [00:36:14] The 2 defining bonds for an atropisomer are co-planar - atoms are: 0 31 - 66/238 Test #77: testMol2ToMol .......................... Passed 0.04 sec -test 78 - Start 78: testSequence - -78: Test command: /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/testSequence -78: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers -78: Test timeout computed to be: 1500 -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: [00:36:14] The 2 defining bonds for an atropisomer are co-planar - atoms are: 15 16 +68: [09:33:08] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 2 ignored +68: [09:33:08] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 2 ignored +68: [09:33:08] The 2 defining bonds for an atropisomer are co-planar - atoms are: 2 8 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 @@ -20612,151 +20596,120 @@ 78: CONECT 27 28 28 29 78: END 78: - 67/238 Test #78: testSequence ........................... Passed 0.05 sec -test 79 - Start 79: testExtendedStereoParsing - -79: Test command: /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/testExtendedStereoParsing -79: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers -79: Test timeout computed to be: 1500 -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: - 68/238 Test #60: cxsmilesTest ........................... Passed 1.24 sec + 68/238 Test #78: testSequence ........................... Passed 0.05 sec + 69/238 Test #79: testExtendedStereoParsing .............. Passed 0.03 sec test 80 Start 80: fileParsersCatchTest 80: Test command: /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest 80: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-aarch64-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-aarch64-linux-gnu/Code/GraphMol/FileParsers/testPropertyLists +81: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers +81: Test timeout computed to be: 1500 68: Test 68: -68: FalseAtropisomer.mrv -68: -68: Test -68: -68: AtropEnhancedStereo.mrv -68: -68: Test -68: -68: AtropManyChirals.mrv -68: -68: Test -68: -68: AtropManyChiralsEnhanced.mrv -68: -68: Test -68: -68: AtropManyChiralsEnhanced2.mrv -68: -68: Test -68: -68: AtropManyChiralsEnhanced3.mrv -68: -68: Test -68: -68: AtropManyChiralsEnhanced4.mrv -68: -68: Test -68: -68: BMS-986142_3d_chiral.mrv -68: -68: Test -68: -68: BMS-986142_3d.mrv -68: -68: Test -68: -68: BMS-986142_atrop1.mrv -68: -68: Test -68: -68: BMS-986142_atrop2.mrv +68: RP-6306_3d.mrv 68: 68: Test 68: -68: BMS-986142_atrop3.mrv +68: Sotorasib_atrop1.mrv 68: 68: Test 68: -68: BMS-986142_atrop4.mrv +68: Sotorasib_atrop2.mrv 68: 68: Test 68: -68: BMS-986142_atrop5.mrv +68: Sotorasib_atrop3.mrv 68: -68: [00:36:14] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored -68: [00:36:14] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored - 69/238 Test #79: testExtendedStereoParsing .............. Passed 0.03 sec -test 81 - Start 81: testPropertyLists - -81: Test command: /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/testPropertyLists -81: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers -81: Test timeout computed to be: 1500 68: Test 68: -68: BMS-986142_atrop6.mrv +68: Sotorasib_atrop4.mrv 68: 68: Test 68: -68: BMS-986142_atrop7.mrv +68: Sotorasib_atrop5.mrv 68: +68: [09:33:08] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored +68: [09:33:08] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored 68: Test 68: -68: BMS-986142_atrop8.mrv +68: Sotorasib_atropBad1.mrv 68: -68: [00:36:14] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored -68: [00:36:14] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored +68: [09:33:08] The 2 defining bonds for an atropisomer are co-planar - atoms are: 7 20 +69: [09:33:08] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 1 ignored +69: [09:33:08] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 1 ignored +69: [09:33:08] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 1 ignored +69: [09:33:08] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 1 ignored 68: Test 68: -68: BMS-986142_atropBad2.mrv +68: Sotorasib_atropBad2.mrv 68: -68: [00:36:14] The bonds on one end of an atropisomer are both UP or both DOWN - atoms are: 7 29 -80: Randomness seeded to: 2128950897 -81: Randomness seeded to: 3697140471 +68: [09:33:08] The bonds on one end of an atropisomer are both UP or both DOWN - atoms are: 7 20 +69: [09:33:08] 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: [09:33:08] +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-aarch64-linux-gnu//lib/libRDKitRDGeneral.so.1 +69: 1# Invar::operator<<(std::ostream&, Invar::Invariant const&) in /build/reproducible-path/rdkit-202503.1/obj-aarch64-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-aarch64-linux-gnu//lib/libRDKitFileParsers.so.1 +69: 3# 0x0000FFFF94E77EA4 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu//lib/libRDKitFileParsers.so.1 +69: 4# 0x0000FFFF94E85AA0 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu//lib/libRDKitFileParsers.so.1 +69: 5# 0x0000FFFF94E869CC in /build/reproducible-path/rdkit-202503.1/obj-aarch64-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-aarch64-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-aarch64-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-aarch64-linux-gnu//lib/libRDKitFileParsers.so.1 +69: 9# 0x0000AAAAABB2F77C in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersTest1 +69: 10# 0x0000AAAAABBA4944 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersTest1 +69: 11# 0x0000AAAAABB15BF8 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersTest1 +69: 12# 0x0000FFFF9453229C in /lib/aarch64-linux-gnu/libc.so.6 +69: 13# __libc_start_main in /lib/aarch64-linux-gnu/libc.so.6 +69: 14# 0x0000AAAAABB15E30 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersTest1 +69: ---------- +69: **** +69: +81: Randomness seeded to: 3009493712 81: =============================================================================== 81: All tests passed (95 assertions in 4 test cases) 81: -80: [00:36:14] SGroup SAP line too short: 'M SAP 1 1 8' on line 29 -80: [00:36:14] SGroup SAP line too short: 'M SAP 1 1 8' on line 28 -80: [00:36:14] Could not infer missing lvIdx on malformed SAP line for SGroup 1 -80: [00:36:14] SGroup 1 is invalid and will be ignored -80: [00:36:14] SGroup SAP line too short: 'M SAP 1 1 8' on line 28 -80: [00:36:14] Could not infer missing lvIdx on malformed SAP line for SGroup 1 -80: [00:36:14] SGroup 1 is invalid and will be ignored -80: [00:36:14] SGroup SAP line too short: 'M SAP 1 1 8' on line 35 -80: [00:36:14] SGroup SAP line too short: 'M SAP 2 1 12' on line 39 -80: [00:36:14] SGroup SAP line too short: 'M SAP 1 1 8' on line 34 -80: [00:36:14] SGroup SAP line too short: 'M SAP 2 1 12' on line 38 -80: [00:36:14] Could not infer missing lvIdx on malformed SAP line for SGroup 1 -80: [00:36:14] SGroup 1 is invalid and will be ignored -80: [00:36:14] SGroup SAP line too short: 'M SAP 1 1 8' on line 34 -80: [00:36:14] SGroup SAP line too short: 'M SAP 2 1 12' on line 39 -80: [00:36:14] Could not infer missing lvIdx on malformed SAP line for SGroup 1 -80: [00:36:14] SGroup 1 is invalid and will be ignored -80: [00:36:14] SGroup 3 referenced on line 40 not found. -80: [00:36:14] + 70/238 Test #81: testPropertyLists ...................... Passed 0.05 sec +test 82 + Start 82: XYZFileParserCatchTest + +82: Test command: /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/XYZFileParserCatchTest +82: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers +82: Test timeout computed to be: 1500 +80: Randomness seeded to: 1744032770 +80: [09:33:08] SGroup SAP line too short: 'M SAP 1 1 8' on line 29 +80: [09:33:08] SGroup SAP line too short: 'M SAP 1 1 8' on line 28 +80: [09:33:08] Could not infer missing lvIdx on malformed SAP line for SGroup 1 +80: [09:33:08] SGroup 1 is invalid and will be ignored +80: [09:33:08] SGroup SAP line too short: 'M SAP 1 1 8' on line 28 +80: [09:33:08] Could not infer missing lvIdx on malformed SAP line for SGroup 1 +80: [09:33:08] SGroup 1 is invalid and will be ignored +80: [09:33:08] SGroup SAP line too short: 'M SAP 1 1 8' on line 35 +80: [09:33:08] SGroup SAP line too short: 'M SAP 2 1 12' on line 39 +80: [09:33:08] SGroup SAP line too short: 'M SAP 1 1 8' on line 34 +80: [09:33:08] SGroup SAP line too short: 'M SAP 2 1 12' on line 38 +80: [09:33:08] Could not infer missing lvIdx on malformed SAP line for SGroup 1 +80: [09:33:08] SGroup 1 is invalid and will be ignored +80: [09:33:08] SGroup SAP line too short: 'M SAP 1 1 8' on line 34 +80: [09:33:08] SGroup SAP line too short: 'M SAP 2 1 12' on line 39 +80: [09:33:08] Could not infer missing lvIdx on malformed SAP line for SGroup 1 +80: [09:33:08] SGroup 1 is invalid and will be ignored +80: [09:33:08] SGroup 3 referenced on line 40 not found. +80: [09:33:08] 80: 80: **** 80: Pre-condition Violation @@ -20769,24 +20722,45 @@ 80: 1# Invar::operator<<(std::ostream&, Invar::Invariant const&) in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu//lib/libRDKitRDGeneral.so.1 80: 2# RDKit::SubstanceGroup::addCState(unsigned int, RDGeom::Point3D const&) in /build/reproducible-path/rdkit-202503.1/obj-aarch64-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-aarch64-linux-gnu//lib/libRDKitFileParsers.so.1 -80: 4# 0x0000FFFFA12FED68 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu//lib/libRDKitFileParsers.so.1 +80: 4# 0x0000FFFFB8EBED68 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-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-aarch64-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-aarch64-linux-gnu//lib/libRDKitFileParsers.so.1 -80: 7# 0x0000AAAAE6299CDC in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -80: 8# 0x0000AAAAE631292C in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -80: 9# 0x0000AAAAE63132E0 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -80: 10# 0x0000AAAAE6313714 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -80: 11# 0x0000AAAAE62E4BB8 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -80: 12# 0x0000AAAAE62E5104 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -80: 13# 0x0000AAAAE625C1B0 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -80: 14# 0x0000FFFFA09B229C in /lib/aarch64-linux-gnu/libc.so.6 +80: 7# 0x0000AAAAE4FE9CDC in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +80: 8# 0x0000AAAAE506292C in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +80: 9# 0x0000AAAAE50632E0 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +80: 10# 0x0000AAAAE5063714 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +80: 11# 0x0000AAAAE5034BB8 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +80: 12# 0x0000AAAAE5035104 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +80: 13# 0x0000AAAAE4FAC1B0 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +80: 14# 0x0000FFFFB857229C in /lib/aarch64-linux-gnu/libc.so.6 80: 15# __libc_start_main in /lib/aarch64-linux-gnu/libc.so.6 -80: 16# 0x0000AAAAE625C270 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +80: 16# 0x0000AAAAE4FAC270 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest 80: ---------- 80: **** 80: -80: [00:36:14] SGroup 3 referenced on line 40 not found. -80: [00:36:14] +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: [09:33:08] The 2 defining bonds for an atropisomer are co-planar - atoms are: 0 31 +80: [09:33:08] SGroup 3 referenced on line 40 not found. +80: [09:33:08] 80: 80: **** 80: Pre-condition Violation @@ -20799,29 +20773,29 @@ 80: 1# Invar::operator<<(std::ostream&, Invar::Invariant const&) in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu//lib/libRDKitRDGeneral.so.1 80: 2# RDKit::SubstanceGroup::addCState(unsigned int, RDGeom::Point3D const&) in /build/reproducible-path/rdkit-202503.1/obj-aarch64-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-aarch64-linux-gnu//lib/libRDKitFileParsers.so.1 -80: 4# 0x0000FFFFA12FED68 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu//lib/libRDKitFileParsers.so.1 +80: 4# 0x0000FFFFB8EBED68 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-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-aarch64-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-aarch64-linux-gnu//lib/libRDKitFileParsers.so.1 -80: 7# 0x0000AAAAE6299D5C in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -80: 8# 0x0000AAAAE631292C in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -80: 9# 0x0000AAAAE63132E0 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -80: 10# 0x0000AAAAE6313714 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -80: 11# 0x0000AAAAE62E4BB8 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -80: 12# 0x0000AAAAE62E5104 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -80: 13# 0x0000AAAAE625C1B0 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -80: 14# 0x0000FFFFA09B229C in /lib/aarch64-linux-gnu/libc.so.6 +80: 7# 0x0000AAAAE4FE9D5C in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +80: 8# 0x0000AAAAE506292C in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +80: 9# 0x0000AAAAE50632E0 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +80: 10# 0x0000AAAAE5063714 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +80: 11# 0x0000AAAAE5034BB8 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +80: 12# 0x0000AAAAE5035104 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +80: 13# 0x0000AAAAE4FAC1B0 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +80: 14# 0x0000FFFFB857229C in /lib/aarch64-linux-gnu/libc.so.6 80: 15# __libc_start_main in /lib/aarch64-linux-gnu/libc.so.6 -80: 16# 0x0000AAAAE625C270 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +80: 16# 0x0000AAAAE4FAC270 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest 80: ---------- 80: **** 80: -80: [00:36:14] no bonds -80: [00:36:14] SGroup 1 is invalid and will be ignored -80: [00:36:14] SGroup line too short: 'M SBV 1 6' on line 42 -80: [00:36:14] SGroup 1 is invalid and will be ignored -80: [00:36:14] SGroup line too short: 'M SBL 2 3 9 10' on line 46 -80: [00:36:14] SGroup 2 is invalid and will be ignored -80: [00:36:14] +80: [09:33:08] no bonds +80: [09:33:08] SGroup 1 is invalid and will be ignored +80: [09:33:08] SGroup line too short: 'M SBV 1 6' on line 42 +80: [09:33:08] SGroup 1 is invalid and will be ignored +80: [09:33:08] SGroup line too short: 'M SBL 2 3 9 10' on line 46 +80: [09:33:08] SGroup 2 is invalid and will be ignored +80: [09:33:08] 80: 80: **** 80: Pre-condition Violation @@ -20835,23 +20809,23 @@ 80: 2# RDKit::ROMol::getUniqueBondWithBookmark(int) in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu//lib/libRDKitGraphMol.so.1 80: 3# RDKit::SubstanceGroup::addBondWithBookmark(int) in /build/reproducible-path/rdkit-202503.1/obj-aarch64-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-aarch64-linux-gnu//lib/libRDKitFileParsers.so.1 -80: 5# 0x0000FFFFA12FECD0 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu//lib/libRDKitFileParsers.so.1 +80: 5# 0x0000FFFFB8EBECD0 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-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-aarch64-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-aarch64-linux-gnu//lib/libRDKitFileParsers.so.1 -80: 8# 0x0000AAAAE629A704 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -80: 9# 0x0000AAAAE631292C in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -80: 10# 0x0000AAAAE63132E0 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -80: 11# 0x0000AAAAE6313714 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -80: 12# 0x0000AAAAE62E4BB8 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -80: 13# 0x0000AAAAE62E5104 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -80: 14# 0x0000AAAAE625C1B0 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -80: 15# 0x0000FFFFA09B229C in /lib/aarch64-linux-gnu/libc.so.6 +80: 8# 0x0000AAAAE4FEA704 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +80: 9# 0x0000AAAAE506292C in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +80: 10# 0x0000AAAAE50632E0 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +80: 11# 0x0000AAAAE5063714 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +80: 12# 0x0000AAAAE5034BB8 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +80: 13# 0x0000AAAAE5035104 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +80: 14# 0x0000AAAAE4FAC1B0 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +80: 15# 0x0000FFFFB857229C in /lib/aarch64-linux-gnu/libc.so.6 80: 16# __libc_start_main in /lib/aarch64-linux-gnu/libc.so.6 -80: 17# 0x0000AAAAE625C270 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +80: 17# 0x0000AAAAE4FAC270 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest 80: ---------- 80: **** 80: -80: [00:36:14] +80: [09:33:08] 80: 80: **** 80: Pre-condition Violation @@ -20865,24 +20839,24 @@ 80: 2# RDKit::ROMol::getUniqueBondWithBookmark(int) in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu//lib/libRDKitGraphMol.so.1 80: 3# RDKit::SubstanceGroup::addBondWithBookmark(int) in /build/reproducible-path/rdkit-202503.1/obj-aarch64-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-aarch64-linux-gnu//lib/libRDKitFileParsers.so.1 -80: 5# 0x0000FFFFA12FECD0 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu//lib/libRDKitFileParsers.so.1 +80: 5# 0x0000FFFFB8EBECD0 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-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-aarch64-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-aarch64-linux-gnu//lib/libRDKitFileParsers.so.1 -80: 8# 0x0000AAAAE629A784 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -80: 9# 0x0000AAAAE631292C in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -80: 10# 0x0000AAAAE63132E0 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -80: 11# 0x0000AAAAE6313714 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -80: 12# 0x0000AAAAE62E4BB8 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -80: 13# 0x0000AAAAE62E5104 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -80: 14# 0x0000AAAAE625C1B0 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -80: 15# 0x0000FFFFA09B229C in /lib/aarch64-linux-gnu/libc.so.6 +80: 8# 0x0000AAAAE4FEA784 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +80: 9# 0x0000AAAAE506292C in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +80: 10# 0x0000AAAAE50632E0 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +80: 11# 0x0000AAAAE5063714 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +80: 12# 0x0000AAAAE5034BB8 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +80: 13# 0x0000AAAAE5035104 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +80: 14# 0x0000AAAAE4FAC1B0 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +80: 15# 0x0000FFFFB857229C in /lib/aarch64-linux-gnu/libc.so.6 80: 16# __libc_start_main in /lib/aarch64-linux-gnu/libc.so.6 -80: 17# 0x0000AAAAE625C270 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +80: 17# 0x0000AAAAE4FAC270 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest 80: ---------- 80: **** 80: -80: [00:36:14] bookmark not found -80: [00:36:14] +80: [09:33:08] bookmark not found +80: [09:33:08] 80: 80: **** 80: Pre-condition Violation @@ -20896,25 +20870,25 @@ 80: 2# RDKit::SubstanceGroup::getBondType(unsigned int) const in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu//lib/libRDKitGraphMol.so.1 80: 3# RDKit::SubstanceGroup::addCState(unsigned int, RDGeom::Point3D const&) in /build/reproducible-path/rdkit-202503.1/obj-aarch64-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-aarch64-linux-gnu//lib/libRDKitFileParsers.so.1 -80: 5# 0x0000FFFFA12FED68 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu//lib/libRDKitFileParsers.so.1 +80: 5# 0x0000FFFFB8EBED68 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-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-aarch64-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-aarch64-linux-gnu//lib/libRDKitFileParsers.so.1 -80: 8# 0x0000AAAAE629A784 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -80: 9# 0x0000AAAAE631292C in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -80: 10# 0x0000AAAAE63132E0 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -80: 11# 0x0000AAAAE6313714 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -80: 12# 0x0000AAAAE62E4BB8 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -80: 13# 0x0000AAAAE62E5104 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -80: 14# 0x0000AAAAE625C1B0 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -80: 15# 0x0000FFFFA09B229C in /lib/aarch64-linux-gnu/libc.so.6 +80: 8# 0x0000AAAAE4FEA784 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +80: 9# 0x0000AAAAE506292C in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +80: 10# 0x0000AAAAE50632E0 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +80: 11# 0x0000AAAAE5063714 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +80: 12# 0x0000AAAAE5034BB8 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +80: 13# 0x0000AAAAE5035104 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +80: 14# 0x0000AAAAE4FAC1B0 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +80: 15# 0x0000FFFFB857229C in /lib/aarch64-linux-gnu/libc.so.6 80: 16# __libc_start_main in /lib/aarch64-linux-gnu/libc.so.6 -80: 17# 0x0000AAAAE625C270 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +80: 17# 0x0000AAAAE4FAC270 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest 80: ---------- 80: **** 80: -80: [00:36:14] bond is not part of the SubstanceGroup -80: [00:36:14] SGroup 2 is invalid and will be ignored -80: [00:36:14] +80: [09:33:08] bond is not part of the SubstanceGroup +80: [09:33:08] SGroup 2 is invalid and will be ignored +80: [09:33:08] 80: 80: **** 80: Pre-condition Violation @@ -20928,23 +20902,23 @@ 80: 2# RDKit::ROMol::getUniqueAtomWithBookmark(int) in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu//lib/libRDKitGraphMol.so.1 80: 3# RDKit::SubstanceGroup::addAtomWithBookmark(int) in /build/reproducible-path/rdkit-202503.1/obj-aarch64-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-aarch64-linux-gnu//lib/libRDKitFileParsers.so.1 -80: 5# 0x0000FFFFA12FECD0 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu//lib/libRDKitFileParsers.so.1 +80: 5# 0x0000FFFFB8EBECD0 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-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-aarch64-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-aarch64-linux-gnu//lib/libRDKitFileParsers.so.1 -80: 8# 0x0000AAAAE629AA74 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -80: 9# 0x0000AAAAE631292C in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -80: 10# 0x0000AAAAE63132E0 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -80: 11# 0x0000AAAAE6313714 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -80: 12# 0x0000AAAAE62E4BB8 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -80: 13# 0x0000AAAAE62E5104 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -80: 14# 0x0000AAAAE625C1B0 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -80: 15# 0x0000FFFFA09B229C in /lib/aarch64-linux-gnu/libc.so.6 +80: 8# 0x0000AAAAE4FEAA74 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +80: 9# 0x0000AAAAE506292C in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +80: 10# 0x0000AAAAE50632E0 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +80: 11# 0x0000AAAAE5063714 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +80: 12# 0x0000AAAAE5034BB8 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +80: 13# 0x0000AAAAE5035104 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +80: 14# 0x0000AAAAE4FAC1B0 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +80: 15# 0x0000FFFFB857229C in /lib/aarch64-linux-gnu/libc.so.6 80: 16# __libc_start_main in /lib/aarch64-linux-gnu/libc.so.6 -80: 17# 0x0000AAAAE625C270 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +80: 17# 0x0000AAAAE4FAC270 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest 80: ---------- 80: **** 80: -80: [00:36:14] +80: [09:33:08] 80: 80: **** 80: Pre-condition Violation @@ -20958,57 +20932,29 @@ 80: 2# RDKit::ROMol::getUniqueAtomWithBookmark(int) in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu//lib/libRDKitGraphMol.so.1 80: 3# RDKit::SubstanceGroup::addAtomWithBookmark(int) in /build/reproducible-path/rdkit-202503.1/obj-aarch64-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-aarch64-linux-gnu//lib/libRDKitFileParsers.so.1 -80: 5# 0x0000FFFFA12FECD0 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu//lib/libRDKitFileParsers.so.1 +80: 5# 0x0000FFFFB8EBECD0 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-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-aarch64-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-aarch64-linux-gnu//lib/libRDKitFileParsers.so.1 -80: 8# 0x0000AAAAE629AAF4 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -80: 9# 0x0000AAAAE631292C in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -80: 10# 0x0000AAAAE63132E0 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -80: 11# 0x0000AAAAE6313714 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -80: 12# 0x0000AAAAE62E4BB8 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -80: 13# 0x0000AAAAE62E5104 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -80: 14# 0x0000AAAAE625C1B0 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -80: 15# 0x0000FFFFA09B229C in /lib/aarch64-linux-gnu/libc.so.6 +80: 8# 0x0000AAAAE4FEAAF4 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +80: 9# 0x0000AAAAE506292C in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +80: 10# 0x0000AAAAE50632E0 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +80: 11# 0x0000AAAAE5063714 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +80: 12# 0x0000AAAAE5034BB8 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +80: 13# 0x0000AAAAE5035104 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +80: 14# 0x0000AAAAE4FAC1B0 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +80: 15# 0x0000FFFFB857229C in /lib/aarch64-linux-gnu/libc.so.6 80: 16# __libc_start_main in /lib/aarch64-linux-gnu/libc.so.6 -80: 17# 0x0000AAAAE625C270 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +80: 17# 0x0000AAAAE4FAC270 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest 80: ---------- 80: **** 80: -80: [00:36:14] bookmark not found -80: [00:36:14] Neither beginning nor ending atoms of bond 9 is in this SubstanceGroup. -80: [00:36:14] SGroup 2 is invalid and will be ignored -80: [00:36:14] WARNING: final character of V3000 array is not ')' -80: [00:36:14] +80: [09:33:08] bookmark not found +80: [09:33:08] Neither beginning nor ending atoms of bond 9 is in this SubstanceGroup. +80: [09:33:08] SGroup 2 is invalid and will be ignored +80: [09:33:08] WARNING: final character of V3000 array is not ')' +80: [09:33:08] 80: 80: **** - 70/238 Test #81: testPropertyLists ...................... Passed 0.04 sec -test 82 - Start 82: XYZFileParserCatchTest - -82: Test command: /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/XYZFileParserCatchTest -82: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers -82: Test timeout computed to be: 1500 -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: [00:36:14] The 2 defining bonds for an atropisomer are co-planar - atoms are: 17 21 80: Pre-condition Violation 80: bookmark not found 80: Violation occurred on line 267 in file ./Code/GraphMol/ROMol.cpp @@ -21024,21 +20970,21 @@ 80: 6# RDKit::FileParserUtils::ParseV3000CTAB(std::istream*, unsigned int&, RDKit::RWMol*, RDKit::Conformer*&, bool&, unsigned int&, unsigned int&, bool, bool) in /build/reproducible-path/rdkit-202503.1/obj-aarch64-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-aarch64-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-aarch64-linux-gnu//lib/libRDKitFileParsers.so.1 -80: 9# 0x0000AAAAE62986E8 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -80: 10# 0x0000AAAAE631292C in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -80: 11# 0x0000AAAAE63132E0 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -80: 12# 0x0000AAAAE6313714 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -80: 13# 0x0000AAAAE62E4BB8 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -80: 14# 0x0000AAAAE62E5104 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -80: 15# 0x0000AAAAE625C1B0 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -80: 16# 0x0000FFFFA09B229C in /lib/aarch64-linux-gnu/libc.so.6 +80: 9# 0x0000AAAAE4FE86E8 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +80: 10# 0x0000AAAAE506292C in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +80: 11# 0x0000AAAAE50632E0 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +80: 12# 0x0000AAAAE5063714 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +80: 13# 0x0000AAAAE5034BB8 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +80: 14# 0x0000AAAAE5035104 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +80: 15# 0x0000AAAAE4FAC1B0 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +80: 16# 0x0000FFFFB857229C in /lib/aarch64-linux-gnu/libc.so.6 80: 17# __libc_start_main in /lib/aarch64-linux-gnu/libc.so.6 -80: 18# 0x0000AAAAE625C270 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +80: 18# 0x0000AAAAE4FAC270 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest 80: ---------- 80: **** 80: -80: [00:36:14] WARNING: final character of V3000 array is not ')' -80: [00:36:14] +80: [09:33:08] WARNING: final character of V3000 array is not ')' +80: [09:33:08] 80: 80: **** 80: Pre-condition Violation @@ -21056,23 +21002,23 @@ 80: 6# RDKit::FileParserUtils::ParseV3000CTAB(std::istream*, unsigned int&, RDKit::RWMol*, RDKit::Conformer*&, bool&, unsigned int&, unsigned int&, bool, bool) in /build/reproducible-path/rdkit-202503.1/obj-aarch64-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-aarch64-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-aarch64-linux-gnu//lib/libRDKitFileParsers.so.1 -80: 9# 0x0000AAAAE6298764 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -80: 10# 0x0000AAAAE631292C in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -80: 11# 0x0000AAAAE63132E0 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -80: 12# 0x0000AAAAE6313714 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -80: 13# 0x0000AAAAE62E4BB8 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -80: 14# 0x0000AAAAE62E5104 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -80: 15# 0x0000AAAAE625C1B0 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -80: 16# 0x0000FFFFA09B229C in /lib/aarch64-linux-gnu/libc.so.6 +80: 9# 0x0000AAAAE4FE8764 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +80: 10# 0x0000AAAAE506292C in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +80: 11# 0x0000AAAAE50632E0 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +80: 12# 0x0000AAAAE5063714 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +80: 13# 0x0000AAAAE5034BB8 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +80: 14# 0x0000AAAAE5035104 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +80: 15# 0x0000AAAAE4FAC1B0 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +80: 16# 0x0000FFFFB857229C in /lib/aarch64-linux-gnu/libc.so.6 80: 17# __libc_start_main in /lib/aarch64-linux-gnu/libc.so.6 -80: 18# 0x0000AAAAE625C270 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +80: 18# 0x0000AAAAE4FAC270 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest 80: ---------- 80: **** 80: -80: [00:36:14] bookmark not found -80: [00:36:14] SGroup 1 is invalid and will be ignored -80: [00:36:14] WARNING: final character of V3000 array is not ')' -80: [00:36:14] +80: [09:33:08] bookmark not found +80: [09:33:08] SGroup 1 is invalid and will be ignored +80: [09:33:08] WARNING: final character of V3000 array is not ')' +80: [09:33:08] 80: 80: **** 80: Pre-condition Violation @@ -21090,21 +21036,21 @@ 80: 6# RDKit::FileParserUtils::ParseV3000CTAB(std::istream*, unsigned int&, RDKit::RWMol*, RDKit::Conformer*&, bool&, unsigned int&, unsigned int&, bool, bool) in /build/reproducible-path/rdkit-202503.1/obj-aarch64-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-aarch64-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-aarch64-linux-gnu//lib/libRDKitFileParsers.so.1 -80: 9# 0x0000AAAAE6298A38 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -80: 10# 0x0000AAAAE631292C in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -80: 11# 0x0000AAAAE63132E0 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -80: 12# 0x0000AAAAE6313714 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -80: 13# 0x0000AAAAE62E4BB8 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -80: 14# 0x0000AAAAE62E5104 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -80: 15# 0x0000AAAAE625C1B0 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -80: 16# 0x0000FFFFA09B229C in /lib/aarch64-linux-gnu/libc.so.6 +80: 9# 0x0000AAAAE4FE8A38 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +80: 10# 0x0000AAAAE506292C in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +80: 11# 0x0000AAAAE50632E0 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +80: 12# 0x0000AAAAE5063714 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +80: 13# 0x0000AAAAE5034BB8 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +80: 14# 0x0000AAAAE5035104 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +80: 15# 0x0000AAAAE4FAC1B0 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +80: 16# 0x0000FFFFB857229C in /lib/aarch64-linux-gnu/libc.so.6 80: 17# __libc_start_main in /lib/aarch64-linux-gnu/libc.so.6 -80: 18# 0x0000AAAAE625C270 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +80: 18# 0x0000AAAAE4FAC270 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest 80: ---------- 80: **** 80: -80: [00:36:14] WARNING: final character of V3000 array is not ')' -80: [00:36:14] +80: [09:33:08] WARNING: final character of V3000 array is not ')' +80: [09:33:08] 80: 80: **** 80: Pre-condition Violation @@ -21122,22 +21068,22 @@ 80: 6# RDKit::FileParserUtils::ParseV3000CTAB(std::istream*, unsigned int&, RDKit::RWMol*, RDKit::Conformer*&, bool&, unsigned int&, unsigned int&, bool, bool) in /build/reproducible-path/rdkit-202503.1/obj-aarch64-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-aarch64-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-aarch64-linux-gnu//lib/libRDKitFileParsers.so.1 -80: 9# 0x0000AAAAE6298AB4 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -80: 10# 0x0000AAAAE631292C in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -80: 11# 0x0000AAAAE63132E0 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -80: 12# 0x0000AAAAE6313714 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -80: 13# 0x0000AAAAE62E4BB8 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -80: 14# 0x0000AAAAE62E5104 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -80: 15# 0x0000AAAAE625C1B0 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -80: 16# 0x0000FFFFA09B229C in /lib/aarch64-linux-gnu/libc.so.6 +80: 9# 0x0000AAAAE4FE8AB4 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +80: 10# 0x0000AAAAE506292C in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +80: 11# 0x0000AAAAE50632E0 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +80: 12# 0x0000AAAAE5063714 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +80: 13# 0x0000AAAAE5034BB8 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +80: 14# 0x0000AAAAE5035104 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +80: 15# 0x0000AAAAE4FAC1B0 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +80: 16# 0x0000FFFFB857229C in /lib/aarch64-linux-gnu/libc.so.6 80: 17# __libc_start_main in /lib/aarch64-linux-gnu/libc.so.6 -80: 18# 0x0000AAAAE625C270 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +80: 18# 0x0000AAAAE4FAC270 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest 80: ---------- 80: **** 80: -80: [00:36:14] bookmark not found -80: [00:36:14] SGroup 1 is invalid and will be ignored -80: [00:36:14] +80: [09:33:08] bookmark not found +80: [09:33:08] SGroup 1 is invalid and will be ignored +80: [09:33:08] 80: 80: **** 80: Pre-condition Violation @@ -21155,20 +21101,20 @@ 80: 6# RDKit::FileParserUtils::ParseV3000CTAB(std::istream*, unsigned int&, RDKit::RWMol*, RDKit::Conformer*&, bool&, unsigned int&, unsigned int&, bool, bool) in /build/reproducible-path/rdkit-202503.1/obj-aarch64-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-aarch64-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-aarch64-linux-gnu//lib/libRDKitFileParsers.so.1 -80: 9# 0x0000AAAAE6298D88 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -80: 10# 0x0000AAAAE631292C in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -80: 11# 0x0000AAAAE63132E0 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -80: 12# 0x0000AAAAE6313714 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -80: 13# 0x0000AAAAE62E4BB8 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -80: 14# 0x0000AAAAE62E5104 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -80: 15# 0x0000AAAAE625C1B0 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -80: 16# 0x0000FFFFA09B229C in /lib/aarch64-linux-gnu/libc.so.6 +80: 9# 0x0000AAAAE4FE8D88 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +80: 10# 0x0000AAAAE506292C in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +80: 11# 0x0000AAAAE50632E0 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +80: 12# 0x0000AAAAE5063714 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +80: 13# 0x0000AAAAE5034BB8 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +80: 14# 0x0000AAAAE5035104 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +80: 15# 0x0000AAAAE4FAC1B0 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +80: 16# 0x0000FFFFB857229C in /lib/aarch64-linux-gnu/libc.so.6 80: 17# __libc_start_main in /lib/aarch64-linux-gnu/libc.so.6 -80: 18# 0x0000AAAAE625C270 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +80: 18# 0x0000AAAAE4FAC270 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest 80: ---------- 80: **** 80: -80: [00:36:14] +80: [09:33:08] 80: 80: **** 80: Pre-condition Violation @@ -21186,22 +21132,22 @@ 80: 6# RDKit::FileParserUtils::ParseV3000CTAB(std::istream*, unsigned int&, RDKit::RWMol*, RDKit::Conformer*&, bool&, unsigned int&, unsigned int&, bool, bool) in /build/reproducible-path/rdkit-202503.1/obj-aarch64-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-aarch64-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-aarch64-linux-gnu//lib/libRDKitFileParsers.so.1 -80: 9# 0x0000AAAAE6298E04 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -80: 10# 0x0000AAAAE631292C in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -80: 11# 0x0000AAAAE63132E0 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -80: 12# 0x0000AAAAE6313714 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -80: 13# 0x0000AAAAE62E4BB8 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -80: 14# 0x0000AAAAE62E5104 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -80: 15# 0x0000AAAAE625C1B0 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -80: 16# 0x0000FFFFA09B229C in /lib/aarch64-linux-gnu/libc.so.6 +80: 9# 0x0000AAAAE4FE8E04 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +80: 10# 0x0000AAAAE506292C in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +80: 11# 0x0000AAAAE50632E0 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +80: 12# 0x0000AAAAE5063714 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +80: 13# 0x0000AAAAE5034BB8 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +80: 14# 0x0000AAAAE5035104 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +80: 15# 0x0000AAAAE4FAC1B0 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +80: 16# 0x0000FFFFB857229C in /lib/aarch64-linux-gnu/libc.so.6 80: 17# __libc_start_main in /lib/aarch64-linux-gnu/libc.so.6 -80: 18# 0x0000AAAAE625C270 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +80: 18# 0x0000AAAAE4FAC270 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest 80: ---------- 80: **** 80: -80: [00:36:14] bookmark not found -80: [00:36:14] SGroup 2 is invalid and will be ignored -80: [00:36:14] +80: [09:33:08] bookmark not found +80: [09:33:08] SGroup 2 is invalid and will be ignored +80: [09:33:08] 80: 80: **** 80: Pre-condition Violation @@ -21219,20 +21165,20 @@ 80: 6# RDKit::FileParserUtils::ParseV3000CTAB(std::istream*, unsigned int&, RDKit::RWMol*, RDKit::Conformer*&, bool&, unsigned int&, unsigned int&, bool, bool) in /build/reproducible-path/rdkit-202503.1/obj-aarch64-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-aarch64-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-aarch64-linux-gnu//lib/libRDKitFileParsers.so.1 -80: 9# 0x0000AAAAE62990D8 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -80: 10# 0x0000AAAAE631292C in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -80: 11# 0x0000AAAAE63132E0 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -80: 12# 0x0000AAAAE6313714 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -80: 13# 0x0000AAAAE62E4BB8 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -80: 14# 0x0000AAAAE62E5104 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -80: 15# 0x0000AAAAE625C1B0 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -80: 16# 0x0000FFFFA09B229C in /lib/aarch64-linux-gnu/libc.so.6 +80: 9# 0x0000AAAAE4FE90D8 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +80: 10# 0x0000AAAAE506292C in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +80: 11# 0x0000AAAAE50632E0 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +80: 12# 0x0000AAAAE5063714 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +80: 13# 0x0000AAAAE5034BB8 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +80: 14# 0x0000AAAAE5035104 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +80: 15# 0x0000AAAAE4FAC1B0 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +80: 16# 0x0000FFFFB857229C in /lib/aarch64-linux-gnu/libc.so.6 80: 17# __libc_start_main in /lib/aarch64-linux-gnu/libc.so.6 -80: 18# 0x0000AAAAE625C270 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +80: 18# 0x0000AAAAE4FAC270 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest 80: ---------- 80: **** 80: -80: [00:36:14] +80: [09:33:08] 80: 80: **** 80: Pre-condition Violation @@ -21250,65 +21196,46 @@ 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-aarch64-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-aarch64-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-aarch64-linux-gnu//lib/libRDKitFileParsers.so.1 -80: 9# 0x0000AAAAE6299154 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -80: 10# 0x0000AAAAE631292C in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -80: 11# 0x0000AAAAE63132E0 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -80: 12# 0x0000AAAAE6313714 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -80: 13# 0x0000AAAAE62E4BB8 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -80: 14# 0x0000AAAAE62E5104 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -80: 15# 0x0000AAAAE625C1B0 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -80: 16# 0x0000FFFFA09B229C in /lib/aarch64-linux-gnu/libc.so.6 +80: 9# 0x0000AAAAE4FE9154 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +80: 10# 0x0000AAAAE506292C in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +80: 11# 0x0000AAAAE50632E0 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +80: 12# 0x0000AAAAE5063714 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +80: 13# 0x0000AAAAE5034BB8 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +80: 14# 0x0000AAAAE5035104 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +80: 15# 0x0000AAAAE4FAC1B0 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +80: 16# 0x0000FFFFB857229C in /lib/aarch64-linux-gnu/libc.so.6 80: 17# __libc_start_main in /lib/aarch64-linux-gnu/libc.so.6 -80: 18# 0x0000AAAAE625C270 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +80: 18# 0x0000AAAAE4FAC270 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest 80: ---------- 80: **** 80: -80: [00:36:14] bookmark not found -80: [00:36:14] SGroup 2 is invalid and will be ignored -80: [00:36:14] Explicit valence for atom # 2 O, 3, is greater than permitted -80: [00:36:14] Explicit valence for atom # 1 O, 3, is greater than permitted -80: [00:36:14] Explicit valence for atom # 1 C, 5, is greater than permitted -68: Test -68: -68: RP-6306_atrop1.mrv -68: -68: Test -68: -68: RP-6306_atrop2.mrv -68: +80: [09:33:08] bookmark not found +80: [09:33:08] SGroup 2 is invalid and will be ignored +82: Randomness seeded to: 4264995793 +82: =============================================================================== +82: All tests passed (100 assertions in 2 test cases) +82: 68: Test 68: -68: RP-6306_atrop3.mrv +68: mrtx1719_3d.mrv 68: 68: Test 68: -68: RP-6306_atrop4.mrv +68: mrtx1719_atrop1.mrv 68: 68: Test 68: -68: RP-6306_atrop5.mrv +68: mrtx1719_atrop2.mrv 68: -68: [00:36:14] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 2 ignored -68: [00:36:14] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 2 ignored -29: Checking against /build/reproducible-path/rdkit-202503.1/Code/ForceField/MMFF/test_data/MMFF94_reference.log... -80: [00:36:14] sanitize [00:36:14] UNK: [00:36:14] Warning: molecule is tagged as 3D, but all Z coords are zero and 2D stereo markers have been found, marking the mol as 2D. 68: Test 68: -68: RP-6306_atropBad1.mrv +68: mrtx1719_atrop3.mrv 68: -68: [00:36:14] The bonds on one end of an atropisomer are both UP or both DOWN - atoms are: 2 8 -82: Randomness seeded to: 1855440979 -82: =============================================================================== -82: All tests passed (100 assertions in 2 test cases) -82: 68: Test 68: -68: RP-6306_atropBad2.mrv +68: mrtx1719_atropBad1.mrv 68: -68: [00:36:14] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 2 ignored -68: [00:36:14] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 2 ignored -68: [00:36:14] The 2 defining bonds for an atropisomer are co-planar - atoms are: 2 8 -75: [00:36:14] Warning: molecule is tagged as 3D, but all Z coords are zero and 2D stereo markers have been found, marking the mol as 2D. +68: [09:33:08] The 2 defining bonds for an atropisomer are co-planar - atoms are: 15 16 71/238 Test #82: XYZFileParserCatchTest ................. Passed 0.04 sec test 83 Start 83: cdxmlParserCatchTest @@ -21316,11 +21243,16 @@ 83: Test command: /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/cdxmlParserCatchTest 83: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers 83: Test timeout computed to be: 1500 -80: [00:36:14] skipping block at line 7: 'BEGIN ATOM' +80: [09:33:08] Explicit valence for atom # 2 O, 3, is greater than permitted +80: [09:33:08] Explicit valence for atom # 1 O, 3, is greater than permitted +80: [09:33:08] Explicit valence for atom # 1 C, 5, is greater than permitted +80: [09:33:08] sanitize [09:33:08] UNK: [09:33:08] 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: [09:33:08] 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: [00:36:14] +75: [09:33:08] 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: [09:33:08] 80: 80: **** 80: Pre-condition Violation @@ -21332,21 +21264,21 @@ 80: 0# Invar::Invariant::toString[abi:cxx11]() const in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu//lib/libRDKitRDGeneral.so.1 80: 1# Invar::operator<<(std::ostream&, Invar::Invariant const&) in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu//lib/libRDKitRDGeneral.so.1 80: 2# RDKit::v2::FileParsers::SDMolSupplier::next() in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu//lib/libRDKitFileParsers.so.1 -80: 3# 0x0000AAAAE62CFC60 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -80: 4# 0x0000AAAAE6281568 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -80: 5# 0x0000AAAAE631292C in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -80: 6# 0x0000AAAAE63132E0 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -80: 7# 0x0000AAAAE6313714 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -80: 8# 0x0000AAAAE62E4BB8 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -80: 9# 0x0000AAAAE62E5104 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -80: 10# 0x0000AAAAE625C1B0 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -80: 11# 0x0000FFFFA09B229C in /lib/aarch64-linux-gnu/libc.so.6 +80: 3# 0x0000AAAAE501FC60 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +80: 4# 0x0000AAAAE4FD1568 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +80: 5# 0x0000AAAAE506292C in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +80: 6# 0x0000AAAAE50632E0 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +80: 7# 0x0000AAAAE5063714 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +80: 8# 0x0000AAAAE5034BB8 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +80: 9# 0x0000AAAAE5035104 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +80: 10# 0x0000AAAAE4FAC1B0 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +80: 11# 0x0000FFFFB857229C in /lib/aarch64-linux-gnu/libc.so.6 80: 12# __libc_start_main in /lib/aarch64-linux-gnu/libc.so.6 -80: 13# 0x0000AAAAE625C270 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +80: 13# 0x0000AAAAE4FAC270 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest 80: ---------- 80: **** 80: -80: [00:36:14] +80: [09:33:08] 80: 80: **** 80: Pre-condition Violation @@ -21358,21 +21290,21 @@ 80: 0# Invar::Invariant::toString[abi:cxx11]() const in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu//lib/libRDKitRDGeneral.so.1 80: 1# Invar::operator<<(std::ostream&, Invar::Invariant const&) in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu//lib/libRDKitRDGeneral.so.1 80: 2# RDKit::v2::FileParsers::ForwardSDMolSupplier::next() in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu//lib/libRDKitFileParsers.so.1 -80: 3# 0x0000AAAAE62CFC60 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -80: 4# 0x0000AAAAE62816D8 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -80: 5# 0x0000AAAAE631292C in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -80: 6# 0x0000AAAAE63132E0 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -80: 7# 0x0000AAAAE6313714 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -80: 8# 0x0000AAAAE62E4BB8 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -80: 9# 0x0000AAAAE62E5104 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -80: 10# 0x0000AAAAE625C1B0 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -80: 11# 0x0000FFFFA09B229C in /lib/aarch64-linux-gnu/libc.so.6 +80: 3# 0x0000AAAAE501FC60 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +80: 4# 0x0000AAAAE4FD16D8 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +80: 5# 0x0000AAAAE506292C in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +80: 6# 0x0000AAAAE50632E0 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +80: 7# 0x0000AAAAE5063714 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +80: 8# 0x0000AAAAE5034BB8 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +80: 9# 0x0000AAAAE5035104 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +80: 10# 0x0000AAAAE4FAC1B0 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +80: 11# 0x0000FFFFB857229C in /lib/aarch64-linux-gnu/libc.so.6 80: 12# __libc_start_main in /lib/aarch64-linux-gnu/libc.so.6 -80: 13# 0x0000AAAAE625C270 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +80: 13# 0x0000AAAAE4FAC270 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest 80: ---------- 80: **** 80: -80: [00:36:14] +80: [09:33:08] 80: 80: **** 80: Pre-condition Violation @@ -21384,21 +21316,21 @@ 80: 0# Invar::Invariant::toString[abi:cxx11]() const in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu//lib/libRDKitRDGeneral.so.1 80: 1# Invar::operator<<(std::ostream&, Invar::Invariant const&) in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu//lib/libRDKitRDGeneral.so.1 80: 2# RDKit::v2::FileParsers::SmilesMolSupplier::next() in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu//lib/libRDKitFileParsers.so.1 -80: 3# 0x0000AAAAE62CFC60 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -80: 4# 0x0000AAAAE6281A0C in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -80: 5# 0x0000AAAAE631292C in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -80: 6# 0x0000AAAAE63132E0 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -80: 7# 0x0000AAAAE6313714 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -80: 8# 0x0000AAAAE62E4BB8 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -80: 9# 0x0000AAAAE62E5104 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -80: 10# 0x0000AAAAE625C1B0 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -80: 11# 0x0000FFFFA09B229C in /lib/aarch64-linux-gnu/libc.so.6 +80: 3# 0x0000AAAAE501FC60 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +80: 4# 0x0000AAAAE4FD1A0C in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +80: 5# 0x0000AAAAE506292C in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +80: 6# 0x0000AAAAE50632E0 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +80: 7# 0x0000AAAAE5063714 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +80: 8# 0x0000AAAAE5034BB8 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +80: 9# 0x0000AAAAE5035104 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +80: 10# 0x0000AAAAE4FAC1B0 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +80: 11# 0x0000FFFFB857229C in /lib/aarch64-linux-gnu/libc.so.6 80: 12# __libc_start_main in /lib/aarch64-linux-gnu/libc.so.6 -80: 13# 0x0000AAAAE625C270 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +80: 13# 0x0000AAAAE4FAC270 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest 80: ---------- 80: **** 80: -80: [00:36:14] +80: [09:33:08] 80: 80: **** 80: Pre-condition Violation @@ -21410,43 +21342,17 @@ 80: 0# Invar::Invariant::toString[abi:cxx11]() const in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu//lib/libRDKitRDGeneral.so.1 80: 1# Invar::operator<<(std::ostream&, Invar::Invariant const&) in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu//lib/libRDKitRDGeneral.so.1 80: 2# RDKit::v2::FileParsers::TDTMolSupplier::next() in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu//lib/libRDKitFileParsers.so.1 -80: 3# 0x0000AAAAE62CFC60 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -80: 4# 0x0000AAAAE6281CA8 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -80: 5# 0x0000AAAAE631292C in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -80: 6# 0x0000AAAAE63132E0 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -80: 7# 0x0000AAAAE6313714 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -80: 8# 0x0000AAAAE62E4BB8 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -80: 9# 0x0000AAAAE62E5104 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -80: 10# 0x0000AAAAE625C1B0 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -80: 11# 0x0000FFFFA09B229C in /lib/aarch64-linux-gnu/libc.so.6 +80: 3# 0x0000AAAAE501FC60 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +80: 4# 0x0000AAAAE4FD1CA8 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +80: 5# 0x0000AAAAE506292C in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +80: 6# 0x0000AAAAE50632E0 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +80: 7# 0x0000AAAAE5063714 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +80: 8# 0x0000AAAAE5034BB8 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +80: 9# 0x0000AAAAE5035104 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +80: 10# 0x0000AAAAE4FAC1B0 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +80: 11# 0x0000FFFFB857229C in /lib/aarch64-linux-gnu/libc.so.6 80: 12# __libc_start_main in /lib/aarch64-linux-gnu/libc.so.6 -80: 13# 0x0000AAAAE625C270 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -80: ---------- -80: **** -80: -80: [00:36:14] -80: -80: **** -80: Pre-condition Violation -80: no stream -80: Violation occurred on line 593 in file ./Code/GraphMol/FileParsers/MaeMolSupplier.cpp -80: Failed Expression: dp_sInStream != nullptr -80: ---------- -80: Stacktrace: -80: 0# Invar::Invariant::toString[abi:cxx11]() const in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu//lib/libRDKitRDGeneral.so.1 -80: 1# Invar::operator<<(std::ostream&, Invar::Invariant const&) in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu//lib/libRDKitRDGeneral.so.1 -80: 2# RDKit::v2::FileParsers::MaeMolSupplier::next() in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu//lib/libRDKitFileParsers.so.1 -80: 3# 0x0000AAAAE62CFC60 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -80: 4# 0x0000AAAAE6281EA0 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -80: 5# 0x0000AAAAE631292C in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -80: 6# 0x0000AAAAE63132E0 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -80: 7# 0x0000AAAAE6313714 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -80: 8# 0x0000AAAAE62E4BB8 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -80: 9# 0x0000AAAAE62E5104 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -80: 10# 0x0000AAAAE625C1B0 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -80: 11# 0x0000FFFFA09B229C in /lib/aarch64-linux-gnu/libc.so.6 -80: 12# __libc_start_main in /lib/aarch64-linux-gnu/libc.so.6 -80: 13# 0x0000AAAAE625C270 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +80: 13# 0x0000AAAAE4FAC270 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest 80: ---------- 80: **** 80: @@ -21471,17 +21377,45 @@ 75: 3.0077234 3.0077234 75: 0.37399312 0.37399312 75: -0.07713336 -0.07713336 -75: [00:36:14] bond with order 0 found on line 11. This is not part of the MDL specification. -75: [00:36:14] bond with order 0 found on line 16. This is not part of the MDL specification. -80: [00:36:14] Found a SCD/SED line with missing/empty SDT specification at line 21 -80: [00:36:14] Found a SCD/SED line with missing/empty SDT specification at line 20 -80: [00:36:14] BEGIN SGROUP line not found on line 14 -80: [00:36:14] Unhandled CTAB feature: 'Unsupported SGroup type '' on line 18'. Molecule skipped. -80: [00:36:14] END SGROUP line not found on line 14 -80: [00:36:14] END SGROUP line not found on line 14 -80: [00:36:14] MRV_COORDINATE_BOND_TYPE SGroup with value 0 does not reference a query bond, ignoring. -80: [00:36:14] MRV_COORDINATE_BOND_TYPE SGroup with value 1 does not reference a query bond, ignoring. -80: [00:36:14] +80: [09:33:08] +80: +80: **** +80: Pre-condition Violation +80: no stream +80: Violation occurred on line 593 in file ./Code/GraphMol/FileParsers/MaeMolSupplier.cpp +80: Failed Expression: dp_sInStream != nullptr +80: ---------- +80: Stacktrace: +80: 0# Invar::Invariant::toString[abi:cxx11]() const in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu//lib/libRDKitRDGeneral.so.1 +80: 1# Invar::operator<<(std::ostream&, Invar::Invariant const&) in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu//lib/libRDKitRDGeneral.so.1 +80: 2# RDKit::v2::FileParsers::MaeMolSupplier::next() in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu//lib/libRDKitFileParsers.so.1 +80: 3# 0x0000AAAAE501FC60 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +80: 4# 0x0000AAAAE4FD1EA0 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +80: 5# 0x0000AAAAE506292C in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +80: 6# 0x0000AAAAE50632E0 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +80: 7# 0x0000AAAAE5063714 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +80: 8# 0x0000AAAAE5034BB8 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +80: 9# 0x0000AAAAE5035104 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +80: 10# 0x0000AAAAE4FAC1B0 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +80: 11# 0x0000FFFFB857229C in /lib/aarch64-linux-gnu/libc.so.6 +80: 12# __libc_start_main in /lib/aarch64-linux-gnu/libc.so.6 +80: 13# 0x0000AAAAE4FAC270 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +80: ---------- +80: **** +80: +80: [09:33:08] Found a SCD/SED line with missing/empty SDT specification at line 21 +75: [09:33:08] bond with order 0 found on line 11. This is not part of the MDL specification. +75: [09:33:08] bond with order 0 found on line 16. This is not part of the MDL specification. +80: [09:33:08] Found a SCD/SED line with missing/empty SDT specification at line 20 +80: [09:33:08] BEGIN SGROUP line not found on line 14 +69: [09:33:08] 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: [09:33:08] 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: [09:33:08] Unhandled CTAB feature: 'Unsupported SGroup type '' on line 18'. Molecule skipped. +80: [09:33:08] END SGROUP line not found on line 14 +80: [09:33:08] END SGROUP line not found on line 14 +80: [09:33:08] MRV_COORDINATE_BOND_TYPE SGroup with value 0 does not reference a query bond, ignoring. +80: [09:33:08] MRV_COORDINATE_BOND_TYPE SGroup with value 1 does not reference a query bond, ignoring. +80: [09:33:08] 80: 80: **** 80: Range Error @@ -21496,40 +21430,41 @@ 80: 3# RDKit::FileParserUtils::finishMolProcessing(RDKit::RWMol*, bool, RDKit::v2::FileParsers::MolFileParserParams const&) in /build/reproducible-path/rdkit-202503.1/obj-aarch64-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-aarch64-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-aarch64-linux-gnu//lib/libRDKitFileParsers.so.1 -80: 6# 0x0000AAAAE62CF8D4 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -80: 7# 0x0000AAAAE6290B04 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -80: 8# 0x0000AAAAE631292C in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -80: 9# 0x0000AAAAE63132E0 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -80: 10# 0x0000AAAAE6313714 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -80: 11# 0x0000AAAAE62E4BB8 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -80: 12# 0x0000AAAAE62E5104 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -80: 13# 0x0000AAAAE625C1B0 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -80: 14# 0x0000FFFFA09B229C in /lib/aarch64-linux-gnu/libc.so.6 +80: 6# 0x0000AAAAE501F8D4 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +80: 7# 0x0000AAAAE4FE0B04 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +80: 8# 0x0000AAAAE506292C in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +80: 9# 0x0000AAAAE50632E0 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +80: 10# 0x0000AAAAE5063714 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +80: 11# 0x0000AAAAE5034BB8 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +80: 12# 0x0000AAAAE5035104 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +80: 13# 0x0000AAAAE4FAC1B0 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +80: 14# 0x0000FFFFB857229C in /lib/aarch64-linux-gnu/libc.so.6 80: 15# __libc_start_main in /lib/aarch64-linux-gnu/libc.so.6 -80: 16# 0x0000AAAAE625C270 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +80: 16# 0x0000AAAAE4FAC270 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest 80: ---------- 80: **** 80: -80: [00:36:14] molecule does not contain a bond matching the MRV_COORDINATE_BOND_TYPE SGroup for bond 99, ignoring. -80: [00:36:14] Multiple ATTCHPT values for atom 2 on line 9 -80: [00:36:14] Found a SCD/SED line with missing/empty SDT specification at line 12 -80: [00:36:14] SMARTS Parse Error: syntax error while parsing: [#6;R -80: [00:36:14] SMARTS Parse Error: Failed parsing SMARTS '[#6;R' for input: '[#6;R' -80: [00:36:14] SMARTS for SMARTSQ '[#6;R' could not be parsed or has no atoms. Ignoring it. -80: [00:36:14] Skipping empty SMARTS value for SMARTSQ. -80: [00:36:14] unrecognized QUERYOP '>' for SMARTSQ. Query ignored. -80: [00:36:14] Found a SCD/SED line with missing/empty SDT specification at line 12 -80: [00:36:14] Can't kekulize mol. Unkekulized atoms: 0 1 2 3 4 -80: [00:36:14] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -80: [00:36:14] WARNING: Skipping property bar because the value includes an illegal blank line -80: [00:36:14] WARNING: Skipping property baz because the value includes an illegal blank line -80: [00:36:14] WARNING: Skipping property bletch +80: [09:33:08] molecule does not contain a bond matching the MRV_COORDINATE_BOND_TYPE SGroup for bond 99, ignoring. +80: [09:33:08] Multiple ATTCHPT values for atom 2 on line 9 +80: [09:33:08] Found a SCD/SED line with missing/empty SDT specification at line 12 +80: [09:33:08] SMARTS Parse Error: syntax error while parsing: [#6;R +80: [09:33:08] SMARTS Parse Error: Failed parsing SMARTS '[#6;R' for input: '[#6;R' +80: [09:33:08] SMARTS for SMARTSQ '[#6;R' could not be parsed or has no atoms. Ignoring it. +80: [09:33:08] Skipping empty SMARTS value for SMARTSQ. +80: [09:33:08] unrecognized QUERYOP '>' for SMARTSQ. Query ignored. +80: [09:33:08] Found a SCD/SED line with missing/empty SDT specification at line 12 +80: [09:33:08] Can't kekulize mol. Unkekulized atoms: 0 1 2 3 4 +80: [09:33:08] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +80: [09:33:08] WARNING: Skipping property bar because the value includes an illegal blank line +80: [09:33:08] WARNING: Skipping property baz because the value includes an illegal blank line +80: [09:33:08] WARNING: Skipping property bletch 80: nope because the name includes a newline -80: [00:36:14] WARNING: Skipping property bletch +80: [09:33:08] WARNING: Skipping property bletch 80: nope2 because the name includes a newline -80: [00:36:14] +80: [09:33:08] 80: 80: **** + 72/238 Test #75: testMolWriter .......................... Passed 0.25 sec 80: Post-condition Violation 80: Element 'QQQ' not found 80: Violation occurred on line 93 in file ./Code/GraphMol/PeriodicTable.h @@ -21539,28 +21474,34 @@ 80: 0# Invar::Invariant::toString[abi:cxx11]() const in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu//lib/libRDKitRDGeneral.so.1 80: 1# Invar::operator<<(std::ostream&, Invar::Invariant const&) in /build/reproducible-path/rdkit-202503.1/obj-aarch64-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-aarch64-linux-gnu//lib/libRDKitFileParsers.so.1 -80: 3# 0x0000FFFFA12E7EA4 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu//lib/libRDKitFileParsers.so.1 -80: 4# 0x0000FFFFA12F8110 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu//lib/libRDKitFileParsers.so.1 -80: 5# 0x0000FFFFA12F8D4C in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu//lib/libRDKitFileParsers.so.1 +80: 3# 0x0000FFFFB8EA7EA4 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu//lib/libRDKitFileParsers.so.1 +80: 4# 0x0000FFFFB8EB8110 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu//lib/libRDKitFileParsers.so.1 +80: 5# 0x0000FFFFB8EB8D4C in /build/reproducible-path/rdkit-202503.1/obj-aarch64-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-aarch64-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-aarch64-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-aarch64-linux-gnu//lib/libRDKitFileParsers.so.1 -80: 9# 0x0000AAAAE6268014 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -80: 10# 0x0000AAAAE631292C in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -80: 11# 0x0000AAAAE63132E0 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -80: 12# 0x0000AAAAE6313714 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -80: 13# 0x0000AAAAE62E4BB8 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -80: 14# 0x0000AAAAE62E5104 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -80: 15# 0x0000AAAAE625C1B0 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -80: 16# 0x0000FFFFA09B229C in /lib/aarch64-linux-gnu/libc.so.6 +80: 9# 0x0000AAAAE4FB8014 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +80: 10# 0x0000AAAAE506292C in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +80: 11# 0x0000AAAAE50632E0 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +80: 12# 0x0000AAAAE5063714 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +80: 13# 0x0000AAAAE5034BB8 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +80: 14# 0x0000AAAAE5035104 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +80: 15# 0x0000AAAAE4FAC1B0 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +80: 16# 0x0000FFFFB857229C in /lib/aarch64-linux-gnu/libc.so.6 80: 17# __libc_start_main in /lib/aarch64-linux-gnu/libc.so.6 -80: 18# 0x0000AAAAE625C270 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +80: 18# 0x0000AAAAE4FAC270 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest 80: ---------- 80: **** 80: -80: [00:36:14] +80: [09:33:08] 80: 80: **** +test 84 + Start 84: molfileStereoCatchTest + +84: Test command: /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/molfileStereoCatchTest +84: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers +84: Test timeout computed to be: 1500 80: Post-condition Violation 80: Element 'QQQ' not found 80: Violation occurred on line 93 in file ./Code/GraphMol/PeriodicTable.h @@ -21570,26 +21511,26 @@ 80: 0# Invar::Invariant::toString[abi:cxx11]() const in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu//lib/libRDKitRDGeneral.so.1 80: 1# Invar::operator<<(std::ostream&, Invar::Invariant const&) in /build/reproducible-path/rdkit-202503.1/obj-aarch64-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-aarch64-linux-gnu//lib/libRDKitFileParsers.so.1 -80: 3# 0x0000FFFFA12E7EA4 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu//lib/libRDKitFileParsers.so.1 -80: 4# 0x0000FFFFA12F8110 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu//lib/libRDKitFileParsers.so.1 -80: 5# 0x0000FFFFA12F8D4C in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu//lib/libRDKitFileParsers.so.1 +80: 3# 0x0000FFFFB8EA7EA4 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu//lib/libRDKitFileParsers.so.1 +80: 4# 0x0000FFFFB8EB8110 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu//lib/libRDKitFileParsers.so.1 +80: 5# 0x0000FFFFB8EB8D4C in /build/reproducible-path/rdkit-202503.1/obj-aarch64-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-aarch64-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-aarch64-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-aarch64-linux-gnu//lib/libRDKitFileParsers.so.1 -80: 9# 0x0000AAAAE6267938 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -80: 10# 0x0000AAAAE631292C in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -80: 11# 0x0000AAAAE63132E0 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -80: 12# 0x0000AAAAE6313714 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -80: 13# 0x0000AAAAE62E4BB8 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -80: 14# 0x0000AAAAE62E5104 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -80: 15# 0x0000AAAAE625C1B0 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -80: 16# 0x0000FFFFA09B229C in /lib/aarch64-linux-gnu/libc.so.6 +80: 9# 0x0000AAAAE4FB7938 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +80: 10# 0x0000AAAAE506292C in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +80: 11# 0x0000AAAAE50632E0 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +80: 12# 0x0000AAAAE5063714 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +80: 13# 0x0000AAAAE5034BB8 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +80: 14# 0x0000AAAAE5035104 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +80: 15# 0x0000AAAAE4FAC1B0 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +80: 16# 0x0000FFFFB857229C in /lib/aarch64-linux-gnu/libc.so.6 80: 17# __libc_start_main in /lib/aarch64-linux-gnu/libc.so.6 -80: 18# 0x0000AAAAE625C270 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +80: 18# 0x0000AAAAE4FAC270 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest 80: ---------- 80: **** 80: -80: [00:36:14] +80: [09:33:08] 80: 80: **** 80: Post-condition Violation @@ -21601,26 +21542,26 @@ 80: 0# Invar::Invariant::toString[abi:cxx11]() const in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu//lib/libRDKitRDGeneral.so.1 80: 1# Invar::operator<<(std::ostream&, Invar::Invariant const&) in /build/reproducible-path/rdkit-202503.1/obj-aarch64-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-aarch64-linux-gnu//lib/libRDKitFileParsers.so.1 -80: 3# 0x0000FFFFA12E7EA4 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu//lib/libRDKitFileParsers.so.1 -80: 4# 0x0000FFFFA12F5AA0 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu//lib/libRDKitFileParsers.so.1 -80: 5# 0x0000FFFFA12F69CC in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu//lib/libRDKitFileParsers.so.1 +80: 3# 0x0000FFFFB8EA7EA4 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu//lib/libRDKitFileParsers.so.1 +80: 4# 0x0000FFFFB8EB5AA0 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu//lib/libRDKitFileParsers.so.1 +80: 5# 0x0000FFFFB8EB69CC in /build/reproducible-path/rdkit-202503.1/obj-aarch64-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-aarch64-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-aarch64-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-aarch64-linux-gnu//lib/libRDKitFileParsers.so.1 -80: 9# 0x0000AAAAE6267FD0 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -80: 10# 0x0000AAAAE631292C in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -80: 11# 0x0000AAAAE63132E0 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -80: 12# 0x0000AAAAE6313714 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -80: 13# 0x0000AAAAE62E4BB8 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -80: 14# 0x0000AAAAE62E5104 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -80: 15# 0x0000AAAAE625C1B0 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -80: 16# 0x0000FFFFA09B229C in /lib/aarch64-linux-gnu/libc.so.6 +80: 9# 0x0000AAAAE4FB7FD0 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +80: 10# 0x0000AAAAE506292C in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +80: 11# 0x0000AAAAE50632E0 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +80: 12# 0x0000AAAAE5063714 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +80: 13# 0x0000AAAAE5034BB8 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +80: 14# 0x0000AAAAE5035104 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +80: 15# 0x0000AAAAE4FAC1B0 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +80: 16# 0x0000FFFFB857229C in /lib/aarch64-linux-gnu/libc.so.6 80: 17# __libc_start_main in /lib/aarch64-linux-gnu/libc.so.6 -80: 18# 0x0000AAAAE625C270 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +80: 18# 0x0000AAAAE4FAC270 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest 80: ---------- 80: **** 80: -80: [00:36:14] +80: [09:33:08] 80: 80: **** 80: Post-condition Violation @@ -21632,71 +21573,100 @@ 80: 0# Invar::Invariant::toString[abi:cxx11]() const in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu//lib/libRDKitRDGeneral.so.1 80: 1# Invar::operator<<(std::ostream&, Invar::Invariant const&) in /build/reproducible-path/rdkit-202503.1/obj-aarch64-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-aarch64-linux-gnu//lib/libRDKitFileParsers.so.1 -80: 3# 0x0000FFFFA12E7EA4 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu//lib/libRDKitFileParsers.so.1 -80: 4# 0x0000FFFFA12F5AA0 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu//lib/libRDKitFileParsers.so.1 -80: 5# 0x0000FFFFA12F69CC in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu//lib/libRDKitFileParsers.so.1 +80: 3# 0x0000FFFFB8EA7EA4 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu//lib/libRDKitFileParsers.so.1 +80: 4# 0x0000FFFFB8EB5AA0 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu//lib/libRDKitFileParsers.so.1 +80: 5# 0x0000FFFFB8EB69CC in /build/reproducible-path/rdkit-202503.1/obj-aarch64-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-aarch64-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-aarch64-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-aarch64-linux-gnu//lib/libRDKitFileParsers.so.1 -80: 9# 0x0000AAAAE6267D08 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -80: 10# 0x0000AAAAE631292C in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -80: 11# 0x0000AAAAE63132E0 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -80: 12# 0x0000AAAAE6313714 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -80: 13# 0x0000AAAAE62E4BB8 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -80: 14# 0x0000AAAAE62E5104 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -80: 15# 0x0000AAAAE625C1B0 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -80: 16# 0x0000FFFFA09B229C in /lib/aarch64-linux-gnu/libc.so.6 +80: 9# 0x0000AAAAE4FB7D08 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +80: 10# 0x0000AAAAE506292C in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +80: 11# 0x0000AAAAE50632E0 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +80: 12# 0x0000AAAAE5063714 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +80: 13# 0x0000AAAAE5034BB8 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +80: 14# 0x0000AAAAE5035104 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +80: 15# 0x0000AAAAE4FAC1B0 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +80: 16# 0x0000FFFFB857229C in /lib/aarch64-linux-gnu/libc.so.6 80: 17# __libc_start_main in /lib/aarch64-linux-gnu/libc.so.6 -80: 18# 0x0000AAAAE625C270 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +80: 18# 0x0000AAAAE4FAC270 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest 80: ---------- 80: **** 80: -80: [00:36:14] atom 3 has a negative isotope value. line: 15 - 72/238 Test #75: testMolWriter .......................... Passed 0.31 sec -test 84 - Start 84: molfileStereoCatchTest - -84: Test command: /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/molfileStereoCatchTest -84: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers -84: Test timeout computed to be: 1500 +80: [09:33:08] atom 3 has a negative isotope value. line: 15 68: Test 68: -68: RP-6306_3d.mrv +68: FalseAtropisomer.mrv 68: 68: Test 68: -68: Sotorasib_atrop1.mrv +68: AtropEnhancedStereo.mrv 68: 68: Test 68: -68: Sotorasib_atrop2.mrv +68: AtropManyChirals.mrv 68: 68: Test 68: -68: Sotorasib_atrop3.mrv +68: AtropManyChiralsEnhanced.mrv 68: 68: Test 68: -68: Sotorasib_atrop4.mrv +68: AtropManyChiralsEnhanced2.mrv 68: 68: Test 68: -68: Sotorasib_atrop5.mrv +68: AtropManyChiralsEnhanced3.mrv 68: -68: [00:36:14] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored -68: [00:36:14] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored 68: Test 68: -68: Sotorasib_atropBad1.mrv +68: AtropManyChiralsEnhanced4.mrv 68: -68: [00:36:14] The 2 defining bonds for an atropisomer are co-planar - atoms are: 7 20 68: Test 68: -68: Sotorasib_atropBad2.mrv +68: BMS-986142_3d_chiral.mrv +68: +68: Test +68: +68: BMS-986142_3d.mrv +68: +68: Test +68: +68: BMS-986142_atrop1.mrv +68: +68: Test +68: +68: BMS-986142_atrop2.mrv +68: +68: Test 68: -68: [00:36:14] The bonds on one end of an atropisomer are both UP or both DOWN - atoms are: 7 20 -80: [00:36:14] Ignoring invalid chirality label: '2_bad_chirality' -80: [00:36:14] +68: BMS-986142_atrop3.mrv +68: +68: Test +68: +68: BMS-986142_atrop4.mrv +68: +68: Test +68: +68: BMS-986142_atrop5.mrv +68: +68: [09:33:08] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored +68: [09:33:08] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored +80: [09:33:08] Ignoring invalid chirality label: '2_bad_chirality' +68: Test +68: +68: BMS-986142_atrop6.mrv +68: +68: Test +68: +68: BMS-986142_atrop7.mrv +68: +68: Test +68: +68: BMS-986142_atrop8.mrv +68: +68: [09:33:08] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored +68: [09:33:08] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored +80: [09:33:09] 80: 80: **** 80: Pre-condition Violation @@ -21709,41 +21679,190 @@ 80: 1# Invar::operator<<(std::ostream&, Invar::Invariant const&) in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu//lib/libRDKitRDGeneral.so.1 80: 2# RDKit::v2::FileParsers::MaeMolSupplier::init() in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu//lib/libRDKitFileParsers.so.1 80: 3# RDKit::v2::FileParsers::MaeMolSupplier::reset() in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu//lib/libRDKitFileParsers.so.1 -80: 4# 0x0000AAAAE62A2054 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -80: 5# 0x0000AAAAE631292C in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -80: 6# 0x0000AAAAE63132E0 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -80: 7# 0x0000AAAAE6313714 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -80: 8# 0x0000AAAAE62E4BB8 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -80: 9# 0x0000AAAAE62E5104 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -80: 10# 0x0000AAAAE625C1B0 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -80: 11# 0x0000FFFFA09B229C in /lib/aarch64-linux-gnu/libc.so.6 +80: 4# 0x0000AAAAE4FF2054 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +80: 5# 0x0000AAAAE506292C in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +80: 6# 0x0000AAAAE50632E0 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +80: 7# 0x0000AAAAE5063714 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +80: 8# 0x0000AAAAE5034BB8 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +80: 9# 0x0000AAAAE5035104 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +80: 10# 0x0000AAAAE4FAC1B0 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +80: 11# 0x0000FFFFB857229C in /lib/aarch64-linux-gnu/libc.so.6 80: 12# __libc_start_main in /lib/aarch64-linux-gnu/libc.so.6 -80: 13# 0x0000AAAAE625C270 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +80: 13# 0x0000AAAAE4FAC270 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest 80: ---------- 80: **** 80: -83: Randomness seeded to: 1339101233 -83: [00:36:14] Invalid or missing fragment id from CDXML fragment, assigning new one... -83: [00:36:14] Explicit valence for atom # 3 N, 4, is greater than permitted -83: [00:36:14] CDXMLParser: failed sanitizing skipping fragment 32 -83: [00:36:14] Bad bond in CDXML skipping fragment 58... -83: [00:36:14] Invalid or missing fragment id from CDXML fragment, assigning new one... -83: [00:36:14] Bad bond in CDXML skipping fragment 58... -84: Randomness seeded to: 2756229938 -84: [00:36:14] Warning: ambiguous stereochemistry - opposing bonds have opposite wedging - at atom 2 ignored. -84: [00:36:14] Warning: ambiguous stereochemistry - opposing bonds have opposite wedging - at atom 2 ignored. -84: [00:36:14] Warning: ambiguous stereochemistry - opposing bonds have opposite wedging - at atom 2 ignored. -84: [00:36:14] Warning: ambiguous stereochemistry - opposing bonds have opposite wedging - at atom 2 ignored. +68: Test +68: +68: BMS-986142_atropBad2.mrv +68: +68: [09:33:09] The bonds on one end of an atropisomer are both UP or both DOWN - atoms are: 7 29 +83: Randomness seeded to: 2072741528 +83: [09:33:09] Invalid or missing fragment id from CDXML fragment, assigning new one... +83: [09:33:09] Explicit valence for atom # 3 N, 4, is greater than permitted +83: [09:33:09] CDXMLParser: failed sanitizing skipping fragment 32 +83: [09:33:09] Bad bond in CDXML skipping fragment 58... +83: [09:33:09] Invalid or missing fragment id from CDXML fragment, assigning new one... +83: [09:33:09] Bad bond in CDXML skipping fragment 58... +69: ---------------------------------- +69: ---------------------------------- +69: [09:33:09] +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-aarch64-linux-gnu//lib/libRDKitRDGeneral.so.1 +69: 1# Invar::operator<<(std::ostream&, Invar::Invariant const&) in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu//lib/libRDKitRDGeneral.so.1 +69: 2# RDKit::setAtomRLabel(RDKit::Atom*, int) in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu//lib/libRDKitGraphMol.so.1 +69: 3# 0x0000AAAAABB3F23C in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersTest1 +69: 4# 0x0000AAAAABBA49A4 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersTest1 +69: 5# 0x0000AAAAABB15BF8 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersTest1 +69: 6# 0x0000FFFF9453229C in /lib/aarch64-linux-gnu/libc.so.6 +69: 7# __libc_start_main in /lib/aarch64-linux-gnu/libc.so.6 +69: 8# 0x0000AAAAABB15E30 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersTest1 +69: ---------- +69: **** +69: +69: [09:33:09] WARNING: could not find number of expected rings. Switching to an approximate ring finding algorithm. +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: [09:33:09] The 2 defining bonds for an atropisomer are co-planar - atoms are: 17 21 +84: Randomness seeded to: 1277314769 +84: [09:33:09] Warning: ambiguous stereochemistry - opposing bonds have opposite wedging - at atom 2 ignored. +84: [09:33:09] Warning: ambiguous stereochemistry - opposing bonds have opposite wedging - at atom 2 ignored. +84: [09:33:09] Warning: ambiguous stereochemistry - opposing bonds have opposite wedging - at atom 2 ignored. +84: [09:33:09] Warning: ambiguous stereochemistry - opposing bonds have opposite wedging - at atom 2 ignored. 84: =============================================================================== 84: All tests passed (142 assertions in 6 test cases) 84: - 73/238 Test #84: molfileStereoCatchTest ................. Passed 0.04 sec +83: [09:33:09] WARNING: not removing hydrogen atom without neighbors +83: [09:33:09] WARNING: not removing hydrogen atom without neighbors + 73/238 Test #84: molfileStereoCatchTest ................. Passed 0.05 sec test 85 Start 85: connectTheDotsTest 85: Test command: /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/connectTheDotsTest 85: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers 85: Test timeout computed to be: 1500 +83: [09:33:09] WARNING: not removing hydrogen atom without neighbors +83: [09:33:09] WARNING: not removing hydrogen atom without neighbors +83: [09:33:09] WARNING: not removing hydrogen atom without neighbors +83: [09:33:09] WARNING: not removing hydrogen atom without neighbors +83: [09:33:09] WARNING: not removing hydrogen atom without neighbors +83: [09:33:09] WARNING: not removing hydrogen atom without neighbors +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: [09:33:09] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 2 ignored +68: [09:33:09] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 2 ignored +83: [09:33:09] WARNING: not removing hydrogen atom without neighbors +83: [09:33:09] WARNING: not removing hydrogen atom without neighbors +83: [09:33:09] CDXMLParser: Schema 80180 step 80181 ReactionStepAgents reaction fragment 64603 not found in document. +68: Test +68: +68: RP-6306_atropBad1.mrv +68: +68: [09:33:09] 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: +68: [09:33:09] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 2 ignored +68: [09:33:09] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 2 ignored +68: [09:33:09] The 2 defining bonds for an atropisomer are co-planar - atoms are: 2 8 +80: [09:33:09] Can't kekulize mol. Unkekulized atoms: 0 1 2 3 4 +83: [09:33:09] Incomplete atom labelling, cannot make bond +83: [09:33:09] Incomplete atom labelling, cannot make bond +80: [09:33:09] 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.[09:33:09] 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: [09:33:09] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +80: [09:33:09] 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: [09:33:09] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +68: Test +68: +68: RP-6306_3d.mrv +68: +68: Test +68: +68: Sotorasib_atrop1.mrv +68: +68: Test +68: +68: Sotorasib_atrop2.mrv +68: +68: Test +68: +68: Sotorasib_atrop3.mrv +68: +68: Test +68: +68: Sotorasib_atrop4.mrv +68: +68: Test +68: +68: Sotorasib_atrop5.mrv +68: +68: [09:33:09] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored +68: [09:33:09] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored +83: [09:33:09] Incomplete atom labelling, cannot make bond +68: Test +68: +68: Sotorasib_atropBad1.mrv +68: +68: [09:33:09] The 2 defining bonds for an atropisomer are co-planar - atoms are: 7 20 +68: Test +68: +68: Sotorasib_atropBad2.mrv +68: +68: [09:33:09] The bonds on one end of an atropisomer are both UP or both DOWN - atoms are: 7 20 +83: [09:33:09] Failed to parse XML fragment 5 node: n attribute: id: mydoghasfleas +83: [09:33:09] Failed to parse XML fragment 5 node: n attribute: id: mydoghasfleas +83: [09:33:09] Failed to parse XML fragment 5 node: b attribute: Order: slartibartfast +83: [09:33:09] Failed to parse XML fragment 5 node: b attribute: Order: 5 +85: Randomness seeded to: 550120836 +85: =============================================================================== +85: All tests passed (8 assertions in 1 test case) +85: +83: [09:33:09] Invalid or missing fragment id from CDXML fragment, assigning new one... + 74/238 Test #85: connectTheDotsTest ..................... Passed 0.06 sec 68: Test 68: 68: Sotorasib_3d.mrv @@ -21764,7 +21883,23 @@ 68: 68: ZM374979_atropBad1.mrv 68: -68: [00:36:14] The 2 defining bonds for an atropisomer are co-planar - atoms are: 0 31 +68: [09:33:09] The 2 defining bonds for an atropisomer are co-planar - atoms are: 0 31 +test 86 + Start 86: v2MolSuppliers + +86: Test command: /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/v2MolSuppliers +86: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers +86: Test timeout computed to be: 1500 +83: =============================================================================== +83: All tests passed (263 assertions in 7 test cases) +83: + 75/238 Test #83: cdxmlParserCatchTest ................... Passed 0.18 sec +test 87 + Start 87: v2FileParsersCatchTest + +87: Test command: /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/v2FileParsersCatchTest +87: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers +87: Test timeout computed to be: 1500 68: Test 68: 68: mrtx1719_3d.mrv @@ -21785,36 +21920,27 @@ 68: 68: mrtx1719_atropBad1.mrv 68: -68: [00:36:15] The 2 defining bonds for an atropisomer are co-planar - atoms are: 15 16 -83: [00:36:15] WARNING: not removing hydrogen atom without neighbors -83: [00:36:15] WARNING: not removing hydrogen atom without neighbors -83: [00:36:15] WARNING: not removing hydrogen atom without neighbors -83: [00:36:15] WARNING: not removing hydrogen atom without neighbors -83: [00:36:15] WARNING: not removing hydrogen atom without neighbors -83: [00:36:15] WARNING: not removing hydrogen atom without neighbors -83: [00:36:15] WARNING: not removing hydrogen atom without neighbors -83: [00:36:15] WARNING: not removing hydrogen atom without neighbors -80: [00:36:15] Can't kekulize mol. Unkekulized atoms: 0 1 2 3 4 -83: [00:36:15] WARNING: not removing hydrogen atom without neighbors -83: [00:36:15] WARNING: not removing hydrogen atom without neighbors -83: [00:36:15] CDXMLParser: Schema 80180 step 80181 ReactionStepAgents reaction fragment 64603 not found in document. -85: Randomness seeded to: 389582844 -85: =============================================================================== -85: All tests passed (8 assertions in 1 test case) -85: -80: [00:36:15] 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.[00:36:15] 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: [00:36:15] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -80: [00:36:15] 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: [00:36:15] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. - 74/238 Test #85: connectTheDotsTest ..................... Passed 0.04 sec -test 86 - Start 86: v2MolSuppliers +68: [09:33:09] The 2 defining bonds for an atropisomer are co-planar - atoms are: 15 16 +87: Randomness seeded to: 814186861 +87: =============================================================================== +87: All tests passed (6 assertions in 1 test case) +87: + 76/238 Test #87: v2FileParsersCatchTest ................. Passed 0.04 sec +test 88 + Start 88: atropisomersCatch -86: Test command: /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/v2MolSuppliers -86: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers -86: Test timeout computed to be: 1500 -83: [00:36:15] Incomplete atom labelling, cannot make bond -83: [00:36:15] Incomplete atom labelling, cannot make bond +88: Test command: /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/atropisomersCatch +88: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers +88: Test timeout computed to be: 1500 +86: Randomness seeded to: 1473890007 +86: [09:33:09] Ignoring invalid chirality label: '12_R_1_3_4_5' +86: [09:33:09] Ignoring invalid chirality label: '12_ANR_1_3_4_15' +86: [09:33:09] Ignoring invalid chirality label: '2_S_1_3_4' +86: [09:33:09] Ignoring invalid chirality label: '2_ANS_1_3_4_5_2' +86: =============================================================================== +86: All tests passed (24 assertions in 6 test cases) +86: + 77/238 Test #86: v2MolSuppliers ......................... Passed 0.06 sec 68: Test 68: 68: AlexRxn.mrv @@ -21855,38 +21981,20 @@ 68: 68: EmptyRxn.mrv 68: -68: [00:36:15] initialization failed -83: [00:36:15] Incomplete atom labelling, cannot make bond -86: Randomness seeded to: 262001081 -86: [00:36:15] Ignoring invalid chirality label: '12_R_1_3_4_5' -86: [00:36:15] Ignoring invalid chirality label: '12_ANR_1_3_4_15' -86: [00:36:15] Ignoring invalid chirality label: '2_S_1_3_4' -86: [00:36:15] Ignoring invalid chirality label: '2_ANS_1_3_4_5_2' -86: =============================================================================== -86: All tests passed (24 assertions in 6 test cases) -86: - 75/238 Test #86: v2MolSuppliers ......................... Passed 0.06 sec -83: [00:36:15] Failed to parse XML fragment 5 node: n attribute: id: mydoghasfleas -83: [00:36:15] Failed to parse XML fragment 5 node: n attribute: id: mydoghasfleas -test 87 - Start 87: v2FileParsersCatchTest - -87: Test command: /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/v2FileParsersCatchTest -87: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers -87: Test timeout computed to be: 1500 -83: [00:36:15] Failed to parse XML fragment 5 node: b attribute: Order: slartibartfast -83: [00:36:15] Failed to parse XML fragment 5 node: b attribute: Order: 5 -83: [00:36:15] Invalid or missing fragment id from CDXML fragment, assigning new one... -83: =============================================================================== -83: All tests passed (263 assertions in 7 test cases) -83: - 76/238 Test #83: cdxmlParserCatchTest ................... Passed 0.19 sec -test 88 - Start 88: atropisomersCatch +68: [09:33:09] initialization failed +test 89 + Start 89: multithreadedSupplierCatchTest -88: Test command: /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/atropisomersCatch -88: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers -88: Test timeout computed to be: 1500 +89: Test command: /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/multithreadedSupplierCatchTest +89: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers +89: Test timeout computed to be: 1500 +69: [09:33:09] SMARTS Parse Error: syntax error while parsing: MyDogHasFleas +69: [09:33:09] SMARTS Parse Error: Failed parsing SMARTS 'MyDogHasFleas' for input: 'MyDogHasFleas' +88: Randomness seeded to: 596992208 +88: =============================================================================== +88: All tests passed (26 assertions in 2 test cases) +88: + 78/238 Test #88: atropisomersCatch ...................... Passed 0.04 sec 68: Test 68: 68: RxnNoCoords.mrv @@ -21975,69 +22083,24 @@ 68: 68: Smiles1 68: - 77/238 Test #68: testMrvToMol ........................... Passed 1.19 sec -test 89 - Start 89: multithreadedSupplierCatchTest - -89: Test command: /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/multithreadedSupplierCatchTest -89: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers -89: Test timeout computed to be: 1500 -87: Randomness seeded to: 2729476006 -87: =============================================================================== -87: All tests passed (6 assertions in 1 test case) -87: - 78/238 Test #87: v2FileParsersCatchTest ................. Passed 0.04 sec test 90 Start 90: testSubstructMatch 90: Test command: /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/Substruct/testSubstructMatch 90: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/Substruct 90: Test timeout computed to be: 1500 -69: [00:36:15] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 1 ignored -69: [00:36:15] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 1 ignored -69: [00:36:15] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 1 ignored -69: [00:36:15] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 1 ignored -88: Randomness seeded to: 3750878470 -88: =============================================================================== -88: All tests passed (26 assertions in 2 test cases) -88: -69: [00:36:15] 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: [00:36:15] -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-aarch64-linux-gnu//lib/libRDKitRDGeneral.so.1 -69: 1# Invar::operator<<(std::ostream&, Invar::Invariant const&) in /build/reproducible-path/rdkit-202503.1/obj-aarch64-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-aarch64-linux-gnu//lib/libRDKitFileParsers.so.1 -69: 3# 0x0000FFFF98E67EA4 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu//lib/libRDKitFileParsers.so.1 -69: 4# 0x0000FFFF98E75AA0 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu//lib/libRDKitFileParsers.so.1 -69: 5# 0x0000FFFF98E769CC in /build/reproducible-path/rdkit-202503.1/obj-aarch64-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-aarch64-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-aarch64-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-aarch64-linux-gnu//lib/libRDKitFileParsers.so.1 -69: 9# 0x0000AAAAE6B2F77C in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersTest1 -69: 10# 0x0000AAAAE6BA4944 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersTest1 -69: 11# 0x0000AAAAE6B15BF8 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersTest1 -69: 12# 0x0000FFFF9852229C in /lib/aarch64-linux-gnu/libc.so.6 -69: 13# __libc_start_main in /lib/aarch64-linux-gnu/libc.so.6 -69: 14# 0x0000AAAAE6B15E30 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersTest1 -69: ---------- -69: **** -69: - 79/238 Test #88: atropisomersCatch ...................... Passed 0.04 sec +40: [09:33:09] done: 500000 +40: [09:33:09] Done + 79/238 Test #68: testMrvToMol ........................... Passed 0.88 sec test 91 Start 91: substructTestCatch 91: Test command: /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/Substruct/substructTestCatch 91: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/Substruct 91: Test timeout computed to be: 1500 +69: [09:33:09] Empty atom list: 'M ALS 1 0 F' on line 8. 90: ----------------- Test 1 +40: [09:33:09] Testing hanoi with a functor. 90: Done 90: 90: ----------------- Test 2 @@ -22061,15 +22124,97 @@ 90: ----------------- Testing serial numbers on recursive queries 90: Done 90: -90: [00:36:15] ------------------------------------- -90: [00:36:15] Test multithreading +90: [09:33:09] ------------------------------------- +90: [09:33:09] Test multithreading +69: de_DE.UTF-8 +69: [09:33:09] ------------------------------------- +69: [09:33:09] Test multithreading Locale Switching 90: reading molecules +40: [09:33:09] Done +40: [09:33:09] Testing basic partition refinement. +40: [09:33:09] Done +40: [09:33:09] Testing partition refinement with neighbors. +40: [09:33:09] Done +40: [09:33:09] testing canonicalization via tie breaking. +40: [09:33:09] Done +40: [09:33:09] testing canonicalization using the wrapper. +40: [09:33:09] Done +40: [09:33:09] testing some specific ordering problems +40: [09:33:09] Finished +40: [09:33:09] testing chiral invariants. +40: [09:33:09] Finished +40: [09:33:09] testing unique ranks in w.r.t. renumbering. +69: [09:33:09] Test multithreading (Done) +69: [09:33:09] ------------------------------------- +69: *************************************** +69: *************************************** 90: hits: 1111110111111111111111011111100011011011111101010111011110111101111111111111111111111011111011111110 90: processing 90: launch :0 +69: [09:33:09] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 90: launch :1 90: launch :2 +69: [09:33:09] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 90: launch :3 +69: [09:33:09] bond with order 0 found on line 7. This is not part of the MDL specification. +40: [09:33:09] Finished +40: [09:33:09] testing mol fragments. +40: [09:33:09] Finished +40: [09:33:09] testing protein round-tripping. +69: [09:33:09] Skipping unrecognized collection type at line 26: MDLV30/HILITE BONDS=(1 7) +69: [09:33:09] Skipping unrecognized collection type at line 27: MDLV30/HILITE ATOMS=(1 7) +69: [09:33:09] 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 +89: Randomness seeded to: 4127312407 +89: [09:33:09] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [09:33:09] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [09:33:09] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [09:33:09] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [09:33:09] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [09:33:09] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [09:33:09] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [09:33:09] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [09:33:09] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [09:33:09] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [09:33:09] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [09:33:09] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [09:33:09] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [09:33:09] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [09:33:09] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [09:33:09] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [09:33:09] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [09:33:09] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [09:33:09] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [09:33:09] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [09:33:09] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [09:33:09] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [09:33:09] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [09:33:09] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [09:33:09] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [09:33:09] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [09:33:09] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [09:33:09] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [09:33:09] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [09:33:09] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [09:33:09] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [09:33:09] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [09:33:09] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [09:33:09] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [09:33:09] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [09:33:09] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [09:33:09] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [09:33:09] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [09:33:09] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [09:33:09] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [09:33:09] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [09:33:09] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [09:33:09] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [09:33:09] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [09:33:09] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [09:33:09] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. 90: done 90: hits2: 1111110111111111111111011111100011011011111101010111011110111101111111111111111111111011111011111110 90: processing2 @@ -22077,236 +22222,199 @@ 90: launch2 :1 90: launch2 :2 90: launch2 :3 +89: [09:33:09] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [09:33:09] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [09:33:09] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [09:33:09] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [09:33:09] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [09:33:09] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [09:33:09] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [09:33:09] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [09:33:09] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [09:33:09] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [09:33:09] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [09:33:09] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [09:33:09] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [09:33:09] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [09:33:09] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [09:33:09] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [09:33:09] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [09:33:09] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [09:33:09] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [09:33:09] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [09:33:09] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [09:33:09] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [09:33:09] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [09:33:09] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [09:33:09] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [09:33:09] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [09:33:09] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [09:33:09] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [09:33:09] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [09:33:09] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [09:33:09] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [09:33:09] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [09:33:09] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [09:33:09] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [09:33:09] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [09:33:09] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [09:33:09] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [09:33:09] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [09:33:09] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [09:33:09] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [09:33:09] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [09:33:09] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [09:33:09] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [09:33:09] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [09:33:09] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [09:33:09] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [09:33:09] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [09:33:09] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [09:33:09] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [09:33:09] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [09:33:09] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [09:33:09] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [09:33:09] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [09:33:09] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [09:33:09] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [09:33:09] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [09:33:09] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [09:33:09] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [09:33:09] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [09:33:09] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. 90: done +89: [09:33:09] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [09:33:09] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. 90: preprocessing 3 +89: [09:33:09] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [09:33:09] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [09:33:09] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [09:33:09] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [09:33:09] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [09:33:09] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. 90: hits3: 1110100011001000010011100110100011011000010101000100110010101111011100101000001111110000010100100110 90: processing3 90: launch3 :0 +89: [09:33:09] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. 90: launch3 :1 +89: [09:33:09] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. 90: launch3 :2 +89: [09:33:09] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. 90: launch3 :3 +89: [09:33:09] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [09:33:09] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [09:33:09] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [09:33:09] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [09:33:09] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [09:33:09] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [09:33:09] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [09:33:09] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [09:33:09] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [09:33:09] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [09:33:09] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [09:33:09] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [09:33:09] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [09:33:09] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [09:33:09] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [09:33:09] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [09:33:09] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [09:33:09] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [09:33:09] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [09:33:09] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [09:33:09] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [09:33:09] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [09:33:09] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [09:33:09] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [09:33:09] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [09:33:09] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [09:33:09] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [09:33:09] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [09:33:09] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [09:33:09] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [09:33:09] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [09:33:09] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [09:33:09] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [09:33:09] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [09:33:09] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [09:33:09] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [09:33:09] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [09:33:09] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [09:33:09] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [09:33:09] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [09:33:09] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [09:33:09] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [09:33:09] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [09:33:09] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [09:33:09] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [09:33:09] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [09:33:09] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [09:33:09] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [09:33:09] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [09:33:09] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [09:33:09] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [09:33:09] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [09:33:09] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [09:33:09] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [09:33:09] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [09:33:09] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [09:33:09] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [09:33:09] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [09:33:09] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [09:33:09] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [09:33:09] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [09:33:09] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [09:33:09] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [09:33:09] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [09:33:09] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [09:33:09] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [09:33:09] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [09:33:09] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [09:33:09] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [09:33:09] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [09:33:09] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [09:33:09] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [09:33:09] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [09:33:09] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [09:33:09] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [09:33:09] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [09:33:09] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [09:33:09] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [09:33:09] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [09:33:09] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [09:33:09] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [09:33:09] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [09:33:09] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [09:33:09] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. 29: All 191 tests passed -89: Randomness seeded to: 4252877975 -89: [00:36:15] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [00:36:15] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [00:36:15] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [00:36:15] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [00:36:15] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [00:36:15] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [00:36:15] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [00:36:15] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [00:36:15] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [00:36:15] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [00:36:15] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [00:36:15] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [00:36:15] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [00:36:15] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [00:36:15] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [00:36:15] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [00:36:15] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [00:36:15] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [00:36:15] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [00:36:15] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [00:36:15] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [00:36:15] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [00:36:15] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [00:36:15] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [00:36:15] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [00:36:15] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [00:36:15] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [00:36:15] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [00:36:15] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [00:36:15] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [00:36:15] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [00:36:15] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [00:36:15] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [00:36:15] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [00:36:15] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [00:36:15] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [00:36:15] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [00:36:15] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [00:36:15] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [00:36:15] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [00:36:15] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [00:36:15] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [00:36:15] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [00:36:15] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [00:36:15] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [00:36:15] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [00:36:15] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [00:36:15] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [00:36:15] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [00:36:15] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [00:36:15] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -69: [00:36:15] Warning: molecule is tagged as 3D, but all Z coords are zero and 2D stereo markers have been found, marking the mol as 2D. -89: [00:36:15] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -69: [00:36:15] Warning: molecule is tagged as 3D, but all Z coords are zero and 2D stereo markers have been found, marking the mol as 2D. -89: [00:36:15] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [00:36:15] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [00:36:15] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [00:36:15] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [00:36:15] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [00:36:15] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [00:36:15] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [00:36:15] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [00:36:15] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [00:36:15] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [00:36:15] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [00:36:15] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [00:36:15] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [00:36:15] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [00:36:15] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [00:36:15] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [00:36:15] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [00:36:15] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [00:36:15] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [00:36:15] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [00:36:15] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [00:36:15] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. 90: done -90: [00:36:15] done -90: [00:36:15] ------------------------------------- -90: [00:36:15] Test GitHub issue 15 -90: [00:36:15] done -90: [00:36:15] ------------------------------------- -90: [00:36:15] Test GitHub issue 409 -90: [00:36:15] done -90: [00:36:15] ------------------------------------- -90: [00:36:15] Test chiral matching -90: [00:36:15] done -90: [00:36:15] ------------------------------------- -90: [00:36:15] Test GitHub issue 688: partially specified chiral substructure queries don't work properly -89: [00:36:15] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [00:36:15] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [00:36:15] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [00:36:15] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [00:36:15] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [00:36:15] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [00:36:15] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [00:36:15] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [00:36:15] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [00:36:15] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -90: [00:36:15] done -90: [00:36:15] ------------------------------------- -90: [00:36:15] Test dative-bond matching -89: [00:36:15] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [00:36:15] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [00:36:15] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [00:36:15] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [00:36:15] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [00:36:15] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -90: [00:36:15] done -89: [00:36:15] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -90: [00:36:15] ------------------------------------- -89: [00:36:15] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [00:36:15] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -90: [00:36:15] Test cis/trans matching -89: [00:36:15] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [00:36:15] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [00:36:15] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [00:36:15] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [00:36:15] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [00:36:15] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [00:36:15] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [00:36:15] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [00:36:15] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [00:36:15] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [00:36:15] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [00:36:15] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [00:36:15] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [00:36:15] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [00:36:15] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [00:36:15] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [00:36:15] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [00:36:15] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [00:36:15] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -90: [00:36:15] done -90: [00:36:15] ------------------------------------- -90: [00:36:15] Test cis/trans matching part 2 -89: [00:36:15] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [00:36:15] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [00:36:15] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [00:36:15] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [00:36:15] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [00:36:15] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [00:36:15] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [00:36:15] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [00:36:15] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [00:36:15] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [00:36:15] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [00:36:15] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [00:36:15] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -90: [00:36:15] done -90: [00:36:15] ------------------------------------- -90: [00:36:15] Testing Github #1389: Substructure matching with chirality failure when query is built from SMARTS -89: [00:36:15] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [00:36:15] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [00:36:15] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [00:36:15] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [00:36:15] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [00:36:15] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [00:36:15] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -90: [00:36:15] done -89: [00:36:15] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [00:36:15] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [00:36:15] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [00:36:15] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [00:36:15] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [00:36:15] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [00:36:15] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [00:36:15] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [00:36:15] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [00:36:15] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [00:36:15] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [00:36:15] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [00:36:15] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [00:36:15] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [00:36:15] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [00:36:15] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [00:36:15] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [00:36:15] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [00:36:15] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [00:36:15] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [00:36:15] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [00:36:15] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [00:36:15] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [00:36:15] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [00:36:15] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [00:36:15] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [00:36:15] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [00:36:15] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [00:36:15] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [00:36:15] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [00:36:15] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [00:36:15] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [00:36:15] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [00:36:15] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [00:36:15] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [00:36:15] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [00:36:15] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [00:36:15] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [00:36:15] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [00:36:15] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [00:36:15] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [00:36:15] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [00:36:15] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [00:36:15] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [00:36:15] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [00:36:15] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [00:36:15] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [00:36:15] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [00:36:15] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [00:36:15] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [00:36:15] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [00:36:15] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [00:36:15] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [00:36:15] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [00:36:15] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [00:36:15] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [00:36:15] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -90: [00:36:15] ------------------------------------- -90: [00:36:15] Testing matching E/Z against Cis/Trans stereo bonds -90: [00:36:15] +90: [09:33:09] done +90: [09:33:09] ------------------------------------- +90: [09:33:09] Test GitHub issue 15 +90: [09:33:09] done +90: [09:33:09] ------------------------------------- +90: [09:33:09] Test GitHub issue 409 +90: [09:33:09] done +90: [09:33:09] ------------------------------------- +90: [09:33:09] Test chiral matching +90: [09:33:09] done +90: [09:33:09] ------------------------------------- +90: [09:33:09] Test GitHub issue 688: partially specified chiral substructure queries don't work properly +90: [09:33:09] done +90: [09:33:09] ------------------------------------- +90: [09:33:09] Test dative-bond matching +90: [09:33:09] done +90: [09:33:09] ------------------------------------- +90: [09:33:09] Test cis/trans matching +90: [09:33:09] done +90: [09:33:09] ------------------------------------- +90: [09:33:09] Test cis/trans matching part 2 +90: [09:33:09] done +90: [09:33:09] ------------------------------------- +90: [09:33:09] Testing Github #1389: Substructure matching with chirality failure when query is built from SMARTS +90: [09:33:09] done +90: [09:33:09] ------------------------------------- +90: [09:33:09] Testing matching E/Z against Cis/Trans stereo bonds +90: [09:33:09] 90: 90: **** 90: Pre-condition Violation @@ -22319,15 +22427,15 @@ 90: 1# Invar::operator<<(std::ostream&, Invar::Invariant const&) in /build/reproducible-path/rdkit-202503.1/obj-aarch64-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-aarch64-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-aarch64-linux-gnu//lib/libRDKitSubstructMatch.so.1 -90: 4# 0x0000AAAAB85EAD90 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/Substruct/testSubstructMatch -90: 5# 0x0000AAAAB85D99A8 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/Substruct/testSubstructMatch -90: 6# 0x0000FFFFBAD4229C in /lib/aarch64-linux-gnu/libc.so.6 +90: 4# 0x0000AAAAC12BAD90 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/Substruct/testSubstructMatch +90: 5# 0x0000AAAAC12A99A8 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/Substruct/testSubstructMatch +90: 6# 0x0000FFFFB373229C in /lib/aarch64-linux-gnu/libc.so.6 90: 7# __libc_start_main in /lib/aarch64-linux-gnu/libc.so.6 -90: 8# 0x0000AAAAB85D9BB0 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/Substruct/testSubstructMatch +90: 8# 0x0000AAAAC12A9BB0 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/Substruct/testSubstructMatch 90: ---------- 90: **** 90: -90: [00:36:15] +90: [09:33:09] 90: 90: **** 90: Pre-condition Violation @@ -22340,269 +22448,216 @@ 90: 1# Invar::operator<<(std::ostream&, Invar::Invariant const&) in /build/reproducible-path/rdkit-202503.1/obj-aarch64-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-aarch64-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-aarch64-linux-gnu//lib/libRDKitSubstructMatch.so.1 -90: 4# 0x0000AAAAB85EB3E0 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/Substruct/testSubstructMatch -90: 5# 0x0000AAAAB85D99A8 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/Substruct/testSubstructMatch -90: 6# 0x0000FFFFBAD4229C in /lib/aarch64-linux-gnu/libc.so.6 +90: 4# 0x0000AAAAC12BB3E0 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/Substruct/testSubstructMatch +90: 5# 0x0000AAAAC12A99A8 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/Substruct/testSubstructMatch +90: 6# 0x0000FFFFB373229C in /lib/aarch64-linux-gnu/libc.so.6 90: 7# __libc_start_main in /lib/aarch64-linux-gnu/libc.so.6 -90: 8# 0x0000AAAAB85D9BB0 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/Substruct/testSubstructMatch +90: 8# 0x0000AAAAC12A9BB0 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/Substruct/testSubstructMatch 90: ---------- 90: **** 90: -90: [00:36:15] ------------------------------------- -90: [00:36:15] Test substructure matching with a pathological case for symmetric SSSR -90: [00:36:15] ------------------------------------- -90: [00:36:15] Test isAtomTerminalRGroupOrQueryHydrogen -89: [00:36:15] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [00:36:15] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [00:36:15] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [00:36:15] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [00:36:15] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [00:36:15] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [00:36:15] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [00:36:15] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [00:36:15] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [00:36:15] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [00:36:15] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [00:36:15] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. - 80/238 Test #90: testSubstructMatch ..................... Passed 0.27 sec +90: [09:33:09] ------------------------------------- +90: [09:33:09] Test substructure matching with a pathological case for symmetric SSSR +90: [09:33:09] ------------------------------------- +90: [09:33:09] Test isAtomTerminalRGroupOrQueryHydrogen + 80/238 Test #90: testSubstructMatch ..................... Passed 0.25 sec test 92 Start 92: testGenericGroups 92: Test command: /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/GenericGroups/testGenericGroups 92: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/GenericGroups 92: Test timeout computed to be: 1500 -69: ---------------------------------- -69: ---------------------------------- -69: [00:36:15] -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-aarch64-linux-gnu//lib/libRDKitRDGeneral.so.1 -69: 1# Invar::operator<<(std::ostream&, Invar::Invariant const&) in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu//lib/libRDKitRDGeneral.so.1 -69: 2# RDKit::setAtomRLabel(RDKit::Atom*, int) in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu//lib/libRDKitGraphMol.so.1 -69: 3# 0x0000AAAAE6B3F23C in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersTest1 -69: 4# 0x0000AAAAE6BA49A4 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersTest1 -69: 5# 0x0000AAAAE6B15BF8 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersTest1 -69: 6# 0x0000FFFF9852229C in /lib/aarch64-linux-gnu/libc.so.6 -69: 7# __libc_start_main in /lib/aarch64-linux-gnu/libc.so.6 -69: 8# 0x0000AAAAE6B15E30 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersTest1 -69: ---------- -69: **** -69: -69: [00:36:15] WARNING: could not find number of expected rings. Switching to an approximate ring finding algorithm. -29: -29: Computing MMFF94 energies for /build/reproducible-path/rdkit-202503.1/Code/ForceField/MMFF/test_data/MMFF94_hypervalent.sdf... -91: Randomness seeded to: 2415866191 +91: Randomness seeded to: 15561268 91: =============================================================================== 91: All tests passed (242 assertions in 12 test cases) 91: - 81/238 Test #91: substructTestCatch ..................... Passed 0.42 sec + 81/238 Test #91: substructTestCatch ..................... Passed 0.27 sec test 93 Start 93: testReaction 93: Test command: /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/ChemReactions/testReaction 93: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/ChemReactions 93: Test timeout computed to be: 1500 +12: .................. +12: ---------------------------------------------------------------------- +12: Ran 18 tests in 1.779s +12: +12: OK 93: smi: O=C1CNC(=O)CN1 93: 1: O=C1CNC(=O)CN1 93: 2: COOC -93: [00:36:15] SMARTS Parse Error: syntax error while parsing: [Q:1][C:2][C:3](=[O:4])[O:5] -93: [00:36:15] 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: [09:33:09] SMARTS Parse Error: syntax error while parsing: [Q:1][C:2][C:3](=[O:4])[O:5] +93: [09:33:09] 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: [00:36:15] product atom-mapping number 1 found multiple times. -93: [00:36:15] mapped atoms in the reactants were not mapped in the products. +93: [09:33:09] product atom-mapping number 1 found multiple times. +93: [09:33:09] mapped atoms in the reactants were not mapped in the products. 93: unmapped numbers are: 4 -93: [00:36:15] atom 0 in product 0 has multiple charge specifications. + 82/238 Test #12: pyBV ................................... Passed 2.18 sec +test 94 + Start 94: testReactionFingerprints + +94: Test command: /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/ChemReactions/testReactionFingerprints +94: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/ChemReactions +94: Test timeout computed to be: 1500 +93: [09:33:09] atom 0 in product 0 has multiple charge specifications. 93: mass: 15.0001 93: Oc1ccccn1 93: Oc1ccc[nH]1 -93: [00:36:15] SMARTS Parse Error: syntax error while parsing: ([C:1](=O)O.[C:2] -93: [00:36:15] SMARTS Parse Error: Failed parsing SMARTS '([C:1](=O)O.[C:2]' for input: '([C:1](=O)O.[C:2]' -93: [00:36:15] SMARTS Parse Error: syntax error while parsing: ([C:2] -93: [00:36:15] SMARTS Parse Error: Failed parsing SMARTS '([C:2]' for input: '([C:2]' -93: [00:36:15] SMARTS Parse Error: syntax error while parsing: [C:1](=O)O).[C:2] -93: [00:36:15] SMARTS Parse Error: Failed parsing SMARTS '[C:1](=O)O).[C:2]' for input: '[C:1](=O)O).[C:2]' -93: [00:36:15] SMARTS Parse Error: syntax error while parsing: [C:2]) -93: [00:36:15] SMARTS Parse Error: Failed parsing SMARTS '[C:2])' for input: '[C:2])' -93: [00:36:15] SMILES Parse Error: syntax error while parsing: [Q:1][C:2][C:3](=[O:4])[O:5] -93: [00:36:15] SMILES Parse Error: check for mistakes around position 2: -93: [00:36:15] [Q:1][C:2][C:3](=[O:4])[O:5] -93: [00:36:15] ~^ -93: [00:36:15] 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: [00:36:15] reactant 2 has no mapped atoms. -93: [00:36:15] >> Atoms within one molecule have different RXN roles. -93: [00:36:15] >> Fragment 0 not included in the reaction, atoms do not have a correct RXN role. -93: [00:36:15] SMARTS Parse Error: syntax error while parsing: ([C:1][C:2] -93: [00:36:15] SMARTS Parse Error: Failed parsing SMARTS '([C:1][C:2]' for input: '([C:1][C:2]' -93: [00:36:15] SMARTS Parse Error: syntax error while parsing: ([C:2] -93: [00:36:15] SMARTS Parse Error: Failed parsing SMARTS '([C:2]' for input: '([C:2]' -93: [00:36:15] SMARTS Parse Error: syntax error while parsing: [C:1][C:2]) -93: [00:36:15] SMARTS Parse Error: Failed parsing SMARTS '[C:1][C:2])' for input: '[C:1][C:2])' -93: [00:36:15] SMARTS Parse Error: syntax error while parsing: [C:1]).[C:2] -93: [00:36:15] SMARTS Parse Error: Failed parsing SMARTS '[C:1]).[C:2]' for input: '[C:1]).[C:2]' -93: [00:36:15] reactant 0 has no mapped atoms. -93: [00:36:15] reactant 1 has no mapped atoms. -93: [00:36:15] reactant 3 has no mapped atoms. -93: [00:36:15] product atom-mapping number 2 found multiple times. -93: [00:36:15] product atom-mapping number 3 found multiple times. -93: [00:36:15] product atom-mapping number 4 found multiple times. -93: [00:36:15] product atom-mapping number 5 found multiple times. -93: [00:36:15] product atom-mapping number 6 found multiple times. -93: [00:36:15] product atom-mapping number 7 found multiple times. -93: [00:36:15] product atom-mapping number 8 found multiple times. -93: [00:36:15] product atom-mapping number 12 found multiple times. -93: [00:36:15] product atom-mapping number 9 found multiple times. -93: [00:36:15] product atom-mapping number 10 found multiple times. -93: [00:36:15] product atom-mapping number 11 found multiple times. -93: [00:36:15] reactant 0 has no mapped atoms. -93: [00:36:15] reactant 1 has no mapped atoms. -93: [00:36:15] reactant 3 has no mapped atoms. -93: [00:36:15] reactant atom-mapping number 19 found multiple times. -93: [00:36:15] reactant atom-mapping number 25 found multiple times. -93: [00:36:15] reactant atom-mapping number 20 found multiple times. -93: [00:36:15] reactant atom-mapping number 21 found multiple times. -93: [00:36:15] reactant atom-mapping number 22 found multiple times. -93: [00:36:15] reactant atom-mapping number 23 found multiple times. -93: [00:36:15] reactant atom-mapping number 24 found multiple times. -93: [00:36:15] product atom-mapping number 1 found multiple times. -93: [00:36:15] product atom-mapping number 1 found multiple times. -93: [00:36:15] product atom-mapping number 1 found multiple times. -93: [00:36:15] product atom-mapping number 1 found multiple times. -93: [00:36:15] product atom-mapping number 2 found multiple times. -93: [00:36:15] product atom-mapping number 1 found multiple times. -93: [00:36:15] product atom-mapping number 2 found multiple times. -93: [00:36:15] product atom-mapping number 1 found multiple times. -93: [00:36:15] product atom-mapping number 2 found multiple times. -93: [00:36:15] product atom-mapping number 1 found multiple times. -93: [00:36:15] product atom-mapping number 2 found multiple times. -93: [00:36:15] product atom-mapping number 1 found multiple times. +29: +29: Computing MMFF94 energies for /build/reproducible-path/rdkit-202503.1/Code/ForceField/MMFF/test_data/MMFF94_hypervalent.sdf... +94: [09:33:09] ------------------------------------- +93: [09:33:09] SMARTS Parse Error: syntax error while parsing: ([C:1](=O)O.[C:2] +93: [09:33:09] SMARTS Parse Error: Failed parsing SMARTS '([C:1](=O)O.[C:2]' for input: '([C:1](=O)O.[C:2]' +93: [09:33:09] SMARTS Parse Error: syntax error while parsing: ([C:2] +93: [09:33:09] SMARTS Parse Error: Failed parsing SMARTS '([C:2]' for input: '([C:2]' +93: [09:33:09] SMARTS Parse Error: syntax error while parsing: [C:1](=O)O).[C:2] +93: [09:33:09] SMARTS Parse Error: Failed parsing SMARTS '[C:1](=O)O).[C:2]' for input: '[C:1](=O)O).[C:2]' +93: [09:33:09] SMARTS Parse Error: syntax error while parsing: [C:2]) +93: [09:33:09] SMARTS Parse Error: Failed parsing SMARTS '[C:2])' for input: '[C:2])' +94: [09:33:09] Test Reaction StructuralFingerprint +93: [09:33:09] SMILES Parse Error: syntax error while parsing: [Q:1][C:2][C:3](=[O:4])[O:5] +93: [09:33:09] SMILES Parse Error: check for mistakes around position 2: +93: [09:33:09] [Q:1][C:2][C:3](=[O:4])[O:5] +93: [09:33:09] ~^ +93: [09:33:09] 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: [09:33:09] reactant 2 has no mapped atoms. +93: [09:33:09] >> Atoms within one molecule have different RXN roles. +93: [09:33:09] >> Fragment 0 not included in the reaction, atoms do not have a correct RXN role. +93: [09:33:09] SMARTS Parse Error: syntax error while parsing: ([C:1][C:2] +93: [09:33:09] SMARTS Parse Error: Failed parsing SMARTS '([C:1][C:2]' for input: '([C:1][C:2]' +93: [09:33:09] SMARTS Parse Error: syntax error while parsing: ([C:2] +93: [09:33:09] SMARTS Parse Error: Failed parsing SMARTS '([C:2]' for input: '([C:2]' +93: [09:33:09] SMARTS Parse Error: syntax error while parsing: [C:1][C:2]) +93: [09:33:09] SMARTS Parse Error: Failed parsing SMARTS '[C:1][C:2])' for input: '[C:1][C:2])' +93: [09:33:09] SMARTS Parse Error: syntax error while parsing: [C:1]).[C:2] +93: [09:33:09] SMARTS Parse Error: Failed parsing SMARTS '[C:1]).[C:2]' for input: '[C:1]).[C:2]' +93: [09:33:09] reactant 0 has no mapped atoms. +93: [09:33:09] reactant 1 has no mapped atoms. +93: [09:33:09] reactant 3 has no mapped atoms. +93: [09:33:09] product atom-mapping number 2 found multiple times. +93: [09:33:09] product atom-mapping number 3 found multiple times. +93: [09:33:09] product atom-mapping number 4 found multiple times. +93: [09:33:09] product atom-mapping number 5 found multiple times. +93: [09:33:09] product atom-mapping number 6 found multiple times. +93: [09:33:09] product atom-mapping number 7 found multiple times. +93: [09:33:09] product atom-mapping number 8 found multiple times. +93: [09:33:09] product atom-mapping number 12 found multiple times. +93: [09:33:09] product atom-mapping number 9 found multiple times. +93: [09:33:09] product atom-mapping number 10 found multiple times. +93: [09:33:09] product atom-mapping number 11 found multiple times. +93: [09:33:09] reactant 0 has no mapped atoms. +93: [09:33:09] reactant 1 has no mapped atoms. +93: [09:33:09] reactant 3 has no mapped atoms. +93: [09:33:09] reactant atom-mapping number 19 found multiple times. +93: [09:33:09] reactant atom-mapping number 25 found multiple times. +93: [09:33:09] reactant atom-mapping number 20 found multiple times. +93: [09:33:09] reactant atom-mapping number 21 found multiple times. +93: [09:33:09] reactant atom-mapping number 22 found multiple times. +93: [09:33:09] reactant atom-mapping number 23 found multiple times. +93: [09:33:09] reactant atom-mapping number 24 found multiple times. +93: [09:33:09] product atom-mapping number 1 found multiple times. +93: [09:33:09] product atom-mapping number 1 found multiple times. +93: [09:33:09] product atom-mapping number 1 found multiple times. +93: [09:33:09] product atom-mapping number 1 found multiple times. +93: [09:33:09] product atom-mapping number 2 found multiple times. +93: [09:33:09] product atom-mapping number 1 found multiple times. +93: [09:33:09] product atom-mapping number 2 found multiple times. +93: [09:33:09] product atom-mapping number 1 found multiple times. +93: [09:33:09] product atom-mapping number 2 found multiple times. +93: [09:33:09] product atom-mapping number 1 found multiple times. +93: [09:33:09] product atom-mapping number 2 found multiple times. +93: [09:33:09] product atom-mapping number 1 found multiple times. 93: F[C@@](Cl)(Br)ONO[C@](F)(Cl)Br -93: [00:36:15] product atom-mapping number 2 found multiple times. -93: [00:36:15] product atom-mapping number 1 found multiple times. -93: [00:36:15] product atom-mapping number 2 found multiple times. -93: [00:36:15] product atom-mapping number 1 found multiple times. +93: [09:33:09] product atom-mapping number 2 found multiple times. +93: [09:33:09] product atom-mapping number 1 found multiple times. +93: [09:33:09] product atom-mapping number 2 found multiple times. +93: [09:33:09] product atom-mapping number 1 found multiple times. 93: F[C@](Cl)(Br)ONO[C@](F)(Cl)Br -93: [00:36:15] product atom-mapping number 5 found multiple times. -93: [00:36:15] product atom-mapping number 2 found multiple times. -93: [00:36:15] product atom-mapping number 3 found multiple times. -93: [00:36:15] product atom-mapping number 1 found multiple times. -93: [00:36:15] product atom-mapping number 4 found multiple times. -93: [00:36:15] product atom-mapping number 5 found multiple times. -93: [00:36:15] product atom-mapping number 2 found multiple times. -93: [00:36:15] product atom-mapping number 3 found multiple times. -93: [00:36:15] product atom-mapping number 1 found multiple times. -93: [00:36:15] product atom-mapping number 4 found multiple times. +93: [09:33:09] product atom-mapping number 5 found multiple times. +93: [09:33:09] product atom-mapping number 2 found multiple times. +93: [09:33:09] product atom-mapping number 3 found multiple times. +93: [09:33:09] product atom-mapping number 1 found multiple times. +93: [09:33:09] product atom-mapping number 4 found multiple times. +93: [09:33:09] product atom-mapping number 5 found multiple times. +93: [09:33:09] product atom-mapping number 2 found multiple times. +93: [09:33:09] product atom-mapping number 3 found multiple times. +93: [09:33:09] product atom-mapping number 1 found multiple times. +93: [09:33:09] product atom-mapping number 4 found multiple times. 93: F[C@@](Cl)(Br)ONO[C@](F)(Cl)Br -93: [00:36:15] product atom-mapping number 5 found multiple times. -93: [00:36:15] product atom-mapping number 2 found multiple times. -93: [00:36:15] product atom-mapping number 3 found multiple times. -93: [00:36:15] product atom-mapping number 1 found multiple times. -93: [00:36:15] product atom-mapping number 4 found multiple times. -93: [00:36:15] product atom-mapping number 5 found multiple times. -93: [00:36:15] product atom-mapping number 2 found multiple times. -93: [00:36:15] product atom-mapping number 3 found multiple times. -93: [00:36:15] product atom-mapping number 1 found multiple times. -93: [00:36:15] product atom-mapping number 4 found multiple times. +93: [09:33:09] product atom-mapping number 5 found multiple times. +93: [09:33:09] product atom-mapping number 2 found multiple times. +93: [09:33:09] product atom-mapping number 3 found multiple times. +93: [09:33:09] product atom-mapping number 1 found multiple times. +93: [09:33:09] product atom-mapping number 4 found multiple times. +93: [09:33:09] product atom-mapping number 5 found multiple times. +93: [09:33:09] product atom-mapping number 2 found multiple times. +93: [09:33:09] product atom-mapping number 3 found multiple times. +93: [09:33:09] product atom-mapping number 1 found multiple times. +93: [09:33:09] product atom-mapping number 4 found multiple times. 93: F[C@](Cl)(Br)ONO[C@](F)(Cl)Br -93: [00:36:15] product atom-mapping number 2 found multiple times. -93: [00:36:15] product atom-mapping number 3 found multiple times. -93: [00:36:15] product atom-mapping number 1 found multiple times. -93: [00:36:15] product atom-mapping number 4 found multiple times. -93: [00:36:15] product atom-mapping number 2 found multiple times. -93: [00:36:15] product atom-mapping number 3 found multiple times. -93: [00:36:15] product atom-mapping number 1 found multiple times. -93: [00:36:15] product atom-mapping number 4 found multiple times. +93: [09:33:09] product atom-mapping number 2 found multiple times. +93: [09:33:09] product atom-mapping number 3 found multiple times. +93: [09:33:09] product atom-mapping number 1 found multiple times. +93: [09:33:09] product atom-mapping number 4 found multiple times. +93: [09:33:09] product atom-mapping number 2 found multiple times. +93: [09:33:09] product atom-mapping number 3 found multiple times. +93: [09:33:09] product atom-mapping number 1 found multiple times. +93: [09:33:09] product atom-mapping number 4 found multiple times. 93: F[C@@](Cl)(Br)O[C@](F)(Cl)Br -93: [00:36:15] product atom-mapping number 2 found multiple times. -93: [00:36:15] product atom-mapping number 3 found multiple times. -93: [00:36:15] product atom-mapping number 1 found multiple times. -93: [00:36:15] product atom-mapping number 4 found multiple times. -93: [00:36:15] product atom-mapping number 2 found multiple times. -93: [00:36:15] product atom-mapping number 3 found multiple times. -93: [00:36:15] product atom-mapping number 1 found multiple times. -93: [00:36:15] product atom-mapping number 4 found multiple times. +93: [09:33:09] product atom-mapping number 2 found multiple times. +93: [09:33:09] product atom-mapping number 3 found multiple times. +93: [09:33:09] product atom-mapping number 1 found multiple times. +93: [09:33:09] product atom-mapping number 4 found multiple times. +93: [09:33:09] product atom-mapping number 2 found multiple times. +93: [09:33:09] product atom-mapping number 3 found multiple times. +93: [09:33:09] product atom-mapping number 1 found multiple times. +93: [09:33:09] product atom-mapping number 4 found multiple times. 93: F[C@](Cl)(Br)O[C@](F)(Cl)Br -93: [00:36:15] product atom-mapping number 4 found multiple times. -93: [00:36:15] product atom-mapping number 3 found multiple times. -93: [00:36:15] product atom-mapping number 2 found multiple times. -93: [00:36:15] product atom-mapping number 1 found multiple times. -93: [00:36:15] product atom-mapping number 4 found multiple times. -93: [00:36:15] product atom-mapping number 3 found multiple times. -93: [00:36:15] product atom-mapping number 2 found multiple times. -93: [00:36:15] product atom-mapping number 1 found multiple times. -93: [00:36:15] product atom-mapping number 4 found multiple times. -93: [00:36:15] product atom-mapping number 3 found multiple times. -93: [00:36:15] product atom-mapping number 2 found multiple times. -93: [00:36:15] product atom-mapping number 1 found multiple times. -93: [00:36:15] product atom-mapping number 4 found multiple times. -93: [00:36:15] product atom-mapping number 3 found multiple times. -93: [00:36:15] product atom-mapping number 2 found multiple times. -93: [00:36:15] product atom-mapping number 1 found multiple times. -93: [00:36:15] product atom-mapping number 3 found multiple times. -93: [00:36:15] product atom-mapping number 2 found multiple times. -93: [00:36:15] product atom-mapping number 1 found multiple times. -93: [00:36:15] mapped atoms in the reactants were not mapped in the products. +93: [09:33:09] product atom-mapping number 4 found multiple times. +93: [09:33:09] product atom-mapping number 3 found multiple times. +93: [09:33:09] product atom-mapping number 2 found multiple times. +93: [09:33:09] product atom-mapping number 1 found multiple times. +93: [09:33:09] product atom-mapping number 4 found multiple times. +93: [09:33:09] product atom-mapping number 3 found multiple times. +93: [09:33:09] product atom-mapping number 2 found multiple times. +93: [09:33:09] product atom-mapping number 1 found multiple times. +93: [09:33:09] product atom-mapping number 4 found multiple times. +93: [09:33:09] product atom-mapping number 3 found multiple times. +93: [09:33:09] product atom-mapping number 2 found multiple times. +93: [09:33:09] product atom-mapping number 1 found multiple times. +93: [09:33:09] product atom-mapping number 4 found multiple times. +93: [09:33:09] product atom-mapping number 3 found multiple times. +93: [09:33:09] product atom-mapping number 2 found multiple times. +93: [09:33:09] product atom-mapping number 1 found multiple times. +93: [09:33:09] product atom-mapping number 3 found multiple times. +93: [09:33:09] product atom-mapping number 2 found multiple times. +93: [09:33:09] product atom-mapping number 1 found multiple times. +93: [09:33:09] mapped atoms in the reactants were not mapped in the products. 93: unmapped numbers are: 4 -93: [00:36:15] product atom-mapping number 3 found multiple times. -93: [00:36:15] product atom-mapping number 2 found multiple times. -93: [00:36:15] product atom-mapping number 1 found multiple times. -93: [00:36:15] mapped atoms in the reactants were not mapped in the products. +93: [09:33:09] product atom-mapping number 3 found multiple times. +93: [09:33:09] product atom-mapping number 2 found multiple times. +93: [09:33:09] product atom-mapping number 1 found multiple times. +93: [09:33:09] mapped atoms in the reactants were not mapped in the products. 93: unmapped numbers are: 4 -93: [00:36:15] product atom-mapping number 6 not found in reactants. -93: [00:36:15] product atom-mapping number 7 not found in reactants. -93: [00:36:15] product atom-mapping number 8 not found in reactants. -93: [00:36:15] product atom-mapping number 7 not found in reactants. -93: [00:36:15] product atom-mapping number 8 not found in reactants. -93: [00:36:15] product atom-mapping number 9 not found in reactants. -93: [00:36:15] product atom-mapping number 10 not found in reactants. -93: [00:36:15] mapped atoms in the reactants were not mapped in the products. +40: [09:33:09] Finished +40: [09:33:09] testing stability w.r.t. renumbering. +93: [09:33:09] product atom-mapping number 6 not found in reactants. +93: [09:33:09] product atom-mapping number 7 not found in reactants. +93: [09:33:09] product atom-mapping number 8 not found in reactants. +93: [09:33:09] product atom-mapping number 7 not found in reactants. +93: [09:33:09] product atom-mapping number 8 not found in reactants. +93: [09:33:09] product atom-mapping number 9 not found in reactants. +93: [09:33:09] product atom-mapping number 10 not found in reactants. +93: [09:33:09] mapped atoms in the reactants were not mapped in the products. 93: unmapped numbers are: 6 -93: [00:36:15] product atom-mapping number 7 not found in reactants. -93: [00:36:15] product atom-mapping number 8 not found in reactants. -93: [00:36:15] product atom-mapping number 9 not found in reactants. -93: [00:36:15] product atom-mapping number 10 not found in reactants. -93: [00:36:15] mapped atoms in the reactants were not mapped in the products. +94: [09:33:09] ------------------------------------- +94: [09:33:09] Test Reaction DifferenceFingerprint +93: [09:33:09] product atom-mapping number 7 not found in reactants. +93: [09:33:09] product atom-mapping number 8 not found in reactants. +93: [09:33:09] product atom-mapping number 9 not found in reactants. +93: [09:33:09] product atom-mapping number 10 not found in reactants. +93: [09:33:09] 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] -89: [00:36:15] Explicit valence for atom # 9 N, 5, is greater than permitted -93: [00:36:15] mapped atoms in the reactants were not mapped in the products. -93: unmapped numbers are: 7 8 9 10 11 12 13 14 15 16 -93: [00:36:15] product atom-mapping number 17 not found in reactants. -93: [00:36:15] product atom-mapping number 18 not found in reactants. -93: [00:36:15] mapped atoms in the reactants were not mapped in the products. -93: unmapped numbers are: 12 -89: [00:36:15] Explicit valence for atom # 3 Al, 6, is greater than permitted -93: [00:36:15] Reaction has explicit hydrogens, reactants will need explicit hydrogens (addHs) -93: [00:36:15] Reaction has explicit hydrogens, reactants will need explicit hydrogens (addHs) -93: -93: [00:36:15] Mismatched potential rlabels: 1 unmapped reactant dummy atom rlabels,0 unmappped product dummy atom rlabels -93: ------------- -93: CCOc1ccccc1 -89: [00:36:15] Explicit valence for atom # 4 Al, 6, is greater than permitted -89: [00:36:15] Explicit valence for atom # 10 Si, 6, is greater than permitted -92: Randomness seeded to: 1204177019 -92: =============================================================================== -92: All tests passed (11480 assertions in 38 test cases) -92: - 82/238 Test #92: testGenericGroups ...................... Passed 0.44 sec -test 94 - Start 94: testReactionFingerprints - -94: Test command: /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/ChemReactions/testReactionFingerprints -94: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/ChemReactions -94: Test timeout computed to be: 1500 -94: [00:36:15] ------------------------------------- -94: [00:36:15] Test Reaction StructuralFingerprint -69: [00:36:15] SMARTS Parse Error: syntax error while parsing: MyDogHasFleas -69: [00:36:15] SMARTS Parse Error: Failed parsing SMARTS 'MyDogHasFleas' for input: 'MyDogHasFleas' -94: [00:36:15] ------------------------------------- -94: [00:36:15] Test Reaction DifferenceFingerprint 83/238 Test #94: testReactionFingerprints ............... Passed 0.05 sec test 95 Start 95: testEnumeration @@ -22610,401 +22665,165 @@ 95: Test command: /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/ChemReactions/testEnumeration 95: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/ChemReactions 95: Test timeout computed to be: 1500 -40: [00:36:15] done: 500000 -40: [00:36:15] Done -69: [00:36:15] Empty atom list: 'M ALS 1 0 F' on line 8. -40: [00:36:15] Testing hanoi with a functor. -93: [00:36:15] reactant 0 has no mapped atoms. -93: [00:36:15] product 0 has no mapped atoms. -93: [00:36:15] WARNING: neither stereo atoms nor CIP codes found for double bond. Stereochemistry info will not be propagated to product. -69: de_DE.UTF-8 -69: [00:36:15] ------------------------------------- -69: [00:36:15] Test multithreading Locale Switching -40: [00:36:15] Done -40: [00:36:15] Testing basic partition refinement. -89: [00:36:15] Explicit valence for atom # 2 O, 4, is greater than permitted - 84/238 Test #93: testReaction ........................... Passed 0.40 sec +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] +40: [09:33:09] Finished +40: [09:33:09] testing smiles round-tripping. +93: [09:33:09] mapped atoms in the reactants were not mapped in the products. +93: unmapped numbers are: 7 8 9 10 11 12 13 14 15 16 +93: [09:33:09] product atom-mapping number 17 not found in reactants. +93: [09:33:09] product atom-mapping number 18 not found in reactants. +93: [09:33:09] mapped atoms in the reactants were not mapped in the products. +93: unmapped numbers are: 12 +89: [09:33:09] Explicit valence for atom # 9 N, 5, is greater than permitted +40: [09:33:09] Finished +40: [09:33:09] testing github #1567: Non-canonical result from MolFragmentToSmiles() +40: [09:33:09] Finished + 84/238 Test #40: hanoiTest .............................. Passed 1.87 sec test 96 Start 96: rxnTestCatch 96: Test command: /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/ChemReactions/rxnTestCatch 96: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/ChemReactions 96: Test timeout computed to be: 1500 -89: [00:36:15] Explicit valence for atom # 3 Al, 6, is greater than permitted -89: [00:36:15] Explicit valence for atom # 3 Be, 4, is greater than permitted -40: [00:36:15] Done -40: [00:36:15] Testing partition refinement with neighbors. -40: [00:36:15] Done -40: [00:36:15] testing canonicalization via tie breaking. -40: [00:36:15] Done -40: [00:36:15] testing canonicalization using the wrapper. -40: [00:36:15] Done -40: [00:36:15] testing some specific ordering problems -40: [00:36:15] Finished -40: [00:36:15] testing chiral invariants. -40: [00:36:16] Finished -40: [00:36:16] testing unique ranks in w.r.t. renumbering. -69: [00:36:16] Test multithreading (Done) -69: [00:36:16] ------------------------------------- -89: [00:36:16] Explicit valence for atom # 27 P, 6, is greater than permitted +93: [09:33:09] Reaction has explicit hydrogens, reactants will need explicit hydrogens (addHs) +93: [09:33:09] Reaction has explicit hydrogens, reactants will need explicit hydrogens (addHs) +93: +93: [09:33:09] Mismatched potential rlabels: 1 unmapped reactant dummy atom rlabels,0 unmappped product dummy atom rlabels +93: ------------- +93: CCOc1ccccc1 95: 30000000 30000000 -69: *************************************** -69: *************************************** -69: [00:36:16] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -69: [00:36:16] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -69: [00:36:16] bond with order 0 found on line 7. This is not part of the MDL specification. -96: Randomness seeded to: 4270363011 -96: [00:36:16] atom 0 in product 0 has multiple charge specifications. -96: [00:36:16] Found a SCD/SED line with missing/empty SDT specification at line 34 -96: [00:36:16] Found a SCD/SED line with missing/empty SDT specification at line 36 -96: [00:36:16] Found a SCD/SED line with missing/empty SDT specification at line 38 -96: [00:36:16] Found a SCD/SED line with missing/empty SDT specification at line 40 -96: [00:36:16] Found a SCD/SED line with missing/empty SDT specification at line 42 -96: [00:36:16] Found a SCD/SED line with missing/empty SDT specification at line 87 -96: [00:36:16] Found a SCD/SED line with missing/empty SDT specification at line 89 -96: [00:36:16] Found a SCD/SED line with missing/empty SDT specification at line 91 -96: [00:36:16] Found a SCD/SED line with missing/empty SDT specification at line 93 -96: [00:36:16] Found a SCD/SED line with missing/empty SDT specification at line 95 -40: [00:36:16] Finished -40: [00:36:16] testing mol fragments. -40: [00:36:16] Finished -40: [00:36:16] testing protein round-tripping. -69: [00:36:16] Skipping unrecognized collection type at line 26: MDLV30/HILITE BONDS=(1 7) -69: [00:36:16] Skipping unrecognized collection type at line 27: MDLV30/HILITE ATOMS=(1 7) -69: [00:36:16] Warning: molecule is tagged as 3D, but all Z coords are zero and 2D stereo markers have been found, marking the mol as 2D. -96: [00:36:16] mapped atoms in the reactants were not mapped in the products. -96: unmapped numbers are: 2 -96: [00:36:16] mapped atoms in the reactants were not mapped in the products. -96: unmapped numbers are: 2 -96: [00:36:16] SMARTS Parse Error: unclosed ring for input: 'CC1' -96: [00:36:16] SMILES Parse Error: unclosed ring for input: 'CC1' -96: [00:36:16] mapped atoms in the reactants were not mapped in the products. -96: unmapped numbers are: 2 -96: [00:36:16] product atom-mapping number 2 not found in reactants. -96: [00:36:16] mapped atoms in the reactants were not mapped in the products. -96: unmapped numbers are: 2 -96: [00:36:16] product atom-mapping number 2 not found in reactants. -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 -96: [00:36:16] CX Extensions: Substance group hierarchy is not always preserved. -96: [00:36:16] CX Extensions: Substance group hierarchy is not always preserved. -69: check isomorphism -96: [00:36:16] reactant 0 has no mapped atoms. -96: [00:36:16] product 0 has no mapped atoms. -96: [00:36:16] Can't kekulize mol. Unkekulized atoms: 0 1 2 3 4 -96: [00:36:16] Can't kekulize mol. Unkekulized atoms: 0 1 2 3 4 -96: [00:36:16] Explicit valence for atom # 1 O, 5, is greater than permitted -96: =============================================================================== -96: All tests passed (722 assertions in 30 test cases) -96: - 85/238 Test #96: rxnTestCatch ........................... Passed 0.14 sec +69: [09:33:09] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 1 ignored +69: [09:33:09] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 1 ignored +69: [09:33:09] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 1 ignored +69: [09:33:09] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 1 ignored +69: [09:33:09] 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: [09:33:09] +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-aarch64-linux-gnu//lib/libRDKitRDGeneral.so.1 +69: 1# Invar::operator<<(std::ostream&, Invar::Invariant const&) in /build/reproducible-path/rdkit-202503.1/obj-aarch64-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-aarch64-linux-gnu//lib/libRDKitFileParsers.so.1 +69: 3# 0x0000FFFF94E77EA4 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu//lib/libRDKitFileParsers.so.1 +69: 4# 0x0000FFFF94E85AA0 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu//lib/libRDKitFileParsers.so.1 +69: 5# 0x0000FFFF94E869CC in /build/reproducible-path/rdkit-202503.1/obj-aarch64-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-aarch64-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-aarch64-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-aarch64-linux-gnu//lib/libRDKitFileParsers.so.1 +69: 9# 0x0000AAAAABB2F77C in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersTest1 +69: 10# 0x0000AAAAABBA4944 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersTest1 +69: 11# 0x0000AAAAABB15C6C in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersTest1 +69: 12# 0x0000FFFF9453229C in /lib/aarch64-linux-gnu/libc.so.6 +69: 13# __libc_start_main in /lib/aarch64-linux-gnu/libc.so.6 +69: 14# 0x0000AAAAABB15E30 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersTest1 +69: ---------- +69: **** +69: +96: Randomness seeded to: 1689488734 +96: [09:33:09] atom 0 in product 0 has multiple charge specifications. +92: Randomness seeded to: 1076196559 +92: =============================================================================== +92: All tests passed (11480 assertions in 38 test cases) +92: + 85/238 Test #92: testGenericGroups ...................... Passed 0.29 sec test 97 Start 97: pyChemReactions 97: Test command: /usr/bin/python3 "/build/reproducible-path/rdkit-202503.1/Code/GraphMol/ChemReactions/Wrap/testReactionWrapper.py" 97: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/ChemReactions/Wrap 97: Test timeout computed to be: 1500 -89: [00:36:16] Explicit valence for atom # 9 N, 5, is greater than permitted -89: [00:36:16] Explicit valence for atom # 3 Al, 6, is greater than permitted -89: [00:36:16] Explicit valence for atom # 4 Al, 6, is greater than permitted -89: [00:36:16] Explicit valence for atom # 10 Si, 6, is greater than permitted -40: [00:36:16] Finished -40: [00:36:16] testing stability w.r.t. renumbering. -97: ...[00:36:16] -97: -97: **** -40: [00:36:16] Finished -40: [00:36:16] testing smiles round-tripping. -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-aarch64-linux-gnu//lib/libRDKitRDGeneral.so.1 -97: 1# Invar::operator<<(std::ostream&, Invar::Invariant const&) in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu//lib/libRDKitRDGeneral.so.1 -97: 2# RDKit::Atom::getNumImplicitHs() const in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu//lib/libRDKitGraphMol.so.1 -97: 3# RDKit::Atom::getTotalNumHs(bool) const in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu//lib/libRDKitGraphMol.so.1 -97: 4# Queries::EqualityQuery::Match(RDKit::Atom const*) const in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu//lib/libRDKitSmilesParse.so.1 -97: 5# Queries::AndQuery::Match(RDKit::Atom const*) const in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu//lib/libRDKitGraphMol.so.1 -97: 6# Queries::AndQuery::Match(RDKit::Atom const*) const in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu//lib/libRDKitGraphMol.so.1 -97: 7# Queries::OrQuery::Match(RDKit::Atom const*) const in /build/reproducible-path/rdkit-202503.1/obj-aarch64-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-aarch64-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-aarch64-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-aarch64-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-aarch64-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-aarch64-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-aarch64-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-aarch64-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-aarch64-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-aarch64-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-aarch64-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-aarch64-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-aarch64-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-aarch64-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-aarch64-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-aarch64-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-aarch64-linux-gnu/rdkit/Chem/rdChemReactions.so -97: 24# boost::python::objects::function::call(_object*, _object*) const in /lib/aarch64-linux-gnu/libboost_python313.so.1.83.0 -97: 25# 0x0000FFFF92A32680 in /lib/aarch64-linux-gnu/libboost_python313.so.1.83.0 -97: 26# boost::python::detail::exception_handler::operator()(boost::function0 const&) const in /lib/aarch64-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-aarch64-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-aarch64-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-aarch64-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-aarch64-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-aarch64-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-aarch64-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-aarch64-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-aarch64-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-aarch64-linux-gnu/rdkit/Chem/rdchem.so -97: 36# 0x0000FFFF90FEC320 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so -97: 37# 0x0000FFFF90FEC2B8 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so -97: 38# 0x0000FFFF90FEC248 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so -97: 39# 0x0000FFFF90FEC1E0 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so -97: 40# 0x0000FFFF90FEC178 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-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-aarch64-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-aarch64-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-aarch64-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-aarch64-linux-gnu/rdkit/rdBase.so -97: 45# boost::python::handle_exception_impl(boost::function0) in /lib/aarch64-linux-gnu/libboost_python313.so.1.83.0 -97: 46# 0x0000FFFF92A2F25C in /lib/aarch64-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# 0x000000000053D3B0 in /usr/bin/python3 -97: 50# _PyEval_EvalFrameDefault in /usr/bin/python3 -97: 51# 0x000000000061C8E0 in /usr/bin/python3 -97: 52# 0x00000000005A787C in /usr/bin/python3 -97: 53# _PyObject_MakeTpCall in /usr/bin/python3 -97: 54# _PyEval_EvalFrameDefault in /usr/bin/python3 -97: 55# 0x000000000053D3B0 in /usr/bin/python3 -97: 56# _PyEval_EvalFrameDefault in /usr/bin/python3 -97: 57# 0x000000000061C8E0 in /usr/bin/python3 -97: 58# 0x00000000005A787C in /usr/bin/python3 -97: 59# _PyObject_MakeTpCall in /usr/bin/python3 -97: 60# _PyEval_EvalFrameDefault in /usr/bin/python3 -97: 61# 0x000000000053D3B0 in /usr/bin/python3 -97: 62# _PyEval_EvalFrameDefault in /usr/bin/python3 -97: 63# 0x000000000061C8E0 in /usr/bin/python3 -97: 64# 0x00000000005A787C in /usr/bin/python3 -97: 65# _PyObject_MakeTpCall in /usr/bin/python3 -97: 66# _PyEval_EvalFrameDefault in /usr/bin/python3 -97: 67# 0x000000000050B150 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# 0x000000000064023C in /usr/bin/python3 -97: 72# 0x000000000063BC30 in /usr/bin/python3 -97: 73# 0x000000000065F810 in /usr/bin/python3 -97: 74# 0x000000000065F0B4 in /usr/bin/python3 -97: 75# 0x000000000065EE50 in /usr/bin/python3 -97: 76# Py_RunMain in /usr/bin/python3 -97: 77# Py_BytesMain in /usr/bin/python3 -97: 78# 0x0000FFFF9356229C in /lib/aarch64-linux-gnu/libc.so.6 -97: 79# __libc_start_main in /lib/aarch64-linux-gnu/libc.so.6 -97: 80# _start in /usr/bin/python3 -97: ---------- -97: **** -97: -97: [00:36:16] -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-aarch64-linux-gnu//lib/libRDKitRDGeneral.so.1 -97: 1# Invar::operator<<(std::ostream&, Invar::Invariant const&) in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu//lib/libRDKitRDGeneral.so.1 -97: 2# RDKit::Atom::getNumImplicitHs() const in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu//lib/libRDKitGraphMol.so.1 -97: 3# RDKit::Atom::getTotalNumHs(bool) const in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu//lib/libRDKitGraphMol.so.1 -97: 4# Queries::EqualityQuery::Match(RDKit::Atom const*) const in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu//lib/libRDKitSmilesParse.so.1 -97: 5# Queries::AndQuery::Match(RDKit::Atom const*) const in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu//lib/libRDKitGraphMol.so.1 -97: 6# Queries::AndQuery::Match(RDKit::Atom const*) const in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu//lib/libRDKitGraphMol.so.1 -97: 7# Queries::OrQuery::Match(RDKit::Atom const*) const in /build/reproducible-path/rdkit-202503.1/obj-aarch64-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-aarch64-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-aarch64-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-aarch64-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-aarch64-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-aarch64-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-aarch64-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-aarch64-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-aarch64-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-aarch64-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-aarch64-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-aarch64-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-aarch64-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-aarch64-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-aarch64-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-aarch64-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-aarch64-linux-gnu/rdkit/Chem/rdChemReactions.so -97: 24# boost::python::objects::function::call(_object*, _object*) const in /lib/aarch64-linux-gnu/libboost_python313.so.1.83.0 -97: 25# 0x0000FFFF92A32680 in /lib/aarch64-linux-gnu/libboost_python313.so.1.83.0 -97: 26# boost::python::detail::exception_handler::operator()(boost::function0 const&) const in /lib/aarch64-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-aarch64-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-aarch64-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-aarch64-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-aarch64-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-aarch64-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-aarch64-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-aarch64-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-aarch64-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-aarch64-linux-gnu/rdkit/Chem/rdchem.so -97: 36# 0x0000FFFF90FEC320 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so -97: 37# 0x0000FFFF90FEC2B8 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so -97: 38# 0x0000FFFF90FEC248 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so -97: 39# 0x0000FFFF90FEC1E0 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so -97: 40# 0x0000FFFF90FEC178 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-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-aarch64-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-aarch64-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-aarch64-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-aarch64-linux-gnu/rdkit/rdBase.so -97: 45# boost::python::handle_exception_impl(boost::function0) in /lib/aarch64-linux-gnu/libboost_python313.so.1.83.0 -97: 46# 0x0000FFFF92A2F25C in /lib/aarch64-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# 0x000000000053D3B0 in /usr/bin/python3 -97: 50# _PyEval_EvalFrameDefault in /usr/bin/python3 -97: 51# 0x000000000061C8E0 in /usr/bin/python3 -97: 52# 0x00000000005A787C in /usr/bin/python3 -97: 53# _PyObject_MakeTpCall in /usr/bin/python3 -97: 54# _PyEval_EvalFrameDefault in /usr/bin/python3 -97: 55# 0x000000000053D3B0 in /usr/bin/python3 -97: 56# _PyEval_EvalFrameDefault in /usr/bin/python3 -97: 57# 0x000000000061C8E0 in /usr/bin/python3 -97: 58# 0x00000000005A787C in /usr/bin/python3 -97: 59# _PyObject_MakeTpCall in /usr/bin/python3 -97: 60# _PyEval_EvalFrameDefault in /usr/bin/python3 -97: 61# 0x000000000053D3B0 in /usr/bin/python3 -97: 62# _PyEval_EvalFrameDefault in /usr/bin/python3 -97: 63# 0x000000000061C8E0 in /usr/bin/python3 -97: 64# 0x00000000005A787C in /usr/bin/python3 -97: 65# _PyObject_MakeTpCall in /usr/bin/python3 -97: 66# _PyEval_EvalFrameDefault in /usr/bin/python3 -97: 67# 0x000000000050B150 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# 0x000000000064023C in /usr/bin/python3 -97: 72# 0x000000000063BC30 in /usr/bin/python3 -97: 73# 0x000000000065F810 in /usr/bin/python3 -97: 74# 0x000000000065F0B4 in /usr/bin/python3 -97: 75# 0x000000000065EE50 in /usr/bin/python3 -97: 76# Py_RunMain in /usr/bin/python3 -97: 77# Py_BytesMain in /usr/bin/python3 -97: 78# 0x0000FFFF9356229C in /lib/aarch64-linux-gnu/libc.so.6 -97: 79# __libc_start_main in /lib/aarch64-linux-gnu/libc.so.6 -97: 80# _start in /usr/bin/python3 -97: ---------- -97: **** -97: -97: .........[00:36:16] stereo atoms in input cannot be mapped to output (atoms are no longer bonded) -97: [00:36:16] stereo atoms in input cannot be mapped to output (atoms are no longer bonded) -97: [00:36:16] stereo atoms in input cannot be mapped to output (atoms are no longer bonded) -97: [00:36:16] stereo atoms in input cannot be mapped to output (atoms are no longer bonded) -97: .[00:36:16] product atom-mapping number 1 found multiple times. -97: [00:36:16] product atom-mapping number 1 found multiple times. -97: ................[00:36:16] mapped atoms in the reactants were not mapped in the products. -97: unmapped numbers are: 3 -97: [00:36:16] 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: [00:36:16] mapped atoms in the reactants were not mapped in the products. -97: unmapped numbers are: 3 -97: ..[00:36:16] reactant 2 has no mapped atoms. -97: [00:36:16] reactant 2 has no mapped atoms. -97: [00:36:16] product 1 has no mapped atoms. -97: ........[00:36:16] SMARTS Parse Error: syntax error while parsing: [C:1](=[O:2])Q -97: [00:36:16] SMARTS Parse Error: Failed parsing SMARTS '[C:1](=[O:2])Q' for input: '[C:1](=[O:2])Q' -97: [00:36:16] SMARTS Parse Error: syntax error while parsing: [C:1](=[O:2])[N:3]Q -97: [00:36:16] SMARTS Parse Error: Failed parsing SMARTS '[C:1](=[O:2])[N:3]Q' for input: '[C:1](=[O:2])[N:3]Q' -97: .[00:36:16] reactant atom-mapping number 1 found multiple times. -97: [00:36:16] product atom-mapping number 2 not found in reactants. -97: [00:36:16] mapped atoms in the reactants were not mapped in the products. -97: unmapped numbers are: 4 -97: [00:36:16] product atom-mapping number 5 not found in reactants. -89: [00:36:16] Explicit valence for atom # 2 O, 4, is greater than permitted -89: [00:36:16] Explicit valence for atom # 3 Be, 4, is greater than permitted[00:36:16] Explicit valence for atom # 3 Al, 6, is greater than permitted -89: -97: ........./build/reproducible-path/rdkit-202503.1/Code/GraphMol/ChemReactions/Wrap/testReactionWrapper.py:745: ResourceWarning: unclosed file <_io.BufferedReader name='/build/reproducible-path/rdkit-202503.1/Code/GraphMol/ChemReactions/testData/reaction1.no_metadata.png'> -97: png = open(fname, 'rb').read() -97: ResourceWarning: Enable tracemalloc to get the object allocation traceback -97: [00:36:16] Found a SCD/SED line with missing/empty SDT specification at line 34 -97: [00:36:16] Found a SCD/SED line with missing/empty SDT specification at line 36 -97: [00:36:16] Found a SCD/SED line with missing/empty SDT specification at line 38 -97: [00:36:16] Found a SCD/SED line with missing/empty SDT specification at line 40 -97: [00:36:16] Found a SCD/SED line with missing/empty SDT specification at line 42 -97: [00:36:16] Found a SCD/SED line with missing/empty SDT specification at line 87 -97: [00:36:16] Found a SCD/SED line with missing/empty SDT specification at line 89 -97: [00:36:16] Found a SCD/SED line with missing/empty SDT specification at line 91 -97: [00:36:16] Found a SCD/SED line with missing/empty SDT specification at line 93 -97: [00:36:16] Found a SCD/SED line with missing/empty SDT specification at line 95 -89: [00:36:16] Explicit valence for atom # 27 P, 6, is greater than permitted -97: ..[00:36:16] SMARTS Parse Error: syntax error while parsing: boromicacid -97: [00:36:16] SMARTS Parse Error: Failed parsing SMARTS 'boromicacid' for input: 'boromicacid' -97: [00:36:16] SMARTS Parse Error: syntax error while parsing: carboxylicacid,acidchlroide -97: [00:36:16] SMARTS Parse Error: Failed parsing SMARTS 'carboxylicacid,acidchlroide' for input: 'carboxylicacid,acidchlroide' -97: [00:36:16] SMARTS Parse Error: syntax error while parsing: carboxyliccaid,acidchloride -97: [00:36:16] SMARTS Parse Error: Failed parsing SMARTS 'carboxyliccaid,acidchloride' for input: 'carboxyliccaid,acidchloride' -97: [00:36:16] reaction has no reactants -97: [00:36:16] reaction has no products -97: [00:36:16] initialization failed -97: [00:36:16] reaction has no reactants -97: [00:36:16] reaction has no products -97: .[00:36:16] SMARTS Parse Error: syntax error while parsing: boromicacid -97: [00:36:16] SMARTS Parse Error: Failed parsing SMARTS 'boromicacid' for input: 'boromicacid' -97: [00:36:16] SMARTS Parse Error: syntax error while parsing: carboxylicacid,acidchlroide -97: [00:36:16] SMARTS Parse Error: Failed parsing SMARTS 'carboxylicacid,acidchlroide' for input: 'carboxylicacid,acidchlroide' -97: [00:36:16] SMARTS Parse Error: syntax error while parsing: carboxyliccaid,acidchloride -97: [00:36:16] SMARTS Parse Error: Failed parsing SMARTS 'carboxyliccaid,acidchloride' for input: 'carboxyliccaid,acidchloride' -97: [00:36:16] reaction has no reactants -97: [00:36:16] reaction has no products -97: [00:36:16] initialization failed -97: [00:36:16] reaction has no reactants -97: [00:36:16] reaction has no products -97: . -97: ---------------------------------------------------------------------- -97: Ran 54 tests in 0.178s -97: -97: OK -97: ******************************************** -97: /build/reproducible-path/rdkit-202503.1/Code/GraphMol/ChemReactions/testData/AmideBond.rxn -97: -89: =============================================================================== -89: All tests passed (21562 assertions in 3 test cases) -89: - 86/238 Test #89: multithreadedSupplierCatchTest ......... Passed 1.66 sec +96: [09:33:09] Found a SCD/SED line with missing/empty SDT specification at line 34 +96: [09:33:09] Found a SCD/SED line with missing/empty SDT specification at line 36 +96: [09:33:09] Found a SCD/SED line with missing/empty SDT specification at line 38 +96: [09:33:09] Found a SCD/SED line with missing/empty SDT specification at line 40 +96: [09:33:09] Found a SCD/SED line with missing/empty SDT specification at line 42 +96: [09:33:09] Found a SCD/SED line with missing/empty SDT specification at line 87 +96: [09:33:09] Found a SCD/SED line with missing/empty SDT specification at line 89 +96: [09:33:09] Found a SCD/SED line with missing/empty SDT specification at line 91 +96: [09:33:09] Found a SCD/SED line with missing/empty SDT specification at line 93 +96: [09:33:09] Found a SCD/SED line with missing/empty SDT specification at line 95 +96: [09:33:09] mapped atoms in the reactants were not mapped in the products. +96: unmapped numbers are: 2 +96: [09:33:09] mapped atoms in the reactants were not mapped in the products. +96: unmapped numbers are: 2 +96: [09:33:09] SMARTS Parse Error: unclosed ring for input: 'CC1' +96: [09:33:09] SMILES Parse Error: unclosed ring for input: 'CC1' +96: [09:33:09] mapped atoms in the reactants were not mapped in the products. +96: unmapped numbers are: 2 +96: [09:33:09] product atom-mapping number 2 not found in reactants. +96: [09:33:09] mapped atoms in the reactants were not mapped in the products. +96: unmapped numbers are: 2 +96: [09:33:09] product atom-mapping number 2 not found in reactants. +89: [09:33:09] Explicit valence for atom # 3 Al, 6, is greater than permitted +96: [09:33:09] CX Extensions: Substance group hierarchy is not always preserved. +96: [09:33:09] CX Extensions: Substance group hierarchy is not always preserved. + 86/238 Test #42: resMolSupplierTest ..................... Passed 1.98 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-aarch64-linux-gnu/Code/GraphMol/ChemReactions/Wrap 98: Test timeout computed to be: 1500 -40: [00:36:16] Finished -40: [00:36:16] testing github #1567: Non-canonical result from MolFragmentToSmiles() -40: [00:36:16] Finished - 87/238 Test #42: resMolSupplierTest ..................... Passed 3.55 sec +96: [09:33:09] reactant 0 has no mapped atoms. +96: [09:33:09] product 0 has no mapped atoms. +96: [09:33:09] Can't kekulize mol. Unkekulized atoms: 0 1 2 3 4 +96: [09:33:09] Can't kekulize mol. Unkekulized atoms: 0 1 2 3 4 +96: [09:33:09] Explicit valence for atom # 1 O, 5, is greater than permitted +96: =============================================================================== +96: All tests passed (722 assertions in 30 test cases) +96: + 87/238 Test #96: rxnTestCatch ........................... Passed 0.12 sec 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-aarch64-linux-gnu/Code/GraphMol/ChemReactions/Wrap 99: Test timeout computed to be: 1500 - 88/238 Test #40: hanoiTest .............................. Passed 3.60 sec +69: [09:33:09] 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: [09:33:09] Warning: molecule is tagged as 3D, but all Z coords are zero and 2D stereo markers have been found, marking the mol as 2D. +89: [09:33:09] Explicit valence for atom # 4 Al, 6, is greater than permitted +93: [09:33:09] reactant 0 has no mapped atoms. +93: [09:33:09] product 0 has no mapped atoms. +93: [09:33:09] WARNING: neither stereo atoms nor CIP codes found for double bond. Stereochemistry info will not be propagated to product. + 88/238 Test #93: testReaction ........................... Passed 0.35 sec test 100 Start 100: testChemTransforms 100: Test command: /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/ChemTransforms/testChemTransforms 100: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/ChemTransforms 100: Test timeout computed to be: 1500 - 89/238 Test #97: pyChemReactions ........................ Passed 0.75 sec -test 101 - Start 101: chemTransformsTestCatch - -101: Test command: /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/ChemTransforms/chemTransformsTestCatch -101: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/ChemTransforms -101: Test timeout computed to be: 1500 +89: [09:33:09] Explicit valence for atom # 10 Si, 6, is greater than permitted +69: ---------------------------------- +69: ---------------------------------- +69: [09:33:09] +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-aarch64-linux-gnu//lib/libRDKitRDGeneral.so.1 +69: 1# Invar::operator<<(std::ostream&, Invar::Invariant const&) in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu//lib/libRDKitRDGeneral.so.1 +69: 2# RDKit::setAtomRLabel(RDKit::Atom*, int) in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu//lib/libRDKitGraphMol.so.1 +69: 3# 0x0000AAAAABB3F23C in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersTest1 +69: 4# 0x0000AAAAABBA49A4 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersTest1 +69: 5# 0x0000AAAAABB15C6C in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersTest1 +69: 6# 0x0000FFFF9453229C in /lib/aarch64-linux-gnu/libc.so.6 +69: 7# __libc_start_main in /lib/aarch64-linux-gnu/libc.so.6 +69: 8# 0x0000AAAAABB15E30 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersTest1 +69: ---------- +69: **** +69: +69: [09:33:09] WARNING: could not find number of expected rings. Switching to an approximate ring finding algorithm. 100: 1 smi: CC 100: 1 smi: CC 100: 2 smi: CCO[C@H](N)P @@ -23013,11 +22832,26 @@ 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 -101: Randomness seeded to: 1050360868 -101: [00:36:16] Incomplete atom labelling, cannot make bond -101: [00:36:16] +100: [09:33:09] SMARTS Parse Error: syntax error while parsing: bar +100: [09:33:09] SMARTS Parse Error: Failed parsing SMARTS 'bar' for input: 'bar' + 89/238 Test #100: testChemTransforms ..................... Passed 0.11 sec +test 101 + Start 101: chemTransformsTestCatch + +101: Test command: /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/ChemTransforms/chemTransformsTestCatch +101: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/ChemTransforms +101: Test timeout computed to be: 1500 +89: [09:33:09] Explicit valence for atom # 2 O, 4, is greater than permitted +69: [09:33:09] SMARTS Parse Error: syntax error while parsing: MyDogHasFleas +69: [09:33:09] SMARTS Parse Error: Failed parsing SMARTS 'MyDogHasFleas' for input: 'MyDogHasFleas' +89: [09:33:09] Explicit valence for atom # 3 Be, 4, is greater than permitted +89: [09:33:09] Explicit valence for atom # 3 Al, 6, is greater than permitted +101: Randomness seeded to: 166024391 +101: [09:33:09] Incomplete atom labelling, cannot make bond +101: [09:33:09] 101: 101: **** +89: [09:33:10] Explicit valence for atom # 27 P, 6, is greater than permitted 101: Invariant Violation 101: molzip: bond info already exists for end atom with label:1 101: Violation occurred on line 1094 in file ./Code/GraphMol/ChemTransforms/MolFragmenter.cpp @@ -23028,23 +22862,21 @@ 101: 1# Invar::operator<<(std::ostream&, Invar::Invariant const&) in /build/reproducible-path/rdkit-202503.1/obj-aarch64-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-aarch64-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-aarch64-linux-gnu//lib/libRDKitChemTransforms.so.1 -101: 4# 0x0000AAAAC72970A4 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/ChemTransforms/chemTransformsTestCatch -101: 5# 0x0000AAAAC72E5FEC in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/ChemTransforms/chemTransformsTestCatch -101: 6# 0x0000AAAAC72E69A0 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/ChemTransforms/chemTransformsTestCatch -101: 7# 0x0000AAAAC72E6DD4 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/ChemTransforms/chemTransformsTestCatch -101: 8# 0x0000AAAAC72BA358 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/ChemTransforms/chemTransformsTestCatch -101: 9# 0x0000AAAAC72BA8A4 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/ChemTransforms/chemTransformsTestCatch -101: 10# 0x0000AAAAC728C550 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/ChemTransforms/chemTransformsTestCatch -101: 11# 0x0000FFFF9F9C229C in /lib/aarch64-linux-gnu/libc.so.6 +101: 4# 0x0000AAAAD89670A4 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/ChemTransforms/chemTransformsTestCatch +101: 5# 0x0000AAAAD89B5FEC in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/ChemTransforms/chemTransformsTestCatch +101: 6# 0x0000AAAAD89B69A0 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/ChemTransforms/chemTransformsTestCatch +101: 7# 0x0000AAAAD89B6DD4 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/ChemTransforms/chemTransformsTestCatch +101: 8# 0x0000AAAAD898A358 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/ChemTransforms/chemTransformsTestCatch +101: 9# 0x0000AAAAD898A8A4 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/ChemTransforms/chemTransformsTestCatch +101: 10# 0x0000AAAAD895C550 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/ChemTransforms/chemTransformsTestCatch +101: 11# 0x0000FFFFA5D6229C in /lib/aarch64-linux-gnu/libc.so.6 101: 12# __libc_start_main in /lib/aarch64-linux-gnu/libc.so.6 -101: 13# 0x0000AAAAC728C630 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/ChemTransforms/chemTransformsTestCatch +101: 13# 0x0000AAAAD895C630 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/ChemTransforms/chemTransformsTestCatch 101: ---------- 101: **** 101: -100: [00:36:16] SMARTS Parse Error: syntax error while parsing: bar -100: [00:36:16] SMARTS Parse Error: Failed parsing SMARTS 'bar' for input: 'bar' -101: [00:36:16] Incomplete atom labelling, cannot make bond -101: [00:36:16] +101: [09:33:10] Incomplete atom labelling, cannot make bond +101: [09:33:10] 101: 101: **** 101: Invariant Violation @@ -23057,23 +22889,31 @@ 101: 1# Invar::operator<<(std::ostream&, Invar::Invariant const&) in /build/reproducible-path/rdkit-202503.1/obj-aarch64-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-aarch64-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-aarch64-linux-gnu//lib/libRDKitChemTransforms.so.1 -101: 4# 0x0000AAAAC72970A4 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/ChemTransforms/chemTransformsTestCatch -101: 5# 0x0000AAAAC72E5FEC in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/ChemTransforms/chemTransformsTestCatch -101: 6# 0x0000AAAAC72E69A0 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/ChemTransforms/chemTransformsTestCatch -101: 7# 0x0000AAAAC72E6DD4 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/ChemTransforms/chemTransformsTestCatch -101: 8# 0x0000AAAAC72BA358 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/ChemTransforms/chemTransformsTestCatch -101: 9# 0x0000AAAAC72BA8A4 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/ChemTransforms/chemTransformsTestCatch -101: 10# 0x0000AAAAC728C550 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/ChemTransforms/chemTransformsTestCatch -101: 11# 0x0000FFFF9F9C229C in /lib/aarch64-linux-gnu/libc.so.6 +101: 4# 0x0000AAAAD89670A4 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/ChemTransforms/chemTransformsTestCatch +101: 5# 0x0000AAAAD89B5FEC in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/ChemTransforms/chemTransformsTestCatch +101: 6# 0x0000AAAAD89B69A0 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/ChemTransforms/chemTransformsTestCatch +101: 7# 0x0000AAAAD89B6DD4 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/ChemTransforms/chemTransformsTestCatch +101: 8# 0x0000AAAAD898A358 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/ChemTransforms/chemTransformsTestCatch +101: 9# 0x0000AAAAD898A8A4 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/ChemTransforms/chemTransformsTestCatch +101: 10# 0x0000AAAAD895C550 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/ChemTransforms/chemTransformsTestCatch +101: 11# 0x0000FFFFA5D6229C in /lib/aarch64-linux-gnu/libc.so.6 101: 12# __libc_start_main in /lib/aarch64-linux-gnu/libc.so.6 -101: 13# 0x0000AAAAC728C630 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/ChemTransforms/chemTransformsTestCatch +101: 13# 0x0000AAAAD895C630 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/ChemTransforms/chemTransformsTestCatch 101: ---------- 101: **** 101: -101: [00:36:16] Incomplete atom labelling, cannot make bond -101: [00:36:16] +69: [09:33:10] Empty atom list: 'M ALS 1 0 F' on line 8. + 90/238 Test #69: fileParsersTest1 ....................... Passed 1.67 sec +101: [09:33:10] Incomplete atom labelling, cannot make bond +101: [09:33:10] 101: 101: **** +test 102 + Start 102: tautomerQueryTestCatch + +102: Test command: /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/TautomerQuery/tautomerQueryTestCatch +102: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/TautomerQuery +102: Test timeout computed to be: 1500 101: Invariant Violation 101: molzip: bond info already exists for end atom with label:1 101: Violation occurred on line 1094 in file ./Code/GraphMol/ChemTransforms/MolFragmenter.cpp @@ -23084,23 +22924,23 @@ 101: 1# Invar::operator<<(std::ostream&, Invar::Invariant const&) in /build/reproducible-path/rdkit-202503.1/obj-aarch64-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-aarch64-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-aarch64-linux-gnu//lib/libRDKitChemTransforms.so.1 -101: 4# 0x0000AAAAC72970A4 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/ChemTransforms/chemTransformsTestCatch -101: 5# 0x0000AAAAC72E5FEC in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/ChemTransforms/chemTransformsTestCatch -101: 6# 0x0000AAAAC72E69A0 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/ChemTransforms/chemTransformsTestCatch -101: 7# 0x0000AAAAC72E6DD4 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/ChemTransforms/chemTransformsTestCatch -101: 8# 0x0000AAAAC72BA358 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/ChemTransforms/chemTransformsTestCatch -101: 9# 0x0000AAAAC72BA8A4 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/ChemTransforms/chemTransformsTestCatch -101: 10# 0x0000AAAAC728C550 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/ChemTransforms/chemTransformsTestCatch -101: 11# 0x0000FFFF9F9C229C in /lib/aarch64-linux-gnu/libc.so.6 +101: 4# 0x0000AAAAD89670A4 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/ChemTransforms/chemTransformsTestCatch +101: 5# 0x0000AAAAD89B5FEC in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/ChemTransforms/chemTransformsTestCatch +101: 6# 0x0000AAAAD89B69A0 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/ChemTransforms/chemTransformsTestCatch +101: 7# 0x0000AAAAD89B6DD4 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/ChemTransforms/chemTransformsTestCatch +101: 8# 0x0000AAAAD898A358 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/ChemTransforms/chemTransformsTestCatch +101: 9# 0x0000AAAAD898A8A4 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/ChemTransforms/chemTransformsTestCatch +101: 10# 0x0000AAAAD895C550 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/ChemTransforms/chemTransformsTestCatch +101: 11# 0x0000FFFFA5D6229C in /lib/aarch64-linux-gnu/libc.so.6 101: 12# __libc_start_main in /lib/aarch64-linux-gnu/libc.so.6 -101: 13# 0x0000AAAAC728C630 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/ChemTransforms/chemTransformsTestCatch +101: 13# 0x0000AAAAD895C630 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/ChemTransforms/chemTransformsTestCatch 101: ---------- 101: **** 101: -101: [00:36:16] Incomplete atom labelling, cannot make bond -101: [00:36:16] Incomplete atom labelling, cannot make bond -101: [00:36:16] Incomplete atom labelling, cannot make bond -101: [00:36:16] +101: [09:33:10] Incomplete atom labelling, cannot make bond +101: [09:33:10] Incomplete atom labelling, cannot make bond +101: [09:33:10] Incomplete atom labelling, cannot make bond +101: [09:33:10] 101: 101: **** 101: Invariant Violation @@ -23113,21 +22953,21 @@ 101: 1# Invar::operator<<(std::ostream&, Invar::Invariant const&) in /build/reproducible-path/rdkit-202503.1/obj-aarch64-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-aarch64-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-aarch64-linux-gnu//lib/libRDKitChemTransforms.so.1 -101: 4# 0x0000AAAAC72970A4 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/ChemTransforms/chemTransformsTestCatch -101: 5# 0x0000AAAAC72E5FEC in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/ChemTransforms/chemTransformsTestCatch -101: 6# 0x0000AAAAC72E69A0 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/ChemTransforms/chemTransformsTestCatch -101: 7# 0x0000AAAAC72E6DD4 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/ChemTransforms/chemTransformsTestCatch -101: 8# 0x0000AAAAC72BA358 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/ChemTransforms/chemTransformsTestCatch -101: 9# 0x0000AAAAC72BA8A4 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/ChemTransforms/chemTransformsTestCatch -101: 10# 0x0000AAAAC728C550 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/ChemTransforms/chemTransformsTestCatch -101: 11# 0x0000FFFF9F9C229C in /lib/aarch64-linux-gnu/libc.so.6 +101: 4# 0x0000AAAAD89670A4 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/ChemTransforms/chemTransformsTestCatch +101: 5# 0x0000AAAAD89B5FEC in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/ChemTransforms/chemTransformsTestCatch +101: 6# 0x0000AAAAD89B69A0 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/ChemTransforms/chemTransformsTestCatch +101: 7# 0x0000AAAAD89B6DD4 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/ChemTransforms/chemTransformsTestCatch +101: 8# 0x0000AAAAD898A358 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/ChemTransforms/chemTransformsTestCatch +101: 9# 0x0000AAAAD898A8A4 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/ChemTransforms/chemTransformsTestCatch +101: 10# 0x0000AAAAD895C550 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/ChemTransforms/chemTransformsTestCatch +101: 11# 0x0000FFFFA5D6229C in /lib/aarch64-linux-gnu/libc.so.6 101: 12# __libc_start_main in /lib/aarch64-linux-gnu/libc.so.6 -101: 13# 0x0000AAAAC728C630 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/ChemTransforms/chemTransformsTestCatch +101: 13# 0x0000AAAAD895C630 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/ChemTransforms/chemTransformsTestCatch 101: ---------- 101: **** 101: -101: [00:36:16] Incomplete atom labelling, cannot make bond -101: [00:36:16] +101: [09:33:10] Incomplete atom labelling, cannot make bond +101: [09:33:10] 101: 101: **** 101: Invariant Violation @@ -23140,20 +22980,20 @@ 101: 1# Invar::operator<<(std::ostream&, Invar::Invariant const&) in /build/reproducible-path/rdkit-202503.1/obj-aarch64-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-aarch64-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-aarch64-linux-gnu//lib/libRDKitChemTransforms.so.1 -101: 4# 0x0000AAAAC72970A4 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/ChemTransforms/chemTransformsTestCatch -101: 5# 0x0000AAAAC72E5FEC in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/ChemTransforms/chemTransformsTestCatch -101: 6# 0x0000AAAAC72E69A0 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/ChemTransforms/chemTransformsTestCatch -101: 7# 0x0000AAAAC72E6DD4 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/ChemTransforms/chemTransformsTestCatch -101: 8# 0x0000AAAAC72BA358 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/ChemTransforms/chemTransformsTestCatch -101: 9# 0x0000AAAAC72BA8A4 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/ChemTransforms/chemTransformsTestCatch -101: 10# 0x0000AAAAC728C550 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/ChemTransforms/chemTransformsTestCatch -101: 11# 0x0000FFFF9F9C229C in /lib/aarch64-linux-gnu/libc.so.6 +101: 4# 0x0000AAAAD89670A4 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/ChemTransforms/chemTransformsTestCatch +101: 5# 0x0000AAAAD89B5FEC in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/ChemTransforms/chemTransformsTestCatch +101: 6# 0x0000AAAAD89B69A0 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/ChemTransforms/chemTransformsTestCatch +101: 7# 0x0000AAAAD89B6DD4 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/ChemTransforms/chemTransformsTestCatch +101: 8# 0x0000AAAAD898A358 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/ChemTransforms/chemTransformsTestCatch +101: 9# 0x0000AAAAD898A8A4 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/ChemTransforms/chemTransformsTestCatch +101: 10# 0x0000AAAAD895C550 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/ChemTransforms/chemTransformsTestCatch +101: 11# 0x0000FFFFA5D6229C in /lib/aarch64-linux-gnu/libc.so.6 101: 12# __libc_start_main in /lib/aarch64-linux-gnu/libc.so.6 -101: 13# 0x0000AAAAC728C630 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/ChemTransforms/chemTransformsTestCatch +101: 13# 0x0000AAAAD895C630 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/ChemTransforms/chemTransformsTestCatch 101: ---------- 101: **** 101: -101: [00:36:16] +101: [09:33:10] 101: 101: **** 101: Invariant Violation @@ -23167,92 +23007,176 @@ 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-aarch64-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-aarch64-linux-gnu//lib/libRDKitChemTransforms.so.1 101: 4# RDKit::molzip(RDKit::ROMol const&, RDKit::MolzipParams const&) in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu//lib/libRDKitChemTransforms.so.1 -101: 5# 0x0000AAAAC728D318 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/ChemTransforms/chemTransformsTestCatch -101: 6# 0x0000AAAAC72E5FEC in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/ChemTransforms/chemTransformsTestCatch -101: 7# 0x0000AAAAC72E69A0 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/ChemTransforms/chemTransformsTestCatch -101: 8# 0x0000AAAAC72E6DD4 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/ChemTransforms/chemTransformsTestCatch -101: 9# 0x0000AAAAC72BA358 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/ChemTransforms/chemTransformsTestCatch -101: 10# 0x0000AAAAC72BA8A4 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/ChemTransforms/chemTransformsTestCatch -101: 11# 0x0000AAAAC728C550 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/ChemTransforms/chemTransformsTestCatch -101: 12# 0x0000FFFF9F9C229C in /lib/aarch64-linux-gnu/libc.so.6 +101: 5# 0x0000AAAAD895D318 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/ChemTransforms/chemTransformsTestCatch +101: 6# 0x0000AAAAD89B5FEC in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/ChemTransforms/chemTransformsTestCatch +101: 7# 0x0000AAAAD89B69A0 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/ChemTransforms/chemTransformsTestCatch +101: 8# 0x0000AAAAD89B6DD4 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/ChemTransforms/chemTransformsTestCatch +101: 9# 0x0000AAAAD898A358 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/ChemTransforms/chemTransformsTestCatch +101: 10# 0x0000AAAAD898A8A4 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/ChemTransforms/chemTransformsTestCatch +101: 11# 0x0000AAAAD895C550 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/ChemTransforms/chemTransformsTestCatch +101: 12# 0x0000FFFFA5D6229C in /lib/aarch64-linux-gnu/libc.so.6 101: 13# __libc_start_main in /lib/aarch64-linux-gnu/libc.so.6 -101: 14# 0x0000AAAAC728C630 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/ChemTransforms/chemTransformsTestCatch +101: 14# 0x0000AAAAD895C630 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/ChemTransforms/chemTransformsTestCatch 101: ---------- 101: **** 101: 101: =============================================================================== 101: All tests passed (675 assertions in 10 test cases) 101: - 90/238 Test #100: testChemTransforms ..................... Passed 0.12 sec -test 102 - Start 102: tautomerQueryTestCatch - -102: Test command: /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/TautomerQuery/tautomerQueryTestCatch -102: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/TautomerQuery -102: Test timeout computed to be: 1500 - 91/238 Test #101: chemTransformsTestCatch ................ Passed 0.11 sec + 91/238 Test #101: chemTransformsTestCatch ................ Passed 0.09 sec test 103 Start 103: pyTautomerQuery 103: Test command: /usr/bin/python3 "/build/reproducible-path/rdkit-202503.1/Code/GraphMol/TautomerQuery/Wrap/rough_test.py" 103: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/TautomerQuery/Wrap 103: Test timeout computed to be: 1500 -98: [00:36:17] == testCartesianProduct -98: .[00:36:17] == testEnumerateLibrary +98: [09:33:10] == testCartesianProduct +99: .[09:33:10] reactant 0 has no mapped atoms. +99: [09:33:10] product 0 has no mapped atoms. +99: [09:33:10] reactant 0 has no mapped atoms. +99: [09:33:10] product 0 has no mapped atoms. +98: .[09:33:10] == testEnumerateLibrary +97: ...[09:33:10] +97: +97: **** +99: .[09:33:10] reactant 0 has no mapped atoms. +99: [09:33:10] reactant 1 has no mapped atoms. +99: [09:33:10] product 0 has no mapped atoms. +99: [09:33:10] reactant 0 has no mapped atoms. 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 -98: ..[00:36:17] == testRGroupState -99: .[00:36:17] reactant 0 has no mapped atoms. -99: [00:36:17] product 0 has no mapped atoms. -99: [00:36:17] reactant 0 has no mapped atoms. -99: [00:36:17] product 0 has no mapped atoms. -99: .[00:36:17] reactant 0 has no mapped atoms. -99: [00:36:17] reactant 1 has no mapped atoms. -99: [00:36:17] product 0 has no mapped atoms. -99: [00:36:17] reactant 0 has no mapped atoms. -99: [00:36:17] reactant 1 has no mapped atoms. -99: [00:36:17] product 0 has no mapped atoms. -99: [00:36:17] reactant 0 has no mapped atoms. -99: [00:36:17] reactant 1 has no mapped atoms. -99: [00:36:17] product 0 has no mapped atoms. -99: [00:36:17] reactant 0 has no mapped atoms. -99: [00:36:17] reactant 1 has no mapped atoms. -99: [00:36:17] product 0 has no mapped atoms. -98: .[00:36:17] == testRandomEnumerateAllBBsLibrary -98: ** [1, 1] -98: ** [0, 2] -98: ** [1, 0] -99: [00:36:17] reactant 0 has no mapped atoms. -99: [00:36:17] reactant 1 has no mapped atoms. -99: [00:36:17] product 0 has no mapped atoms. -99: [00:36:17] reactant 0 has no mapped atoms. -99: [00:36:17] reactant 1 has no mapped atoms. -99: [00:36:17] product 0 has no mapped atoms. -99: [00:36:17] reactant 0 has no mapped atoms. -99: [00:36:17] reactant 1 has no mapped atoms. -99: [00:36:17] product 0 has no mapped atoms. -99: [00:36:17] reactant 0 has no mapped atoms. -99: [00:36:17] reactant 1 has no mapped atoms. -99: [00:36:17] product 0 has no mapped atoms. -99: [00:36:17] reactant 0 has no mapped atoms. -99: [00:36:17] reactant 1 has no mapped atoms. -99: [00:36:17] product 0 has no mapped atoms. -99: [00:36:17] reactant 0 has no mapped atoms. -99: [00:36:17] reactant 1 has no mapped atoms. -99: [00:36:17] product 0 has no mapped atoms. -99: [00:36:17] reactant 0 has no mapped atoms. -99: [00:36:17] reactant 1 has no mapped atoms. -99: [00:36:17] product 0 has no mapped atoms. -99: [00:36:17] reactant 0 has no mapped atoms. -99: [00:36:17] reactant 1 has no mapped atoms. -99: [00:36:17] product 0 has no mapped atoms. -99: [00:36:17] reactant 0 has no mapped atoms. -99: [00:36:17] reactant 1 has no mapped atoms. -99: [00:36:17] product 0 has no mapped atoms. -99: [00:36:17] reactant 0 has no mapped atoms. -99: [00:36:17] reactant 1 has no mapped atoms. -99: [00:36:17] product 0 has no mapped atoms. +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-aarch64-linux-gnu//lib/libRDKitRDGeneral.so.1 +97: 1# Invar::operator<<(std::ostream&, Invar::Invariant const&) in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu//lib/libRDKitRDGeneral.so.1 +97: 2# RDKit::Atom::getNumImplicitHs() const in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu//lib/libRDKitGraphMol.so.1 +97: 3# RDKit::Atom::getTotalNumHs(bool) const in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu//lib/libRDKitGraphMol.so.1 +97: 4# Queries::EqualityQuery::Match(RDKit::Atom const*) const in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu//lib/libRDKitSmilesParse.so.1 +97: 5# Queries::AndQuery::Match(RDKit::Atom const*) const in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu//lib/libRDKitGraphMol.so.1 +97: 6# Queries::AndQuery::Match(RDKit::Atom const*) const in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu//lib/libRDKitGraphMol.so.1 +97: 7# Queries::OrQuery::Match(RDKit::Atom const*) const in /build/reproducible-path/rdkit-202503.1/obj-aarch64-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-aarch64-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-aarch64-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-aarch64-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-aarch64-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-aarch64-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-aarch64-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-aarch64-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-aarch64-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-aarch64-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-aarch64-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-aarch64-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-aarch64-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-aarch64-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-aarch64-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-aarch64-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-aarch64-linux-gnu/rdkit/Chem/rdChemReactions.so +97: 24# boost::python::objects::function::call(_object*, _object*) const in /lib/aarch64-linux-gnu/libboost_python313.so.1.83.0 +97: 25# 0x0000FFFF98A42680 in /lib/aarch64-linux-gnu/libboost_python313.so.1.83.0 +97: 26# boost::python::detail::exception_handler::operator()(boost::function0 const&) const in /lib/aarch64-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-aarch64-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-aarch64-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-aarch64-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-aarch64-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-aarch64-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-aarch64-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-aarch64-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-aarch64-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-aarch64-linux-gnu/rdkit/Chem/rdchem.so +97: 36# 0x0000FFFF96FFC320 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so +97: 37# 0x0000FFFF96FFC2B8 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so +97: 38# 0x0000FFFF96FFC248 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so +97: 39# 0x0000FFFF96FFC1E0 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so +97: 40# 0x0000FFFF96FFC178 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-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-aarch64-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-aarch64-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-aarch64-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-aarch64-linux-gnu/rdkit/rdBase.so +97: 45# boost::python::handle_exception_impl(boost::function0) in /lib/aarch64-linux-gnu/libboost_python313.so.1.83.0 +97: 46# 0x0000FFFF98A3F25C in /lib/aarch64-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# 0x000000000053D3B0 in /usr/bin/python3 +97: 50# _PyEval_EvalFrameDefault in /usr/bin/python3 +97: 51# 0x000000000061C8E0 in /usr/bin/python3 +97: 52# 0x00000000005A787C in /usr/bin/python3 +97: 53# _PyObject_MakeTpCall in /usr/bin/python3 +97: 54# _PyEval_EvalFrameDefault in /usr/bin/python3 +97: 55# 0x000000000053D3B0 in /usr/bin/python3 +97: 56# _PyEval_EvalFrameDefault in /usr/bin/python3 +97: 57# 0x000000000061C8E0 in /usr/bin/python3 +97: 58# 0x00000000005A787C in /usr/bin/python3 +97: 59# _PyObject_MakeTpCall in /usr/bin/python3 +97: 60# _PyEval_EvalFrameDefault in /usr/bin/python3 +97: 61# 0x000000000053D3B0 in /usr/bin/python3 +97: 62# _PyEval_EvalFrameDefault in /usr/bin/python3 +97: 63# 0x000000000061C8E0 in /usr/bin/python3 +97: 64# 0x00000000005A787C in /usr/bin/python3 +97: 65# _PyObject_MakeTpCall in /usr/bin/python3 +97: 66# _PyEval_EvalFrameDefault in /usr/bin/python3 +97: 67# 0x000000000050B150 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# 0x000000000064023C in /usr/bin/python3 +97: 72# 0x000000000063BC30 in /usr/bin/python3 +97: 73# 0x000000000065F810 in /usr/bin/python3 +97: 74# 0x000000000065F0B4 in /usr/bin/python3 +97: 75# 0x000000000065EE50 in /usr/bin/python3 +97: 76# Py_RunMain in /usr/bin/python3 +97: 77# Py_BytesMain in /usr/bin/python3 +97: 78# 0x0000FFFF9957229C in /lib/aarch64-linux-gnu/libc.so.6 +97: 79# __libc_start_main in /lib/aarch64-linux-gnu/libc.so.6 +97: 80# _start in /usr/bin/python3 +97: ---------- +99: [09:33:10] reactant 1 has no mapped atoms. +99: [09:33:10] product 0 has no mapped atoms. +99: [09:33:10] reactant 0 has no mapped atoms. +99: [09:33:10] reactant 1 has no mapped atoms. +99: [09:33:10] product 0 has no mapped atoms. +99: [09:33:10] reactant 0 has no mapped atoms. +99: [09:33:10] reactant 1 has no mapped atoms. +99: [09:33:10] product 0 has no mapped atoms. +99: [09:33:10] reactant 0 has no mapped atoms. +99: [09:33:10] reactant 1 has no mapped atoms. +99: [09:33:10] product 0 has no mapped atoms. +99: [09:33:10] reactant 0 has no mapped atoms. +99: [09:33:10] reactant 1 has no mapped atoms. +99: [09:33:10] product 0 has no mapped atoms. +99: [09:33:10] reactant 0 has no mapped atoms. +99: [09:33:10] reactant 1 has no mapped atoms. +99: [09:33:10] product 0 has no mapped atoms. +99: [09:33:10] reactant 0 has no mapped atoms. +99: [09:33:10] reactant 1 has no mapped atoms. +99: [09:33:10] product 0 has no mapped atoms. +99: [09:33:10] reactant 0 has no mapped atoms. +99: [09:33:10] reactant 1 has no mapped atoms. +99: [09:33:10] product 0 has no mapped atoms. +97: **** +97: +99: [09:33:10] reactant 0 has no mapped atoms. +99: [09:33:10] reactant 1 has no mapped atoms. +99: [09:33:10] product 0 has no mapped atoms. +97: [09:33:10] +97: +97: **** +99: [09:33:10] reactant 0 has no mapped atoms. +99: [09:33:10] reactant 1 has no mapped atoms. +99: [09:33:10] product 0 has no mapped atoms. +99: [09:33:10] reactant 0 has no mapped atoms. +99: [09:33:10] reactant 1 has no mapped atoms. +99: [09:33:10] product 0 has no mapped atoms. +99: [09:33:10] reactant 0 has no mapped atoms. +99: [09:33:10] reactant 1 has no mapped atoms. +99: [09:33:10] product 0 has no mapped atoms. +99: [09:33:10] reactant 0 has no mapped atoms. +99: [09:33:10] reactant 1 has no mapped atoms. +99: [09:33:10] product 0 has no mapped atoms. 99: () 99: ******************************************** 99: $RXN @@ -23616,16 +23540,16 @@ 99: 1 2 1 0 99: M ISO 2 1 1 2 2 99: M END -99: [00:36:17] reactant 0 has no mapped atoms. -99: [00:36:17] reactant 1 has no mapped atoms. -99: [00:36:17] product 0 has no mapped atoms. -99: [00:36:17] Could not find RLabel mapping for atom: 0 in template: 1 -99: [00:36:17] reactant 1 has no mapped atoms. -99: [00:36:17] reactant 1 has no mapped atoms. -99: [00:36:17] reactant 1 has no mapped atoms. +99: [09:33:10] reactant 0 has no mapped atoms. +99: [09:33:10] reactant 1 has no mapped atoms. +99: [09:33:10] product 0 has no mapped atoms. +99: [09:33:10] Could not find RLabel mapping for atom: 0 in template: 1 +99: [09:33:10] reactant 1 has no mapped atoms. +99: [09:33:10] reactant 1 has no mapped atoms. +99: [09:33:10] reactant 1 has no mapped atoms. 99: .. 99: ---------------------------------------------------------------------- -99: Ran 4 tests in 0.024s +99: Ran 4 tests in 0.035s 99: 99: OK 99: @@ -23682,83 +23606,153 @@ 99: M END 99: 99: $RXN Failed -98: .[00:36:17] == testRandomEnumerateLibrary -98: .[00:36:17] == testRandomSample -98: .[00:36:17] == testRandomSampleAllBBs -98: .[00:36:17] deprecated -- please use MatchOnlyAtRgroupsAdjustParams instead -98: [00:36:17] deprecated -- please use MatchOnlyAtRgroupsAdjustParams instead -98: .[00:36:17] == testRemoveBadMatches -98: .[00:36:17] == testTimings - 92/238 Test #99: pyChemReactionSanitize ................. Passed 0.43 sec +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-aarch64-linux-gnu//lib/libRDKitRDGeneral.so.1 +97: 1# Invar::operator<<(std::ostream&, Invar::Invariant const&) in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu//lib/libRDKitRDGeneral.so.1 +97: 2# RDKit::Atom::getNumImplicitHs() const in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu//lib/libRDKitGraphMol.so.1 +97: 3# RDKit::Atom::getTotalNumHs(bool) const in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu//lib/libRDKitGraphMol.so.1 +97: 4# Queries::EqualityQuery::Match(RDKit::Atom const*) const in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu//lib/libRDKitSmilesParse.so.1 +97: 5# Queries::AndQuery::Match(RDKit::Atom const*) const in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu//lib/libRDKitGraphMol.so.1 +97: 6# Queries::AndQuery::Match(RDKit::Atom const*) const in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu//lib/libRDKitGraphMol.so.1 +97: 7# Queries::OrQuery::Match(RDKit::Atom const*) const in /build/reproducible-path/rdkit-202503.1/obj-aarch64-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-aarch64-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-aarch64-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-aarch64-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-aarch64-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-aarch64-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-aarch64-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-aarch64-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-aarch64-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-aarch64-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-aarch64-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-aarch64-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-aarch64-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-aarch64-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-aarch64-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-aarch64-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-aarch64-linux-gnu/rdkit/Chem/rdChemReactions.so +97: 24# boost::python::objects::function::call(_object*, _object*) const in /lib/aarch64-linux-gnu/libboost_python313.so.1.83.0 +97: 25# 0x0000FFFF98A42680 in /lib/aarch64-linux-gnu/libboost_python313.so.1.83.0 +97: 26# boost::python::detail::exception_handler::operator()(boost::function0 const&) const in /lib/aarch64-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-aarch64-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-aarch64-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-aarch64-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-aarch64-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-aarch64-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-aarch64-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-aarch64-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-aarch64-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-aarch64-linux-gnu/rdkit/Chem/rdchem.so +97: 36# 0x0000FFFF96FFC320 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so +97: 37# 0x0000FFFF96FFC2B8 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so +97: 38# 0x0000FFFF96FFC248 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so +97: 39# 0x0000FFFF96FFC1E0 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so +97: 40# 0x0000FFFF96FFC178 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-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-aarch64-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-aarch64-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-aarch64-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-aarch64-linux-gnu/rdkit/rdBase.so +97: 45# boost::python::handle_exception_impl(boost::function0) in /lib/aarch64-linux-gnu/libboost_python313.so.1.83.0 +97: 46# 0x0000FFFF98A3F25C in /lib/aarch64-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# 0x000000000053D3B0 in /usr/bin/python3 +97: 50# _PyEval_EvalFrameDefault in /usr/bin/python3 +97: 51# 0x000000000061C8E0 in /usr/bin/python3 +97: 52# 0x00000000005A787C in /usr/bin/python3 +97: 53# _PyObject_MakeTpCall in /usr/bin/python3 +97: 54# _PyEval_EvalFrameDefault in /usr/bin/python3 +97: 55# 0x000000000053D3B0 in /usr/bin/python3 +97: 56# _PyEval_EvalFrameDefault in /usr/bin/python3 +97: 57# 0x000000000061C8E0 in /usr/bin/python3 +97: 58# 0x00000000005A787C in /usr/bin/python3 +97: 59# _PyObject_MakeTpCall in /usr/bin/python3 +97: 60# _PyEval_EvalFrameDefault in /usr/bin/python3 +97: 61# 0x000000000053D3B0 in /usr/bin/python3 +97: 62# _PyEval_EvalFrameDefault in /usr/bin/python3 +97: 63# 0x000000000061C8E0 in /usr/bin/python3 +97: 64# 0x00000000005A787C in /usr/bin/python3 +97: 65# _PyObject_MakeTpCall in /usr/bin/python3 +97: 66# _PyEval_EvalFrameDefault in /usr/bin/python3 +97: 67# 0x000000000050B150 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# 0x000000000064023C in /usr/bin/python3 +97: 72# 0x000000000063BC30 in /usr/bin/python3 +97: 73# 0x000000000065F810 in /usr/bin/python3 +97: 74# 0x000000000065F0B4 in /usr/bin/python3 +97: 75# 0x000000000065EE50 in /usr/bin/python3 +97: 76# Py_RunMain in /usr/bin/python3 +97: 77# Py_BytesMain in /usr/bin/python3 +97: 78# 0x0000FFFF9957229C in /lib/aarch64-linux-gnu/libc.so.6 +97: 79# __libc_start_main in /lib/aarch64-linux-gnu/libc.so.6 +97: 80# _start in /usr/bin/python3 +97: ---------- +97: **** +97: +97: .........[09:33:10] stereo atoms in input cannot be mapped to output (atoms are no longer bonded) +97: [09:33:10] stereo atoms in input cannot be mapped to output (atoms are no longer bonded) +97: [09:33:10] stereo atoms in input cannot be mapped to output (atoms are no longer bonded) +97: [09:33:10] stereo atoms in input cannot be mapped to output (atoms are no longer bonded) +97: .[09:33:10] product atom-mapping number 1 found multiple times. +97: [09:33:10] product atom-mapping number 1 found multiple times. +102: Randomness seeded to: 1889719235 +102: =============================================================================== +102: All tests passed (93 assertions in 13 test cases) +102: + 92/238 Test #102: tautomerQueryTestCatch ................. Passed 0.12 sec test 104 Start 104: testSubgraphs1 104: Test command: /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/Subgraphs/testSubgraphs1 104: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/Subgraphs 104: Test timeout computed to be: 1500 +97: ................[09:33:10] mapped atoms in the reactants were not mapped in the products. +97: unmapped numbers are: 3 +97: [09:33:10] mapped atoms in the reactants were not mapped in the products. +97: unmapped numbers are: 3 +98: ..[09:33:10] == testRGroupState +98: .[09:33:10] == testRandomEnumerateAllBBsLibrary +98: ** [1, 1] +98: ** [0, 2] +98: ** [1, 0] 104: ----------------------- 104: Subgraph retrieval 104: Finished 104: ----------------------- 104: testSubgraphs2a +98: .[09:33:10] == testRandomEnumerateLibrary +97: .:488: RuntimeWarning: to-Python converter for boost::shared_ptr already registered; second conversion method ignored. +97: [09:33:10] mapped atoms in the reactants were not mapped in the products. +97: unmapped numbers are: 3 +98: .[09:33:10] == testRandomSample 104: Finished 104: ----------------------- 104: testSubgraphs2 -69: [00:36:17] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 1 ignored -69: [00:36:17] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 1 ignored -69: [00:36:17] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 1 ignored -69: [00:36:17] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 1 ignored -69: [00:36:17] 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: [00:36:17] -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-aarch64-linux-gnu//lib/libRDKitRDGeneral.so.1 -69: 1# Invar::operator<<(std::ostream&, Invar::Invariant const&) in /build/reproducible-path/rdkit-202503.1/obj-aarch64-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-aarch64-linux-gnu//lib/libRDKitFileParsers.so.1 -69: 3# 0x0000FFFF98E67EA4 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu//lib/libRDKitFileParsers.so.1 -69: 4# 0x0000FFFF98E75AA0 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu//lib/libRDKitFileParsers.so.1 -69: 5# 0x0000FFFF98E769CC in /build/reproducible-path/rdkit-202503.1/obj-aarch64-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-aarch64-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-aarch64-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-aarch64-linux-gnu//lib/libRDKitFileParsers.so.1 -69: 9# 0x0000AAAAE6B2F77C in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersTest1 -69: 10# 0x0000AAAAE6BA4944 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersTest1 -69: 11# 0x0000AAAAE6B15C6C in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersTest1 -69: 12# 0x0000FFFF9852229C in /lib/aarch64-linux-gnu/libc.so.6 -69: 13# __libc_start_main in /lib/aarch64-linux-gnu/libc.so.6 -69: 14# 0x0000AAAAE6B15E30 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersTest1 -69: ---------- -69: **** -69: -103: ..... -103: ---------------------------------------------------------------------- -103: Ran 5 tests in 0.058s -103: -103: OK -102: Randomness seeded to: 1736180351 -102: =============================================================================== -102: All tests passed (93 assertions in 13 test cases) -102: -104: Finished -104: ----------------------- -104: Path retrieval -104: Finished -104: ----------------------- -104: Path retrieval2 -104: Finished -104: ----------------------- -104: Unique Subgraph retrieval -104: Finished -104: ----------------------- -104: testUniqueSubgraphs2 - 93/238 Test #102: tautomerQueryTestCatch ................. Passed 0.38 sec +98: .[09:33:10] == testRandomSampleAllBBs +97: ..[09:33:10] reactant 2 has no mapped atoms. +97: [09:33:10] reactant 2 has no mapped atoms. +97: [09:33:10] product 1 has no mapped atoms. +98: .[09:33:10] deprecated -- please use MatchOnlyAtRgroupsAdjustParams instead +98: [09:33:10] deprecated -- please use MatchOnlyAtRgroupsAdjustParams instead +98: .[09:33:10] == testRemoveBadMatches +98: .[09:33:10] == testTimings +97: ........[09:33:10] SMARTS Parse Error: syntax error while parsing: [C:1](=[O:2])Q +97: [09:33:10] SMARTS Parse Error: Failed parsing SMARTS '[C:1](=[O:2])Q' for input: '[C:1](=[O:2])Q' +97: [09:33:10] SMARTS Parse Error: syntax error while parsing: [C:1](=[O:2])[N:3]Q +97: [09:33:10] SMARTS Parse Error: Failed parsing SMARTS '[C:1](=[O:2])[N:3]Q' for input: '[C:1](=[O:2])[N:3]Q' +97: .[09:33:10] reactant atom-mapping number 1 found multiple times. +97: [09:33:10] product atom-mapping number 2 not found in reactants. +97: [09:33:10] mapped atoms in the reactants were not mapped in the products. +97: unmapped numbers are: 4 +97: [09:33:10] product atom-mapping number 5 not found in reactants. + 93/238 Test #99: pyChemReactionSanitize ................. Passed 0.40 sec test 105 Start 105: testSubgraphs2 @@ -23767,6 +23761,19 @@ 105: Test timeout computed to be: 1500 105: ----------------------- 105: Test1: pathToSubmol +97: ........./build/reproducible-path/rdkit-202503.1/Code/GraphMol/ChemReactions/Wrap/testReactionWrapper.py:745: ResourceWarning: unclosed file <_io.BufferedReader name='/build/reproducible-path/rdkit-202503.1/Code/GraphMol/ChemReactions/testData/reaction1.no_metadata.png'> +97: png = open(fname, 'rb').read() +97: ResourceWarning: Enable tracemalloc to get the object allocation traceback +97: [09:33:10] Found a SCD/SED line with missing/empty SDT specification at line 34 +97: [09:33:10] Found a SCD/SED line with missing/empty SDT specification at line 36 +97: [09:33:10] Found a SCD/SED line with missing/empty SDT specification at line 38 +97: [09:33:10] Found a SCD/SED line with missing/empty SDT specification at line 40 +97: [09:33:10] Found a SCD/SED line with missing/empty SDT specification at line 42 +97: [09:33:10] Found a SCD/SED line with missing/empty SDT specification at line 87 +97: [09:33:10] Found a SCD/SED line with missing/empty SDT specification at line 89 +97: [09:33:10] Found a SCD/SED line with missing/empty SDT specification at line 91 +97: [09:33:10] Found a SCD/SED line with missing/empty SDT specification at line 93 +97: [09:33:10] Found a SCD/SED line with missing/empty SDT specification at line 95 105: Finished 105: ----------------------- 105: Test2: Atom Environments @@ -23780,6 +23787,8 @@ 105: ----------------------- 105: Testing github Issue103: more stereochemistry and pathToSubmol (path needs to be in sorted order) 105: Finished +97: ..[09:33:10] SMARTS Parse Error: syntax error while parsing: boromicacid +97: [09:33:10] SMARTS Parse Error: Failed parsing SMARTS 'boromicacid' for input: 'boromicacid' 94/238 Test #105: testSubgraphs2 ......................... Passed 0.03 sec test 106 Start 106: subgraphsCatch @@ -23787,27 +23796,70 @@ 106: Test command: /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/Subgraphs/subgraphsCatch 106: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/Subgraphs 106: Test timeout computed to be: 1500 -106: Randomness seeded to: 722324802 +103: ..... +103: ---------------------------------------------------------------------- +103: Ran 5 tests in 0.025s +103: +103: OK +104: Finished +104: ----------------------- +104: Path retrieval +104: Finished +104: ----------------------- +104: Path retrieval2 +104: Finished +104: ----------------------- +104: Unique Subgraph retrieval +104: Finished +104: ----------------------- +104: testUniqueSubgraphs2 +97: [09:33:10] SMARTS Parse Error: syntax error while parsing: carboxylicacid,acidchlroide +97: [09:33:10] SMARTS Parse Error: Failed parsing SMARTS 'carboxylicacid,acidchlroide' for input: 'carboxylicacid,acidchlroide' +97: [09:33:10] SMARTS Parse Error: syntax error while parsing: carboxyliccaid,acidchloride +97: [09:33:10] SMARTS Parse Error: Failed parsing SMARTS 'carboxyliccaid,acidchloride' for input: 'carboxyliccaid,acidchloride' +97: [09:33:10] reaction has no reactants +97: [09:33:10] reaction has no products +97: [09:33:10] initialization failed +97: [09:33:10] reaction has no reactants +97: [09:33:10] reaction has no products +97: .[09:33:10] SMARTS Parse Error: syntax error while parsing: boromicacid +97: [09:33:10] SMARTS Parse Error: Failed parsing SMARTS 'boromicacid' for input: 'boromicacid' +97: [09:33:10] SMARTS Parse Error: syntax error while parsing: carboxylicacid,acidchlroide +97: [09:33:10] SMARTS Parse Error: Failed parsing SMARTS 'carboxylicacid,acidchlroide' for input: 'carboxylicacid,acidchlroide' +97: [09:33:10] SMARTS Parse Error: syntax error while parsing: carboxyliccaid,acidchloride +97: [09:33:10] SMARTS Parse Error: Failed parsing SMARTS 'carboxyliccaid,acidchloride' for input: 'carboxyliccaid,acidchloride' +97: [09:33:10] reaction has no reactants +97: [09:33:10] reaction has no products +97: [09:33:10] initialization failed +97: [09:33:10] reaction has no reactants +97: [09:33:10] reaction has no products +97: . +97: ---------------------------------------------------------------------- +97: Ran 54 tests in 0.192s +97: +97: OK +97: ******************************************** +97: /build/reproducible-path/rdkit-202503.1/Code/GraphMol/ChemReactions/testData/AmideBond.rxn +97: +106: Randomness seeded to: 2560766200 106: --------- 106: =============================================================================== 106: All tests passed (11 assertions in 1 test case) 106: - 95/238 Test #103: pyTautomerQuery ........................ Passed 0.44 sec - 96/238 Test #106: subgraphsCatch ......................... Passed 0.03 sec + 95/238 Test #103: pyTautomerQuery ........................ Passed 0.23 sec test 107 Start 107: filterCatalogTest 107: Test command: /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FilterCatalog/filterCatalogTest 107: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FilterCatalog 107: Test timeout computed to be: 1500 + 96/238 Test #106: subgraphsCatch ......................... Passed 0.05 sec test 108 Start 108: pyFilterCatalog 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-aarch64-linux-gnu/Code/GraphMol/FilterCatalog/Wrap 108: Test timeout computed to be: 1500 -69: [00:36:17] 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: [00:36:17] Warning: molecule is tagged as 3D, but all Z coords are zero and 2D stereo markers have been found, marking the mol as 2D. 107: Warning: molecule failed filter 107: Warning: molecule failed filter: reason hzone_phenol_A(479) 107: v = { @@ -23867,6 +23919,13 @@ 107: 12,16}, 107: } 107: Warning: molecule failed filter + 97/238 Test #97: pyChemReactions ........................ Passed 0.61 sec +test 109 + Start 109: testFragCatalog + +109: Test command: /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FragCatalog/testFragCatalog +109: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FragCatalog +109: Test timeout computed to be: 1500 107: Warning: molecule failed filter: reason keto_keto_gamma(5) 107: v = { 107: 0,0}, @@ -23896,11 +23955,8 @@ 107: 10,15}, 107: 11,16}, 107: } -12: .................. -12: ---------------------------------------------------------------------- -12: Ran 18 tests in 4.369s -12: -12: OK +89: [09:33:10] Explicit valence for atom # 9 N, 5, is greater than permitted +109: 21 104: Finished 104: ----------------------- 104: testRootedSubgraphs @@ -23908,125 +23964,47 @@ 104: ----------------------- 104: testRootedPaths 104: Finished - 97/238 Test #104: testSubgraphs1 ......................... Passed 0.28 sec -test 109 - Start 109: testFragCatalog - -109: Test command: /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FragCatalog/testFragCatalog -109: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FragCatalog -109: Test timeout computed to be: 1500 -69: ---------------------------------- -69: ---------------------------------- -69: [00:36:17] -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-aarch64-linux-gnu//lib/libRDKitRDGeneral.so.1 -69: 1# Invar::operator<<(std::ostream&, Invar::Invariant const&) in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu//lib/libRDKitRDGeneral.so.1 -69: 2# RDKit::setAtomRLabel(RDKit::Atom*, int) in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu//lib/libRDKitGraphMol.so.1 -69: 3# 0x0000AAAAE6B3F23C in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersTest1 -69: 4# 0x0000AAAAE6BA49A4 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersTest1 -69: 5# 0x0000AAAAE6B15C6C in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersTest1 -69: 6# 0x0000FFFF9852229C in /lib/aarch64-linux-gnu/libc.so.6 -69: 7# __libc_start_main in /lib/aarch64-linux-gnu/libc.so.6 -69: 8# 0x0000AAAAE6B15E30 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersTest1 -69: ---------- -69: **** -69: -69: [00:36:17] WARNING: could not find number of expected rings. Switching to an approximate ring finding algorithm. -109: 21 - 98/238 Test #12: pyBV ................................... Passed 4.90 sec + 98/238 Test #104: testSubgraphs1 ......................... Passed 0.27 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-aarch64-linux-gnu/Code/GraphMol/FragCatalog/Wrap 110: Test timeout computed to be: 1500 - 99/238 Test #107: filterCatalogTest ...................... Passed 0.24 sec +89: [09:33:10] Explicit valence for atom # 3 Al, 6, is greater than permitted +89: [09:33:10] Explicit valence for atom # 4 Al, 6, is greater than permitted + 99/238 Test #107: filterCatalogTest ...................... Passed 0.27 sec test 111 Start 111: testDescriptors 111: Test command: /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/Descriptors/testDescriptors 111: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/Descriptors 111: Test timeout computed to be: 1500 -111: [00:36:17] ------------------------------------- -111: [00:36:17] Test Crippen parameter acquisition. -111: [00:36:17] done -111: [00:36:17] ------------------------------------- -111: [00:36:17] Test Crippen calculation. -69: [00:36:17] SMARTS Parse Error: syntax error while parsing: MyDogHasFleas -69: [00:36:17] SMARTS Parse Error: Failed parsing SMARTS 'MyDogHasFleas' for input: 'MyDogHasFleas' -111: [00:36:17] done -111: [00:36:17] ------------------------------------- -111: [00:36:17] Test Issue262: problems with Crippen calculation from pickles. -111: [00:36:17] done -111: [00:36:17] ------------------------------------- -111: [00:36:17] Test AMW calculation. -111: [00:36:17] done -111: [00:36:17] ------------------------------------- -111: [00:36:17] Test Exact MW calculation. -111: [00:36:17] done -111: [00:36:17] ------------------------------------- -111: [00:36:17] Test Labute ASA descriptors. +89: [09:33:10] Explicit valence for atom # 10 Si, 6, is greater than permitted +111: [09:33:10] ------------------------------------- +111: [09:33:10] Test Crippen parameter acquisition. +111: [09:33:10] done +111: [09:33:10] ------------------------------------- +111: [09:33:10] Test Crippen calculation. +111: [09:33:10] done +111: [09:33:10] ------------------------------------- +111: [09:33:10] Test Issue262: problems with Crippen calculation from pickles. +111: [09:33:10] done +111: [09:33:10] ------------------------------------- +111: [09:33:10] Test AMW calculation. +111: [09:33:10] done +111: [09:33:10] ------------------------------------- +111: [09:33:10] Test Exact MW calculation. +111: [09:33:10] done +111: [09:33:10] ------------------------------------- +111: [09:33:10] Test Labute ASA descriptors. +111: [09:33:10] done +111: [09:33:10] ------------------------------------- +111: [09:33:10] Test TPSA descriptors. 108: :488: RuntimeWarning: to-Python converter for boost::shared_ptr already registered; second conversion method ignored. -111: [00:36:17] done -111: [00:36:17] ------------------------------------- -111: [00:36:17] Test TPSA descriptors. -69: [00:36:17] Empty atom list: 'M ALS 1 0 F' on line 8. -100/238 Test #69: fileParsersTest1 ....................... Passed 3.73 sec -test 112 - Start 112: testAUTOCORR2D - -112: Test command: /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/Descriptors/testAUTOCORR2D -112: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/Descriptors -112: Test timeout computed to be: 1500 -111: [00:36:17] done -111: [00:36:17] ------------------------------------- -111: [00:36:17] Test Lipinski parameters. -112: [00:36:17] ---------------------------- -112: start test autocorr2D -111: [00:36:17] done -111: [00:36:17] ------------------------------------- -111: [00:36:17] Test VSA descriptors. -111: [00:36:17] done -111: [00:36:17] ------------------------------------- -111: [00:36:17] Test molecular formula calculation. -111: [00:36:17] done -111: [00:36:17] ------------------------------------- -111: [00:36:17] Test Issue 3415534. -111: [00:36:17] done -111: [00:36:17] ------------------------------------- -111: [00:36:17] Test Issue3433771: Bad definition for Crippen atom type O11. -111: [00:36:17] done -111: [00:36:17] ------------------------------------- -111: [00:36:17] Test multithreading -111: reading molecules -111: processing -111: launch :0 -111: launch :1 -111: launch :2 -111: launch :3 -110: ......... -110: ---------------------------------------------------------------------- -110: Ran 9 tests in 0.069s -110: -110: OK -101/238 Test #110: pyFragCatalog .......................... Passed 0.46 sec -test 113 - Start 113: testATF - -113: Test command: /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/Descriptors/testATF -113: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/Descriptors -113: Test timeout computed to be: 1500 -29: Checking against /build/reproducible-path/rdkit-202503.1/Code/ForceField/MMFF/test_data/MMFF94_reference.log... 98: . 98: ---------------------------------------------------------------------- -98: Ran 11 tests in 0.958s +98: Ran 11 tests in 0.558s 98: 98: OK 98: True @@ -24039,129 +24017,25 @@ 98: 0 10 out of 10 98: 1 5 out of 5 98: 2 6 out of 6 -98: Skipped 10000000 in 0.06383872032165527 seconds -98: Skipped 10000000 in 0.4793984889984131 seconds -98: Skipped 10000000 in 0.1541287899017334 seconds -102/238 Test #113: testATF ................................ Passed 0.03 sec -test 114 - Start 114: testBCUT - -114: Test command: /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/Descriptors/testBCUT -114: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/Descriptors -114: Test timeout computed to be: 1500 -114: [00:36:18] ------------------------------------- -114: [00:36:18] Basic BCUT tests. -114: [00:36:18] done -114: [00:36:18] ------------------------------------- -114: [00:36:18] Larger BCUT tests. -103/238 Test #98: pyChemReactionEnumerations ............. Passed 1.34 sec -test 115 - Start 115: testEEM - -115: Test command: /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/Descriptors/testEEM -115: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/Descriptors -115: Test timeout computed to be: 1500 -115: =>start test EEM -115: [00:36:18] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: 0 -115: [00:36:18] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [00:36:18] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [00:36:18] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -29: All 191 tests passed -115: [00:36:18] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [00:36:18] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [00:36:18] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [00:36:18] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [00:36:18] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [00:36:18] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [00:36:18] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [00:36:18] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [00:36:18] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [00:36:18] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [00:36:18] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [00:36:18] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [00:36:18] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [00:36:18] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [00:36:18] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [00:36:18] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [00:36:18] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [00:36:18] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [00:36:18] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [00:36:18] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [00:36:18] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -112: [00:36:18] done -115: [00:36:18] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -112: [00:36:18] ------------------------------------- -112: [00:36:18] Test Github #3806: NaNs from AUTOCORR2D descriptor -112: [00:36:18] done -115: [00:36:18] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [00:36:18] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [00:36:18] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -104/238 Test #112: testAUTOCORR2D ......................... Passed 0.47 sec -115: [00:36:18] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -test 116 - Start 116: testPBF +98: Skipped 10000000 in 0.0342409610748291 seconds +98: Skipped 10000000 in 0.2587602138519287 seconds +98: Skipped 10000000 in 0.07390689849853516 seconds +110: ......... +110: ---------------------------------------------------------------------- +110: Ran 9 tests in 0.067s +110: +110: OK +111: [09:33:10] done +111: [09:33:10] ------------------------------------- +111: [09:33:10] Test Lipinski parameters. +100/238 Test #98: pyChemReactionEnumerations ............. Passed 0.89 sec +test 112 + Start 112: testAUTOCORR2D -116: Test command: /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/Descriptors/testPBF -116: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/Descriptors -116: Test timeout computed to be: 1500 -115: [00:36:18] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [00:36:18] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [00:36:18] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [00:36:18] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [00:36:18] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [00:36:18] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [00:36:18] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [00:36:18] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [00:36:18] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [00:36:18] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [00:36:18] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [00:36:18] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [00:36:18] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [00:36:18] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [00:36:18] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -116: [00:36:18] ------------------------------------- -116: [00:36:18] Basic PBF tests. -115: [00:36:18] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [00:36:18] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [00:36:18] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [00:36:18] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [00:36:18] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [00:36:18] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [00:36:18] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [00:36:18] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [00:36:18] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [00:36:18] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [00:36:18] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [00:36:18] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [00:36:18] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [00:36:18] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [00:36:18] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [00:36:18] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [00:36:18] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [00:36:18] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [00:36:18] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [00:36:18] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [00:36:18] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [00:36:18] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [00:36:18] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [00:36:18] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [00:36:18] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [00:36:18] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [00:36:18] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [00:36:18] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [00:36:18] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [00:36:18] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [00:36:18] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [00:36:18] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [00:36:18] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [00:36:18] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [00:36:18] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [00:36:18] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [00:36:18] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [00:36:18] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [00:36:18] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -109: [00:36:18] +112: Test command: /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/Descriptors/testAUTOCORR2D +112: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/Descriptors +112: Test timeout computed to be: 1500 +109: [09:33:10] 109: 109: **** 109: Invariant Violation @@ -24172,17 +24046,17 @@ 109: Stacktrace: 109: 0# Invar::Invariant::toString[abi:cxx11]() const in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu//lib/libRDKitRDGeneral.so.1 109: 1# Invar::operator<<(std::ostream&, Invar::Invariant const&) in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu//lib/libRDKitRDGeneral.so.1 -109: 2# 0x0000FFFF86831948 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu//lib/libRDKitFragCatalog.so.1 +109: 2# 0x0000FFFFAAAE1948 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu//lib/libRDKitFragCatalog.so.1 109: 3# RDKit::readFuncGroups(std::istream&, int) in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu//lib/libRDKitFragCatalog.so.1 -109: 4# 0x0000AAAACED27B08 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FragCatalog/testFragCatalog -109: 5# 0x0000AAAACED24960 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FragCatalog/testFragCatalog -109: 6# 0x0000FFFF85DF229C in /lib/aarch64-linux-gnu/libc.so.6 +109: 4# 0x0000AAAADEB47B08 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FragCatalog/testFragCatalog +109: 5# 0x0000AAAADEB44960 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FragCatalog/testFragCatalog +109: 6# 0x0000FFFFAA0A229C in /lib/aarch64-linux-gnu/libc.so.6 109: 7# __libc_start_main in /lib/aarch64-linux-gnu/libc.so.6 -109: 8# 0x0000AAAACED24B30 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FragCatalog/testFragCatalog +109: 8# 0x0000AAAADEB44B30 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FragCatalog/testFragCatalog 109: ---------- 109: **** 109: -109: [00:36:18] +109: [09:33:10] 109: 109: **** 109: Invariant Violation @@ -24193,17 +24067,17 @@ 109: Stacktrace: 109: 0# Invar::Invariant::toString[abi:cxx11]() const in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu//lib/libRDKitRDGeneral.so.1 109: 1# Invar::operator<<(std::ostream&, Invar::Invariant const&) in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu//lib/libRDKitRDGeneral.so.1 -109: 2# 0x0000FFFF86831948 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu//lib/libRDKitFragCatalog.so.1 +109: 2# 0x0000FFFFAAAE1948 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu//lib/libRDKitFragCatalog.so.1 109: 3# RDKit::readFuncGroups(std::istream&, int) in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu//lib/libRDKitFragCatalog.so.1 -109: 4# 0x0000AAAACED27B08 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FragCatalog/testFragCatalog -109: 5# 0x0000AAAACED24960 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FragCatalog/testFragCatalog -109: 6# 0x0000FFFF85DF229C in /lib/aarch64-linux-gnu/libc.so.6 +109: 4# 0x0000AAAADEB47B08 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FragCatalog/testFragCatalog +109: 5# 0x0000AAAADEB44960 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FragCatalog/testFragCatalog +109: 6# 0x0000FFFFAA0A229C in /lib/aarch64-linux-gnu/libc.so.6 109: 7# __libc_start_main in /lib/aarch64-linux-gnu/libc.so.6 -109: 8# 0x0000AAAACED24B30 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FragCatalog/testFragCatalog +109: 8# 0x0000AAAADEB44B30 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FragCatalog/testFragCatalog 109: ---------- 109: **** 109: -109: [00:36:18] +109: [09:33:10] 109: 109: **** 109: Invariant Violation @@ -24214,519 +24088,614 @@ 109: Stacktrace: 109: 0# Invar::Invariant::toString[abi:cxx11]() const in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu//lib/libRDKitRDGeneral.so.1 109: 1# Invar::operator<<(std::ostream&, Invar::Invariant const&) in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu//lib/libRDKitRDGeneral.so.1 -109: 2# 0x0000FFFF86831948 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu//lib/libRDKitFragCatalog.so.1 +109: 2# 0x0000FFFFAAAE1948 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu//lib/libRDKitFragCatalog.so.1 109: 3# RDKit::readFuncGroups(std::istream&, int) in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu//lib/libRDKitFragCatalog.so.1 -109: 4# 0x0000AAAACED27B08 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FragCatalog/testFragCatalog -109: 5# 0x0000AAAACED24960 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FragCatalog/testFragCatalog -109: 6# 0x0000FFFF85DF229C in /lib/aarch64-linux-gnu/libc.so.6 +109: 4# 0x0000AAAADEB47B08 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FragCatalog/testFragCatalog +109: 5# 0x0000AAAADEB44960 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FragCatalog/testFragCatalog +109: 6# 0x0000FFFFAA0A229C in /lib/aarch64-linux-gnu/libc.so.6 109: 7# __libc_start_main in /lib/aarch64-linux-gnu/libc.so.6 -109: 8# 0x0000AAAACED24B30 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FragCatalog/testFragCatalog +109: 8# 0x0000AAAADEB44B30 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FragCatalog/testFragCatalog 109: ---------- 109: **** 109: -115: [00:36:18] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [00:36:18] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -105/238 Test #109: testFragCatalog ........................ Passed 0.78 sec +101/238 Test #109: testFragCatalog ........................ Passed 0.35 sec +test 113 + Start 113: testATF + +113: Test command: /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/Descriptors/testATF +113: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/Descriptors +113: Test timeout computed to be: 1500 +112: [09:33:10] ---------------------------- +112: start test autocorr2D +29: Checking against /build/reproducible-path/rdkit-202503.1/Code/ForceField/MMFF/test_data/MMFF94_reference.log... +102/238 Test #110: pyFragCatalog .......................... Passed 0.32 sec +test 114 + Start 114: testBCUT + +114: Test command: /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/Descriptors/testBCUT +114: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/Descriptors +114: Test timeout computed to be: 1500 +103/238 Test #113: testATF ................................ Passed 0.03 sec +test 115 + Start 115: testEEM + +115: Test command: /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/Descriptors/testEEM +115: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/Descriptors +115: Test timeout computed to be: 1500 +89: [09:33:10] Explicit valence for atom # 2 O, 4, is greater than permitted +114: [09:33:10] ------------------------------------- +114: [09:33:10] Basic BCUT tests. +89: [09:33:10] Explicit valence for atom # 3 Al, 6, is greater than permitted +115: =>start test EEM +115: [09:33:10] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +89: [09:33:10] Explicit valence for atom # 3 Be, 4, is greater than permitted +115: 0 +115: [09:33:10] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +29: All 191 tests passed +114: [09:33:10] done +114: [09:33:10] ------------------------------------- +114: [09:33:10] Larger BCUT tests. +115: [09:33:10] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [09:33:10] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [09:33:10] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [09:33:10] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [09:33:10] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [09:33:10] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [09:33:10] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [09:33:10] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +111: [09:33:10] done +111: [09:33:10] ------------------------------------- +111: [09:33:10] Test VSA descriptors. +115: [09:33:10] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +111: [09:33:10] done +111: [09:33:10] ------------------------------------- +111: [09:33:10] Test molecular formula calculation. +115: [09:33:10] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [09:33:10] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +111: [09:33:10] done +111: [09:33:10] ------------------------------------- +111: [09:33:10] Test Issue 3415534. +115: [09:33:10] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +111: [09:33:10] done +111: [09:33:10] ------------------------------------- +111: [09:33:10] Test Issue3433771: Bad definition for Crippen atom type O11. +111: [09:33:10] done +111: [09:33:10] ------------------------------------- +111: [09:33:10] Test multithreading +111: reading molecules +115: [09:33:10] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [09:33:10] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [09:33:10] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [09:33:10] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [09:33:10] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [09:33:10] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [09:33:10] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [09:33:10] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [09:33:10] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [09:33:10] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [09:33:10] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [09:33:10] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [09:33:10] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [09:33:10] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [09:33:10] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +111: processing +111: launch :0 +111: launch :1 +111: launch :2 +111: launch :3 +89: [09:33:10] Explicit valence for atom # 27 P, 6, is greater than permitted +115: [09:33:10] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [09:33:10] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [09:33:10] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [09:33:10] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [09:33:10] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [09:33:10] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [09:33:10] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [09:33:10] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [09:33:10] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [09:33:10] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [09:33:10] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [09:33:10] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [09:33:10] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [09:33:10] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [09:33:10] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [09:33:10] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [09:33:10] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [09:33:10] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [09:33:10] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [09:33:10] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [09:33:10] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [09:33:10] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [09:33:10] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [09:33:10] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [09:33:10] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [09:33:10] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [09:33:10] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [09:33:10] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [09:33:10] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [09:33:10] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [09:33:10] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [09:33:10] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [09:33:10] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [09:33:10] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [09:33:10] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [09:33:10] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [09:33:10] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [09:33:10] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [09:33:10] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [09:33:10] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [09:33:10] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [09:33:10] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +89: =============================================================================== +89: All tests passed (21562 assertions in 3 test cases) +89: +104/238 Test #89: multithreadedSupplierCatchTest ......... Passed 1.70 sec +test 116 + Start 116: testPBF + +116: Test command: /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/Descriptors/testPBF +116: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/Descriptors +116: Test timeout computed to be: 1500 +29: +29: Computing MMFF94 energies for /build/reproducible-path/rdkit-202503.1/Code/ForceField/MMFF/test_data/MMFF94_dative.smi... +115: [09:33:10] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [09:33:10] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [09:33:10] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [09:33:10] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [09:33:10] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [09:33:10] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [09:33:10] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [09:33:10] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [09:33:10] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [09:33:10] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [09:33:10] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [09:33:10] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +116: [09:33:10] ------------------------------------- +116: [09:33:10] Basic PBF tests. +115: [09:33:10] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [09:33:10] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [09:33:10] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [09:33:10] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [09:33:10] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [09:33:10] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [09:33:10] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [09:33:10] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [09:33:10] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [09:33:10] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [09:33:10] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [09:33:10] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [09:33:10] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [09:33:10] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [09:33:10] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [09:33:10] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [09:33:10] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [09:33:10] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: 100 +115: [09:33:10] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [09:33:10] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [09:33:10] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [09:33:10] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [09:33:10] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [09:33:10] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [09:33:10] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [09:33:10] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [09:33:10] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [09:33:10] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [09:33:10] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [09:33:10] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [09:33:10] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [09:33:10] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [09:33:10] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [09:33:10] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [09:33:10] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [09:33:10] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [09:33:10] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [09:33:10] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [09:33:10] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [09:33:10] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [09:33:10] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [09:33:10] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [09:33:10] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [09:33:10] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [09:33:10] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [09:33:10] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [09:33:10] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [09:33:10] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [09:33:10] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [09:33:10] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [09:33:10] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [09:33:10] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [09:33:10] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [09:33:10] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [09:33:10] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [09:33:10] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [09:33:10] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [09:33:10] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [09:33:10] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [09:33:10] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [09:33:10] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [09:33:10] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [09:33:10] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [09:33:10] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [09:33:10] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [09:33:10] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [09:33:10] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [09:33:10] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [09:33:10] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [09:33:10] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [09:33:10] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [09:33:10] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [09:33:10] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [09:33:10] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [09:33:10] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [09:33:11] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [09:33:11] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [09:33:11] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [09:33:11] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [09:33:11] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [09:33:11] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [09:33:11] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [09:33:11] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [09:33:11] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [09:33:11] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [09:33:11] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [09:33:11] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [09:33:11] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [09:33:11] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [09:33:11] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [09:33:11] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [09:33:11] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [09:33:11] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [09:33:11] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [09:33:11] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [09:33:11] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [09:33:11] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [09:33:11] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [09:33:11] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [09:33:11] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [09:33:11] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [09:33:11] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [09:33:11] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [09:33:11] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [09:33:11] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [09:33:11] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [09:33:11] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [09:33:11] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [09:33:11] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [09:33:11] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [09:33:11] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [09:33:11] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [09:33:11] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [09:33:11] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [09:33:11] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [09:33:11] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [09:33:11] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [09:33:11] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: 200 +115: [09:33:11] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [09:33:11] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [09:33:11] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +116: [09:33:11] done +116: [09:33:11] ------------------------------------- +115: [09:33:11] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +116: [09:33:11] PBF edge cases. +115: [09:33:11] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [09:33:11] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +116: [09:33:11] done +115: [09:33:11] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [09:33:11] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +105/238 Test #116: testPBF ................................ Passed 0.22 sec +115: [09:33:11] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. test 117 Start 117: testRDFcustom 117: Test command: /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/Descriptors/testRDFcustom 117: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/Descriptors 117: Test timeout computed to be: 1500 -115: [00:36:18] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [00:36:18] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [00:36:18] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [00:36:18] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [00:36:18] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [00:36:18] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [00:36:18] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [00:36:18] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [00:36:18] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [00:36:18] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [00:36:18] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [00:36:18] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [00:36:18] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -29: -29: Computing MMFF94 energies for /build/reproducible-path/rdkit-202503.1/Code/ForceField/MMFF/test_data/MMFF94_dative.smi... -115: [00:36:18] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [00:36:18] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: 100 -115: [00:36:18] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [00:36:18] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [00:36:18] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [00:36:18] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [00:36:18] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [00:36:18] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [00:36:18] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [00:36:18] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [00:36:18] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [00:36:18] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [00:36:18] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [00:36:18] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [00:36:18] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [00:36:18] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [00:36:18] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [00:36:18] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [00:36:18] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [00:36:18] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [00:36:18] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [00:36:18] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [00:36:18] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [00:36:18] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [00:36:18] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [00:36:18] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [00:36:18] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [00:36:18] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [00:36:18] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [00:36:18] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [00:36:18] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [00:36:18] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [00:36:18] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [00:36:18] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [00:36:18] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [00:36:18] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [00:36:18] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [00:36:18] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [00:36:18] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [00:36:18] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [00:36:18] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [00:36:18] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [00:36:18] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [00:36:18] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [00:36:18] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [00:36:18] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [00:36:18] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [00:36:18] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [00:36:18] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [00:36:18] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [00:36:18] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [00:36:18] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [00:36:18] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [00:36:18] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [00:36:18] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [00:36:18] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [00:36:18] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [00:36:18] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [00:36:18] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [00:36:18] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [00:36:18] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [00:36:18] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [00:36:18] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [00:36:18] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [00:36:18] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [00:36:18] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [00:36:18] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [00:36:18] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [00:36:18] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [00:36:18] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [00:36:18] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [00:36:18] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [00:36:18] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [00:36:18] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [00:36:18] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [00:36:18] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [00:36:18] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [00:36:18] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [00:36:18] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [00:36:18] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [00:36:18] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [00:36:18] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [00:36:18] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [00:36:18] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [00:36:18] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [00:36:18] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -108: .............[00:36:18] SMILES Parse Error: syntax error while parsing: --- -108: [00:36:18] SMILES Parse Error: check for mistakes around position 1: -108: [00:36:18] --- -108: [00:36:18] ^ -108: [00:36:18] SMILES Parse Error: Failed parsing SMILES '---' for input: '---' -108: [00:36:18] dasfsadf -108: [00:36:18] SMILES Parse Error: syntax error while parsing: --- -108: [00:36:18] SMILES Parse Error: check for mistakes around position 1: -108: [00:36:18] --- -108: [00:36:18] ^ -108: [00:36:18] SMILES Parse Error: Failed parsing SMILES '---' for input: '---' -108: [00:36:18] dasfsadf -108: [00:36:18] SMILES Parse Error: syntax error while parsing: --- -108: [00:36:18] SMILES Parse Error: check for mistakes around position 1: -108: [00:36:18] --- -108: [00:36:18] ^ -108: [00:36:18] SMILES Parse Error: Failed parsing SMILES '---' for input: '---' -108: [00:36:18] dasfsadf -108: [00:36:18] SMILES Parse Error: syntax error while parsing: --- -108: [00:36:18] SMILES Parse Error: check for mistakes around position 1: -108: [00:36:18] --- -108: [00:36:18] ^ -108: [00:36:18] SMILES Parse Error: Failed parsing SMILES '---' for input: '---' -108: [00:36:18] dasfsadf -108: [00:36:18] SMILES Parse Error: syntax error while parsing: --- -108: [00:36:18] SMILES Parse Error: check for mistakes around position 1: -108: [00:36:18] --- -108: [00:36:18] ^ -108: [00:36:18] SMILES Parse Error: Failed parsing SMILES '---' for input: '---' -108: [00:36:18] dasfsadf -108: [00:36:18] SMILES Parse Error: syntax error while parsing: --- -108: [00:36:18] SMILES Parse Error: check for mistakes around position 1: -108: [00:36:18] --- -108: [00:36:18] ^ -108: [00:36:18] SMILES Parse Error: Failed parsing SMILES '---' for input: '---' -108: [00:36:18] dasfsadf -108: [00:36:18] SMILES Parse Error: syntax error while parsing: --- -108: [00:36:18] SMILES Parse Error: check for mistakes around position 1: -108: [00:36:18] --- -108: [00:36:18] ^ -108: [00:36:18] SMILES Parse Error: Failed parsing SMILES '---' for input: '---' -108: [00:36:18] dasfsadf -108: [00:36:18] SMILES Parse Error: syntax error while parsing: --- -108: [00:36:18] SMILES Parse Error: check for mistakes around position 1: -108: [00:36:18] --- -108: [00:36:18] ^ -108: [00:36:18] SMILES Parse Error: Failed parsing SMILES '---' for input: '---' -108: [00:36:18] dasfsadf -108: [00:36:18] SMILES Parse Error: syntax error while parsing: --- -108: [00:36:18] SMILES Parse Error: check for mistakes around position 1: -108: [00:36:18] --- -108: [00:36:18] ^ -108: [00:36:18] SMILES Parse Error: Failed parsing SMILES '---' for input: '---' -108: [00:36:18] dasfsadf -108: [00:36:18] SMILES Parse Error: syntax error while parsing: --- -108: [00:36:18] SMILES Parse Error: check for mistakes around position 1: -108: [00:36:18] --- -108: [00:36:18] ^ -108: [00:36:18] SMILES Parse Error: Failed parsing SMILES '---' for input: '---' -108: [00:36:18] dasfsadf -108: [00:36:18] SMILES Parse Error: syntax error while parsing: --- -108: [00:36:18] SMILES Parse Error: check for mistakes around position 1: -108: [00:36:18] --- -108: [00:36:18] ^ -108: [00:36:18] SMILES Parse Error: Failed parsing SMILES '---' for input: '---' -108: [00:36:18] dasfsadf -108: [00:36:18] SMILES Parse Error: syntax error while parsing: --- -108: [00:36:18] SMILES Parse Error: check for mistakes around position 1: -108: [00:36:18] --- -108: [00:36:18] ^ -108: [00:36:18] SMILES Parse Error: Failed parsing SMILES '---' for input: '---' -108: [00:36:18] dasfsadf -108: [00:36:18] SMILES Parse Error: syntax error while parsing: --- -108: [00:36:18] SMILES Parse Error: check for mistakes around position 1: -108: [00:36:18] --- -108: [00:36:18] ^ -108: [00:36:18] SMILES Parse Error: Failed parsing SMILES '---' for input: '---' -108: [00:36:18] dasfsadf -108: [00:36:18] SMILES Parse Error: syntax error while parsing: --- -108: [00:36:18] SMILES Parse Error: check for mistakes around position 1: -108: [00:36:18] --- -108: [00:36:18] ^ -108: [00:36:18] SMILES Parse Error: Failed parsing SMILES '---' for input: '---' -108: [00:36:18] dasfsadf -108: [00:36:18] SMILES Parse Error: syntax error while parsing: --- -108: [00:36:18] SMILES Parse Error: check for mistakes around position 1: -108: [00:36:18] --- -108: [00:36:18] ^ -108: [00:36:18] SMILES Parse Error: Failed parsing SMILES '---' for input: '---' -108: [00:36:18] dasfsadf -115: [00:36:18] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -108: [00:36:18] SMILES Parse Error: syntax error while parsing: --- -108: [00:36:18] SMILES Parse Error: check for mistakes around position 1: -108: [00:36:18] --- -108: [00:36:18] ^ -108: [00:36:18] SMILES Parse Error: Failed parsing SMILES '---' for input: '---' -108: [00:36:18] dasfsadf -115: [00:36:18] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -108: [00:36:18] SMILES Parse Error: syntax error while parsing: --- -108: [00:36:18] SMILES Parse Error: check for mistakes around position 1: -108: [00:36:18] --- -108: [00:36:18] ^ -108: [00:36:18] SMILES Parse Error: Failed parsing SMILES '---' for input: '---' -108: [00:36:18] dasfsadf -115: [00:36:18] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -108: [00:36:18] SMILES Parse Error: syntax error while parsing: --- -108: [00:36:18] SMILES Parse Error: check for mistakes around position 1: -108: [00:36:18] --- -108: [00:36:18] ^ -108: [00:36:18] SMILES Parse Error: Failed parsing SMILES '---' for input: '---' -108: [00:36:18] dasfsadf -108: [00:36:18] SMILES Parse Error: syntax error while parsing: --- -115: [00:36:18] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -108: [00:36:18] SMILES Parse Error: check for mistakes around position 1: -108: [00:36:18] --- -108: [00:36:18] ^ -108: [00:36:18] SMILES Parse Error: Failed parsing SMILES '---' for input: '---' -108: [00:36:18] dasfsadf -115: [00:36:18] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [00:36:18] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -108: [00:36:18] SMILES Parse Error: syntax error while parsing: --- -108: [00:36:18] SMILES Parse Error: check for mistakes around position 1: -108: [00:36:18] --- -108: [00:36:18] ^ -108: [00:36:18] SMILES Parse Error: Failed parsing SMILES '---' for input: '---' -108: [00:36:18] dasfsadf -108: [00:36:18] SMILES Parse Error: syntax error while parsing: --- -108: [00:36:18] SMILES Parse Error: check for mistakes around position 1: -108: [00:36:18] --- -108: [00:36:18] ^ -108: [00:36:18] SMILES Parse Error: Failed parsing SMILES '---' for input: '---' -108: [00:36:18] dasfsadf -108: [00:36:18] SMILES Parse Error: syntax error while parsing: --- -108: [00:36:18] SMILES Parse Error: check for mistakes around position 1: -108: [00:36:18] --- -108: [00:36:18] ^ -108: [00:36:18] SMILES Parse Error: Failed parsing SMILES '---' for input: '---' -108: [00:36:18] dasfsadf -108: [00:36:18] SMILES Parse Error: syntax error while parsing: --- -108: [00:36:18] SMILES Parse Error: check for mistakes around position 1: -108: [00:36:18] --- -108: [00:36:18] ^ -108: [00:36:18] SMILES Parse Error: Failed parsing SMILES '---' for input: '---' -108: [00:36:18] dasfsadf -108: [00:36:18] SMILES Parse Error: syntax error while parsing: --- -108: [00:36:18] SMILES Parse Error: check for mistakes around position 1: -108: [00:36:18] --- -108: [00:36:18] ^ -108: [00:36:18] SMILES Parse Error: Failed parsing SMILES '---' for input: '---' -108: [00:36:18] dasfsadf -108: [00:36:18] SMILES Parse Error: syntax error while parsing: --- -108: [00:36:18] SMILES Parse Error: check for mistakes around position 1: -108: [00:36:18] --- -108: [00:36:18] ^ -108: [00:36:18] SMILES Parse Error: Failed parsing SMILES '---' for input: '---' -108: [00:36:18] dasfsadf -108: [00:36:18] SMILES Parse Error: syntax error while parsing: --- -108: [00:36:18] SMILES Parse Error: check for mistakes around position 1: -108: [00:36:18] --- -108: [00:36:18] ^ -108: [00:36:18] SMILES Parse Error: Failed parsing SMILES '---' for input: '---' -108: [00:36:18] dasfsadf -108: [00:36:18] SMILES Parse Error: syntax error while parsing: --- -108: [00:36:18] SMILES Parse Error: check for mistakes around position 1: -108: [00:36:18] --- -108: [00:36:18] ^ -108: [00:36:18] SMILES Parse Error: Failed parsing SMILES '---' for input: '---' -108: [00:36:18] dasfsadf -108: [00:36:18] SMILES Parse Error: syntax error while parsing: --- -108: [00:36:18] SMILES Parse Error: check for mistakes around position 1: -108: [00:36:18] --- -108: [00:36:18] ^ -108: [00:36:18] SMILES Parse Error: Failed parsing SMILES '---' for input: '---' -108: [00:36:18] dasfsadf -108: [00:36:18] SMILES Parse Error: syntax error while parsing: --- -108: [00:36:18] SMILES Parse Error: check for mistakes around position 1: -108: [00:36:18] --- -108: [00:36:18] ^ -108: [00:36:18] SMILES Parse Error: Failed parsing SMILES '---' for input: '---' -108: [00:36:18] dasfsadf -115: [00:36:18] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [00:36:18] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [00:36:18] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -108: [00:36:18] SMILES Parse Error: syntax error while parsing: --- -108: [00:36:18] SMILES Parse Error: check for mistakes around position 1: -108: [00:36:18] --- -108: [00:36:18] ^ -108: [00:36:18] SMILES Parse Error: Failed parsing SMILES '---' for input: '---' -108: [00:36:18] dasfsadf -115: [00:36:18] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [00:36:18] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [00:36:18] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [00:36:18] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [00:36:18] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [00:36:18] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [00:36:18] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: 200 -115: [00:36:18] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [00:36:18] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [00:36:18] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [00:36:18] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -116: [00:36:18] done -116: [00:36:18] ------------------------------------- -116: [00:36:18] PBF edge cases. -115: [00:36:18] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [00:36:18] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [00:36:18] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -116: [00:36:18] done -115: [00:36:18] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [00:36:18] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -106/238 Test #116: testPBF ................................ Passed 0.31 sec +115: [09:33:11] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [09:33:11] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [09:33:11] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [09:33:11] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [09:33:11] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [09:33:11] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [09:33:11] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [09:33:11] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [09:33:11] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [09:33:11] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +112: [09:33:11] done +112: [09:33:11] ------------------------------------- +112: [09:33:11] Test Github #3806: NaNs from AUTOCORR2D descriptor +112: [09:33:11] done +115: [09:33:11] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [09:33:11] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +106/238 Test #112: testAUTOCORR2D ......................... Passed 0.42 sec +115: [09:33:11] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +108: .............[09:33:11] SMILES Parse Error: syntax error while parsing: --- +108: [09:33:11] SMILES Parse Error: check for mistakes around position 1: +108: [09:33:11] --- +108: [09:33:11] ^ +108: [09:33:11] SMILES Parse Error: Failed parsing SMILES '---' for input: '---' +108: [09:33:11] dasfsadf test 118 Start 118: testRDF 118: Test command: /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/Descriptors/testRDF 118: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/Descriptors 118: Test timeout computed to be: 1500 -115: [00:36:18] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [00:36:18] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [00:36:18] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [00:36:18] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [00:36:18] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [00:36:18] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [00:36:18] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [00:36:18] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [00:36:18] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [00:36:18] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [00:36:18] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [00:36:18] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [00:36:18] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [00:36:18] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [00:36:18] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [00:36:18] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [00:36:18] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [00:36:18] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [00:36:18] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [00:36:18] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [00:36:18] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [00:36:18] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [00:36:18] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [00:36:18] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [00:36:18] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [00:36:18] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [00:36:18] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [00:36:18] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [00:36:18] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [00:36:18] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [00:36:18] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [00:36:18] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [00:36:18] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [00:36:18] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [00:36:18] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [00:36:18] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [00:36:18] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [00:36:18] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [00:36:18] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [00:36:18] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [00:36:18] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [00:36:18] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [00:36:18] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [00:36:18] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [00:36:18] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [00:36:18] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [00:36:18] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [00:36:18] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [00:36:18] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [00:36:18] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [00:36:18] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [00:36:18] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [00:36:18] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [00:36:18] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [00:36:18] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [00:36:18] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [00:36:18] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [00:36:18] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [00:36:18] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [00:36:18] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [00:36:18] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [00:36:18] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [00:36:18] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [00:36:18] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [00:36:18] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [00:36:18] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -108: .[00:36:18] SMILES Parse Error: syntax error while parsing: mydoghasfleas -108: [00:36:18] SMILES Parse Error: check for mistakes around position 1: -108: [00:36:18] mydoghasfleas -108: [00:36:18] ^ -108: [00:36:18] SMILES Parse Error: Failed parsing SMILES 'mydoghasfleas' for input: 'mydoghasfleas' -115: [00:36:18] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [00:36:18] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [00:36:18] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [00:36:18] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [00:36:18] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [00:36:18] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [00:36:18] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [00:36:18] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [00:36:18] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [00:36:18] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [00:36:18] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [00:36:18] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [00:36:18] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [00:36:18] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [00:36:18] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [00:36:18] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [00:36:18] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [00:36:18] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [00:36:18] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [00:36:18] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [00:36:18] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [00:36:18] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [00:36:18] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [00:36:18] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [00:36:18] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [09:33:11] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [09:33:11] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [09:33:11] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [09:33:11] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [09:33:11] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [09:33:11] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +108: [09:33:11] SMILES Parse Error: syntax error while parsing: --- +108: [09:33:11] SMILES Parse Error: check for mistakes around position 1: +108: [09:33:11] --- +108: [09:33:11] ^ +108: [09:33:11] SMILES Parse Error: Failed parsing SMILES '---' for input: '---' +108: [09:33:11] dasfsadf +108: [09:33:11] SMILES Parse Error: syntax error while parsing: --- +108: [09:33:11] SMILES Parse Error: check for mistakes around position 1: +108: [09:33:11] --- +108: [09:33:11] ^ +108: [09:33:11] SMILES Parse Error: Failed parsing SMILES '---' for input: '---' +108: [09:33:11] dasfsadf +108: [09:33:11] SMILES Parse Error: syntax error while parsing: --- +108: [09:33:11] SMILES Parse Error: check for mistakes around position 1: +108: [09:33:11] --- +108: [09:33:11] ^ +108: [09:33:11] SMILES Parse Error: Failed parsing SMILES '---' for input: '---' +108: [09:33:11] dasfsadf +108: [09:33:11] SMILES Parse Error: syntax error while parsing: --- +108: [09:33:11] SMILES Parse Error: check for mistakes around position 1: +108: [09:33:11] --- +108: [09:33:11] ^ +108: [09:33:11] SMILES Parse Error: Failed parsing SMILES '---' for input: '---' +108: [09:33:11] dasfsadf +108: [09:33:11] SMILES Parse Error: syntax error while parsing: --- +108: [09:33:11] SMILES Parse Error: check for mistakes around position 1: +108: [09:33:11] --- +108: [09:33:11] ^ +108: [09:33:11] SMILES Parse Error: Failed parsing SMILES '---' for input: '---' +108: [09:33:11] dasfsadf +108: [09:33:11] SMILES Parse Error: syntax error while parsing: --- +108: [09:33:11] SMILES Parse Error: check for mistakes around position 1: +108: [09:33:11] --- +108: [09:33:11] ^ +108: [09:33:11] SMILES Parse Error: Failed parsing SMILES '---' for input: '---' +108: [09:33:11] dasfsadf +108: [09:33:11] SMILES Parse Error: syntax error while parsing: --- +108: [09:33:11] SMILES Parse Error: check for mistakes around position 1: +108: [09:33:11] --- +108: [09:33:11] ^ +108: [09:33:11] SMILES Parse Error: Failed parsing SMILES '---' for input: '---' +108: [09:33:11] dasfsadf +108: [09:33:11] SMILES Parse Error: syntax error while parsing: --- +108: [09:33:11] SMILES Parse Error: check for mistakes around position 1: +108: [09:33:11] --- +108: [09:33:11] ^ +108: [09:33:11] SMILES Parse Error: Failed parsing SMILES '---' for input: '---' +108: [09:33:11] dasfsadf +108: [09:33:11] SMILES Parse Error: syntax error while parsing: --- +108: [09:33:11] SMILES Parse Error: check for mistakes around position 1: +108: [09:33:11] --- +108: [09:33:11] ^ +108: [09:33:11] SMILES Parse Error: Failed parsing SMILES '---' for input: '---' +108: [09:33:11] dasfsadf +108: [09:33:11] SMILES Parse Error: syntax error while parsing: --- +108: [09:33:11] SMILES Parse Error: check for mistakes around position 1: +108: [09:33:11] --- +108: [09:33:11] ^ +108: [09:33:11] SMILES Parse Error: Failed parsing SMILES '---' for input: '---' +108: [09:33:11] dasfsadf +108: [09:33:11] SMILES Parse Error: syntax error while parsing: --- +108: [09:33:11] SMILES Parse Error: check for mistakes around position 1: +108: [09:33:11] --- +108: [09:33:11] ^ +108: [09:33:11] SMILES Parse Error: Failed parsing SMILES '---' for input: '---' +108: [09:33:11] dasfsadf +108: [09:33:11] SMILES Parse Error: syntax error while parsing: --- +108: [09:33:11] SMILES Parse Error: check for mistakes around position 1: +108: [09:33:11] --- +108: [09:33:11] ^ +108: [09:33:11] SMILES Parse Error: Failed parsing SMILES '---' for input: '---' +108: [09:33:11] dasfsadf +108: [09:33:11] SMILES Parse Error: syntax error while parsing: --- +108: [09:33:11] SMILES Parse Error: check for mistakes around position 1: +108: [09:33:11] --- +108: [09:33:11] ^ +108: [09:33:11] SMILES Parse Error: Failed parsing SMILES '---' for input: '---' +108: [09:33:11] dasfsadf +108: [09:33:11] SMILES Parse Error: syntax error while parsing: --- +108: [09:33:11] SMILES Parse Error: check for mistakes around position 1: +108: [09:33:11] --- +108: [09:33:11] ^ +108: [09:33:11] SMILES Parse Error: Failed parsing SMILES '---' for input: '---' +108: [09:33:11] dasfsadf +108: [09:33:11] SMILES Parse Error: syntax error while parsing: --- +108: [09:33:11] SMILES Parse Error: check for mistakes around position 1: +108: [09:33:11] --- +108: [09:33:11] ^ +108: [09:33:11] SMILES Parse Error: Failed parsing SMILES '---' for input: '---' +108: [09:33:11] dasfsadf +108: [09:33:11] SMILES Parse Error: syntax error while parsing: --- +108: [09:33:11] SMILES Parse Error: check for mistakes around position 1: +108: [09:33:11] --- +108: [09:33:11] ^ +108: [09:33:11] SMILES Parse Error: Failed parsing SMILES '---' for input: '---' +108: [09:33:11] dasfsadf +108: [09:33:11] SMILES Parse Error: syntax error while parsing: --- +108: [09:33:11] SMILES Parse Error: check for mistakes around position 1: +108: [09:33:11] --- +108: [09:33:11] ^ +108: [09:33:11] SMILES Parse Error: Failed parsing SMILES '---' for input: '---' +108: [09:33:11] dasfsadf +108: [09:33:11] SMILES Parse Error: syntax error while parsing: --- +108: [09:33:11] SMILES Parse Error: check for mistakes around position 1: +108: [09:33:11] --- +108: [09:33:11] ^ +108: [09:33:11] SMILES Parse Error: Failed parsing SMILES '---' for input: '---' +108: [09:33:11] dasfsadf +108: [09:33:11] SMILES Parse Error: syntax error while parsing: --- +108: [09:33:11] SMILES Parse Error: check for mistakes around position 1: +108: [09:33:11] --- +108: [09:33:11] ^ +108: [09:33:11] SMILES Parse Error: Failed parsing SMILES '---' for input: '---' +108: [09:33:11] dasfsadf +108: [09:33:11] SMILES Parse Error: syntax error while parsing: --- +108: [09:33:11] SMILES Parse Error: check for mistakes around position 1: +108: [09:33:11] --- +108: [09:33:11] ^ +108: [09:33:11] SMILES Parse Error: Failed parsing SMILES '---' for input: '---' +108: [09:33:11] dasfsadf +108: [09:33:11] SMILES Parse Error: syntax error while parsing: --- +108: [09:33:11] SMILES Parse Error: check for mistakes around position 1: +108: [09:33:11] --- +108: [09:33:11] ^ +108: [09:33:11] SMILES Parse Error: Failed parsing SMILES '---' for input: '---' +108: [09:33:11] dasfsadf +108: [09:33:11] SMILES Parse Error: syntax error while parsing: --- +108: [09:33:11] SMILES Parse Error: check for mistakes around position 1: +108: [09:33:11] --- +108: [09:33:11] ^ +108: [09:33:11] SMILES Parse Error: Failed parsing SMILES '---' for input: '---' +108: [09:33:11] dasfsadf +108: [09:33:11] SMILES Parse Error: syntax error while parsing: --- +108: [09:33:11] SMILES Parse Error: check for mistakes around position 1: +108: [09:33:11] --- +108: [09:33:11] ^ +108: [09:33:11] SMILES Parse Error: Failed parsing SMILES '---' for input: '---' +108: [09:33:11] dasfsadf +108: [09:33:11] SMILES Parse Error: syntax error while parsing: --- +108: [09:33:11] SMILES Parse Error: check for mistakes around position 1: +108: [09:33:11] --- +108: [09:33:11] ^ +108: [09:33:11] SMILES Parse Error: Failed parsing SMILES '---' for input: '---' +108: [09:33:11] dasfsadf +108: [09:33:11] SMILES Parse Error: syntax error while parsing: --- +108: [09:33:11] SMILES Parse Error: check for mistakes around position 1: +108: [09:33:11] --- +108: [09:33:11] ^ +108: [09:33:11] SMILES Parse Error: Failed parsing SMILES '---' for input: '---' +108: [09:33:11] dasfsadf +108: [09:33:11] SMILES Parse Error: syntax error while parsing: --- +108: [09:33:11] SMILES Parse Error: check for mistakes around position 1: +108: [09:33:11] --- +108: [09:33:11] ^ +108: [09:33:11] SMILES Parse Error: Failed parsing SMILES '---' for input: '---' +108: [09:33:11] dasfsadf +108: [09:33:11] SMILES Parse Error: syntax error while parsing: --- +108: [09:33:11] SMILES Parse Error: check for mistakes around position 1: +108: [09:33:11] --- +108: [09:33:11] ^ +108: [09:33:11] SMILES Parse Error: Failed parsing SMILES '---' for input: '---' +108: [09:33:11] dasfsadf +108: [09:33:11] SMILES Parse Error: syntax error while parsing: --- +108: [09:33:11] SMILES Parse Error: check for mistakes around position 1: +108: [09:33:11] --- +108: [09:33:11] ^ +108: [09:33:11] SMILES Parse Error: Failed parsing SMILES '---' for input: '---' +108: [09:33:11] dasfsadf +108: [09:33:11] SMILES Parse Error: syntax error while parsing: --- +108: [09:33:11] SMILES Parse Error: check for mistakes around position 1: +108: [09:33:11] --- +108: [09:33:11] ^ +108: [09:33:11] SMILES Parse Error: Failed parsing SMILES '---' for input: '---' +108: [09:33:11] dasfsadf +115: [09:33:11] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [09:33:11] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [09:33:11] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [09:33:11] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [09:33:11] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [09:33:11] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [09:33:11] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [09:33:11] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [09:33:11] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [09:33:11] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [09:33:11] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [09:33:11] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [09:33:11] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [09:33:11] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [09:33:11] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [09:33:11] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [09:33:11] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [09:33:11] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [09:33:11] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [09:33:11] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [09:33:11] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [09:33:11] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [09:33:11] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [09:33:11] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [09:33:11] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [09:33:11] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [09:33:11] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [09:33:11] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [09:33:11] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [09:33:11] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [09:33:11] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [09:33:11] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [09:33:11] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [09:33:11] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [09:33:11] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [09:33:11] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [09:33:11] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [09:33:11] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [09:33:11] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [09:33:11] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [09:33:11] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [09:33:11] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [09:33:11] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [09:33:11] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [09:33:11] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [09:33:11] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [09:33:11] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [09:33:11] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [09:33:11] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [09:33:11] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [09:33:11] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [09:33:11] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +108: .[09:33:11] SMILES Parse Error: syntax error while parsing: mydoghasfleas +108: [09:33:11] SMILES Parse Error: check for mistakes around position 1: +108: [09:33:11] mydoghasfleas +108: [09:33:11] ^ +108: [09:33:11] SMILES Parse Error: Failed parsing SMILES 'mydoghasfleas' for input: 'mydoghasfleas' +115: [09:33:11] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [09:33:11] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [09:33:11] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [09:33:11] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [09:33:11] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [09:33:11] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [09:33:11] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [09:33:11] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [09:33:11] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [09:33:11] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [09:33:11] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [09:33:11] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [09:33:11] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [09:33:11] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [09:33:11] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [09:33:11] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [09:33:11] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [09:33:11] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [09:33:11] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [09:33:11] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 115: 300 -115: [00:36:18] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [00:36:18] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [00:36:18] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [00:36:18] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [00:36:18] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [00:36:18] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [00:36:18] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [00:36:18] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [00:36:18] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [00:36:18] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [00:36:18] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [00:36:18] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [00:36:18] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [00:36:18] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [00:36:18] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [00:36:18] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [00:36:18] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [00:36:18] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [00:36:18] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [00:36:18] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [00:36:18] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [00:36:18] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [00:36:18] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [00:36:18] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [00:36:18] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [00:36:18] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [00:36:18] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [00:36:18] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [00:36:18] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [00:36:18] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [00:36:18] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [00:36:18] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [00:36:18] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [00:36:18] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [00:36:18] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [00:36:18] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [00:36:18] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [00:36:18] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [00:36:18] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [00:36:18] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [00:36:18] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [00:36:18] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [00:36:18] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [00:36:18] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [00:36:18] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [00:36:18] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [00:36:18] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [00:36:18] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [00:36:18] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [00:36:18] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [00:36:18] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [00:36:18] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [00:36:18] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [00:36:18] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [00:36:18] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [00:36:18] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [00:36:18] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [00:36:18] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [00:36:18] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -117: =>start test rdf custom -117: [00:36:18] test on : 365 molecules done -115: [00:36:18] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [00:36:18] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [00:36:18] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [00:36:18] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [00:36:18] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [00:36:18] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [00:36:18] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [00:36:18] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [00:36:18] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [00:36:18] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [00:36:18] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [00:36:18] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [00:36:18] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [00:36:18] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [09:33:11] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [09:33:11] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [09:33:11] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [09:33:11] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [09:33:11] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [09:33:11] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [09:33:11] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [09:33:11] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [09:33:11] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [09:33:11] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [09:33:11] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [09:33:11] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [09:33:11] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 108: ....... 108: ---------------------------------------------------------------------- -108: Ran 21 tests in 1.017s +108: Ran 21 tests in 0.578s 108: 108: OK 108: (Five aromatic carbons And (Not any of Five aromatic carbons)) @@ -24748,155 +24717,217 @@ 108: 1 108: 2 108: running -115: [00:36:18] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [00:36:18] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [00:36:18] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [00:36:18] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [00:36:18] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [00:36:18] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [00:36:18] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [00:36:18] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [00:36:18] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [00:36:18] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [00:36:18] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [00:36:18] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [00:36:18] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [00:36:18] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [00:36:18] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [00:36:18] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [00:36:18] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [00:36:18] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [00:36:18] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [00:36:18] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [00:36:18] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [00:36:18] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [00:36:18] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [00:36:18] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [00:36:18] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [00:36:18] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [00:36:18] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: 400 -115: [00:36:18] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [00:36:18] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [00:36:18] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [00:36:18] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [00:36:18] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [00:36:18] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [00:36:18] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [00:36:18] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [00:36:18] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [00:36:18] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [00:36:18] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [00:36:18] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [00:36:18] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [00:36:18] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [00:36:18] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [00:36:18] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [00:36:18] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [00:36:18] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [00:36:18] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [00:36:18] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [00:36:18] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [00:36:18] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [00:36:18] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [00:36:18] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [00:36:18] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [00:36:18] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [00:36:18] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [00:36:18] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [00:36:18] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [00:36:18] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [00:36:18] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [00:36:18] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [00:36:18] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [00:36:18] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [00:36:18] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [00:36:18] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [00:36:18] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [00:36:18] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [00:36:18] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [00:36:18] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [00:36:18] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [00:36:18] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [00:36:18] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [00:36:18] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [00:36:18] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [00:36:18] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [00:36:18] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [00:36:18] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [00:36:18] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [00:36:18] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [00:36:18] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [00:36:18] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [00:36:18] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [00:36:18] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [00:36:18] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [00:36:18] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [00:36:18] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [00:36:18] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [00:36:18] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [00:36:18] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [00:36:18] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [00:36:18] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [00:36:18] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [00:36:18] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -114: [00:36:18] ------------------------------------- -114: [00:36:18] Test empty molecule BCUT. -107/238 Test #114: testBCUT ............................... Passed 0.80 sec +115: [09:33:11] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [09:33:11] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [09:33:11] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [09:33:11] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [09:33:11] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [09:33:11] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [09:33:11] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [09:33:11] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [09:33:11] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [09:33:11] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [09:33:11] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [09:33:11] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [09:33:11] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [09:33:11] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [09:33:11] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [09:33:11] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [09:33:11] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [09:33:11] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [09:33:11] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [09:33:11] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [09:33:11] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [09:33:11] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [09:33:11] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [09:33:11] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [09:33:11] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [09:33:11] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [09:33:11] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [09:33:11] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [09:33:11] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [09:33:11] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [09:33:11] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [09:33:11] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [09:33:11] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [09:33:11] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [09:33:11] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [09:33:11] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [09:33:11] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [09:33:11] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +107/238 Test #108: pyFilterCatalog ........................ Passed 0.99 sec test 119 Start 119: testMORSE 119: Test command: /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/Descriptors/testMORSE 119: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/Descriptors 119: Test timeout computed to be: 1500 -115: [00:36:18] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [00:36:18] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [00:36:18] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [00:36:18] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [00:36:18] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [00:36:18] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [00:36:18] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [00:36:18] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [00:36:18] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [00:36:18] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [00:36:18] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [00:36:18] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [00:36:18] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -108/238 Test #108: pyFilterCatalog ........................ Passed 1.48 sec +115: [09:33:11] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [09:33:11] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [09:33:11] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [09:33:11] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [09:33:11] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [09:33:11] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [09:33:11] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [09:33:11] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [09:33:11] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [09:33:11] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [09:33:11] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [09:33:11] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [09:33:11] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [09:33:11] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [09:33:11] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [09:33:11] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [09:33:11] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [09:33:11] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [09:33:11] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [09:33:11] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [09:33:11] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [09:33:11] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +114: [09:33:11] ------------------------------------- +114: [09:33:11] Test empty molecule BCUT. +108/238 Test #114: testBCUT ............................... Passed 0.59 sec test 120 Start 120: test3D 120: Test command: /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/Descriptors/test3D 120: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/Descriptors 120: Test timeout computed to be: 1500 -115: [00:36:18] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [00:36:18] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [00:36:18] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [00:36:18] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [00:36:18] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [00:36:18] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [00:36:18] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [00:36:18] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [00:36:18] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [00:36:18] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [00:36:18] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [00:36:18] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [00:36:18] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [00:36:18] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [00:36:18] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [00:36:18] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [00:36:18] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -120: [00:36:18] ------------------------------------- -120: [00:36:18] Basic PMI tests. -115: [00:36:18] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [00:36:18] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [00:36:18] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [00:36:18] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [00:36:18] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: Elapsed time: 0.776985 s +115: [09:33:11] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [09:33:11] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [09:33:11] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [09:33:11] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [09:33:11] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [09:33:11] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [09:33:11] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [09:33:11] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [09:33:11] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [09:33:11] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [09:33:11] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [09:33:11] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [09:33:11] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [09:33:11] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [09:33:11] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [09:33:11] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [09:33:11] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [09:33:11] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [09:33:11] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [09:33:11] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [09:33:11] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [09:33:11] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [09:33:11] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [09:33:11] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +120: [09:33:11] ------------------------------------- +120: [09:33:11] Basic PMI tests. +117: =>start test rdf custom +117: [09:33:11] test on : 365 molecules done +115: [09:33:11] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [09:33:11] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [09:33:11] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: 400 +115: [09:33:11] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [09:33:11] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [09:33:11] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [09:33:11] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [09:33:11] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [09:33:11] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [09:33:11] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [09:33:11] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [09:33:11] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [09:33:11] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [09:33:11] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [09:33:11] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [09:33:11] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [09:33:11] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [09:33:11] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [09:33:11] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [09:33:11] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [09:33:11] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [09:33:11] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [09:33:11] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [09:33:11] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [09:33:11] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [09:33:11] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [09:33:11] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [09:33:11] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [09:33:11] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [09:33:11] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [09:33:11] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [09:33:11] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [09:33:11] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [09:33:11] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [09:33:11] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [09:33:11] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [09:33:11] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [09:33:11] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [09:33:11] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [09:33:11] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [09:33:11] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [09:33:11] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [09:33:11] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [09:33:11] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [09:33:11] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [09:33:11] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [09:33:11] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [09:33:11] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [09:33:11] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [09:33:11] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [09:33:11] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [09:33:11] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [09:33:11] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [09:33:11] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [09:33:11] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [09:33:11] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [09:33:11] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [09:33:11] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [09:33:11] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [09:33:11] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [09:33:11] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [09:33:11] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [09:33:11] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [09:33:11] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [09:33:11] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [09:33:11] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [09:33:11] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [09:33:11] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [09:33:11] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [09:33:11] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [09:33:11] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [09:33:11] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [09:33:11] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [09:33:11] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [09:33:11] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [09:33:11] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [09:33:11] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [09:33:11] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [09:33:11] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [09:33:11] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [09:33:11] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [09:33:11] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [09:33:11] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [09:33:11] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [09:33:11] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [09:33:11] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [09:33:11] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [09:33:11] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [09:33:11] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [09:33:11] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [09:33:11] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [09:33:11] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [09:33:11] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [09:33:11] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [09:33:11] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [09:33:11] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [09:33:11] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [09:33:11] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [09:33:11] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [09:33:11] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [09:33:11] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [09:33:11] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: Elapsed time: 0.752587 s 115: Errors:0 -115: [00:36:18] test on : 500 molecules done -109/238 Test #115: testEEM ................................ Passed 0.80 sec +115: [09:33:11] test on : 500 molecules done +109/238 Test #115: testEEM ................................ Passed 0.77 sec test 121 Start 121: testWHIM @@ -24904,46 +24935,46 @@ 121: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/Descriptors 121: Test timeout computed to be: 1500 118: =>start test rdf -118: [00:36:19] test on : 365 molecules done -110/238 Test #118: testRDF ................................ Passed 0.52 sec +118: [09:33:11] test on : 365 molecules done +110/238 Test #118: testRDF ................................ Passed 0.49 sec test 122 Start 122: testGETAWAY 122: Test command: /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/Descriptors/testGETAWAY 122: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/Descriptors 122: Test timeout computed to be: 1500 -120: [00:36:19] done -120: [00:36:19] ------------------------------------- -120: [00:36:19] More PMI/NPR tests. -120: [00:36:19] done -120: [00:36:19] ------------------------------------- -120: [00:36:19] Basic NPR tests. -121: =>start test WHIM -121: [00:36:19] test on : 365 molecules done -111/238 Test #121: testWHIM ............................... Passed 0.31 sec +120: [09:33:11] done +120: [09:33:11] ------------------------------------- +120: [09:33:11] More PMI/NPR tests. +120: [09:33:11] done +120: [09:33:11] ------------------------------------- +120: [09:33:11] Basic NPR tests. +120: [09:33:11] done +120: [09:33:11] ------------------------------------- +120: [09:33:11] PMI edge cases. +120: [09:33:11] done +120: [09:33:11] ------------------------------------- +120: [09:33:11] NPR edge cases. +120: [09:33:11] done +120: [09:33:11] ------------------------------------- +120: [09:33:11] 3D descriptors. +120: [09:33:11] done +120: [09:33:11] ------------------------------------- +120: [09:33:11] 3D descriptor edge cases. +120: [09:33:11] done +120: [09:33:11] ------------------------------------- +120: [09:33:11] Inertial shape factor. +120: [09:33:11] done +111/238 Test #120: test3D ................................. Passed 0.51 sec test 123 Start 123: testAUTOCORR3D 123: Test command: /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/Descriptors/testAUTOCORR3D 123: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/Descriptors 123: Test timeout computed to be: 1500 -120: [00:36:19] done -120: [00:36:19] ------------------------------------- -120: [00:36:19] PMI edge cases. -120: [00:36:19] done -120: [00:36:19] ------------------------------------- -120: [00:36:19] NPR edge cases. -120: [00:36:19] done -120: [00:36:19] ------------------------------------- -120: [00:36:19] 3D descriptors. -120: [00:36:19] done -120: [00:36:19] ------------------------------------- -120: [00:36:19] 3D descriptor edge cases. -120: [00:36:19] done -120: [00:36:19] ------------------------------------- -120: [00:36:19] Inertial shape factor. -120: [00:36:19] done -112/238 Test #120: test3D ................................. Passed 0.46 sec +121: =>start test WHIM +121: [09:33:11] test on : 365 molecules done +112/238 Test #121: testWHIM ............................... Passed 0.36 sec test 124 Start 124: testCoulombMat @@ -24952,14 +24983,14 @@ 124: Test timeout computed to be: 1500 124: ===================== Testing CoulombMat ======================= 124: CM test 1 mat Done -113/238 Test #124: testCoulombMat ......................... Passed 0.03 sec +113/238 Test #124: testCoulombMat ......................... Passed 0.04 sec test 125 Start 125: descriptorsTestCatch 125: Test command: /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/Descriptors/descriptorsTestCatch 125: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/Descriptors 125: Test timeout computed to be: 1500 -125: Randomness seeded to: 1084225923 +125: Randomness seeded to: 4027320459 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 @@ -24967,10 +24998,10 @@ 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 -125: Warning: Atom Count for residue GLU5A does not match expected count -123: =>start test autocorr3D -123: [00:36:19] test on : 365 molecules done -114/238 Test #123: testAUTOCORR3D ......................... Passed 0.39 sec +119: =>start test MORSE +119: =>read file +119: [09:33:12] test on : 365 molecules done +114/238 Test #119: testMORSE .............................. Passed 0.78 sec test 126 Start 126: pyMolDescriptors @@ -24978,52 +25009,128 @@ 126: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/Descriptors/Wrap 126: Test timeout computed to be: 1500 117: =>start test morse custom -117: [00:36:19] test on : 365 molecules done -125: Warning: Atom Count for residue ASN39A does not match expected count -119: =>start test MORSE -119: =>read file -119: [00:36:19] test on : 365 molecules done -115/238 Test #119: testMORSE .............................. Passed 1.09 sec +117: [09:33:12] test on : 365 molecules done +125: Warning: Atom Count for residue GLU5A does not match expected count +123: =>start test autocorr3D +123: [09:33:12] test on : 365 molecules done +115/238 Test #123: testAUTOCORR3D ......................... Passed 0.31 sec 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-aarch64-linux-gnu/Code/GraphMol/Descriptors/Wrap 127: Test timeout computed to be: 1500 -126: [00:36:20] DEPRECATION WARNING: please use AtomPairGenerator -126: [00:36:20] DEPRECATION WARNING: please use AtomPairGenerator -126: [00:36:20] DEPRECATION WARNING: please use AtomPairGenerator -126: [00:36:20] DEPRECATION WARNING: please use AtomPairGenerator -126: [00:36:20] DEPRECATION WARNING: please use AtomPairGenerator -126: [00:36:20] DEPRECATION WARNING: please use AtomPairGenerator -126: [00:36:20] DEPRECATION WARNING: please use AtomPairGenerator -126: [00:36:20] DEPRECATION WARNING: please use AtomPairGenerator -126: [00:36:20] DEPRECATION WARNING: please use AtomPairGenerator -126: [00:36:20] DEPRECATION WARNING: please use AtomPairGenerator -126: [00:36:20] DEPRECATION WARNING: please use AtomPairGenerator -126: [00:36:20] DEPRECATION WARNING: please use AtomPairGenerator -126: [00:36:20] DEPRECATION WARNING: please use TopologicalTorsionGenerator -126: [00:36:20] DEPRECATION WARNING: please use TopologicalTorsionGenerator -126: [00:36:20] DEPRECATION WARNING: please use TopologicalTorsionGenerator -126: [00:36:20] DEPRECATION WARNING: please use TopologicalTorsionGenerator -126: [00:36:20] DEPRECATION WARNING: please use TopologicalTorsionGenerator -126: [00:36:20] DEPRECATION WARNING: please use TopologicalTorsionGenerator -126: [00:36:20] DEPRECATION WARNING: please use TopologicalTorsionGenerator -126: [00:36:20] DEPRECATION WARNING: please use TopologicalTorsionGenerator -126: [00:36:20] DEPRECATION WARNING: please use TopologicalTorsionGenerator -126: [00:36:20] DEPRECATION WARNING: please use TopologicalTorsionGenerator -126: [00:36:20] DEPRECATION WARNING: please use TopologicalTorsionGenerator -126: [00:36:20] DEPRECATION WARNING: please use TopologicalTorsionGenerator -126: ..[00:36:20] DEPRECATION WARNING: please use AtomPairGenerator -126: [00:36:20] DEPRECATION WARNING: please use AtomPairGenerator -126: [00:36:20] DEPRECATION WARNING: please use AtomPairGenerator -126: [00:36:20] DEPRECATION WARNING: please use AtomPairGenerator -126: [00:36:20] DEPRECATION WARNING: please use AtomPairGenerator -126: [00:36:20] DEPRECATION WARNING: please use AtomPairGenerator -126: .[00:36:20] DEPRECATION WARNING: please use AtomPairGenerator -126: [00:36:20] DEPRECATION WARNING: please use AtomPairGenerator -126: [00:36:20] DEPRECATION WARNING: please use AtomPairGenerator -126: ..[00:36:20] +117: =>start test AUTOCORR3D custom +117: [09:33:12] test on : 365 molecules done +111: [09:33:12] done +111: [09:33:12] ------------------------------------- +111: [09:33:12] Test Issue252: Bad definitions for Crippen atom types. +111: [09:33:12] done +111: [09:33:12] ------------------------------------- +111: [09:33:12] Test calculation of ChiVs. +111: [09:33:12] done +111: [09:33:12] ------------------------------------- +111: [09:33:12] Test calculation of ChiNs. +111: [09:33:12] done +111: [09:33:12] ------------------------------------- +111: [09:33:12] Test calculation of HallKierAlpha. +111: [09:33:12] done +111: [09:33:12] ------------------------------------- +111: [09:33:12] Test calculation of Kappa1. +111: [09:33:12] done +111: [09:33:12] ------------------------------------- +111: [09:33:12] Test calculation of Kappa2. +111: [09:33:12] done +111: [09:33:12] ------------------------------------- +111: [09:33:12] Test calculation of Kappa3. +111: [09:33:12] done +111: [09:33:12] ------------------------------------- +111: [09:33:12] Test Crippen atom type calculations. +111: [09:33:12] done +111: [09:33:12] ------------------------------------- +111: [09:33:12] Test ring descriptors +111: [09:33:12] done +111: [09:33:12] ------------------------------------- +111: [09:33:12] Test other count descriptors. +111: [09:33:12] done +111: [09:33:12] ------------------------------------- +111: [09:33:12] Test MQN +111: [09:33:12] done +111: [09:33:12] ------------------------------------- +111: [09:33:12] Test GitHub Issue 56. +111: [09:33:12] WARNING: not removing hydrogen atom without neighbors +111: [09:33:12] WARNING: not removing hydrogen atom without neighbors +111: [09:33:12] WARNING: not removing hydrogen atom without neighbors +111: [09:33:12] WARNING: not removing hydrogen atom without neighbors +111: [09:33:12] done +111: [09:33:12] ------------------------------------- +111: [09:33:12] Test Github92: Bad Crippen atom type for pyrrole H. +111: [09:33:12] done +111: [09:33:12] ------------------------------------- +111: [09:33:12] Test Github362: order dependence in Kier-Hall descriptors. +111: [09:33:12] done +111: [09:33:12] ------------------------------------- +111: [09:33:12] Test calculation of spiro and bridgehead counts. +111: [09:33:12] done +111: [09:33:12] ------------------------------------- +111: [09:33:12] Test Github694: ExactMolWt ignoring the mass of the electron +111: [09:33:12] done +111: [09:33:12] ------------------------------------- +111: [09:33:12] Testing Properties and KitchenSink +111: [09:33:12] ---Caught keyerror (bad property name)--- +111: [09:33:12] ------------------------------------- +111: [09:33:12] Test USR Descriptor +111: [09:33:12] done +111: [09:33:12] ------------------------------------- +111: [09:33:12] Test Github #1702: AUTOCORR2D.h not installed unless RDK_BUILD_DESCRIPTORS3D but is required +111: [09:33:12] done +111: [09:33:12] ------------------------------------- +111: [09:33:12] Test Github #1973: support P and S terms for TPSA calculation +111: [09:33:12] done +111: [09:33:12] ------------------------------------- +111: [09:33:12] Test Github #2948: Empty molecule has non-zero LabuteASA +111: [09:33:12] done +116/238 Test #111: testDescriptors ........................ Passed 1.83 sec +test 128 + Start 128: testFingerprints + +128: Test command: /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/Fingerprints/testFingerprints +128: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/Fingerprints +128: Test timeout computed to be: 1500 +126: [09:33:12] DEPRECATION WARNING: please use AtomPairGenerator +126: [09:33:12] DEPRECATION WARNING: please use AtomPairGenerator +126: [09:33:12] DEPRECATION WARNING: please use AtomPairGenerator +126: [09:33:12] DEPRECATION WARNING: please use AtomPairGenerator +126: [09:33:12] DEPRECATION WARNING: please use AtomPairGenerator +126: [09:33:12] DEPRECATION WARNING: please use AtomPairGenerator +126: [09:33:12] DEPRECATION WARNING: please use AtomPairGenerator +126: [09:33:12] DEPRECATION WARNING: please use AtomPairGenerator +126: [09:33:12] DEPRECATION WARNING: please use AtomPairGenerator +126: [09:33:12] DEPRECATION WARNING: please use AtomPairGenerator +126: [09:33:12] DEPRECATION WARNING: please use AtomPairGenerator +126: [09:33:12] DEPRECATION WARNING: please use AtomPairGenerator +126: [09:33:12] DEPRECATION WARNING: please use TopologicalTorsionGenerator +126: [09:33:12] DEPRECATION WARNING: please use TopologicalTorsionGenerator +126: [09:33:12] DEPRECATION WARNING: please use TopologicalTorsionGenerator +126: [09:33:12] DEPRECATION WARNING: please use TopologicalTorsionGenerator +126: [09:33:12] DEPRECATION WARNING: please use TopologicalTorsionGenerator +126: [09:33:12] DEPRECATION WARNING: please use TopologicalTorsionGenerator +126: [09:33:12] DEPRECATION WARNING: please use TopologicalTorsionGenerator +126: [09:33:12] DEPRECATION WARNING: please use TopologicalTorsionGenerator +126: [09:33:12] DEPRECATION WARNING: please use TopologicalTorsionGenerator +126: [09:33:12] DEPRECATION WARNING: please use TopologicalTorsionGenerator +126: [09:33:12] DEPRECATION WARNING: please use TopologicalTorsionGenerator +126: [09:33:12] DEPRECATION WARNING: please use TopologicalTorsionGenerator +126: ..[09:33:12] DEPRECATION WARNING: please use AtomPairGenerator +126: [09:33:12] DEPRECATION WARNING: please use AtomPairGenerator +126: [09:33:12] DEPRECATION WARNING: please use AtomPairGenerator +126: [09:33:12] DEPRECATION WARNING: please use AtomPairGenerator +126: [09:33:12] DEPRECATION WARNING: please use AtomPairGenerator +126: [09:33:12] DEPRECATION WARNING: please use AtomPairGenerator +126: .[09:33:12] DEPRECATION WARNING: please use AtomPairGenerator +126: [09:33:12] DEPRECATION WARNING: please use AtomPairGenerator +126: [09:33:12] DEPRECATION WARNING: please use AtomPairGenerator +126: ..[09:33:12] 126: 126: **** 126: Pre-condition Violation @@ -25035,10 +25142,10 @@ 126: 0# Invar::Invariant::toString[abi:cxx11]() const in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu//lib/libRDKitRDGeneral.so.1 126: 1# Invar::operator<<(std::ostream&, Invar::Invariant const&) in /build/reproducible-path/rdkit-202503.1/obj-aarch64-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-aarch64-linux-gnu//lib/libRDKitDescriptors.so.1 -126: 3# 0x0000FFFF85FAD0B8 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdMolDescriptors.so -126: 4# 0x0000FFFF85FC2370 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdMolDescriptors.so +126: 3# 0x0000FFFF977ED0B8 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdMolDescriptors.so +126: 4# 0x0000FFFF97802370 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdMolDescriptors.so 126: 5# boost::python::objects::function::call(_object*, _object*) const in /lib/aarch64-linux-gnu/libboost_python313.so.1.83.0 -126: 6# 0x0000FFFF89E72680 in /lib/aarch64-linux-gnu/libboost_python313.so.1.83.0 +126: 6# 0x0000FFFF9B6B2680 in /lib/aarch64-linux-gnu/libboost_python313.so.1.83.0 126: 7# boost::python::detail::exception_handler::operator()(boost::function0 const&) const in /lib/aarch64-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-aarch64-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-aarch64-linux-gnu/rdkit/Chem/rdDepictor.so @@ -25049,17 +25156,17 @@ 126: 14# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202503.1/obj-aarch64-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-aarch64-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-aarch64-linux-gnu/rdkit/Chem/rdchem.so -126: 17# 0x0000FFFF883FC320 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so -126: 18# 0x0000FFFF883FC2B8 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so -126: 19# 0x0000FFFF883FC248 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so -126: 20# 0x0000FFFF883FC1E0 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so -126: 21# 0x0000FFFF883FC178 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so +126: 17# 0x0000FFFF99C3C320 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so +126: 18# 0x0000FFFF99C3C2B8 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so +126: 19# 0x0000FFFF99C3C248 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so +126: 20# 0x0000FFFF99C3C1E0 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so +126: 21# 0x0000FFFF99C3C178 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-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-aarch64-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-aarch64-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-aarch64-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-aarch64-linux-gnu/rdkit/rdBase.so 126: 26# boost::python::handle_exception_impl(boost::function0) in /lib/aarch64-linux-gnu/libboost_python313.so.1.83.0 -126: 27# 0x0000FFFF89E6F25C in /lib/aarch64-linux-gnu/libboost_python313.so.1.83.0 +126: 27# 0x0000FFFF9B6AF25C in /lib/aarch64-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# 0x000000000053D3B0 in /usr/bin/python3 @@ -25091,101 +25198,12 @@ 126: 56# 0x000000000065EE50 in /usr/bin/python3 126: 57# Py_RunMain in /usr/bin/python3 126: 58# Py_BytesMain in /usr/bin/python3 -126: 59# 0x0000FFFF8A77229C in /lib/aarch64-linux-gnu/libc.so.6 +126: 59# 0x0000FFFF9BFB229C in /lib/aarch64-linux-gnu/libc.so.6 126: 60# __libc_start_main in /lib/aarch64-linux-gnu/libc.so.6 126: 61# _start in /usr/bin/python3 126: ---------- 126: **** 126: -117: =>start test AUTOCORR3D custom -117: [00:36:20] test on : 365 molecules done -126: ...Warning: Atom Count for residue GLU5A does not match expected count -126: Warning: Atom Count for residue ASN39A does not match expected count -126: Warning: Atom Count for residue GLU53A does not match expected count -126: Warning: Atom Count for residue ARG64A does not match expected count -126: Warning: Atom Count for residue LYS80A does not match expected count -125: Warning: Atom Count for residue GLU53A 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: Warning: Atom Count for residue GLU5A does not match expected count -125: Warning: Atom Count for residue ARG64A does not match expected count -111: [00:36:20] done -111: [00:36:20] ------------------------------------- -111: [00:36:20] Test Issue252: Bad definitions for Crippen atom types. -111: [00:36:20] done -111: [00:36:20] ------------------------------------- -111: [00:36:20] Test calculation of ChiVs. -111: [00:36:20] done -111: [00:36:20] ------------------------------------- -111: [00:36:20] Test calculation of ChiNs. -111: [00:36:20] done -111: [00:36:20] ------------------------------------- -111: [00:36:20] Test calculation of HallKierAlpha. -111: [00:36:20] done -111: [00:36:20] ------------------------------------- -111: [00:36:20] Test calculation of Kappa1. -111: [00:36:20] done -111: [00:36:20] ------------------------------------- -111: [00:36:20] Test calculation of Kappa2. -111: [00:36:20] done -111: [00:36:20] ------------------------------------- -111: [00:36:20] Test calculation of Kappa3. -111: [00:36:20] done -111: [00:36:20] ------------------------------------- -111: [00:36:20] Test Crippen atom type calculations. -111: [00:36:20] done -111: [00:36:20] ------------------------------------- -111: [00:36:20] Test ring descriptors -111: [00:36:20] done -111: [00:36:20] ------------------------------------- -111: [00:36:20] Test other count descriptors. -111: [00:36:20] done -111: [00:36:20] ------------------------------------- -111: [00:36:20] Test MQN -111: [00:36:20] done -111: [00:36:20] ------------------------------------- -111: [00:36:20] Test GitHub Issue 56. -111: [00:36:20] WARNING: not removing hydrogen atom without neighbors -111: [00:36:20] WARNING: not removing hydrogen atom without neighbors -111: [00:36:20] WARNING: not removing hydrogen atom without neighbors -111: [00:36:20] WARNING: not removing hydrogen atom without neighbors -111: [00:36:20] done -111: [00:36:20] ------------------------------------- -111: [00:36:20] Test Github92: Bad Crippen atom type for pyrrole H. -111: [00:36:20] done -111: [00:36:20] ------------------------------------- -111: [00:36:20] Test Github362: order dependence in Kier-Hall descriptors. -111: [00:36:20] done -111: [00:36:20] ------------------------------------- -111: [00:36:20] Test calculation of spiro and bridgehead counts. -111: [00:36:20] done -111: [00:36:20] ------------------------------------- -111: [00:36:20] Test Github694: ExactMolWt ignoring the mass of the electron -111: [00:36:20] done -111: [00:36:20] ------------------------------------- -111: [00:36:20] Testing Properties and KitchenSink -111: [00:36:20] ---Caught keyerror (bad property name)--- -111: [00:36:20] ------------------------------------- -111: [00:36:20] Test USR Descriptor -111: [00:36:20] done -111: [00:36:20] ------------------------------------- -111: [00:36:20] Test Github #1702: AUTOCORR2D.h not installed unless RDK_BUILD_DESCRIPTORS3D but is required -111: [00:36:20] done -111: [00:36:20] ------------------------------------- -111: [00:36:20] Test Github #1973: support P and S terms for TPSA calculation -111: [00:36:20] done -111: [00:36:20] ------------------------------------- -111: [00:36:20] Test Github #2948: Empty molecule has non-zero LabuteASA -111: [00:36:20] done -116/238 Test #111: testDescriptors ........................ Passed 2.68 sec -test 128 - Start 128: testFingerprints - -128: Test command: /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/Fingerprints/testFingerprints -128: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/Fingerprints -128: Test timeout computed to be: 1500 -117: =>start test 2 WHIM custom -117: [00:36:20] test on : 365 molecules done 128: 128: 128: @@ -25206,6 +25224,7 @@ 128: 128: 128: ------------------- +126: ...Warning: Atom Count for residue GLU5A does not match expected count 128: Atoms: 128: 0 8 O chg: 0 deg: 1 exp: 1 imp: 1 hyb: SP2 128: 1 6 C chg: 0 deg: 3 exp: 4 imp: 0 hyb: SP2 arom?: 1 @@ -25648,6 +25667,13 @@ 128: 128: ------------------- 128: +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 +125: Warning: Atom Count for residue ASN39A 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 128: 128: 128: @@ -25669,626 +25695,624 @@ 128: 128: ------------------- 128: -125: Warning: Atom Count for residue LYS80A does not match expected count -128: [00:36:20] ------------------------------------- -128: [00:36:20] Test Morgan Fingerprints. -128: [00:36:20] done -128: [00:36:20] ------------------------------------- -128: [00:36:20] Test Morgan Fingerprints using fromAtoms argument. -128: [00:36:20] done -128: [00:36:20] ------------------------------------- -128: [00:36:20] Test Morgan Fingerprints as bit vects. -128: [00:36:20] done -128: [00:36:20] ------------------------------------- -128: [00:36:20] Test Morgan Fingerprints with feature invariants. -128: [00:36:20] done -128: [00:36:20] ------------------------------------- -128: [00:36:20] Test additional Morgan fingerprints options. -128: [00:36:20] done -128: [00:36:20] ------------------------------------- -128: [00:36:20] Test Atom Codes. -128: [00:36:20] done -128: [00:36:20] ------------------------------------- -128: [00:36:20] Test Atom Pairs. -128: [00:36:20] DEPRECATION WARNING: please use AtomPairGenerator -128: [00:36:20] DEPRECATION WARNING: please use AtomPairGenerator -128: [00:36:20] done -128: [00:36:20] ------------------------------------- -128: [00:36:20] Test Atom Pairs part 2. -128: [00:36:20] DEPRECATION WARNING: please use AtomPairGenerator -128: [00:36:20] DEPRECATION WARNING: please use AtomPairGenerator -128: [00:36:20] done -128: [00:36:20] ------------------------------------- -128: [00:36:20] Test Topological Torsions. -128: [00:36:20] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [00:36:20] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [00:36:20] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [00:36:20] done -128: [00:36:20] ------------------------------------- -128: [00:36:20] Test Bulk Topological Torsions. -128: [00:36:20] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [00:36:20] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [00:36:20] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [00:36:20] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [00:36:20] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [00:36:20] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [00:36:20] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [00:36:20] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [00:36:20] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [00:36:20] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [00:36:20] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [00:36:20] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [00:36:20] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [00:36:20] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [00:36:20] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [00:36:20] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [00:36:20] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [00:36:20] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [00:36:20] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [00:36:20] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [00:36:20] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [00:36:20] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [00:36:20] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [00:36:20] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [00:36:20] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [00:36:20] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [00:36:20] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [00:36:20] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [00:36:20] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [00:36:20] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [00:36:20] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [00:36:20] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [00:36:20] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [00:36:20] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [00:36:20] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [00:36:20] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [00:36:20] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [00:36:20] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [00:36:20] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [00:36:20] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [00:36:20] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [00:36:20] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [00:36:20] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [00:36:20] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [00:36:20] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [00:36:20] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [00:36:20] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [00:36:20] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [00:36:20] DEPRECATION WARNING: please use TopologicalTorsionGenerator -126: Warning: Atom Count for residue ASN39A does not match expected count -128: [00:36:20] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [00:36:20] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [00:36:20] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [00:36:20] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [00:36:20] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [00:36:20] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [00:36:20] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [00:36:20] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [00:36:20] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [00:36:20] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [00:36:20] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [00:36:20] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [00:36:20] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [00:36:20] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [00:36:20] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [00:36:20] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [00:36:20] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [00:36:20] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [00:36:20] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [00:36:20] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [00:36:20] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [00:36:20] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [00:36:20] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [00:36:20] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [00:36:20] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [00:36:20] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [00:36:20] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [00:36:20] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [00:36:20] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [00:36:20] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [00:36:20] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [00:36:20] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [00:36:20] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [00:36:20] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [00:36:20] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [00:36:20] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [00:36:20] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [00:36:20] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [00:36:20] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [00:36:20] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [00:36:20] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [00:36:20] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [00:36:20] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [00:36:20] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [00:36:20] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [00:36:20] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [00:36:20] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [00:36:20] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [00:36:20] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [00:36:20] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [00:36:20] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [00:36:20] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [00:36:20] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [00:36:20] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [00:36:20] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [00:36:20] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [00:36:20] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [00:36:20] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [00:36:20] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [00:36:20] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [00:36:20] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [00:36:20] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [00:36:20] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [00:36:20] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [00:36:20] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [00:36:20] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [00:36:20] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [00:36:20] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [00:36:20] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [00:36:20] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [00:36:20] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [00:36:20] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [00:36:20] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [00:36:20] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [00:36:20] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [00:36:20] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [00:36:20] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [00:36:20] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [00:36:20] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [00:36:20] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [00:36:20] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [00:36:20] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [00:36:20] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [00:36:20] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [00:36:20] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [00:36:20] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [00:36:20] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [00:36:20] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [00:36:20] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [00:36:20] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [00:36:20] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [00:36:20] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [00:36:20] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [00:36:20] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [00:36:20] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [00:36:20] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [00:36:20] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [00:36:20] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [00:36:20] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [00:36:20] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [00:36:20] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [00:36:20] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [00:36:20] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [00:36:20] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [00:36:20] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [00:36:20] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [00:36:20] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [00:36:20] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [00:36:20] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [00:36:20] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [00:36:20] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [00:36:20] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [00:36:20] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [00:36:20] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [00:36:20] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [00:36:20] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [00:36:20] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [09:33:12] ------------------------------------- +128: [09:33:12] Test Morgan Fingerprints. +128: [09:33:12] done +128: [09:33:12] ------------------------------------- +128: [09:33:12] Test Morgan Fingerprints using fromAtoms argument. +128: [09:33:12] done +128: [09:33:12] ------------------------------------- +128: [09:33:12] Test Morgan Fingerprints as bit vects. +128: [09:33:12] done +128: [09:33:12] ------------------------------------- +128: [09:33:12] Test Morgan Fingerprints with feature invariants. +128: [09:33:12] done +128: [09:33:12] ------------------------------------- +128: [09:33:12] Test additional Morgan fingerprints options. +128: [09:33:12] done +128: [09:33:12] ------------------------------------- +128: [09:33:12] Test Atom Codes. +128: [09:33:12] done +128: [09:33:12] ------------------------------------- +128: [09:33:12] Test Atom Pairs. +128: [09:33:12] DEPRECATION WARNING: please use AtomPairGenerator +128: [09:33:12] DEPRECATION WARNING: please use AtomPairGenerator +128: [09:33:12] done +128: [09:33:12] ------------------------------------- +128: [09:33:12] Test Atom Pairs part 2. +128: [09:33:12] DEPRECATION WARNING: please use AtomPairGenerator +128: [09:33:12] DEPRECATION WARNING: please use AtomPairGenerator +128: [09:33:12] done +128: [09:33:12] ------------------------------------- +128: [09:33:12] Test Topological Torsions. +128: [09:33:12] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [09:33:12] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [09:33:12] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [09:33:12] done +128: [09:33:12] ------------------------------------- +128: [09:33:12] Test Bulk Topological Torsions. +128: [09:33:12] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [09:33:12] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [09:33:12] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [09:33:12] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [09:33:12] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [09:33:12] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [09:33:12] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [09:33:12] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [09:33:12] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [09:33:12] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [09:33:12] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [09:33:12] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [09:33:12] DEPRECATION WARNING: please use TopologicalTorsionGenerator +126: Warning: Atom Count for residue GLU5A does not match expected count +128: [09:33:12] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [09:33:12] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [09:33:12] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [09:33:12] DEPRECATION WARNING: please use TopologicalTorsionGenerator +117: =>start test 2 WHIM custom +117: [09:33:12] test on : 365 molecules done +128: [09:33:12] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [09:33:12] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [09:33:12] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [09:33:12] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [09:33:12] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [09:33:12] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [09:33:12] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [09:33:12] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [09:33:12] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [09:33:12] DEPRECATION WARNING: please use TopologicalTorsionGenerator 127: ........ 127: ---------------------------------------------------------------------- -127: Ran 8 tests in 0.202s +127: Ran 8 tests in 0.169s 127: 127: OK -128: [00:36:20] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [00:36:20] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [00:36:20] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [00:36:20] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [00:36:20] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [00:36:20] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [00:36:20] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [00:36:20] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [00:36:20] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [00:36:20] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [00:36:20] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [00:36:20] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [00:36:20] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [00:36:20] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [00:36:20] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [00:36:20] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [00:36:20] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [00:36:20] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [00:36:20] DEPRECATION WARNING: please use TopologicalTorsionGenerator -126: Warning: Atom Count for residue GLU53A does not match expected count -128: [00:36:20] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [00:36:20] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [00:36:20] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [00:36:20] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [00:36:20] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [00:36:20] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [00:36:20] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [00:36:20] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [00:36:20] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [00:36:20] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [00:36:20] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [00:36:20] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [00:36:20] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [00:36:20] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [00:36:20] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [00:36:20] done -128: [00:36:20] ------------------------------------- -128: [00:36:20] Test Hashed Atom Pairs. -128: [00:36:20] DEPRECATION WARNING: please use AtomPairGenerator -128: [00:36:20] DEPRECATION WARNING: please use AtomPairGenerator -128: [00:36:20] DEPRECATION WARNING: please use AtomPairGenerator -128: [00:36:20] DEPRECATION WARNING: please use AtomPairGenerator -128: [00:36:20] DEPRECATION WARNING: please use AtomPairGenerator -128: [00:36:20] DEPRECATION WARNING: please use AtomPairGenerator -128: [00:36:20] done -128: [00:36:20] ------------------------------------- -128: [00:36:20] Test Hashed torsions. -128: [00:36:20] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [00:36:20] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [00:36:20] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [00:36:20] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [00:36:20] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [00:36:20] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [00:36:20] done -128: [00:36:20] ------------------------------------- -128: [00:36:20] Test Rooted Atom Pairs. -128: [00:36:20] DEPRECATION WARNING: please use AtomPairGenerator -128: [00:36:20] DEPRECATION WARNING: please use AtomPairGenerator -128: [00:36:20] done -128: [00:36:20] ------------------------------------- -128: [00:36:20] Test ignoring atoms in Atom Pairs. -128: [00:36:20] DEPRECATION WARNING: please use AtomPairGenerator -128: [00:36:20] DEPRECATION WARNING: please use AtomPairGenerator -128: [00:36:20] DEPRECATION WARNING: please use AtomPairGenerator -128: [00:36:20] DEPRECATION WARNING: please use AtomPairGenerator -128: [00:36:20] DEPRECATION WARNING: please use AtomPairGenerator -128: [00:36:20] done -128: [00:36:20] ------------------------------------- -128: [00:36:20] Test Rooted Topological Torsions. -128: [00:36:20] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [00:36:20] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [00:36:20] done -128: [00:36:20] ------------------------------------- -128: [00:36:20] Test ignoring atoms in Topological Torsions. -128: [00:36:20] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [00:36:20] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [00:36:20] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [00:36:20] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [00:36:20] done -128: [00:36:20] ------------------------------------- -128: [00:36:20] Test atom info from morgan fingerprints. -128: [00:36:20] done -128: [00:36:20] ------------------------------------- -128: [00:36:20] Test atom info from morgan fingerprints including Info Redundant Environments. -128: [00:36:20] done -128: [00:36:20] ------------------------------------- -128: [00:36:20] ------------------------------------- -128: [00:36:20] DEPRECATION WARNING: please use AtomPairGenerator -128: [00:36:20] DEPRECATION WARNING: please use AtomPairGenerator -128: [00:36:20] DEPRECATION WARNING: please use AtomPairGenerator -128: [00:36:20] DEPRECATION WARNING: please use AtomPairGenerator -128: [00:36:20] DEPRECATION WARNING: please use AtomPairGenerator -128: [00:36:20] DEPRECATION WARNING: please use AtomPairGenerator -128: [00:36:20] DEPRECATION WARNING: please use AtomPairGenerator -128: [00:36:20] DEPRECATION WARNING: please use AtomPairGenerator -128: [00:36:20] DEPRECATION WARNING: please use AtomPairGenerator -128: [00:36:20] DEPRECATION WARNING: please use AtomPairGenerator -128: [00:36:20] DEPRECATION WARNING: please use AtomPairGenerator -128: [00:36:20] DEPRECATION WARNING: please use AtomPairGenerator -128: [00:36:20] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [00:36:20] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [00:36:20] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [00:36:20] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [00:36:20] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [00:36:20] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [00:36:20] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [00:36:20] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [00:36:20] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [00:36:20] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [00:36:20] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [00:36:20] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [00:36:20] ------------------------------------- -128: [00:36:20] ------------------------------------- -128: [00:36:20] ------------------------------------- -128: [00:36:20] ------------------------------------- -128: [00:36:20] Test Atom Pairs including info about chirality. -128: [00:36:20] DEPRECATION WARNING: please use AtomPairGenerator -128: [00:36:20] DEPRECATION WARNING: please use AtomPairGenerator -128: [00:36:20] DEPRECATION WARNING: please use AtomPairGenerator -128: [00:36:20] DEPRECATION WARNING: please use AtomPairGenerator -128: [00:36:20] DEPRECATION WARNING: please use AtomPairGenerator -128: [00:36:20] DEPRECATION WARNING: please use AtomPairGenerator -128: [00:36:20] DEPRECATION WARNING: please use AtomPairGenerator -128: [00:36:20] DEPRECATION WARNING: please use AtomPairGenerator -128: [00:36:20] DEPRECATION WARNING: please use AtomPairGenerator -128: [00:36:20] DEPRECATION WARNING: please use AtomPairGenerator -128: [00:36:20] DEPRECATION WARNING: please use AtomPairGenerator -128: [00:36:20] DEPRECATION WARNING: please use AtomPairGenerator -128: [00:36:20] done -128: [00:36:20] ------------------------------------- -128: [00:36:20] Test Topological Torsions including info about chirality. -128: [00:36:20] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [00:36:20] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [00:36:20] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [00:36:20] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [00:36:20] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [00:36:20] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [00:36:20] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [00:36:20] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [00:36:20] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [00:36:20] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [00:36:20] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [00:36:20] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [00:36:20] done -128: [00:36:20] ------------------------------------- -128: [00:36:20] Test GitHub Issue 25: fingerprint backwards compatibility. -128: [00:36:20] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [00:36:20] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [00:36:20] DEPRECATION WARNING: please use AtomPairGenerator -128: [00:36:20] DEPRECATION WARNING: please use AtomPairGenerator -128: [00:36:20] done -128: [00:36:20] ------------------------------------- -128: [00:36:20] Test GitHub Issue 151: PatternFingerprint problems -128: [00:36:20] done -128: [00:36:20] ------------------------------------- -128: [00:36:20] Test 3D atom pairs. -128: [00:36:20] DEPRECATION WARNING: please use AtomPairGenerator -117: =>start test 1 WHIM custom -128: [00:36:20] DEPRECATION WARNING: please use AtomPairGenerator -128: [00:36:20] DEPRECATION WARNING: please use AtomPairGenerator -128: [00:36:20] DEPRECATION WARNING: please use AtomPairGenerator -128: [00:36:20] DEPRECATION WARNING: please use AtomPairGenerator -128: [00:36:20] done -128: [00:36:20] ------------------------------------- -128: [00:36:20] Test GitHub Issue 195: GenMACCSKeys() raises an exception with an empty molecule -128: [00:36:20] done -128: [00:36:20] ------------------------------------- -128: [00:36:20] Test multithreading with the pattern FP -128: reading molecules -117: [00:36:20] test on : 365 molecules done -117/238 Test #127: pyMolDescriptors3D ..................... Passed 0.67 sec +128: [09:33:12] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [09:33:12] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [09:33:12] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [09:33:12] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [09:33:12] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [09:33:12] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [09:33:12] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [09:33:12] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [09:33:12] DEPRECATION WARNING: please use TopologicalTorsionGenerator +125: Warning: Atom Count for residue GLU53A does not match expected count +128: [09:33:12] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [09:33:12] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [09:33:12] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [09:33:12] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [09:33:12] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [09:33:12] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [09:33:12] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [09:33:12] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [09:33:12] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [09:33:12] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [09:33:12] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [09:33:12] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [09:33:12] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [09:33:12] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [09:33:12] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [09:33:12] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [09:33:12] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [09:33:12] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [09:33:12] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [09:33:12] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [09:33:12] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [09:33:12] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [09:33:12] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [09:33:12] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [09:33:12] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [09:33:12] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [09:33:12] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [09:33:12] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [09:33:12] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [09:33:12] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [09:33:12] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [09:33:12] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [09:33:12] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [09:33:12] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [09:33:12] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [09:33:12] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [09:33:12] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [09:33:12] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [09:33:12] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [09:33:12] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [09:33:12] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [09:33:12] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [09:33:12] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [09:33:12] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [09:33:12] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [09:33:12] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [09:33:12] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [09:33:12] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [09:33:12] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [09:33:12] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [09:33:12] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [09:33:12] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [09:33:12] DEPRECATION WARNING: please use TopologicalTorsionGenerator +125: Warning: Atom Count for residue ARG64A does not match expected count +128: [09:33:12] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [09:33:12] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [09:33:12] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [09:33:12] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [09:33:12] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [09:33:12] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [09:33:12] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [09:33:12] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [09:33:12] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [09:33:12] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [09:33:12] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [09:33:12] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [09:33:12] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [09:33:12] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [09:33:12] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [09:33:12] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [09:33:12] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [09:33:12] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [09:33:12] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [09:33:12] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [09:33:12] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [09:33:12] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [09:33:12] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [09:33:12] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [09:33:12] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [09:33:12] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [09:33:12] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [09:33:12] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [09:33:12] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [09:33:12] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [09:33:12] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [09:33:12] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [09:33:12] DEPRECATION WARNING: please use TopologicalTorsionGenerator +117/238 Test #127: pyMolDescriptors3D ..................... Passed 0.44 sec test 129 Start 129: testMHFPFingerprint 129: Test command: /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/Fingerprints/testMHFPFingerprint 129: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/Fingerprints 129: Test timeout computed to be: 1500 -129: [00:36:20] ------------------------------------- -129: [00:36:20] Test MHFP fingerprint encoder initialization -128: pass 1 -128: launch :0 -128: launch :1 -128: launch :2 -128: launch :3 -129: [00:36:20] done -129: [00:36:20] ------------------------------------- -129: [00:36:20] Test MHFP shingling creation -126: Warning: Atom Count for residue ARG64A does not match expected count -129: [00:36:20] done -129: [00:36:20] ------------------------------------- -129: [00:36:20] Test MHFP hashing of string and uint arrays -129: [00:36:20] done -129: [00:36:20] ------------------------------------- -129: [00:36:20] Test SECFP fingerprint functionality -129: [00:36:20] done +128: [09:33:12] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [09:33:12] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [09:33:12] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [09:33:12] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [09:33:12] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [09:33:12] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [09:33:12] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [09:33:12] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [09:33:12] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [09:33:12] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [09:33:12] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [09:33:12] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [09:33:12] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [09:33:12] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [09:33:12] DEPRECATION WARNING: please use TopologicalTorsionGenerator +129: [09:33:12] ------------------------------------- +129: [09:33:12] Test MHFP fingerprint encoder initialization +128: [09:33:12] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [09:33:12] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [09:33:12] DEPRECATION WARNING: please use TopologicalTorsionGenerator +117: =>start test 1 WHIM custom +117: [09:33:12] test on : 365 molecules done +128: [09:33:12] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [09:33:12] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [09:33:12] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [09:33:12] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [09:33:12] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [09:33:12] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [09:33:12] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [09:33:12] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [09:33:12] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [09:33:12] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [09:33:12] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [09:33:12] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [09:33:12] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [09:33:12] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [09:33:12] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [09:33:12] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [09:33:12] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [09:33:12] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [09:33:12] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [09:33:12] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [09:33:12] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [09:33:12] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [09:33:12] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [09:33:12] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [09:33:12] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [09:33:12] DEPRECATION WARNING: please use TopologicalTorsionGenerator +129: [09:33:12] done +129: [09:33:12] ------------------------------------- +129: [09:33:12] Test MHFP shingling creation +128: [09:33:12] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [09:33:12] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [09:33:12] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [09:33:12] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [09:33:12] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [09:33:12] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [09:33:12] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [09:33:12] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [09:33:12] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [09:33:12] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [09:33:12] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [09:33:12] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [09:33:12] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [09:33:12] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [09:33:12] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [09:33:12] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [09:33:12] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [09:33:12] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [09:33:12] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [09:33:12] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [09:33:12] DEPRECATION WARNING: please use TopologicalTorsionGenerator +129: [09:33:12] done +129: [09:33:12] ------------------------------------- +129: [09:33:12] Test MHFP hashing of string and uint arrays +129: [09:33:12] done +129: [09:33:12] ------------------------------------- +129: [09:33:12] Test SECFP fingerprint functionality +128: [09:33:12] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [09:33:12] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [09:33:12] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [09:33:12] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [09:33:12] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [09:33:12] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [09:33:12] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [09:33:12] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [09:33:12] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [09:33:12] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [09:33:12] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [09:33:12] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [09:33:12] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [09:33:12] done +128: [09:33:12] ------------------------------------- +128: [09:33:12] Test Hashed Atom Pairs. +128: [09:33:12] DEPRECATION WARNING: please use AtomPairGenerator +128: [09:33:12] DEPRECATION WARNING: please use AtomPairGenerator +128: [09:33:12] DEPRECATION WARNING: please use AtomPairGenerator +126: Warning: Atom Count for residue ASN39A does not match expected count +128: [09:33:12] DEPRECATION WARNING: please use AtomPairGenerator +128: [09:33:12] DEPRECATION WARNING: please use AtomPairGenerator +128: [09:33:12] DEPRECATION WARNING: please use AtomPairGenerator +128: [09:33:12] done +128: [09:33:12] ------------------------------------- +128: [09:33:12] Test Hashed torsions. +128: [09:33:12] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [09:33:12] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [09:33:12] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [09:33:12] DEPRECATION WARNING: please use TopologicalTorsionGenerator +125: Warning: Atom Count for residue LYS80A does not match expected count +129: [09:33:12] done +128: [09:33:12] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [09:33:12] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [09:33:12] done +128: [09:33:12] ------------------------------------- +128: [09:33:12] Test Rooted Atom Pairs. +128: [09:33:12] DEPRECATION WARNING: please use AtomPairGenerator +128: [09:33:12] DEPRECATION WARNING: please use AtomPairGenerator +128: [09:33:12] done +128: [09:33:12] ------------------------------------- +128: [09:33:12] Test ignoring atoms in Atom Pairs. +128: [09:33:12] DEPRECATION WARNING: please use AtomPairGenerator +128: [09:33:12] DEPRECATION WARNING: please use AtomPairGenerator +128: [09:33:12] DEPRECATION WARNING: please use AtomPairGenerator +128: [09:33:12] DEPRECATION WARNING: please use AtomPairGenerator +128: [09:33:12] DEPRECATION WARNING: please use AtomPairGenerator +128: [09:33:12] done +128: [09:33:12] ------------------------------------- +128: [09:33:12] Test Rooted Topological Torsions. +128: [09:33:12] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [09:33:12] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [09:33:12] done 118/238 Test #129: testMHFPFingerprint .................... Passed 0.08 sec +128: [09:33:12] ------------------------------------- +128: [09:33:12] Test ignoring atoms in Topological Torsions. +128: [09:33:12] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [09:33:12] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [09:33:12] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [09:33:12] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [09:33:12] done +128: [09:33:12] ------------------------------------- +128: [09:33:12] Test atom info from morgan fingerprints. test 130 Start 130: testFingerprintGenerators 130: Test command: /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/Fingerprints/testFingerprintGenerators 130: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/Fingerprints 130: Test timeout computed to be: 1500 -130: [00:36:20] ------------------------------------- -130: [00:36:20] Test atom-pair fp generator -130: [00:36:20] done -130: [00:36:20] ------------------------------------- -130: [00:36:20] Test atom-pair fp generator with different arguments -130: [00:36:20] done -130: [00:36:20] ------------------------------------- -130: [00:36:20] Test compatibility between atom pair implementation for FingerprintGenerator and old atom pairs implementation -130: [00:36:20] DEPRECATION WARNING: please use AtomPairGenerator -130: [00:36:20] DEPRECATION WARNING: please use AtomPairGenerator -130: [00:36:20] DEPRECATION WARNING: please use AtomPairGenerator -130: [00:36:20] DEPRECATION WARNING: please use AtomPairGenerator -130: [00:36:20] DEPRECATION WARNING: please use AtomPairGenerator -130: [00:36:20] DEPRECATION WARNING: please use AtomPairGenerator -130: [00:36:20] DEPRECATION WARNING: please use AtomPairGenerator -130: [00:36:20] DEPRECATION WARNING: please use AtomPairGenerator -130: [00:36:20] DEPRECATION WARNING: please use AtomPairGenerator -130: [00:36:20] DEPRECATION WARNING: please use AtomPairGenerator -130: [00:36:20] done -130: [00:36:20] ------------------------------------- -130: [00:36:20] Test atom-pair additional output -130: [00:36:20] done -130: [00:36:20] ------------------------------------- -130: [00:36:20] Test Folded Atom Pairs. -130: [00:36:20] done -130: [00:36:20] ------------------------------------- -130: [00:36:20] Test Rooted Atom Pairs. -130: [00:36:20] done -130: [00:36:20] ------------------------------------- -130: [00:36:20] Test ignoring atoms in Atom Pairs. -130: [00:36:20] done -130: [00:36:20] ------------------------------------- -130: [00:36:20] Test Atom Pairs including info about chirality. -130: [00:36:20] done -130: [00:36:20] ------------------------------------- -130: [00:36:20] Test Morgan Fingerprints. -130: [00:36:20] done -130: [00:36:20] ------------------------------------- -130: [00:36:20] Test morgan fp generator -130: [00:36:20] done -130: [00:36:20] ------------------------------------- -130: [00:36:20] Test Morgan Fingerprints using fromAtoms argument. -130: [00:36:20] done -130: [00:36:20] ------------------------------------- -130: [00:36:20] Test Morgan Fingerprints as bit vects. -130: [00:36:20] done -130: [00:36:20] ------------------------------------- -130: [00:36:20] Test Morgan Fingerprints with feature invariants. -130: [00:36:20] done -130: [00:36:20] ------------------------------------- -130: [00:36:20] Test additional Morgan fingerprints options. -130: [00:36:20] done -130: [00:36:20] ------------------------------------- -130: [00:36:20] Test GitHub Issue 695: Include cis/trans stereochemistry when useChirality=true with the morgan fingerprints -130: [00:36:20] done -130: [00:36:20] ------------------------------------- -130: [00:36:20] Single atoms setting radius 1 bits in Morgan fingerprints -130: [00:36:20] done -130: [00:36:20] ------------------------------------- -130: [00:36:20] Test different invariant generator combinations -130: [00:36:20] done -130: [00:36:20] ------------------------------------- -130: [00:36:20] Test invariant overriding -130: [00:36:20] done -130: [00:36:20] ------------------------------------- -130: [00:36:20] Test RDKit fp generator +128: [09:33:12] done +128: [09:33:12] ------------------------------------- +128: [09:33:12] Test atom info from morgan fingerprints including Info Redundant Environments. +128: [09:33:12] done +128: [09:33:12] ------------------------------------- +128: [09:33:12] ------------------------------------- +128: [09:33:12] DEPRECATION WARNING: please use AtomPairGenerator +128: [09:33:12] DEPRECATION WARNING: please use AtomPairGenerator +128: [09:33:12] DEPRECATION WARNING: please use AtomPairGenerator +128: [09:33:12] DEPRECATION WARNING: please use AtomPairGenerator +128: [09:33:12] DEPRECATION WARNING: please use AtomPairGenerator +128: [09:33:12] DEPRECATION WARNING: please use AtomPairGenerator +128: [09:33:12] DEPRECATION WARNING: please use AtomPairGenerator +128: [09:33:12] DEPRECATION WARNING: please use AtomPairGenerator +128: [09:33:12] DEPRECATION WARNING: please use AtomPairGenerator +128: [09:33:12] DEPRECATION WARNING: please use AtomPairGenerator +128: [09:33:12] DEPRECATION WARNING: please use AtomPairGenerator +128: [09:33:12] DEPRECATION WARNING: please use AtomPairGenerator +128: [09:33:12] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [09:33:12] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [09:33:12] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [09:33:12] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [09:33:12] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [09:33:12] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [09:33:12] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [09:33:12] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [09:33:12] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [09:33:12] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [09:33:12] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [09:33:12] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [09:33:12] ------------------------------------- +128: [09:33:12] ------------------------------------- +128: [09:33:12] ------------------------------------- +128: [09:33:12] ------------------------------------- +128: [09:33:12] Test Atom Pairs including info about chirality. +128: [09:33:12] DEPRECATION WARNING: please use AtomPairGenerator +128: [09:33:12] DEPRECATION WARNING: please use AtomPairGenerator +128: [09:33:12] DEPRECATION WARNING: please use AtomPairGenerator +128: [09:33:12] DEPRECATION WARNING: please use AtomPairGenerator +128: [09:33:12] DEPRECATION WARNING: please use AtomPairGenerator +128: [09:33:12] DEPRECATION WARNING: please use AtomPairGenerator +128: [09:33:12] DEPRECATION WARNING: please use AtomPairGenerator +128: [09:33:12] DEPRECATION WARNING: please use AtomPairGenerator +128: [09:33:12] DEPRECATION WARNING: please use AtomPairGenerator +128: [09:33:12] DEPRECATION WARNING: please use AtomPairGenerator +128: [09:33:12] DEPRECATION WARNING: please use AtomPairGenerator +128: [09:33:12] DEPRECATION WARNING: please use AtomPairGenerator +128: [09:33:12] done +128: [09:33:12] ------------------------------------- +128: [09:33:12] Test Topological Torsions including info about chirality. +128: [09:33:12] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [09:33:12] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [09:33:12] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [09:33:12] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [09:33:12] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [09:33:12] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [09:33:12] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [09:33:12] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [09:33:12] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [09:33:12] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [09:33:12] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [09:33:12] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [09:33:12] done +128: [09:33:12] ------------------------------------- +128: [09:33:12] Test GitHub Issue 25: fingerprint backwards compatibility. +128: [09:33:12] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [09:33:12] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [09:33:12] DEPRECATION WARNING: please use AtomPairGenerator +128: [09:33:12] DEPRECATION WARNING: please use AtomPairGenerator +128: [09:33:12] done +128: [09:33:12] ------------------------------------- +128: [09:33:12] Test GitHub Issue 151: PatternFingerprint problems +128: [09:33:12] done +128: [09:33:12] ------------------------------------- +128: [09:33:12] Test 3D atom pairs. +128: [09:33:12] DEPRECATION WARNING: please use AtomPairGenerator +128: [09:33:12] DEPRECATION WARNING: please use AtomPairGenerator +128: [09:33:12] DEPRECATION WARNING: please use AtomPairGenerator +128: [09:33:12] DEPRECATION WARNING: please use AtomPairGenerator +128: [09:33:12] DEPRECATION WARNING: please use AtomPairGenerator +128: [09:33:12] done +128: [09:33:12] ------------------------------------- +128: [09:33:12] Test GitHub Issue 195: GenMACCSKeys() raises an exception with an empty molecule +128: [09:33:12] done +128: [09:33:12] ------------------------------------- +128: [09:33:12] Test multithreading with the pattern FP +128: reading molecules +130: [09:33:12] ------------------------------------- +130: [09:33:12] Test atom-pair fp generator +130: [09:33:12] done +130: [09:33:12] ------------------------------------- +130: [09:33:12] Test atom-pair fp generator with different arguments +130: [09:33:12] done +130: [09:33:12] ------------------------------------- +130: [09:33:12] Test compatibility between atom pair implementation for FingerprintGenerator and old atom pairs implementation +130: [09:33:12] DEPRECATION WARNING: please use AtomPairGenerator +130: [09:33:12] DEPRECATION WARNING: please use AtomPairGenerator +130: [09:33:12] DEPRECATION WARNING: please use AtomPairGenerator +130: [09:33:12] DEPRECATION WARNING: please use AtomPairGenerator +128: pass 1 +128: launch :0 +128: launch :1 +128: launch :2 +128: launch :3 +130: [09:33:12] DEPRECATION WARNING: please use AtomPairGenerator +130: [09:33:12] DEPRECATION WARNING: please use AtomPairGenerator +130: [09:33:12] DEPRECATION WARNING: please use AtomPairGenerator +130: [09:33:12] DEPRECATION WARNING: please use AtomPairGenerator +130: [09:33:12] DEPRECATION WARNING: please use AtomPairGenerator +130: [09:33:12] DEPRECATION WARNING: please use AtomPairGenerator +130: [09:33:12] done +130: [09:33:12] ------------------------------------- +130: [09:33:12] Test atom-pair additional output +130: [09:33:12] done +130: [09:33:12] ------------------------------------- +130: [09:33:12] Test Folded Atom Pairs. +130: [09:33:12] done +130: [09:33:12] ------------------------------------- +130: [09:33:12] Test Rooted Atom Pairs. +130: [09:33:12] done +130: [09:33:12] ------------------------------------- +130: [09:33:12] Test ignoring atoms in Atom Pairs. +130: [09:33:12] done +130: [09:33:12] ------------------------------------- +130: [09:33:12] Test Atom Pairs including info about chirality. +130: [09:33:12] done +130: [09:33:12] ------------------------------------- +130: [09:33:12] Test Morgan Fingerprints. +126: Warning: Atom Count for residue GLU53A does not match expected count +130: [09:33:12] done +130: [09:33:12] ------------------------------------- +130: [09:33:12] Test morgan fp generator +130: [09:33:12] done +130: [09:33:12] ------------------------------------- +130: [09:33:12] Test Morgan Fingerprints using fromAtoms argument. +130: [09:33:12] done +130: [09:33:12] ------------------------------------- +130: [09:33:12] Test Morgan Fingerprints as bit vects. +130: [09:33:12] done +130: [09:33:12] ------------------------------------- +130: [09:33:12] Test Morgan Fingerprints with feature invariants. +130: [09:33:12] done +130: [09:33:12] ------------------------------------- +130: [09:33:12] Test additional Morgan fingerprints options. +130: [09:33:12] done +130: [09:33:12] ------------------------------------- +130: [09:33:12] Test GitHub Issue 695: Include cis/trans stereochemistry when useChirality=true with the morgan fingerprints +130: [09:33:12] done +130: [09:33:12] ------------------------------------- +130: [09:33:12] Single atoms setting radius 1 bits in Morgan fingerprints +130: [09:33:12] done +130: [09:33:12] ------------------------------------- +130: [09:33:12] Test different invariant generator combinations +130: [09:33:12] done +130: [09:33:12] ------------------------------------- +130: [09:33:12] Test invariant overriding +130: [09:33:12] done +130: [09:33:12] ------------------------------------- +130: [09:33:12] Test RDKit fp generator +126: Warning: Atom Count for residue ARG64A does not match expected count +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 122: =>start test GETAWAY -122: [00:36:20] test on : 365 molecules done -119/238 Test #122: testGETAWAY ............................ Passed 1.75 sec +122: [09:33:12] test on : 365 molecules done +119/238 Test #122: testGETAWAY ............................ Passed 1.33 sec test 131 Start 131: fpTestCatch 131: Test command: /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/Fingerprints/fpTestCatch 131: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/Fingerprints 131: Test timeout computed to be: 1500 -131: Randomness seeded to: 201453573 +131: Randomness seeded to: 171881504 131: =============================================================================== 131: All tests passed (188 assertions in 16 test cases) 131: -120/238 Test #131: fpTestCatch ............................ Passed 0.02 sec +120/238 Test #131: fpTestCatch ............................ Passed 0.08 sec test 132 Start 132: fpGenTestCatch 132: Test command: /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/Fingerprints/fpGenTestCatch 132: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/Fingerprints 132: Test timeout computed to be: 1500 -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 -132: Randomness seeded to: 695951052 +130: [09:33:13] done +130: [09:33:13] ------------------------------------- +130: [09:33:13] Test unfolded version of RDKFP +130: [09:33:13] ------------------------------------- +130: [09:33:13] Test topological torsion fp generator +130: [09:33:13] DEPRECATION WARNING: please use TopologicalTorsionGenerator +130: [09:33:13] DEPRECATION WARNING: please use TopologicalTorsionGenerator +130: [09:33:13] DEPRECATION WARNING: please use TopologicalTorsionGenerator +130: [09:33:13] DEPRECATION WARNING: please use TopologicalTorsionGenerator +130: [09:33:13] DEPRECATION WARNING: please use TopologicalTorsionGenerator +130: [09:33:13] DEPRECATION WARNING: please use TopologicalTorsionGenerator +130: [09:33:13] DEPRECATION WARNING: please use TopologicalTorsionGenerator +130: [09:33:13] DEPRECATION WARNING: please use TopologicalTorsionGenerator +130: [09:33:13] DEPRECATION WARNING: please use TopologicalTorsionGenerator +130: [09:33:13] DEPRECATION WARNING: please use TopologicalTorsionGenerator +125: Warning: Atom Count for residue GLU150A does not match expected count +130: [09:33:13] done +130: [09:33:13] ------------------------------------- +130: [09:33:13] Test Topological Torsions. +130: [09:33:13] done +130: [09:33:13] ------------------------------------- +130: [09:33:13] Test Folded torsions. +130: [09:33:13] done +130: [09:33:13] ------------------------------------- +130: [09:33:13] Test Bulk Topological Torsions. +132: Randomness seeded to: 566018005 132: =============================================================================== 132: All tests passed (2737 assertions in 7 test cases) 132: -121/238 Test #132: fpGenTestCatch ......................... Passed 0.08 sec +121/238 Test #132: fpGenTestCatch ......................... Passed 0.11 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-aarch64-linux-gnu/Code/GraphMol/Fingerprints/Wrap 133: Test timeout computed to be: 1500 -130: [00:36:21] done -130: [00:36:21] ------------------------------------- -130: [00:36:21] Test unfolded version of RDKFP -130: [00:36:21] ------------------------------------- -130: [00:36:21] Test topological torsion fp generator -130: [00:36:21] DEPRECATION WARNING: please use TopologicalTorsionGenerator -130: [00:36:21] DEPRECATION WARNING: please use TopologicalTorsionGenerator -130: [00:36:21] DEPRECATION WARNING: please use TopologicalTorsionGenerator -130: [00:36:21] DEPRECATION WARNING: please use TopologicalTorsionGenerator -130: [00:36:21] DEPRECATION WARNING: please use TopologicalTorsionGenerator -130: [00:36:21] DEPRECATION WARNING: please use TopologicalTorsionGenerator -130: [00:36:21] DEPRECATION WARNING: please use TopologicalTorsionGenerator -130: [00:36:21] DEPRECATION WARNING: please use TopologicalTorsionGenerator -130: [00:36:21] DEPRECATION WARNING: please use TopologicalTorsionGenerator -130: [00:36:21] DEPRECATION WARNING: please use TopologicalTorsionGenerator -130: [00:36:21] done -130: [00:36:21] ------------------------------------- -130: [00:36:21] Test Topological Torsions. -130: [00:36:21] done -130: [00:36:21] ------------------------------------- -130: [00:36:21] Test Folded torsions. -130: [00:36:21] done -130: [00:36:21] ------------------------------------- -130: [00:36:21] Test Bulk Topological Torsions. -125: Warning: Atom Count for residue GLU150A does not match expected count 125: Warning: Atom Count for residue ASN157A does not match expected count -130: [00:36:21] done -130: [00:36:21] ------------------------------------- -130: [00:36:21] Test Rooted Topological Torsions. -130: [00:36:21] done -130: [00:36:21] ------------------------------------- -130: [00:36:21] Test ignoring atoms in Topological Torsions. -130: [00:36:21] done -130: [00:36:21] ------------------------------------- -130: [00:36:21] ------------------------------------- -130: [00:36:21] Test Topological Torsions including info about chirality. -130: [00:36:21] done -130: [00:36:21] ------------------------------------- -130: [00:36:21] Test GitHub Issue 25: fingerprint backwards compatibility. -130: [00:36:21] done -130: [00:36:21] ------------------------------------- -130: [00:36:21] Test GitHub Issue 334: explicit Hs in SMILES modifies atom pair (and topological torsion) FP. -130: [00:36:21] done -130: [00:36:21] ------------------------------------- -130: [00:36:21] Test GitHub Issue 811: rooted atom fingerprint non identical for the same molecules #811 -130: [00:36:21] done -130: [00:36:21] ------------------------------------- -130: [00:36:21] Test convenience and bulk fp calculation functions -133: .............. -133: ---------------------------------------------------------------------- -133: Ran 14 tests in 0.131s -133: -133: OK -122/238 Test #133: pyTestGenerator ........................ Passed 0.58 sec +130: [09:33:13] done +130: [09:33:13] ------------------------------------- +130: [09:33:13] Test Rooted Topological Torsions. +130: [09:33:13] done +130: [09:33:13] ------------------------------------- +130: [09:33:13] Test ignoring atoms in Topological Torsions. +130: [09:33:13] done +130: [09:33:13] ------------------------------------- +130: [09:33:13] ------------------------------------- +130: [09:33:13] Test Topological Torsions including info about chirality. +130: [09:33:13] done +130: [09:33:13] ------------------------------------- +130: [09:33:13] Test GitHub Issue 25: fingerprint backwards compatibility. +130: [09:33:13] done +130: [09:33:13] ------------------------------------- +130: [09:33:13] Test GitHub Issue 334: explicit Hs in SMILES modifies atom pair (and topological torsion) FP. +130: [09:33:13] done +130: [09:33:13] ------------------------------------- +130: [09:33:13] Test GitHub Issue 811: rooted atom fingerprint non identical for the same molecules #811 +130: [09:33:13] done +130: [09:33:13] ------------------------------------- +130: [09:33:13] Test convenience and bulk fp calculation functions +126: Warning: Atom Count for residue GLU150A does not match expected count +126: Warning: Atom Count for residue ASN157A does not match expected count +74: [09:33:13] Finished: testSmiCorrectness() +74: [09:33:13] ----------------------------------------- +74: +74: [09:33:13] +74: ----------------------------------------- +74: [09:33:13] Spurious data before the first property will be ignored +74: [09:33:13] Property will be truncated after the first blank line +74: [09:33:13] Property will be truncated after the first blank line +74: [09:33:13] Property will be truncated after the first blank line +130: [09:33:13] done +130: [09:33:13] ------------------------------------- +130: [09:33:13] Test GitHub Issue #6958 +130: [09:33:13] DEPRECATION WARNING: please use AtomPairGenerator +122/238 Test #130: testFingerprintGenerators .............. Passed 0.81 sec 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-aarch64-linux-gnu/Code/GraphMol/Fingerprints/Wrap 134: Test timeout computed to be: 1500 -130: [00:36:21] done -130: [00:36:21] ------------------------------------- -130: [00:36:21] Test GitHub Issue #6958 -130: [00:36:21] DEPRECATION WARNING: please use AtomPairGenerator -123/238 Test #130: testFingerprintGenerators .............. Passed 0.88 sec +133: .............. +133: ---------------------------------------------------------------------- +133: Ran 14 tests in 0.140s +133: +133: OK +80: =============================================================================== +80: All tests passed (1596 assertions in 100 test cases) +80: +123/238 Test #80: fileParsersCatchTest ................... Passed 4.73 sec test 135 Start 135: testPartialCharges 135: Test command: /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/PartialCharges/testPartialCharges 135: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/PartialCharges 135: Test timeout computed to be: 1500 -124/238 Test #135: testPartialCharges ..................... Passed 0.01 sec +124/238 Test #135: testPartialCharges ..................... Passed 0.03 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-aarch64-linux-gnu/Code/GraphMol/PartialCharges/Wrap 136: Test timeout computed to be: 1500 -74: [00:36:21] Finished: testSmiCorrectness() -74: [00:36:21] ----------------------------------------- -74: -74: [00:36:21] -74: ----------------------------------------- -74: [00:36:21] Spurious data before the first property will be ignored -74: [00:36:21] Property will be truncated after the first blank line -74: [00:36:21] Property will be truncated after the first blank line -74: [00:36:21] Property will be truncated after the first blank line -126: Warning: Atom Count for residue GLU150A does not match expected count -134: .. -134: ---------------------------------------------------------------------- -134: Ran 2 tests in 0.026s -134: -134: OK -125/238 Test #134: pyTestMHFP ............................. Passed 0.40 sec +125/238 Test #133: pyTestGenerator ........................ Passed 0.51 sec test 137 Start 137: testMolTransforms 137: Test command: /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/MolTransforms/testMolTransforms 137: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/MolTransforms 137: Test timeout computed to be: 1500 -136: ....... -136: ---------------------------------------------------------------------- -136: Ran 7 tests in 0.113s -136: -136: OK -126: Warning: Atom Count for residue ASN157A does not match expected count 137: *********************************************************** 137: Testing MolTransforms 137: --------------------------------- @@ -26319,68 +26343,67 @@ 137: testWeightedCentroid 137: 137: *********************************************************** -126/238 Test #137: testMolTransforms ...................... Passed 0.04 sec +126/238 Test #137: testMolTransforms ...................... Passed 0.05 sec test 138 Start 138: molTransformsTestCatch 138: Test command: /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/MolTransforms/molTransformsTestCatch 138: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/MolTransforms 138: Test timeout computed to be: 1500 -138: Randomness seeded to: 1225280975 +134: .. +134: ---------------------------------------------------------------------- +134: Ran 2 tests in 0.029s +134: +134: OK +138: Randomness seeded to: 117686534 138: =============================================================================== 138: All tests passed (4 assertions in 1 test case) 138: -127/238 Test #138: molTransformsTestCatch ................. Passed 0.05 sec +127/238 Test #138: molTransformsTestCatch ................. Passed 0.04 sec test 139 Start 139: pyMolTransforms 139: Test command: /usr/bin/python3 "/build/reproducible-path/rdkit-202503.1/Code/GraphMol/MolTransforms/Wrap/testMolTransforms.py" 139: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/MolTransforms/Wrap 139: Test timeout computed to be: 1500 -128/238 Test #136: pyPartialCharges ....................... Passed 0.39 sec +128/238 Test #134: pyTestMHFP ............................. Passed 0.25 sec test 140 Start 140: forceFieldHelpersCatch 140: Test command: /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/ForceFieldHelpers/forceFieldHelpersCatch 140: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/ForceFieldHelpers 140: Test timeout computed to be: 1500 -140: Randomness seeded to: 1466916524 -140: =============================================================================== -140: All tests passed (17 assertions in 2 test cases) -140: -129/238 Test #140: forceFieldHelpersCatch ................. Passed 0.04 sec +74: [09:33:13] Finished: testSDCorrectness() +74: [09:33:13] ----------------------------------------- +74: +129/238 Test #74: testMultithreadedMolSupplier ........... Passed 5.02 sec test 141 Start 141: testMMFFForceFieldHelpers 141: Test command: /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/ForceFieldHelpers/MMFF/testMMFFForceFieldHelpers 141: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/ForceFieldHelpers/MMFF 141: Test timeout computed to be: 1500 -141: [00:36:22] ------------------------------------- -141: [00:36:22] Test MMFF atom types. -141: [00:36:22] done -141: [00:36:22] ------------------------------------- -141: [00:36:22] Testing MMFF builder tools. -141: [00:36:22] done -141: [00:36:22] ------------------------------------- -141: [00:36:22] Testing MMFF builder+minimization. -74: [00:36:22] Finished: testSDCorrectness() -74: [00:36:22] ----------------------------------------- -74: -130/238 Test #74: testMultithreadedMolSupplier ........... Passed 7.61 sec +140: Randomness seeded to: 3512592842 +140: =============================================================================== +140: All tests passed (17 assertions in 2 test cases) +140: +130/238 Test #140: forceFieldHelpersCatch ................. Passed 0.04 sec test 142 Start 142: testMMFFForceFieldHelpersMultiThread 142: Test command: /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/ForceFieldHelpers/MMFF/testMMFFForceFieldHelpersMultiThread 142: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/ForceFieldHelpers/MMFF 142: Test timeout computed to be: 1500 -142: [00:36:22] ------------------------------------- -142: [00:36:22] Test MMFF multithreading -141: [00:36:22] done -141: [00:36:22] ------------------------------------- -141: [00:36:22] Testing Issue239. -141: [00:36:22] done -141: [00:36:22] ------------------------------------- -141: [00:36:22] Testing calcEnergy with passed coords. +141: [09:33:13] ------------------------------------- +141: [09:33:13] Test MMFF atom types. +142: [09:33:13] ------------------------------------- +142: [09:33:13] Test MMFF multithreading +141: [09:33:13] done +141: [09:33:13] ------------------------------------- +141: [09:33:13] Testing MMFF builder tools. +141: [09:33:13] done +141: [09:33:13] ------------------------------------- +141: [09:33:13] Testing MMFF builder+minimization. 142: processing 142: launch :0 142: launch :1 @@ -26394,14 +26417,9 @@ 142: launch :9 142: launch :10 142: launch :11 -117: =>start test GETAWAY custom -141: [00:36:22] done -141: [00:36:22] ------------------------------------- -141: [00:36:22] Testing calcGrad. 142: launch :12 142: launch :13 142: launch :14 -117: [00:36:22] test on : 365 molecules done 142: launch :15 142: launch :16 142: launch :17 @@ -26411,623 +26429,534 @@ 142: launch :21 142: launch :22 142: launch :23 -131/238 Test #117: testRDFcustom .......................... Passed 3.89 sec +141: [09:33:13] done +141: [09:33:13] ------------------------------------- +141: [09:33:13] Testing Issue239. +141: [09:33:13] done +141: [09:33:13] ------------------------------------- +141: [09:33:13] Testing calcEnergy with passed coords. +29: Checking against /build/reproducible-path/rdkit-202503.1/Code/ForceField/MMFF/test_data/MMFF94_reference.log... +141: [09:33:13] done +141: [09:33:13] ------------------------------------- +141: [09:33:13] Testing calcGrad. +141: [09:33:13] done +141: [09:33:13] ------------------------------------- +141: [09:33:13] Testing Issue242. +141: [09:33:13] done +141: [09:33:13] ------------------------------------- +141: [09:33:13] Testing github 308: crash during MMFF parameterization . +141: [09:33:13] ------------------------------------- +141: [09:33:13] Testing SFIssue1653802. +141: [09:33:13] done +141: [09:33:13] ------------------------------------- +141: [09:33:13] Testing SFIssue2378119. +141: [09:33:13] done +141: [09:33:13] ------------------------------------- +141: [09:33:13] Test MMFF force-field parameter getters. +141: [09:33:13] ------------------------------------- +141: [09:33:13] Test MMFF multithreading +29: All 191 tests passed +142: done +141: generating reference data +142: [09:33:13] done +136: ....... +136: ---------------------------------------------------------------------- +136: Ran 7 tests in 0.109s +136: +136: OK +131/238 Test #142: testMMFFForceFieldHelpersMultiThread ... Passed 0.26 sec test 143 Start 143: testUFFForceFieldHelpers 143: Test command: /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/ForceFieldHelpers/UFF/testUFFForceFieldHelpers 143: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/ForceFieldHelpers/UFF 143: Test timeout computed to be: 1500 -141: [00:36:22] done -141: [00:36:22] ------------------------------------- -141: [00:36:22] Testing Issue242. -141: [00:36:22] done -141: [00:36:22] ------------------------------------- -141: [00:36:22] Testing github 308: crash during MMFF parameterization . -141: [00:36:22] ------------------------------------- -141: [00:36:22] Testing SFIssue1653802. -141: [00:36:22] done -141: [00:36:22] ------------------------------------- -141: [00:36:22] Testing SFIssue2378119. -141: [00:36:22] done -141: [00:36:22] ------------------------------------- -141: [00:36:22] Test MMFF force-field parameter getters. -141: [00:36:22] ------------------------------------- -141: [00:36:22] Test MMFF multithreading -143: [00:36:22] ------------------------------------- -143: [00:36:22] Test UFF atom labels. -143: [00:36:22] done -143: [00:36:22] ------------------------------------- -143: [00:36:22] Test UFF atom typer. -141: generating reference data -143: [00:36:22] done -143: [00:36:22] ------------------------------------- -143: [00:36:22] Testing UFF builder tools. -143: [00:36:22] done -143: [00:36:22] ------------------------------------- -143: [00:36:22] Testing UFF builder+minimization. -139: ........ -139: ---------------------------------------------------------------------- -139: Ran 8 tests in 0.053s -139: -139: OK -143: [00:36:22] done -143: [00:36:22] ------------------------------------- -143: [00:36:22] Testing UFF special cases. -143: [00:36:22] UFFTYPER: Unrecognized charge state for atom: 0 -143: [00:36:22] done -143: [00:36:22] ------------------------------------- -143: [00:36:22] Testing Issue239. -143: [00:36:22] done -143: [00:36:22] ------------------------------------- -143: [00:36:22] Testing calcEnergy with passed coords. -143: [00:36:22] done -143: [00:36:22] ------------------------------------- -143: [00:36:22] Testing calcGrad. -143: [00:36:22] done -143: [00:36:22] ------------------------------------- -143: [00:36:22] Testing SFIssue1653802. -142: done -142: [00:36:22] done -143: [00:36:22] done -143: [00:36:22] ------------------------------------- -143: [00:36:22] Testing SFIssue2378119. -143: [00:36:22] done -143: [00:36:22] ------------------------------------- -143: [00:36:22] Test UFF force-field parameter getters. -143: [00:36:22] ------------------------------------- -143: [00:36:22] Testing handling missing parameters. -143: [00:36:22] UFFTYPER: Unrecognized hybridization for atom: 0 -143: [00:36:22] UFFTYPER: Unrecognized atom type: Cu+1 (0) -143: [00:36:22] UFFTYPER: Unrecognized hybridization for atom: 0 -143: [00:36:22] UFFTYPER: Unrecognized atom type: Cu+1 (0) -143: [00:36:22] done -143: [00:36:22] ------------------------------------- -143: [00:36:22] Testing SFIssue3009337. -143: [00:36:22] done -143: [00:36:22] ------------------------------------- -143: [00:36:22] Test UFF multithreading -143: generating reference data -132/238 Test #139: pyMolTransforms ........................ Passed 0.48 sec +117: =>start test GETAWAY custom +117: [09:33:14] test on : 365 molecules done +132/238 Test #117: testRDFcustom .......................... Passed 2.97 sec test 144 Start 144: testCrystalForceField 144: Test command: /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/ForceFieldHelpers/CrystalFF/testCrystalForceField 144: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/ForceFieldHelpers/CrystalFF 144: Test timeout computed to be: 1500 -133/238 Test #142: testMMFFForceFieldHelpersMultiThread ... Passed 0.35 sec +143: [09:33:14] ------------------------------------- +143: [09:33:14] Test UFF atom labels. +143: [09:33:14] done +143: [09:33:14] ------------------------------------- +143: [09:33:14] Test UFF atom typer. +144: ------------------------------------- +144: Test CrystalFF torsional term. +143: [09:33:14] done +143: [09:33:14] ------------------------------------- +143: [09:33:14] Testing UFF builder tools. +143: [09:33:14] done +143: [09:33:14] ------------------------------------- +143: [09:33:14] Testing UFF builder+minimization. +133/238 Test #136: pyPartialCharges ....................... Passed 0.50 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-aarch64-linux-gnu/Code/GraphMol/ForceFieldHelpers/Wrap 145: Test timeout computed to be: 1500 -144: ------------------------------------- -144: Test CrystalFF torsional term. +139: ........ +139: ---------------------------------------------------------------------- +139: Ran 8 tests in 0.055s +139: +139: OK +29: +29: Computing MMFF94 energies for /build/reproducible-path/rdkit-202503.1/Code/ForceField/MMFF/test_data/MMFF94_hypervalent.smi... 141: processing 141: launch :0 141: launch :1 -141: launch :2 -141: launch :3 -141: [00:36:22] Rep: 0 Mol:2 -141: [00:36:22] Rep: 0 Mol:0 -141: [00:36:22] Rep: 0 Mol:1 -141: [00:36:22] Rep: 0 Mol:5 -141: [00:36:22] Rep: 0 Mol:9 -141: [00:36:22] Rep: 0 Mol:3 -141: [00:36:22] Rep: 0 Mol:6 -141: [00:36:22] Rep: 0 Mol:10 -141: [00:36:22] Rep: 0 Mol:4 -141: [00:36:22] Rep: 0 Mol:13 -141: [00:36:22] Rep: 0 Mol:17 -141: [00:36:22] Rep: 0 Mol:8 -141: [00:36:22] Rep: 0 Mol:14 -141: [00:36:22] Rep: 0 Mol:7 -141: [00:36:22] Rep: 0 Mol:11 -141: [00:36:22] Rep: 0 Mol:12 -141: [00:36:22] Rep: 0 Mol:18 -141: [00:36:22] Rep: 0 Mol:16 -141: [00:36:22] Rep: 0 Mol:15 -141: [00:36:22] Rep: 0 Mol:21 -141: [00:36:22] Rep: 0 Mol:25 -141: [00:36:22] Rep: 0 Mol:22 -141: [00:36:22] Rep: 0 Mol:20 -141: [00:36:22] Rep: 0 Mol:19 -141: [00:36:22] Rep: 0 Mol:23 -141: [00:36:22] Rep: 0 Mol:27 -134/238 Test #144: testCrystalForceField .................. Passed 0.12 sec -141: [00:36:22] Rep: 0 Mol:26 -141: [00:36:22] Rep: 0 Mol:29 +134/238 Test #139: pyMolTransforms ........................ Passed 0.48 sec test 146 Start 146: testDistGeomHelpers 146: Test command: /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/DistGeomHelpers/testDistGeomHelpers 146: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/DistGeomHelpers 146: Test timeout computed to be: 1500 -141: [00:36:22] Rep: 0 Mol:31 -141: [00:36:22] Rep: 0 Mol:24 -141: [00:36:22] Rep: 0 Mol:28 -146: [00:36:22] ******************************************************** -146: [00:36:22] Testing DistGeomHelpers -146: [00:36:22] --------------------------------- -146: [00:36:22] test2 +141: launch :[09:33:14] Rep: [09:33:14] Rep: 0 Mol:1 +141: [09:33:14] Rep: 0 Mol:5 +141: 2 +143: [09:33:14] done +143: [09:33:14] ------------------------------------- +143: [09:33:14] Testing UFF special cases. +143: [09:33:14] UFFTYPER: Unrecognized charge state for atom: 0 +143: [09:33:14] done +143: [09:33:14] ------------------------------------- +143: [09:33:14] Testing Issue239. +141: launch :3 +141: [09:33:14] Rep: 0 Mol:3 +141: [09:33:14] Rep: 0 Mol:2 +141: 0 Mol:0 +135/238 Test #144: testCrystalForceField .................. Passed 0.15 sec +test 147 + Start 147: distGeomHelpersCatch + +147: Test command: /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/DistGeomHelpers/distGeomHelpersCatch +147: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/DistGeomHelpers +147: Test timeout computed to be: 1500 +141: [09:33:14] Rep: 0 Mol:9 +141: [09:33:14] Rep: 0 Mol:13 +143: [09:33:14] done +143: [09:33:14] ------------------------------------- +143: [09:33:14] Testing calcEnergy with passed coords. +141: [09:33:14] Rep: 0 Mol:4 +141: [09:33:14] Rep: 0 Mol:17 +143: [09:33:14] done +143: [09:33:14] ------------------------------------- +143: [09:33:14] Testing calcGrad. +141: [09:33:14] Rep: 0 Mol:6 +141: [09:33:14] Rep: 0 Mol:8 +141: [09:33:14] Rep: 0 Mol:10 +143: [09:33:14] done +143: [09:33:14] ------------------------------------- +143: [09:33:14] Testing SFIssue1653802. +143: [09:33:14] done +143: [09:33:14] ------------------------------------- +143: [09:33:14] Testing SFIssue2378119. +143: [09:33:14] done +143: [09:33:14] ------------------------------------- +143: [09:33:14] Test UFF force-field parameter getters. +143: [09:33:14] ------------------------------------- +143: [09:33:14] Testing handling missing parameters. +143: [09:33:14] UFFTYPER: Unrecognized hybridization for atom: 0 +143: [09:33:14] UFFTYPER: Unrecognized atom type: Cu+1 (0) +143: [09:33:14] UFFTYPER: Unrecognized hybridization for atom: 0 +143: [09:33:14] UFFTYPER: Unrecognized atom type: Cu+1 (0) +147: Randomness seeded to: 1130210512 +141: [09:33:14] Rep: 0 Mol:7[09:33:14] Rep: 0 Mol:21 +146: [09:33:14] ******************************************************** +146: [09:33:14] Testing DistGeomHelpers +146: [09:33:14] --------------------------------- +146: [09:33:14] test2 146: 146: go -141: [00:36:22] Rep: 0 Mol:30 +141: +141: [09:33:14] Rep: 0 Mol:12 +141: [09:33:14] Rep: 0 Mol:11 +141: [09:33:14] Rep: 0 Mol:16 +141: [09:33:14] Rep: 0 Mol:15 +141: [09:33:14] Rep: 0 Mol:25 +143: [09:33:14] done +143: [09:33:14] ------------------------------------- +143: [09:33:14] Testing SFIssue3009337. +143: [09:33:14] done 146: ------------------------------------- 146: +143: [09:33:14] ------------------------------------- +143: [09:33:14] Test UFF multithreading +141: [09:33:14] Rep: 0 Mol:19 +141: [09:33:14] Rep: 0 Mol:23 +141: [09:33:14] Rep: 0 Mol:27 +141: [09:33:14] Rep: 0 Mol:31 +141: [09:33:14] Rep: 0 Mol:14 +141: [09:33:14] Rep: 0 Mol:29 +143: generating reference data +141: [09:33:14] Rep: 0 Mol:20 +147: [09:33:14] [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)] +141: [09:33:14] Rep: 0 Mol:18 +147: [09:33:14] [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)] +141: [09:33:14] Rep: 0 Mol:24 +147: [09:33:14] [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: [09:33:14] [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: [09:33:14] [!#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: [09:33:14] [!#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: [09:33:14] [!#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: [09:33:14] [!#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: [09:33:14] [!#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: [09:33:14] [!#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: [09:33:14] [!#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: [09:33:14] [!#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: [09:33:14] [!#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: [09:33:14] [!#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: [09:33:14] [!#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: [09:33:14] [!#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: [09:33:14] [!#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: [09:33:14] [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)] +141: [09:33:14] Rep: 0 Mol:28 +147: [09:33:14] [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: [09:33:14] [*:1][X3,X2:2]=[X3,X2:3][*:4]: 101 102 104 220, [(1 0), (-1 100), (1 0), (1 0), (1 0), (1 0)] +141: [09:33:14] Rep: 0 Mol:22 +147: [09:33:14] [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: [09:33:14] [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: [09:33:14] [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: [09:33:14] [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: [09:33:14] [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: [09:33:14] [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: [09:33:14] [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: [09:33:14] [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: [09:33:14] [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: [09:33:14] [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: [09:33:14] [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: [09:33:14] [$([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: [09:33:14] [$(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: [09:33:14] [$(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: [09:33:14] [$(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: [09:33:14] [$(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: [09:33:14] [$(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: [09:33:14] [$(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: [09:33:14] [$(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: [09:33:14] [$(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: [09:33:14] [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: [09:33:14] [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: [09:33:14] [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: [09:33:14] [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: [09:33:14] [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)] +141: [09:33:14] Rep: 0 Mol:26 +147: [09:33:14] 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: [09:33:14] [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: [09:33:14] [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: [09:33:14] [!#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: [09:33:14] [!#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: [09:33:14] [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: [09:33:14] [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: [09:33:14] [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: [09:33:14] [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: [09:33:14] [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: [09:33:14] [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: [09:33:14] [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: [09:33:14] [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: [09:33:14] [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: [09:33:14] [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: [09:33:14] [$([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: [09:33:14] [$([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: [09:33:14] [$(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: [09:33:14] [$(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: [09:33:14] [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: [09:33:14] [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: [09:33:14] 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: [09:33:14] 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: [09:33:14] [!#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: [09:33:14] [!#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: [09:33:14] [!#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)] +141: [09:33:14] Rep: 0 Mol:30 +147: [09:33:14] [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: [09:33:14] [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: ----------- +147: [09:33:14] [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: [09:33:14] [$([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: [09:33:14] [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: [09:33:14] 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: ----------- +147: ----------- +147: [09:33:14] [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: [09:33:14] [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: [09:33:14] [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: [09:33:14] [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: [09:33:14] [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: [09:33:14] [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: [09:33:14] [$(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: [09:33:14] [$(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: [09:33:14] [$(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: [09:33:14] [$(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: [09:33:14] [$(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: [09:33:14] [$(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: [09:33:14] [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: [09:33:14] [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: [09:33:14] [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: [09:33:14] [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: [09:33:14] [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: [09:33:14] [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)] +141: [09:33:14] Rep: 20 Mol:3 +141: [09:33:14] Rep: 20 Mol:7 +141: [09:33:14] Rep: 20 Mol:11 +141: [09:33:14] Rep: 20 Mol:15 +141: [09:33:14] Rep: 20 Mol:19 +141: [09:33:14] Rep: 20 Mol:23 +141: [09:33:14] Rep: 20 Mol:27 +141: [09:33:14] Rep: 20 Mol:31 +145: [09:33:14] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +145: [09:33:14] Molecule does not have explicit Hs. Consider calling AddHs() +145: [09:33:14] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +145: [09:33:14] Molecule does not have explicit Hs. Consider calling AddHs() +145: [09:33:14] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +145: [09:33:14] Molecule does not have explicit Hs. Consider calling AddHs() +145: [09:33:14] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +145: [09:33:14] Molecule does not have explicit Hs. Consider calling AddHs() +145: [09:33:14] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +145: [09:33:14] Molecule does not have explicit Hs. Consider calling AddHs() +145: ..[09:33:14] Molecule does not have explicit Hs. Consider calling AddHs() +145: [09:33:14] Molecule does not have explicit Hs. Consider calling AddHs() +145: .[09:33:14] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +145: [09:33:14] Molecule does not have explicit Hs. Consider calling AddHs() +141: [09:33:14] Rep: 20 Mol:1 +141: [09:33:14] Rep: 20 Mol:5 +145: .[09:33:14] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +141: [09:33:14] Rep: 20 Mol:9 +145: [09:33:14] Molecule does not have explicit Hs. Consider calling AddHs() +141: [09:33:14] Rep: 20 Mol:13 +141: [09:33:14] Rep: 20 Mol:17 +141: [09:33:14] Rep: 20 Mol:21 +141: [09:33:14] Rep: 20 Mol:25 +141: [09:33:14] Rep: 20 Mol:29 +147: [09:33:14] UFFTYPER: Unrecognized atom type: Pt5+2 (1) +147: [09:33:14] UFFTYPER: Unrecognized charge state for atom: 1 +141: [09:33:14] Rep: 20 Mol:0 +147: [09:33:14] UFFTYPER: Unrecognized charge state for atom: 1 +141: [09:33:14] Rep: 20 Mol:4 +141: [09:33:14] Rep: 20 Mol:8 +141: [09:33:14] Rep: 20 Mol:12 +141: [09:33:14] Rep: 20 Mol:16 +141: [09:33:14] Rep: 20 Mol:20 +141: [09:33:14] Rep: 20 Mol:24 +141: [09:33:14] Rep: 20 Mol:28 +145: .[09:33:14] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +145: [09:33:14] Molecule does not have explicit Hs. Consider calling AddHs() +147: [09:33:14] UFFTYPER: Unrecognized charge state for atom: 1 +145: .[09:33:14] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +145: [09:33:14] Molecule does not have explicit Hs. Consider calling AddHs() +141: [09:33:14] Rep: 40 Mol:3 +141: [09:33:14] Rep: 40 Mol:7 +141: [09:33:14] Rep: 40 Mol:11 +141: [09:33:14] Rep: 40 Mol:15 +141: [09:33:14] Rep: 40 Mol:19 +141: [09:33:14] Rep: 40 Mol:23 +145: .[09:33:14] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +145: [09:33:14] Molecule does not have explicit Hs. Consider calling AddHs() +141: [09:33:14] Rep: 40 Mol:27 +145: .[09:33:14] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +145: [09:33:14] Molecule does not have explicit Hs. Consider calling AddHs() +141: [09:33:14] Rep: 40 Mol:31 +145: .[09:33:14] UFFTYPER: Unrecognized hybridization for atom: 0 +145: [09:33:14] UFFTYPER: Unrecognized atom type: Cu+1 (0) +145: .[09:33:14] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +145: [09:33:14] Molecule does not have explicit Hs. Consider calling AddHs() +145: [09:33:14] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +145: [09:33:14] Molecule does not have explicit Hs. Consider calling AddHs() +145: [09:33:14] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +145: [09:33:14] Molecule does not have explicit Hs. Consider calling AddHs() +145: [09:33:14] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +145: [09:33:14] Molecule does not have explicit Hs. Consider calling AddHs() +145: [09:33:14] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +145: [09:33:14] Molecule does not have explicit Hs. Consider calling AddHs() +145: .[09:33:14] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +145: [09:33:14] Molecule does not have explicit Hs. Consider calling AddHs() +145: .[09:33:14] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +145: [09:33:14] Molecule does not have explicit Hs. Consider calling AddHs() +145: .[09:33:14] Molecule does not have explicit Hs. Consider calling AddHs() +145: [09:33:14] Molecule does not have explicit Hs. Consider calling AddHs() +145: ...[09:33:14] Molecule does not have explicit Hs. Consider calling AddHs() +145: [09:33:14] Molecule does not have explicit Hs. Consider calling AddHs() +141: [09:33:14] Rep: 20 Mol:2 +141: [09:33:14] Rep: 20 Mol:6 +141: [09:33:14] Rep: 20 Mol:10 +141: [09:33:14] Rep: 20 Mol:14 +141: [09:33:14] Rep: 20 Mol:18 +141: [09:33:14] Rep: 20 Mol:22 +141: [09:33:14] Rep: 20 Mol:26 +141: [09:33:14] Rep: 20 Mol:30 +145: [09:33:14] Molecule does not have explicit Hs. Consider calling AddHs() 143: processing 143: launch :0 +141: [09:33:14] Rep: 40 Mol:1 143: launch :1 +143: [09:33:14] Rep: 0 Mol:0 143: launch :2 -143: [00:36:22] Rep: 0 Mol: launch :3 -143: [00:36:22] Rep: 0 Mol:2 -143: [00:36:22] Rep: 0 Mol:1 -143: [00:36:22] Rep: 0 Mol:3 -143: [00:36:22] Rep: 0 Mol:5 -143: [00:36:22] Rep: 0 Mol:9 -143: [00:36:22] Rep: 0 Mol:13 -143: 0 -143: [00:36:22] Rep: 0 Mol:7 -143: [00:36:22] Rep: 0 Mol:11 -143: [00:36:22] Rep: 0 Mol:4 -143: [00:36:22] Rep: 0 Mol:15 -143: [00:36:22] Rep: 0 Mol:6 -143: [00:36:22] Rep: 0 Mol:17 -143: [00:36:22] Rep: 0 Mol:19 -143: [00:36:22] Rep: 0 Mol:10 -143: [00:36:22] Rep: 0 Mol:23 -143: [00:36:22] Rep: 0 Mol:27 -143: [00:36:22] Rep: 0 Mol:31[00:36:22] Rep: 0 Mol:21 -143: -143: [00:36:22] Rep: 0 Mol:25 -143: [00:36:22] Rep: 0 Mol:8 -143: [00:36:22] Rep: 0 Mol:29 -143: [00:36:22] Rep: 0 Mol:12 -143: [00:36:22] Rep: 0 Mol:16 -143: [00:36:22] Rep: 0 Mol:14 -143: [00:36:22] Rep: [00:36:22] Rep: 0 Mol:18 -143: 0 Mol:20 -143: [00:36:22] Rep: 0 Mol:24 -141: [00:36:22] Rep: 20 Mol:3 -143: [00:36:22] Rep: 0 Mol:28 -143: [00:36:22] Rep: 0 Mol:22 -143: [00:36:22] Rep: 0 Mol:26 -141: [00:36:22] Rep: 20 Mol:7 -141: [00:36:22] Rep: 20 Mol:11 -141: [00:36:22] Rep: 20 Mol:15 -141: [00:36:22] Rep: 20 Mol:19 -141: [00:36:22] Rep: 20 Mol:23 -141: [00:36:22] Rep: 20 Mol:27 -141: [00:36:22] Rep: 20 Mol:31 -143: [00:36:22] Rep: 0 Mol:30 -141: [00:36:22] Rep: 20 Mol:2 -141: [00:36:22] Rep: 20 Mol:6 -141: [00:36:22] Rep: 20 Mol:10 -141: [00:36:22] Rep: 20 Mol:14 -141: [00:36:22] Rep: 20 Mol:18 -141: [00:36:22] Rep: 20 Mol:22 -141: [00:36:22] Rep: 20 Mol:26 -141: [00:36:22] Rep: 20 Mol:30 -141: [00:36:22] Rep: 20 Mol:1[00:36:22] Rep: 20 Mol:0 -141: [00:36:22] Rep: 20 Mol:4 -141: [00:36:22] Rep: 20 Mol:8 -141: [00:36:22] Rep: 20 Mol:12 -141: [00:36:22] Rep: 20 Mol:16 -141: [00:36:22] Rep: 20 Mol:20 -141: [00:36:22] Rep: 20 Mol:24 -141: [00:36:22] Rep: 20 Mol:28 -141: -141: [00:36:22] Rep: 20 Mol:5 -141: [00:36:22] Rep: 20 Mol:9 -141: [00:36:22] Rep: 20 Mol:13 -141: [00:36:22] Rep: 20 Mol:17 -141: [00:36:22] Rep: 20 Mol:21 -141: [00:36:22] Rep: 20 Mol:25 -141: [00:36:22] Rep: 20 Mol:29 -145: [00:36:22] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -145: [00:36:22] Molecule does not have explicit Hs. Consider calling AddHs() -145: [00:36:22] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -145: [00:36:22] Molecule does not have explicit Hs. Consider calling AddHs() -145: [00:36:22] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -145: [00:36:22] Molecule does not have explicit Hs. Consider calling AddHs() -145: [00:36:22] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -145: [00:36:22] Molecule does not have explicit Hs. Consider calling AddHs() -145: [00:36:22] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -145: [00:36:22] Molecule does not have explicit Hs. Consider calling AddHs() -145: ..[00:36:22] Molecule does not have explicit Hs. Consider calling AddHs() -145: [00:36:22] Molecule does not have explicit Hs. Consider calling AddHs() -145: .[00:36:22] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -145: [00:36:22] 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... -145: .[00:36:22] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -145: [00:36:22] Molecule does not have explicit Hs. Consider calling AddHs() -141: [00:36:22] Rep: 40 Mol:3 -145: .[00:36:22] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -145: [00:36:22] Molecule does not have explicit Hs. Consider calling AddHs() -141: [00:36:22] Rep: 40 Mol:7 -141: [00:36:22] Rep: 40 Mol:11 -141: [00:36:22] Rep: 40 Mol:15 -141: [00:36:22] Rep: 40 Mol:19 -141: [00:36:22] Rep: 40 Mol:23 -141: [00:36:22] Rep: 40 Mol:27 -141: [00:36:22] Rep: 40 Mol:31 -145: .[00:36:23] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -145: [00:36:23] Molecule does not have explicit Hs. Consider calling AddHs() -145: .[00:36:23] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -145: [00:36:23] Molecule does not have explicit Hs. Consider calling AddHs() -145: .[00:36:23] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -145: [00:36:23] Molecule does not have explicit Hs. Consider calling AddHs() -145: .[00:36:23] UFFTYPER: Unrecognized hybridization for atom: 0 -145: [00:36:23] UFFTYPER: Unrecognized atom type: Cu+1 (0) -145: .[00:36:23] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -145: [00:36:23] Molecule does not have explicit Hs. Consider calling AddHs() -145: [00:36:23] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -145: [00:36:23] Molecule does not have explicit Hs. Consider calling AddHs() -145: [00:36:23] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -145: [00:36:23] Molecule does not have explicit Hs. Consider calling AddHs() -145: [00:36:23] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -145: [00:36:23] Molecule does not have explicit Hs. Consider calling AddHs() -145: [00:36:23] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -145: [00:36:23] Molecule does not have explicit Hs. Consider calling AddHs() -145: .[00:36:23] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -145: [00:36:23] Molecule does not have explicit Hs. Consider calling AddHs() -145: .[00:36:23] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -145: [00:36:23] Molecule does not have explicit Hs. Consider calling AddHs() -145: .[00:36:23] Molecule does not have explicit Hs. Consider calling AddHs() -145: [00:36:23] Molecule does not have explicit Hs. Consider calling AddHs() -29: All 191 tests passed -145: ...[00:36:23] Molecule does not have explicit Hs. Consider calling AddHs() -145: [00:36:23] Molecule does not have explicit Hs. Consider calling AddHs() -141: [00:36:23] Rep: 40 Mol:0 -141: [00:36:23] Rep: 40 Mol:4 -141: [00:36:23] Rep: 40 Mol:8 -141: [00:36:23] Rep: 40 Mol:12 -141: [00:36:23] Rep: 40 Mol:16 -141: [00:36:23] Rep: 40 Mol:20 -141: [00:36:23] Rep: 40 Mol:24 -141: [00:36:23] Rep: 40 Mol:28 -145: [00:36:23] Molecule does not have explicit Hs. Consider calling AddHs() -141: [00:36:23] Rep: 40 Mol:1 -141: [00:36:23] Rep: 40 Mol:5 -141: [00:36:23] Rep: 40 Mol:9 -141: [00:36:23] Rep: 40 Mol:13 -141: [00:36:23] Rep: 40 Mol:17 -141: [00:36:23] Rep: 40 Mol:21 -141: [00:36:23] Rep: 40 Mol:25 -141: [00:36:23] Rep: 40 Mol:29 -141: [00:36:23] Rep: 40 Mol:2 -141: [00:36:23] Rep: 40 Mol:6 -141: [00:36:23] Rep: 40 Mol:10 +143: launch :3 +143: [09:33:14] Rep: 0 Mol:3 +147: [09:33:14] UFFTYPER: Unrecognized charge state for atom: 5 +143: [09:33:14] Rep: [09:33:14] Rep: 0[09:33:14] Mol:4 +141: [09:33:14] Rep: 40 Mol:5 +143: Rep: 0 Mol:2 +141: [09:33:14] Rep: 40 Mol:9 +143: 0 Mol:1 +141: [09:33:14] Rep: 40 Mol:13 +141: [09:33:14] Rep: 40 Mol:17 +143: [09:33:14] Rep: 0 Mol:5 +141: [09:33:14] Rep: 40 Mol:21 +141: [09:33:14] Rep: 40 Mol:25 +141: [09:33:14] Rep: 40 Mol:29 +147: [09:33:14] UFFTYPER: Unrecognized charge state for atom: 5 +143: [09:33:14] Rep: 0 Mol:9 145: ... 145: ---------------------------------------------------------------------- -145: Ran 19 tests in 0.253s +145: Ran 19 tests in 0.176s 145: 145: OK -141: [00:36:23] Rep: 40 Mol:14 -141: [00:36:23] Rep: 40 Mol:18 -141: [00:36:23] Rep: 40 Mol:22 -141: [00:36:23] Rep: 60 Mol:3 -141: [00:36:23] Rep: 40 Mol:26 -141: [00:36:23] Rep: 60 Mol:7 -141: [00:36:23] Rep: 40 Mol:30 -141: [00:36:23] Rep: 60 Mol:11 -141: [00:36:23] Rep: 60 Mol:15 -141: [00:36:23] Rep: 60 Mol:19 -141: [00:36:23] Rep: 60 Mol:23 -141: [00:36:23] Rep: 60 Mol:27 -141: [00:36:23] Rep: 60 Mol:31 -29: -29: Computing MMFF94 energies for /build/reproducible-path/rdkit-202503.1/Code/ForceField/MMFF/test_data/MMFF94_hypervalent.smi... -143: [00:36:23] Rep: 100 Mol:3 -143: [00:36:23] Rep: 100 Mol:7 -143: [00:36:23] Rep: 100 Mol:11 -143: [00:36:23] Rep: 100 Mol:15 -143: [00:36:23] Rep: 100 Mol:19 -143: [00:36:23] Rep: 100 Mol:23 -143: [00:36:23] Rep: 100 Mol:27 -143: [00:36:23] Rep: 100 Mol:31 -135/238 Test #145: pyForceFieldHelpers .................... Passed 0.80 sec -test 147 - Start 147: distGeomHelpersCatch - -147: Test command: /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/DistGeomHelpers/distGeomHelpersCatch -147: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/DistGeomHelpers -147: Test timeout computed to be: 1500 -141: [00:36:23] Rep: 60 Mol:0 -147: Randomness seeded to: 670610737 -141: [00:36:23] Rep: 60 Mol:4 -141: [00:36:23] Rep: 60 Mol:8 -141: [00:36:23] Rep: 60 Mol:12 -141: [00:36:23] Rep: 60 Mol:16 -141: [00:36:23] Rep: 60 Mol:20 -141: [00:36:23] Rep: 60 Mol:24 -141: [00:36:23] Rep: 60 Mol:28 -141: [00:36:23] Rep: 80 Mol:3 -141: [00:36:23] Rep: 80 Mol:7 -141: [00:36:23] Rep: 80 Mol:11 -141: [00:36:23] Rep: 80 Mol:15 -141: [00:36:23] Rep: 80 Mol:19 -141: [00:36:23] Rep: 80 Mol:23 -141: [00:36:23] Rep: 80 Mol:27 -141: [00:36:23] Rep: 80 Mol:31 -141: [00:36:23] Rep: 60 Mol:1 -141: [00:36:23] Rep: 60 Mol:5 -141: [00:36:23] Rep: 60 Mol:9 -141: [00:36:23] Rep: 60 Mol:13 -141: [00:36:23] Rep: 60 Mol:17 -141: [00:36:23] Rep: 60 Mol:21 -141: [00:36:23] Rep: 60 Mol:25 -141: [00:36:23] Rep: 60 Mol:29 -143: [00:36:23] Rep: 100 Mol:1 -143: [00:36:23] Rep: 100 Mol:5 -143: [00:36:23] Rep: 100 Mol:9 -143: [00:36:23] Rep: 100 Mol:13 -143: [00:36:23] Rep: 100 Mol:17 -143: [00:36:23] Rep: 100 Mol:21 -143: [00:36:23] Rep: 100 Mol:25 -143: [00:36:23] Rep: 100 Mol:29 -147: [00:36:23] [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: [00:36:23] [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: [00:36:23] [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: [00:36:23] [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: [00:36:23] [!#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: [00:36:23] [!#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: [00:36:23] [!#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: [00:36:23] [!#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: [00:36:23] [!#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: [00:36:23] [!#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: [00:36:23] [!#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: [00:36:23] [!#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: [00:36:23] [!#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: [00:36:23] [!#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: [00:36:23] [!#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: [00:36:23] [!#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: [00:36:23] [!#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: [00:36:23] [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: [00:36:23] [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: [00:36:23] [*: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: [00:36:23] [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: [00:36:23] [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: [00:36:23] [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: [00:36:23] [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: [00:36:23] [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: [00:36:23] [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: [00:36:23] [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: [00:36:23] [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: [00:36:23] [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: [00:36:23] [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: [00:36:23] [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: [00:36:23] [$([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: [00:36:23] [$(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: [00:36:23] [$(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: [00:36:23] [$(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: [00:36:23] [$(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: [00:36:23] [$(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: [00:36:23] [$(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: [00:36:23] [$(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: [00:36:23] [$(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: [00:36:23] [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: [00:36:23] [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: [00:36:23] [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: [00:36:23] [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: [00:36:23] [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: [00:36:23] 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: [00:36:23] [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: [00:36:23] [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: [00:36:23] [!#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: [00:36:23] [!#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: [00:36:23] [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: [00:36:23] [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: [00:36:23] [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: [00:36:23] [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: [00:36:23] [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: [00:36:23] [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: [00:36:23] [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: [00:36:23] [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: [00:36:23] [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: [00:36:23] [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: [00:36:23] [$([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: [00:36:23] [$([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: [00:36:23] [$(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: [00:36:23] [$(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: [00:36:23] [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: [00:36:23] [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: [00:36:23] 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: [00:36:23] 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: [00:36:23] [!#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: [00:36:23] [!#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: [00:36:23] [!#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: [00:36:23] [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: [00:36:23] [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: ----------- -147: [00:36:23] [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: [00:36:23] [$([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)] -141: [00:36:23] Rep: 60 Mol:2 -147: [00:36:23] [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)] -141: [00:36:23] Rep: 60 Mol:6 -147: [00:36:23] 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)] -141: [00:36:23] Rep: 60 Mol:10 -141: [00:36:23] Rep: 60 Mol:14 -141: [00:36:23] Rep: 60 Mol:18 -141: [00:36:23] Rep: 60 Mol:22 -147: ----------- -141: [00:36:23] Rep: 60 Mol:26 -141: [00:36:23] Rep: 60 Mol:30 -147: ----------- -147: [00:36:23] [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: [00:36:23] [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: [00:36:23] [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: [00:36:23] [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: [00:36:23] [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: [00:36:23] [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: [00:36:23] [$(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: [00:36:23] [$(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: [00:36:23] [$(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: [00:36:23] [$(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: [00:36:23] [$(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: [00:36:23] [$(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: [00:36:23] [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: [00:36:23] [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: [00:36:23] [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: [00:36:23] [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: [00:36:23] [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: [00:36:23] [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)] -141: [00:36:23] Rep: 80 Mol:0 -141: [00:36:23] Rep: 80 Mol:4 -141: [00:36:23] Rep: 80 Mol:8 -141: [00:36:23] Rep: 80 Mol:12 -141: [00:36:23] Rep: 80 Mol:16 -141: [00:36:23] Rep: 80 Mol:20 -141: [00:36:23] Rep: 80 Mol:24 -141: [00:36:23] Rep: 80 Mol:28 -143: [00:36:23] Rep: 100 Mol:0 -143: [00:36:23] Rep: 100 Mol:4 -143: [00:36:23] Rep: 100 Mol:8 -143: [00:36:23] Rep: 100 Mol:12 -143: [00:36:23] Rep: 100 Mol:16 -143: [00:36:23] Rep: 100 Mol:20 -143: [00:36:23] Rep: 100 Mol:24 -143: [00:36:23] Rep: 100 Mol:28 -141: [00:36:23] Rep: 80 Mol:2 -141: [00:36:23] Rep: 80 Mol:6 -141: [00:36:23] Rep: 80 Mol:10 -141: [00:36:23] Rep: 80 Mol:14 -141: [00:36:23] Rep: 80 Mol:18 -141: [00:36:23] Rep: 80 Mol:22 -141: [00:36:23] Rep: 80 Mol:26 -141: [00:36:23] Rep: 80 Mol:30 -141: [00:36:23] Rep: 80 Mol:1 -147: [00:36:23] UFFTYPER: Unrecognized atom type: Pt5+2 (1) -141: [00:36:23] Rep: 80 Mol:5 -141: [00:36:23] Rep: 80 Mol:9 -141: [00:36:23] Rep: 80 Mol:13 -141: [00:36:23] Rep: 80 Mol:17 -141: [00:36:23] Rep: 80 Mol:21 -141: [00:36:23] Rep: 80 Mol:25 -141: [00:36:23] Rep: 80 Mol:29 -147: [00:36:23] UFFTYPER: Unrecognized charge state for atom: 1 -147: [00:36:23] UFFTYPER: Unrecognized charge state for atom: 1 -147: [00:36:23] UFFTYPER: Unrecognized charge state for atom: 1 -143: [00:36:23] Rep: 100 Mol:2 -143: [00:36:23] Rep: 100 Mol:6 -143: [00:36:23] Rep: 100 Mol:10 -143: [00:36:23] Rep: 100 Mol:14 -143: [00:36:23] Rep: 100 Mol:18 -143: [00:36:23] Rep: 100 Mol:22 -143: [00:36:23] Rep: 100 Mol:26 -143: [00:36:23] Rep: 100 Mol:30 -147: [00:36:23] UFFTYPER: Unrecognized charge state for atom: 5 -147: [00:36:23] UFFTYPER: Unrecognized charge state for atom: 5 -147: [00:36:23] UFFTYPER: Unrecognized charge state for atom: 5 -141: [00:36:23] done -141: [00:36:23] ------------------------------------- -141: [00:36:23] Test MMFF multithreading2 -147: [00:36:23] UFFTYPER: Unrecognized charge state for atom: 6 -147: [00:36:23] UFFTYPER: Unrecognized charge state for atom: 6 -147: [00:36:23] UFFTYPER: Unrecognized charge state for atom: 6 -80: =============================================================================== -80: All tests passed (1596 assertions in 100 test cases) -80: -136/238 Test #80: fileParsersCatchTest ................... Passed 9.43 sec +143: [09:33:14] Rep: 0 Mol:13 +143: [09:33:14] Rep: 0 Mol:7 +143: [09:33:14] Rep: 0 Mol:11 +143: [09:33:14] Rep: 0 Mol:15 +147: [09:33:14] UFFTYPER: Unrecognized charge state for atom: 5 +143: [09:33:14] Rep: 0 Mol:6 +143: [09:33:14] Rep: 0 Mol:8 +143: [09:33:14] Rep: 0 Mol:10 +143: [09:33:14] Rep: 0 Mol:17 +143: [09:33:14] Rep: 0 Mol:19 +143: [09:33:14] Rep: 0 Mol:12 +143: [09:33:14] Rep: 0 Mol:16 +143: [09:33:14] Rep: 0 Mol:23 +143: [09:33:14] Rep: 0 Mol:27 +141: [09:33:14] Rep: 60 Mol:3 +143: [09:33:14] Rep: 0 Mol:31 +141: [09:33:14] Rep: 60 Mol:7 +143: [09:33:14] Rep: 0 Mol:20 +141: [09:33:14] Rep: 60 Mol:11 +141: [09:33:14] Rep: 60 Mol:15 +143: [09:33:14] Rep: 0 Mol:21 +141: [09:33:14] Rep: 60 Mol:19 +143: [09:33:14] Rep: 0 Mol:14 +141: [09:33:14] Rep: 60 Mol:23 +141: [09:33:14] Rep: 60 Mol:27 +141: [09:33:14] Rep: 60 Mol:31 +143: [09:33:14] Rep: 0 Mol:25 +143: [09:33:14] Rep: 0 Mol:24 +143: [09:33:14] Rep: 0 Mol:28 +141: [09:33:14] Rep: 40 Mol:0 +141: [09:33:14] Rep: 40 Mol:4 +141: [09:33:14] Rep: 40 Mol:8 +141: [09:33:14] Rep: 40 Mol:12 +143: [09:33:14] Rep: [09:33:14] Rep: 0 Mol:18 +143: 0 Mol:29 +141: [09:33:14] Rep: 40 Mol:16 +141: [09:33:14] Rep: 40 Mol:20 +141: [09:33:14] Rep: 40 Mol:24 +141: [09:33:14] Rep: 40 Mol:28 +143: [09:33:14] Rep: 0 Mol:22 +143: [09:33:14] Rep: 0 Mol:26 +143: [09:33:14] Rep: 0 Mol:30 +147: [09:33:14] UFFTYPER: Unrecognized charge state for atom: 6 +147: [09:33:14] UFFTYPER: Unrecognized charge state for atom: 6 +136/238 Test #145: pyForceFieldHelpers .................... Passed 0.57 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-aarch64-linux-gnu/Code/GraphMol/DistGeomHelpers/Wrap 148: Test timeout computed to be: 1500 -141: [00:36:24] done -141: [00:36:24] ------------------------------------- -141: [00:36:24] Test MMFF multithreading3 -146: [00:36:22] --------------------------------- -146: [00:36:22] test3 -146: -146: [00:36:22] --------------------------------- -146: [00:36:22] test4 -146: -146: [00:36:22] --------------------------------- -146: [00:36:22] test5 -146: -146: [00:36:24] --------------------------------- -146: [00:36:24] test6 -146: -146: [00:36:24] --------------------------------- -146: [00:36:24] test15Dists -146: -146: [00:36:24] --------------------------------- -146: [00:36:24] test Issue 215 -146: -146: [00:36:24] --------------------------------- -146: [00:36:24] testMultipleConfs -146: -146: [00:36:24] --------------------------------- -146: [00:36:24] testMultipleConfsExpTors -146: -146: [00:36:24] --------------------------------- -146: [00:36:24] testIssue227 -146: -146: [00:36:24] --------------------------------- -146: [00:36:24] testIssue236 -146: -146: [00:36:24] --------------------------------- -146: [00:36:24] testOrdering -146: -146: [00:36:24] --------------------------------- -146: [00:36:24] testIssue244 -146: -146: [00:36:24] --------------------------------- -146: [00:36:24] testIssue251 -146: -146: [00:36:24] --------------------------------- -146: [00:36:24] testIssue276 -146: [00:36:24] --------------------------------- -146: [00:36:24] testIssue284 -146: -146: [00:36:24] --------------------------------- -146: [00:36:24] testIssue285 -146: -146: [00:36:24] --------------------------------- -146: [00:36:24] testIssue355 -146: -146: [00:36:24] --------------------------------- -146: [00:36:24] testRandomCoords -146: -146: [00:36:24] --------------------------------- -146: [00:36:24] test sf.net issue 1989539 -146: -146: [00:36:24] --------------------------------- -146: [00:36:24] test sf.net issue 2091864 -146: -146: [00:36:24] --------------------------------- -146: [00:36:24] test constrained embedding -146: -146: [00:36:24] ssd: 0.0752641 -146: [00:36:24] ssd: 0.0659363 -128: [00:36:24] done -128: [00:36:24] ------------------------------------- -128: [00:36:24] Test GitHub Issue 258: Bad pattern fingerprint for query molecule -128: [00:36:24] done -128: [00:36:24] ------------------------------------- -128: [00:36:24] Test GitHub Issue 334: explicit Hs in SMILES modifies atom pair (and topological torsion) FP. -128: [00:36:24] DEPRECATION WARNING: please use AtomPairGenerator -128: [00:36:24] DEPRECATION WARNING: please use AtomPairGenerator -128: [00:36:24] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [00:36:24] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [00:36:24] done -128: [00:36:24] ------------------------------------- -128: [00:36:24] Test GitHub Issue 695: Include cis/trans stereochemistry when useChirality=true with the morgan fingerprints -128: [00:36:24] done -128: [00:36:24] ------------------------------------- -128: [00:36:24] Test GitHub Issue 811: rooted atom fingerprint non identical for the same molecules #811 -128: [00:36:24] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [00:36:24] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [00:36:24] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [00:36:24] done -128: [00:36:24] ------------------------------------- -128: [00:36:24] Test unfolded version of RDKFP -128: [00:36:24] ------------------------------------- -128: [00:36:24] Test bitinfo of RDKFP +147: [09:33:14] UFFTYPER: Unrecognized charge state for atom: 6 +141: [09:33:14] Rep: 40 Mol:2 +141: [09:33:14] Rep: 80 Mol:3 +141: [09:33:14] Rep: 40 Mol:6 +141: [09:33:14] Rep: 80 Mol:7 +141: [09:33:14] Rep: 60 Mol:1 +141: [09:33:14] Rep: 40 Mol:10 +141: [09:33:14] Rep: 60 Mol:5 +141: [09:33:14] Rep: 80[09:33:14] Rep: 60 Mol:9 +141: Mol:11 +141: [09:33:14] Rep: 40 Mol:14 +141: [09:33:14] Rep: 60 Mol:13 +141: [09:33:14] [09:33:14] Rep: 80 Mol:15 +141: [09:33:14] Rep: 80 Mol:19 +141: [09:33:14] Rep: 80 Mol:23 +141: [09:33:14] Rep: Rep: 40 Mol:1860[09:33:14] +141: Rep: 80 Mol:27 +141: Mol:17 +141: [09:33:14] Rep: 40 Mol:22 +141: [09:33:14] Rep: 80 Mol:31 +141: [09:33:14] Rep: 60 Mol:21 +141: [09:33:14] Rep: 40 Mol:26 +141: [09:33:14] Rep: 60 Mol:25 +141: [09:33:14] Rep: 40 Mol:30 +141: [09:33:14] Rep: 60 Mol:29 +141: [09:33:14] Rep: 60 Mol:0 +141: [09:33:14] Rep: 60 Mol:4 +141: [09:33:14] Rep: 60 Mol:8 +141: [09:33:14] Rep: 60 Mol:12 +141: [09:33:14] Rep: 60 Mol:16 +141: [09:33:14] Rep: 60 Mol:20 +141: [09:33:14] Rep: 60 Mol:24 +141: [09:33:14] Rep: 60 Mol:28 +141: [09:33:14] Rep: 80 Mol:1 +141: [09:33:14] Rep: 80 Mol:5 +141: [09:33:14] Rep: 80 Mol:9 +141: [09:33:14] Rep: 80 Mol:13 +141: [09:33:14] Rep: 80 Mol:17 +141: [09:33:14] Rep: 80 Mol:21 +141: [09:33:14] Rep: 80 Mol:25 +141: [09:33:14] Rep: 80 Mol:29 +141: [09:33:14] Rep: 60 Mol:2 +141: [09:33:14] Rep: 60 Mol:6 +141: [09:33:14] Rep: 60 Mol:10 +141: [09:33:14] Rep: 60 Mol:14 +141: [09:33:14] Rep: 60 Mol:18 +141: [09:33:14] Rep: 60 Mol:22 +141: [09:33:14] Rep: 60 Mol:26 +141: [09:33:14] Rep: 60 Mol:30 +141: [09:33:14] Rep: 80 Mol:0 +141: [09:33:14] Rep: 80 Mol:4 +141: [09:33:14] Rep: 80 Mol:8 +141: [09:33:14] Rep: 80 Mol:12 +141: [09:33:14] Rep: 80 Mol:16 +141: [09:33:14] Rep: 80 Mol:20 +141: [09:33:14] Rep: 80 Mol:24 +141: [09:33:14] Rep: 80 Mol:28 +143: [09:33:14] Rep: 100 Mol:3 +143: [09:33:14] Rep: 100 Mol:7 +143: [09:33:14] Rep: 100 Mol:11 +143: [09:33:14] Rep: 100 Mol:15 +143: [09:33:14] Rep: 100 Mol:19 +143: [09:33:14] Rep: 100 Mol:23 +143: [09:33:14] Rep: 100 Mol:27 +143: [09:33:14] Rep: 100 Mol:31 +128: [09:33:14] done +128: [09:33:14] ------------------------------------- +128: [09:33:14] Test GitHub Issue 258: Bad pattern fingerprint for query molecule +128: [09:33:14] done +128: [09:33:14] ------------------------------------- +128: [09:33:14] Test GitHub Issue 334: explicit Hs in SMILES modifies atom pair (and topological torsion) FP. +128: [09:33:14] DEPRECATION WARNING: please use AtomPairGenerator +128: [09:33:14] DEPRECATION WARNING: please use AtomPairGenerator +128: [09:33:14] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [09:33:14] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [09:33:14] done +128: [09:33:14] ------------------------------------- +128: [09:33:14] Test GitHub Issue 695: Include cis/trans stereochemistry when useChirality=true with the morgan fingerprints +128: [09:33:14] done +128: [09:33:14] ------------------------------------- +128: [09:33:14] Test GitHub Issue 811: rooted atom fingerprint non identical for the same molecules #811 +128: [09:33:14] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [09:33:14] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [09:33:14] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [09:33:14] done +128: [09:33:14] ------------------------------------- +128: [09:33:14] Test unfolded version of RDKFP +128: [09:33:14] ------------------------------------- +128: [09:33:14] Test bitinfo of RDKFP 128: 562: [ 2 ], 128: 709: [ 0 1 ], 128: 1118: [ 0 1 2 ], @@ -27039,86 +26968,126 @@ 128: 1772: [ 0 ], [ 1 ], 128: 1813: [ 0 1 ], 128: ------------ -128: [00:36:24] ------------------------------------- -128: [00:36:24] Single atoms setting radius 1 bits in Morgan fingerprints -128: [00:36:24] done -128: [00:36:24] ------------------------------------- -128: [00:36:24] Github #879: Pattern fingerprint should set bits for single-atom fragments. -128: [00:36:24] done -128: [00:36:24] ------------------------------------- -128: [00:36:24] Github #1496: Pattern fingerprint setting bad bits for degree zero atoms -128: [00:36:24] done -128: [00:36:24] ------------------------------------- -128: [00:36:24] Github #1793: Fingerprint segfaults with branchedPaths=False and useHs=False -128: [00:36:24] done -128: [00:36:24] ------------------------------------- -128: [00:36:24] Github #1993: fingerprinters that use R/S labels should force a call to assignStereochemistry() if it hasn't already been called -128: [00:36:24] DEPRECATION WARNING: please use AtomPairGenerator -128: [00:36:24] DEPRECATION WARNING: please use AtomPairGenerator -128: [00:36:24] DEPRECATION WARNING: please use AtomPairGenerator -128: [00:36:24] DEPRECATION WARNING: please use AtomPairGenerator -128: [00:36:24] DEPRECATION WARNING: please use AtomPairGenerator -128: [00:36:24] DEPRECATION WARNING: please use AtomPairGenerator -128: [00:36:24] DEPRECATION WARNING: please use AtomPairGenerator -128: [00:36:24] DEPRECATION WARNING: please use AtomPairGenerator -128: [00:36:24] DEPRECATION WARNING: please use AtomPairGenerator -128: [00:36:24] DEPRECATION WARNING: please use AtomPairGenerator -128: [00:36:24] DEPRECATION WARNING: please use AtomPairGenerator -128: [00:36:24] DEPRECATION WARNING: please use AtomPairGenerator -128: [00:36:24] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [00:36:24] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [00:36:24] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [00:36:24] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [00:36:24] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [00:36:24] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [00:36:24] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [00:36:24] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [00:36:24] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [00:36:24] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [00:36:24] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [00:36:24] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [00:36:24] done -128: [00:36:24] ------------------------------------- -128: [00:36:24] Github #2115: BitInfo not complete for RDKFingerprint -128: [00:36:24] done -128: [00:36:24] ------------------------------------- -128: [00:36:24] Github #3723: Fingerprint crash for mols with Zero order bonds -128: [00:36:24] done -137/238 Test #128: testFingerprints ....................... Passed 4.01 sec +128: [09:33:14] ------------------------------------- +128: [09:33:14] Single atoms setting radius 1 bits in Morgan fingerprints +128: [09:33:14] done +128: [09:33:14] ------------------------------------- +128: [09:33:14] Github #879: Pattern fingerprint should set bits for single-atom fragments. +128: [09:33:14] done +128: [09:33:14] ------------------------------------- +128: [09:33:14] Github #1496: Pattern fingerprint setting bad bits for degree zero atoms +128: [09:33:14] done +128: [09:33:14] ------------------------------------- +128: [09:33:14] Github #1793: Fingerprint segfaults with branchedPaths=False and useHs=False +128: [09:33:14] done +128: [09:33:14] ------------------------------------- +128: [09:33:14] Github #1993: fingerprinters that use R/S labels should force a call to assignStereochemistry() if it hasn't already been called +128: [09:33:14] DEPRECATION WARNING: please use AtomPairGenerator +128: [09:33:14] DEPRECATION WARNING: please use AtomPairGenerator +128: [09:33:14] DEPRECATION WARNING: please use AtomPairGenerator +128: [09:33:14] DEPRECATION WARNING: please use AtomPairGenerator +128: [09:33:14] DEPRECATION WARNING: please use AtomPairGenerator +128: [09:33:14] DEPRECATION WARNING: please use AtomPairGenerator +128: [09:33:14] DEPRECATION WARNING: please use AtomPairGenerator +128: [09:33:14] DEPRECATION WARNING: please use AtomPairGenerator +128: [09:33:14] DEPRECATION WARNING: please use AtomPairGenerator +128: [09:33:14] DEPRECATION WARNING: please use AtomPairGenerator +128: [09:33:14] DEPRECATION WARNING: please use AtomPairGenerator +128: [09:33:14] DEPRECATION WARNING: please use AtomPairGenerator +128: [09:33:14] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [09:33:14] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [09:33:14] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [09:33:14] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [09:33:14] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [09:33:14] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [09:33:14] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [09:33:14] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [09:33:14] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [09:33:14] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [09:33:14] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [09:33:14] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [09:33:14] done +128: [09:33:14] ------------------------------------- +128: [09:33:14] Github #2115: BitInfo not complete for RDKFingerprint +128: [09:33:14] done +128: [09:33:14] ------------------------------------- +128: [09:33:14] Github #3723: Fingerprint crash for mols with Zero order bonds +128: [09:33:14] done +137/238 Test #128: testFingerprints ....................... Passed 2.62 sec test 149 Start 149: testMolAlign 149: Test command: /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/MolAlign/testMolAlign 149: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/MolAlign 149: Test timeout computed to be: 1500 -143: [00:36:24] done -143: [00:36:24] ------------------------------------- -143: [00:36:24] Test UFF multithreading2 -146: [00:36:24] --------------------------------- -146: [00:36:24] test sf.net issue 2091974 -146: -146: [00:36:24] --------------------------------- -146: [00:36:24] test sf.net issue 2835784 -146: -146: [00:36:24] --------------------------------- -146: [00:36:24] test sf.net issue 3019283 -146: -146: [00:36:24] --------------------------------- -146: [00:36:24] test sf.net issue 3238580 -146: -146: [00:36:24] --------------------------------- -146: [00:36:24] test sf.net issue 3483968 -146: -146: [00:36:24] --------------------------------- -146: [00:36:24] test github issue 55 -146: -146: [00:36:24] --------------------------------- -146: [00:36:24] test1 -146: -146: [00:36:24] --------------------------------- -146: [00:36:24] test multi-threading -146: -146: building molecules +143: [09:33:14] Rep: 100 Mol:0 +143: [09:33:15] Rep: 100 Mol:4 +141: [09:33:15] Rep: 80 Mol:2 +143: [09:33:15] Rep: 100 Mol:8 +141: [09:33:15] Rep: 80 Mol:6 +143: [09:33:15] Rep: 100 Mol:12 +95: 0,0 0 +95: 0,1 0 +95: 1,0 0 +95: 1,1 0 +143: [09:33:15] Rep: 100 Mol:16 +141: [09:33:15] Rep: 80 Mol:10 +95: 2,0 0 +95: 2,1 0 +143: [09:33:15] Rep: 100 Mol:20 +141: [09:33:15] Rep: 80 Mol:14 +143: [09:33:15] Rep: 100 Mol:24 +141: [09:33:15] Rep: 80 Mol:18 +141: [09:33:15] Rep: 80 Mol:22 +141: [09:33:15] Rep: 80 Mol:26 +141: [09:33:15] Rep: 80 Mol:30 +143: [09:33:15] Rep: 100 Mol:28 +138/238 Test #95: testEnumeration ........................ Passed 5.45 sec +test 150 + Start 150: testO3AAlign + +150: Test command: /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/MolAlign/testO3AAlign +150: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/MolAlign +150: Test timeout computed to be: 1500 +148: .[09:33:15] Molecule does not have explicit Hs. Consider calling AddHs() +143: [09:33:15] Rep: 100 Mol:1 +143: [09:33:15] Rep: 100 Mol:5 +143: [09:33:15] Rep: 100 Mol:9 +143: [09:33:15] Rep: 100 Mol:13 +143: [09:33:15] Rep: 100 Mol:17 +143: [09:33:15] Rep: 100 Mol:21 +143: [09:33:15] Rep: 100 Mol:25 +143: [09:33:15] Rep: 100 Mol:29 +148: [09:33:15] Molecule does not have explicit Hs. Consider calling AddHs() +148: [09:33:15] Molecule does not have explicit Hs. Consider calling AddHs() +148: [09:33:15] Molecule does not have explicit Hs. Consider calling AddHs() +148: ..[09:33:15] Molecule does not have explicit Hs. Consider calling AddHs() +148: [09:33:15] Molecule does not have explicit Hs. Consider calling AddHs() +148: [09:33:15] Molecule does not have explicit Hs. Consider calling AddHs() +148: [09:33:15] Molecule does not have explicit Hs. Consider calling AddHs() +148: [09:33:15] Molecule does not have explicit Hs. Consider calling AddHs() +148: [09:33:15] Molecule does not have explicit Hs. Consider calling AddHs() +148: [09:33:15] Molecule does not have explicit Hs. Consider calling AddHs() +148: [09:33:15] Molecule does not have explicit Hs. Consider calling AddHs() +148: [09:33:15] Molecule does not have explicit Hs. Consider calling AddHs() +148: [09:33:15] Molecule does not have explicit Hs. Consider calling AddHs() +148: [09:33:15] Molecule does not have explicit Hs. Consider calling AddHs() +148: ..[09:33:15] Molecule does not have explicit Hs. Consider calling AddHs() +148: .[09:33:15] Molecule does not have explicit Hs. Consider calling AddHs() +148: [09:33:15] Molecule does not have explicit Hs. Consider calling AddHs() +141: [09:33:15] done +141: [09:33:15] ------------------------------------- +141: [09:33:15] Test MMFF multithreading2 +148: [09:33:15] Molecule does not have explicit Hs. Consider calling AddHs() +148: [09:33:15] Molecule does not have explicit Hs. Consider calling AddHs() +148: [09:33:15] Molecule does not have explicit Hs. Consider calling AddHs() +148: [09:33:15] Molecule does not have explicit Hs. Consider calling AddHs() +148: [09:33:15] Molecule does not have explicit Hs. Consider calling AddHs() +148: [09:33:15] Molecule does not have explicit Hs. Consider calling AddHs() +148: [09:33:15] Molecule does not have explicit Hs. Consider calling AddHs() +148: [09:33:15] Molecule does not have explicit Hs. Consider calling AddHs() +148: [09:33:15] Molecule does not have explicit Hs. Consider calling AddHs() +148: [09:33:15] Molecule does not have explicit Hs. Consider calling AddHs() 149: *********************************************************** 149: Testing MolAlign 149: --------------------------------- @@ -27140,227 +27109,361 @@ 149: testIssue241 149: 149: *********************************************************** -146: generating reference data -138/238 Test #149: testMolAlign ........................... Passed 0.25 sec -test 150 - Start 150: testO3AAlign - -150: Test command: /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/MolAlign/testO3AAlign -150: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/MolAlign -150: Test timeout computed to be: 1500 -141: [00:36:24] done -141: [00:36:24] ------------------------------------- -141: [00:36:24] Testing github 162: Incorrect SMILES after MMFF parameterization . -141: [00:36:24] done -141: [00:36:24] ------------------------------------- -141: [00:36:24] Testing github 224: crash during MMFF parameterization . -141: [00:36:24] done -141: [00:36:24] ------------------------------------- -141: [00:36:24] Testing github6728: crash due to missing stretch-bend params. -139/238 Test #141: testMMFFForceFieldHelpers .............. Passed 2.74 sec +148: [09:33:15] Molecule does not have explicit Hs. Consider calling AddHs() +139/238 Test #149: testMolAlign ........................... Passed 0.13 sec test 151 Start 151: molAlignCatchTest 151: Test command: /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/MolAlign/molAlignCatchTest 151: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/MolAlign 151: Test timeout computed to be: 1500 -148: .[00:36:24] Molecule does not have explicit Hs. Consider calling AddHs() -151: Randomness seeded to: 89288962 -148: [00:36:24] Molecule does not have explicit Hs. Consider calling AddHs() -151: 58192513 -148: [00:36:24] Molecule does not have explicit Hs. Consider calling AddHs() -148: [00:36:24] Molecule does not have explicit Hs. Consider calling AddHs() -148: ..[00:36:24] Molecule does not have explicit Hs. Consider calling AddHs() -148: [00:36:24] Molecule does not have explicit Hs. Consider calling AddHs() -148: [00:36:24] Molecule does not have explicit Hs. Consider calling AddHs() -148: [00:36:24] Molecule does not have explicit Hs. Consider calling AddHs() -148: [00:36:24] Molecule does not have explicit Hs. Consider calling AddHs() -148: [00:36:24] Molecule does not have explicit Hs. Consider calling AddHs() -148: [00:36:24] Molecule does not have explicit Hs. Consider calling AddHs() -148: [00:36:24] Molecule does not have explicit Hs. Consider calling AddHs() -148: [00:36:24] Molecule does not have explicit Hs. Consider calling AddHs() -148: [00:36:24] Molecule does not have explicit Hs. Consider calling AddHs() -148: [00:36:24] Molecule does not have explicit Hs. Consider calling AddHs() -148: ..[00:36:24] Molecule does not have explicit Hs. Consider calling AddHs() -151: 37227611 -148: .[00:36:24] Molecule does not have explicit Hs. Consider calling AddHs() -148: [00:36:24] Molecule does not have explicit Hs. Consider calling AddHs() -148: [00:36:24] Molecule does not have explicit Hs. Consider calling AddHs() -148: [00:36:24] Molecule does not have explicit Hs. Consider calling AddHs() -148: [00:36:24] Molecule does not have explicit Hs. Consider calling AddHs() -148: [00:36:24] Molecule does not have explicit Hs. Consider calling AddHs() -148: [00:36:24] Molecule does not have explicit Hs. Consider calling AddHs() -148: [00:36:24] Molecule does not have explicit Hs. Consider calling AddHs() -148: [00:36:24] Molecule does not have explicit Hs. Consider calling AddHs() -148: [00:36:24] Molecule does not have explicit Hs. Consider calling AddHs() -148: [00:36:24] Molecule does not have explicit Hs. Consider calling AddHs() -148: [00:36:24] Molecule does not have explicit Hs. Consider calling AddHs() -148: [00:36:24] Molecule does not have explicit Hs. Consider calling AddHs() -148: [00:36:24] Molecule does not have explicit Hs. Consider calling AddHs() -148: [00:36:24] Molecule does not have explicit Hs. Consider calling AddHs() -148: [00:36:24] Molecule does not have explicit Hs. Consider calling AddHs() -148: [00:36:25] Molecule does not have explicit Hs. Consider calling AddHs() -148: [00:36:25] Molecule does not have explicit Hs. Consider calling AddHs() -148: [00:36:25] Molecule does not have explicit Hs. Consider calling AddHs() -148: [00:36:25] Molecule does not have explicit Hs. Consider calling AddHs() -148: [00:36:25] Molecule does not have explicit Hs. Consider calling AddHs() -148: [00:36:25] Molecule does not have explicit Hs. Consider calling AddHs() -148: [00:36:25] Molecule does not have explicit Hs. Consider calling AddHs() -148: [00:36:25] Molecule does not have explicit Hs. Consider calling AddHs() -148: [00:36:25] Molecule does not have explicit Hs. Consider calling AddHs() -148: [00:36:25] Molecule does not have explicit Hs. Consider calling AddHs() -143: [00:36:25] done -143: [00:36:25] ------------------------------------- -143: [00:36:25] Test UFF multithreading3 -148: [00:36:25] Molecule does not have explicit Hs. Consider calling AddHs() -148: [00:36:25] Molecule does not have explicit Hs. Consider calling AddHs() -148: [00:36:25] Molecule does not have explicit Hs. Consider calling AddHs() -148: [00:36:25] Molecule does not have explicit Hs. Consider calling AddHs() -148: [00:36:25] Molecule does not have explicit Hs. Consider calling AddHs() -148: [00:36:25] Molecule does not have explicit Hs. Consider calling AddHs() -147: [00:36:25] UFFTYPER: Warning: hybridization set to SP3 for atom 6 -148: [00:36:25] Molecule does not have explicit Hs. Consider calling AddHs() -148: [00:36:25] Molecule does not have explicit Hs. Consider calling AddHs() -148: [00:36:25] Molecule does not have explicit Hs. Consider calling AddHs() -148: [00:36:25] Molecule does not have explicit Hs. Consider calling AddHs() -148: [00:36:25] Molecule does not have explicit Hs. Consider calling AddHs() -148: [00:36:25] Molecule does not have explicit Hs. Consider calling AddHs() -148: [00:36:25] Molecule does not have explicit Hs. Consider calling AddHs() -148: [00:36:25] Molecule does not have explicit Hs. Consider calling AddHs() -148: [00:36:25] Molecule does not have explicit Hs. Consider calling AddHs() -148: [00:36:25] Molecule does not have explicit Hs. Consider calling AddHs() -148: [00:36:25] Molecule does not have explicit Hs. Consider calling AddHs() -147: [00:36:25] UFFTYPER: Warning: hybridization set to SP3 for atom 6 -148: [00:36:25] Molecule does not have explicit Hs. Consider calling AddHs() -148: [00:36:25] Molecule does not have explicit Hs. Consider calling AddHs() -147: [00:36:25] UFFTYPER: Warning: hybridization set to SP3 for atom 6 -148: [00:36:25] Molecule does not have explicit Hs. Consider calling AddHs() -148: [00:36:25] Molecule does not have explicit Hs. Consider calling AddHs() -148: [00:36:25] Molecule does not have explicit Hs. Consider calling AddHs() -148: [00:36:25] Molecule does not have explicit Hs. Consider calling AddHs() -147: [00:36:25] UFFTYPER: Warning: hybridization set to SP3 for atom 11 -147: [00:36:25] UFFTYPER: Warning: hybridization set to SP3 for atom 11 -147: [00:36:25] UFFTYPER: Warning: hybridization set to SP3 for atom 11 -148: [00:36:25] Molecule does not have explicit Hs. Consider calling AddHs() -148: [00:36:25] Molecule does not have explicit Hs. Consider calling AddHs() -148: [00:36:25] Molecule does not have explicit Hs. Consider calling AddHs() -148: [00:36:25] Molecule does not have explicit Hs. Consider calling AddHs() -148: [00:36:25] Molecule does not have explicit Hs. Consider calling AddHs() -148: [00:36:25] Molecule does not have explicit Hs. Consider calling AddHs() -148: [00:36:25] Molecule does not have explicit Hs. Consider calling AddHs() -148: [00:36:25] Molecule does not have explicit Hs. Consider calling AddHs() -148: [00:36:25] Molecule does not have explicit Hs. Consider calling AddHs() -148: [00:36:25] Molecule does not have explicit Hs. Consider calling AddHs() -148: [00:36:25] Molecule does not have explicit Hs. Consider calling AddHs() -148: [00:36:25] Molecule does not have explicit Hs. Consider calling AddHs() -148: [00:36:25] Molecule does not have explicit Hs. Consider calling AddHs() -148: .[00:36:25] Molecule does not have explicit Hs. Consider calling AddHs() -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 -125: =============================================================================== -125: All tests passed (515 assertions in 10 test cases) -125: -143: [00:36:25] done -143: [00:36:25] ------------------------------------- -143: [00:36:25] Testing GitHubIssue62. -140/238 Test #125: descriptorsTestCatch ................... Passed 6.19 sec +148: [09:33:15] Molecule does not have explicit Hs. Consider calling AddHs() +148: [09:33:15] Molecule does not have explicit Hs. Consider calling AddHs() +148: [09:33:15] Molecule does not have explicit Hs. Consider calling AddHs() +143: [09:33:15] Rep: 100 Mol:2 +143: [09:33:15] Rep: 100 Mol:6 +143: [09:33:15] Rep: 100 Mol:10 +143: [09:33:15] Rep: 100 Mol:14 +143: [09:33:15] Rep: 100 Mol:18 +143: [09:33:15] Rep: 100 Mol:22 +143: [09:33:15] Rep: 100 Mol:26 +143: [09:33:15] Rep: 100 Mol:30 +148: [09:33:15] Molecule does not have explicit Hs. Consider calling AddHs() +148: [09:33:15] Molecule does not have explicit Hs. Consider calling AddHs() +148: [09:33:15] Molecule does not have explicit Hs. Consider calling AddHs() +148: [09:33:15] Molecule does not have explicit Hs. Consider calling AddHs() +148: [09:33:15] Molecule does not have explicit Hs. Consider calling AddHs() +148: [09:33:15] Molecule does not have explicit Hs. Consider calling AddHs() +148: [09:33:15] Molecule does not have explicit Hs. Consider calling AddHs() +148: [09:33:15] Molecule does not have explicit Hs. Consider calling AddHs() +148: [09:33:15] Molecule does not have explicit Hs. Consider calling AddHs() +148: [09:33:15] Molecule does not have explicit Hs. Consider calling AddHs() +148: [09:33:15] Molecule does not have explicit Hs. Consider calling AddHs() +148: [09:33:15] Molecule does not have explicit Hs. Consider calling AddHs() +148: [09:33:15] Molecule does not have explicit Hs. Consider calling AddHs() +148: [09:33:15] Molecule does not have explicit Hs. Consider calling AddHs() +148: [09:33:15] Molecule does not have explicit Hs. Consider calling AddHs() +148: [09:33:15] Molecule does not have explicit Hs. Consider calling AddHs() +148: [09:33:15] Molecule does not have explicit Hs. Consider calling AddHs() +148: [09:33:15] Molecule does not have explicit Hs. Consider calling AddHs() +148: [09:33:15] Molecule does not have explicit Hs. Consider calling AddHs() +148: [09:33:15] Molecule does not have explicit Hs. Consider calling AddHs() +148: [09:33:15] Molecule does not have explicit Hs. Consider calling AddHs() +148: [09:33:15] Molecule does not have explicit Hs. Consider calling AddHs() +148: [09:33:15] Molecule does not have explicit Hs. Consider calling AddHs() +148: [09:33:15] Molecule does not have explicit Hs. Consider calling AddHs() +148: [09:33:15] Molecule does not have explicit Hs. Consider calling AddHs() +148: [09:33:15] Molecule does not have explicit Hs. Consider calling AddHs() +148: [09:33:15] Molecule does not have explicit Hs. Consider calling AddHs() +151: Randomness seeded to: 1584252720 +148: [09:33:15] Molecule does not have explicit Hs. Consider calling AddHs() +151: 42064680 +148: [09:33:15] Molecule does not have explicit Hs. Consider calling AddHs() +148: [09:33:15] Molecule does not have explicit Hs. Consider calling AddHs() +151: 22273720 +148: [09:33:15] Molecule does not have explicit Hs. Consider calling AddHs() +148: [09:33:15] Molecule does not have explicit Hs. Consider calling AddHs() +148: [09:33:15] Molecule does not have explicit Hs. Consider calling AddHs() +147: [09:33:15] UFFTYPER: Warning: hybridization set to SP3 for atom 6 +148: [09:33:15] Molecule does not have explicit Hs. Consider calling AddHs() +148: [09:33:15] Molecule does not have explicit Hs. Consider calling AddHs() +148: [09:33:15] Molecule does not have explicit Hs. Consider calling AddHs() +148: [09:33:15] Molecule does not have explicit Hs. Consider calling AddHs() +147: [09:33:15] UFFTYPER: Warning: hybridization set to SP3 for atom 6 +148: [09:33:15] Molecule does not have explicit Hs. Consider calling AddHs() +148: [09:33:15] Molecule does not have explicit Hs. Consider calling AddHs() +148: [09:33:15] Molecule does not have explicit Hs. Consider calling AddHs() +148: [09:33:15] Molecule does not have explicit Hs. Consider calling AddHs() +147: [09:33:15] UFFTYPER: Warning: hybridization set to SP3 for atom 6 +148: [09:33:15] Molecule does not have explicit Hs. Consider calling AddHs() +148: [09:33:15] Molecule does not have explicit Hs. Consider calling AddHs() +148: [09:33:15] Molecule does not have explicit Hs. Consider calling AddHs() +148: [09:33:15] Molecule does not have explicit Hs. Consider calling AddHs() +148: [09:33:15] Molecule does not have explicit Hs. Consider calling AddHs() +141: [09:33:15] done +141: [09:33:15] ------------------------------------- +141: [09:33:15] Test MMFF multithreading3 +147: [09:33:15] UFFTYPER: Warning: hybridization set to SP3 for atom 11 +147: [09:33:15] UFFTYPER: Warning: hybridization set to SP3 for atom 11 +148: .[09:33:15] Molecule does not have explicit Hs. Consider calling AddHs() +147: [09:33:15] UFFTYPER: Warning: hybridization set to SP3 for atom 11 +143: [09:33:15] done +143: [09:33:15] ------------------------------------- +143: [09:33:15] Test UFF multithreading2 +146: [09:33:14] --------------------------------- +146: [09:33:14] test3 +146: +146: [09:33:14] --------------------------------- +146: [09:33:14] test4 +146: +146: [09:33:14] --------------------------------- +146: [09:33:14] test5 +146: +146: [09:33:15] --------------------------------- +146: [09:33:15] test6 +146: +146: [09:33:15] --------------------------------- +146: [09:33:15] test15Dists +146: +146: [09:33:15] --------------------------------- +146: [09:33:15] test Issue 215 +146: +146: [09:33:15] --------------------------------- +146: [09:33:15] testMultipleConfs +146: +146: [09:33:15] --------------------------------- +146: [09:33:15] testMultipleConfsExpTors +146: +146: [09:33:15] --------------------------------- +146: [09:33:15] testIssue227 +146: +146: [09:33:15] --------------------------------- +146: [09:33:15] testIssue236 +146: +146: [09:33:15] --------------------------------- +146: [09:33:15] testOrdering +146: +146: [09:33:15] --------------------------------- +146: [09:33:15] testIssue244 +146: +146: [09:33:15] --------------------------------- +146: [09:33:15] testIssue251 +146: +146: [09:33:15] --------------------------------- +146: [09:33:15] testIssue276 +146: [09:33:15] --------------------------------- +146: [09:33:15] testIssue284 +146: +146: [09:33:15] --------------------------------- +146: [09:33:15] testIssue285 +146: +146: [09:33:15] --------------------------------- +146: [09:33:15] testIssue355 +146: +146: [09:33:15] --------------------------------- +146: [09:33:15] testRandomCoords +146: +146: [09:33:15] --------------------------------- +146: [09:33:15] test sf.net issue 1989539 +146: +146: [09:33:15] --------------------------------- +146: [09:33:15] test sf.net issue 2091864 +146: +146: [09:33:15] --------------------------------- +146: [09:33:15] test constrained embedding +146: +146: [09:33:15] ssd: 0.0752641 +146: [09:33:15] ssd: 0.0659363 +126: Warning: Atom Count for residue GLU5A does not match expected count +126: Warning: Atom Count for residue ASN39A does not match expected count +126: Warning: Atom Count for residue GLU53A does not match expected count +126: Warning: Atom Count for residue ARG64A does not match expected count +126: Warning: Atom Count for residue LYS80A does not match expected count +148: [09:33:15] Molecule does not have explicit Hs. Consider calling AddHs() +126: Warning: Atom Count for residue GLU150A does not match expected count +126: Warning: Atom Count for residue ASN157A does not match expected count +126: .[09:33:15] DEPRECATION WARNING: please use MorganGenerator +126: .[09:33:15] DEPRECATION WARNING: please use MorganGenerator +126: ..[09:33:15] DEPRECATION WARNING: please use AtomPairGenerator +126: [09:33:15] DEPRECATION WARNING: please use AtomPairGenerator +126: [09:33:15] DEPRECATION WARNING: please use AtomPairGenerator +126: [09:33:15] DEPRECATION WARNING: please use AtomPairGenerator +126: [09:33:15] DEPRECATION WARNING: please use AtomPairGenerator +126: [09:33:15] DEPRECATION WARNING: please use AtomPairGenerator +126: .[09:33:15] DEPRECATION WARNING: please use TopologicalTorsionGenerator +126: [09:33:15] DEPRECATION WARNING: please use TopologicalTorsionGenerator +126: ...[09:33:15] DEPRECATION WARNING: please use MorganGenerator +126: [09:33:15] DEPRECATION WARNING: please use MorganGenerator +126: [09:33:15] DEPRECATION WARNING: please use MorganGenerator +126: [09:33:15] DEPRECATION WARNING: please use MorganGenerator +126: [09:33:15] DEPRECATION WARNING: please use MorganGenerator +126: [09:33:15] DEPRECATION WARNING: please use MorganGenerator +126: [09:33:15] DEPRECATION WARNING: please use MorganGenerator +126: [09:33:15] DEPRECATION WARNING: please use MorganGenerator +126: [09:33:15] DEPRECATION WARNING: please use MorganGenerator +126: [09:33:15] DEPRECATION WARNING: please use MorganGenerator +126: [09:33:15] DEPRECATION WARNING: please use MorganGenerator +126: [09:33:15] DEPRECATION WARNING: please use MorganGenerator +126: [09:33:15] DEPRECATION WARNING: please use MorganGenerator +126: [09:33:15] DEPRECATION WARNING: please use MorganGenerator +126: [09:33:15] DEPRECATION WARNING: please use MorganGenerator +126: [09:33:15] DEPRECATION WARNING: please use MorganGenerator +126: [09:33:15] DEPRECATION WARNING: please use MorganGenerator +126: [09:33:15] DEPRECATION WARNING: please use MorganGenerator +126: [09:33:15] DEPRECATION WARNING: please use MorganGenerator +126: [09:33:15] DEPRECATION WARNING: please use MorganGenerator +126: [09:33:15] DEPRECATION WARNING: please use MorganGenerator +126: [09:33:15] DEPRECATION WARNING: please use MorganGenerator +126: ....[09:33:15] DEPRECATION WARNING: please use AtomPairGenerator +126: [09:33:15] DEPRECATION WARNING: please use AtomPairGenerator +126: ....[09:33:15] DEPRECATION WARNING: please use AtomPairGenerator +126: [09:33:15] DEPRECATION WARNING: please use AtomPairGenerator +126: .[09:33:15] DEPRECATION WARNING: please use TopologicalTorsionGenerator +126: [09:33:15] DEPRECATION WARNING: please use TopologicalTorsionGenerator +126: [09:33:15] DEPRECATION WARNING: please use TopologicalTorsionGenerator +126: [09:33:15] DEPRECATION WARNING: please use TopologicalTorsionGenerator +126: [09:33:15] DEPRECATION WARNING: please use TopologicalTorsionGenerator +126: ..[09:33:15] DEPRECATION WARNING: please use TopologicalTorsionGenerator +126: [09:33:15] DEPRECATION WARNING: please use TopologicalTorsionGenerator +126: [09:33:15] DEPRECATION WARNING: please use TopologicalTorsionGenerator +126: [09:33:15] DEPRECATION WARNING: please use TopologicalTorsionGenerator +126: [09:33:15] DEPRECATION WARNING: please use TopologicalTorsionGenerator +126: [09:33:15] DEPRECATION WARNING: please use TopologicalTorsionGenerator +126: .[09:33:15] DEPRECATION WARNING: please use TopologicalTorsionGenerator +126: [09:33:15] DEPRECATION WARNING: please use TopologicalTorsionGenerator +126: ... +126: ---------------------------------------------------------------------- +126: Ran 31 tests in 3.336s +126: +126: OK +126: exactmw 78.046950192 +126: amw 78.11399999999999 +126: lipinskiHBA 0.0 +126: lipinskiHBD 0.0 +126: NumRotatableBonds 0.0 +126: NumHBD 0.0 +126: NumHBA 0.0 +126: NumHeavyAtoms 6.0 +126: NumAtoms 12.0 +126: NumHeteroatoms 0.0 +126: NumAmideBonds 0.0 +126: FractionCSP3 0.0 +126: NumRings 1.0 +126: NumAromaticRings 1.0 +126: NumAliphaticRings 0.0 +126: NumSaturatedRings 0.0 +126: NumHeterocycles 0.0 +126: NumAromaticHeterocycles 0.0 +126: NumSaturatedHeterocycles 0.0 +126: NumAliphaticHeterocycles 0.0 +126: NumSpiroAtoms 0.0 +126: NumBridgeheadAtoms 0.0 +126: NumAtomStereoCenters 0.0 +126: NumUnspecifiedAtomStereoCenters 0.0 +126: labuteASA 37.43140311949697 +126: tpsa 0.0 +126: CrippenClogP 1.6866 +126: CrippenMR 26.441999999999993 +126: chi0v 3.464101615137755 +126: chi1v 2.0000000000000004 +126: chi2v 0.6666666666666671 +126: chi3v 0.6666666666666671 +126: chi4v 0.38490017945975075 +126: chi0n 3.464101615137755 +126: chi1n 2.0000000000000004 +126: chi2n 0.6666666666666671 +126: chi3n 0.6666666666666671 +126: chi4n 0.38490017945975075 +126: hallKierAlpha -0.78 +126: kappa1 3.4115708812260532 +126: kappa2 1.6057694396735218 +126: kappa3 0.5823992601400448 +126: Phi 0.9130327103921437 +126: CustomNumAtoms 6.0 +126: exactmw 78.046950192 +126: lipinskiHBA 0.0 +146: [09:33:15] --------------------------------- +146: [09:33:15] test sf.net issue 2091974 +146: +146: [09:33:15] --------------------------------- +146: [09:33:15] test sf.net issue 2835784 +146: +146: [09:33:15] --------------------------------- +146: [09:33:15] test sf.net issue 3019283 +146: +146: [09:33:15] --------------------------------- +146: [09:33:15] test sf.net issue 3238580 +146: +146: [09:33:15] --------------------------------- +146: [09:33:15] test sf.net issue 3483968 +146: +146: [09:33:15] --------------------------------- +146: [09:33:15] test github issue 55 +146: +146: [09:33:15] --------------------------------- +146: [09:33:15] test1 +146: +146: [09:33:15] --------------------------------- +146: [09:33:15] test multi-threading +146: +146: building molecules +146: generating reference data +141: [09:33:15] done +141: [09:33:15] ------------------------------------- +141: [09:33:15] Testing github 162: Incorrect SMILES after MMFF parameterization . +141: [09:33:15] done +141: [09:33:15] ------------------------------------- +141: [09:33:15] Testing github 224: crash during MMFF parameterization . +141: [09:33:15] done +141: [09:33:15] ------------------------------------- +141: [09:33:15] Testing github6728: crash due to missing stretch-bend params. +140/238 Test #126: pyMolDescriptors ....................... Passed 3.83 sec test 152 Start 152: pyMolAlign 152: Test command: /usr/bin/python3 "/build/reproducible-path/rdkit-202503.1/Code/GraphMol/MolAlign/Wrap/testMolAlign.py" 152: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/MolAlign/Wrap 152: Test timeout computed to be: 1500 -143: [00:36:25] beta-lactam 39.6387 -143: [00:36:25] cyclopropanone 174.698 -143: [00:36:25] aziridine 337.986 -143: [00:36:25] aziridinone 115.248 -143: [00:36:25] isobutene 2.48217 -143: [00:36:25] acetone 1.91788 -143: [00:36:25] cyclopentanone 10.1648 -143: [00:36:25] cyclopropene 99.4921 -143: [00:36:25] cyclobutene 41.0156 -143: [00:36:25] cyclopropane 267.236 -143: [00:36:25] gamma-lactam 15.7471 -148: [00:36:25] Molecule does not have explicit Hs. Consider calling AddHs() -143: [00:36:25] trans-2,3-diphenylcyclopropan-1-one 203.398 -143: [00:36:25] cis-2,3-diphenylcyclopropan-1-one 206.852 -143: [00:36:25] 2,3-diphenylcyclopropa-2-en-1-one 20.0443 -143: [00:36:25] cyclopropylidencyclobutane 218.879 -143: [00:36:25] diphenylmethylidencyclobutane 79.6139 -143: [00:36:25] done -143: [00:36:25] ------------------------------------- -143: [00:36:25] Test Github Issue 613: UFF Atom type not properly assigned to lanthanides. -143: [00:36:25] done -143: [00:36:25] ------------------------------------- -143: [00:36:25] Test square planar complexes -143: [00:36:25] done -143: [00:36:25] ------------------------------------- -143: [00:36:25] Test octahedral complexes -143: [00:36:25] done -141/238 Test #143: testUFFForceFieldHelpers ............... Passed 3.52 sec +141/238 Test #141: testMMFFForceFieldHelpers .............. Passed 2.14 sec test 153 Start 153: testFeatures 153: Test command: /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/MolChemicalFeatures/testFeatures 153: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/MolChemicalFeatures 153: Test timeout computed to be: 1500 -153: [00:36:25] ------------------------------------- -153: [00:36:25] AtomType parser testing. -153: [00:36:25] SMARTS Parse Error: syntax error while parsing: [$([!$([NH0])_100;N,O,$([S])_101,$([N,O)_102])_103] -153: [00:36:25] 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: [00:36:25] done -153: [00:36:25] ------------------------------------- -153: [00:36:25] FeatureDefinition parser testing. -153: [00:36:25] done -153: [00:36:25] ------------------------------------- -153: [00:36:25] Test pulling feat defs from a string. -153: [00:36:25] done -153: [00:36:25] ------------------------------------- -153: [00:36:25] FeatureDef functionality testing. -153: [00:36:25] done -153: [00:36:25] ------------------------------------- -153: [00:36:25] FeatureFactory testing. -153: [00:36:25] 1 -153: [00:36:25] 2 -153: [00:36:25] 3 -153: [00:36:25] 4 -153: [00:36:25] 5 -153: [00:36:25] 6 -153: [00:36:25] done -153: [00:36:25] ------------------------------------- -153: [00:36:25] Feature Location testing. -153: [00:36:25] done -153: [00:36:25] ------------------------------------- -153: [00:36:25] Test building a FeatureFactory from a file -153: [00:36:25] done -153: [00:36:25] ------------------------------------- -153: [00:36:25] Testing Issue 224. -153: [00:36:25] done -153: [00:36:25] ------------------------------------- -153: [00:36:25] Testing Issue 225. -153: [00:36:25] done -153: [00:36:25] ------------------------------------- -153: [00:36:25] Test Issue346 -153: [00:36:25] done -153: [00:36:25] ------------------------------------- -153: [00:36:25] Test Issue347 -153: [00:36:25] done -153: [00:36:25] ------------------------------------- -153: [00:36:25] Testing Issue 348. -153: [00:36:25] SMARTS Parse Error: syntax error while parsing: [C[C] -153: [00:36:25] SMARTS Parse Error: Failed parsing SMARTS '[C[C]' for input: '[C[C]' -153: [00:36:25] ------------------------------------- -153: [00:36:25] Testing Nested AtomType definitions. +153: [09:33:15] ------------------------------------- +153: [09:33:15] AtomType parser testing. +153: [09:33:15] SMARTS Parse Error: syntax error while parsing: [$([!$([NH0])_100;N,O,$([S])_101,$([N,O)_102])_103] +153: [09:33:15] 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: [09:33:15] done +153: [09:33:15] ------------------------------------- +153: [09:33:15] FeatureDefinition parser testing. +153: [09:33:15] done +153: [09:33:15] ------------------------------------- +153: [09:33:15] Test pulling feat defs from a string. +153: [09:33:15] done +153: [09:33:15] ------------------------------------- +153: [09:33:15] FeatureDef functionality testing. +153: [09:33:15] done +153: [09:33:15] ------------------------------------- +153: [09:33:15] FeatureFactory testing. +153: [09:33:15] 1 +153: [09:33:15] 2 +153: [09:33:15] 3 +153: [09:33:15] 4 +153: [09:33:15] 5 +153: [09:33:15] 6 +153: [09:33:15] done +153: [09:33:15] ------------------------------------- +153: [09:33:15] Feature Location testing. +153: [09:33:15] done +153: [09:33:15] ------------------------------------- +153: [09:33:15] Test building a FeatureFactory from a file +153: [09:33:15] done +153: [09:33:15] ------------------------------------- +153: [09:33:15] Testing Issue 224. +153: [09:33:15] done +153: [09:33:15] ------------------------------------- +153: [09:33:15] Testing Issue 225. +153: [09:33:15] done +153: [09:33:15] ------------------------------------- +153: [09:33:15] Test Issue346 +153: [09:33:15] done +148: [09:33:15] Molecule does not have explicit Hs. Consider calling AddHs() +153: [09:33:15] ------------------------------------- +153: [09:33:15] Test Issue347 +153: [09:33:15] done +153: [09:33:15] ------------------------------------- +153: [09:33:15] Testing Issue 348. +153: [09:33:15] SMARTS Parse Error: syntax error while parsing: [C[C] +153: [09:33:15] SMARTS Parse Error: Failed parsing SMARTS '[C[C]' for input: '[C[C]' +153: [09:33:15] ------------------------------------- +153: [09:33:15] Testing Nested AtomType definitions. 153: [$([$([$([C;!$(C=[O,N,P,S]);!$(C#N)]),c]);R])] -153: [00:36:25] ------------------------------------- -153: [00:36:25] Testing Github Issue #252: crash when calling getPos() with no conformer. -153: [00:36:25] expect a precondition failure message below -153: [00:36:25] +153: [09:33:15] ------------------------------------- +153: [09:33:15] Testing Github Issue #252: crash when calling getPos() with no conformer. +153: [09:33:15] expect a precondition failure message below +153: [09:33:15] 153: 153: **** 153: Pre-condition Violation @@ -27373,18 +27476,18 @@ 153: 1# Invar::operator<<(std::ostream&, Invar::Invariant const&) in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu//lib/libRDKitRDGeneral.so.1 153: 2# RDKit::MolChemicalFeature::getPos(int) const in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu//lib/libRDKitMolChemicalFeatures.so.1 153: 3# RDKit::MolChemicalFeature::getPos() const in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu//lib/libRDKitMolChemicalFeatures.so.1 -153: 4# 0x0000AAAAE0C31AB0 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/MolChemicalFeatures/testFeatures -153: 5# 0x0000AAAAE0C24568 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/MolChemicalFeatures/testFeatures -153: 6# 0x0000FFFFB1BD229C in /lib/aarch64-linux-gnu/libc.so.6 +153: 4# 0x0000AAAAE9931AB0 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/MolChemicalFeatures/testFeatures +153: 5# 0x0000AAAAE9924568 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/MolChemicalFeatures/testFeatures +153: 6# 0x0000FFFFB054229C in /lib/aarch64-linux-gnu/libc.so.6 153: 7# __libc_start_main in /lib/aarch64-linux-gnu/libc.so.6 -153: 8# 0x0000AAAAE0C24730 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/MolChemicalFeatures/testFeatures +153: 8# 0x0000AAAAE9924730 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/MolChemicalFeatures/testFeatures 153: ---------- 153: **** 153: -153: [00:36:25] Done -153: [00:36:25] ------------------------------------- -153: [00:36:25] Testing github 2077: add confId argument to MolChemicalFeatureFactor::getFeaturesForMol() -153: [00:36:25] done +153: [09:33:15] Done +153: [09:33:15] ------------------------------------- +153: [09:33:15] Testing github 2077: add confId argument to MolChemicalFeatureFactor::getFeaturesForMol() +153: [09:33:15] done 142/238 Test #153: testFeatures ........................... Passed 0.04 sec test 154 Start 154: pyChemicalFeatures @@ -27392,21 +27495,29 @@ 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-aarch64-linux-gnu/Code/GraphMol/MolChemicalFeatures/Wrap 154: Test timeout computed to be: 1500 -148: [00:36:25] Molecule does not have explicit Hs. Consider calling AddHs() -151: 974345026 -95: 0,0 0 -95: 0,1 0 -95: 1,0 0 -95: 1,1 0 -95: 2,0 0 -95: 2,1 0 -143/238 Test #95: testEnumeration ........................ Passed 10.04 sec +148: [09:33:16] Molecule does not have explicit Hs. Consider calling AddHs() +143: [09:33:16] done +143: [09:33:16] ------------------------------------- +143: [09:33:16] Test UFF multithreading3 +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 +154: .[09:33:16] Molecule does not have explicit Hs. Consider calling AddHs() +125: =============================================================================== +125: All tests passed (515 assertions in 10 test cases) +125: +143/238 Test #125: descriptorsTestCatch ................... Passed 4.23 sec test 155 Start 155: testShapeHelpers 155: Test command: /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/ShapeHelpers/testShapeHelpers 155: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/ShapeHelpers 155: Test timeout computed to be: 1500 +154: .[09:33:16] Molecule does not have explicit Hs. Consider calling AddHs() 155: *********************************************************** 155: Testing ShapeHelpers 155: --------------------------------- @@ -27426,20 +27537,17 @@ 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-aarch64-linux-gnu/Code/GraphMol/ShapeHelpers/Wrap 156: Test timeout computed to be: 1500 -148: [00:36:26] Molecule does not have explicit Hs. Consider calling AddHs() -154: .[00:36:26] Molecule does not have explicit Hs. Consider calling AddHs() -154: .[00:36:26] Molecule does not have explicit Hs. Consider calling AddHs() -154: ..[00:36:26] Molecule does not have explicit Hs. Consider calling AddHs() -154: .[00:36:26] Molecule does not have explicit Hs. Consider calling AddHs() -154: .[00:36:26] SMARTS Parse Error: syntax error while parsing: [N,O;!HQ] -154: [00:36:26] SMARTS Parse Error: Failed parsing SMARTS '[N,O;!HQ]' for input: '[N,O;!HQ]' +154: ..[09:33:16] Molecule does not have explicit Hs. Consider calling AddHs() +154: .[09:33:16] Molecule does not have explicit Hs. Consider calling AddHs() +154: .[09:33:16] SMARTS Parse Error: syntax error while parsing: [N,O;!HQ] +154: [09:33:16] SMARTS Parse Error: Failed parsing SMARTS '[N,O;!HQ]' for input: '[N,O;!HQ]' 154: ... 154: ---------------------------------------------------------------------- -154: Ran 9 tests in 0.127s +154: Ran 9 tests in 0.125s 154: 154: OK -148: [00:36:26] Molecule does not have explicit Hs. Consider calling AddHs() -145/238 Test #154: pyChemicalFeatures ..................... Passed 0.60 sec +148: [09:33:16] Molecule does not have explicit Hs. Consider calling AddHs() +145/238 Test #154: pyChemicalFeatures ..................... Passed 0.42 sec test 157 Start 157: testMolCatalog @@ -27453,269 +27561,195 @@ 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-aarch64-linux-gnu/Code/GraphMol/MolCatalog/Wrap 158: Test timeout computed to be: 1500 -151: 478414793 -151: =============================================================================== -151: All tests passed (73 assertions in 3 test cases) -151: -147/238 Test #151: molAlignCatchTest ...................... Passed 1.67 sec +148: [09:33:16] Molecule does not have explicit Hs. Consider calling AddHs() +143: [09:33:16] done +143: [09:33:16] ------------------------------------- +143: [09:33:16] Testing GitHubIssue62. +143: [09:33:16] beta-lactam 39.6387 +143: [09:33:16] cyclopropanone 174.698 +143: [09:33:16] aziridine 337.986 +143: [09:33:16] aziridinone 115.248 +156: . +156: ---------------------------------------------------------------------- +156: Ran 1 test in 0.026s +156: +156: OK +156: Testing Shape Helpers wrapper +143: [09:33:16] isobutene 2.48217 +143: [09:33:16] acetone 1.91788 +143: [09:33:16] cyclopentanone 10.1648 +143: [09:33:16] cyclopropene 99.4921 +143: [09:33:16] cyclobutene 41.0156 +143: [09:33:16] cyclopropane 267.236 +143: [09:33:16] gamma-lactam 15.7471 +151: 1181231880 +143: [09:33:16] trans-2,3-diphenylcyclopropan-1-one 203.398 +147/238 Test #156: pyShapeHelpers ......................... Passed 0.32 sec test 159 Start 159: moldraw2DTest1 159: Test command: /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/MolDraw2D/moldraw2DTest1 159: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/MolDraw2D 159: Test timeout computed to be: 1500 -156: . -156: ---------------------------------------------------------------------- -156: Ran 1 test in 0.073s -156: -156: OK -156: Testing Shape Helpers wrapper -126: Warning: Atom Count for residue GLU5A does not match expected count -126: Warning: Atom Count for residue ASN39A does not match expected count -126: Warning: Atom Count for residue GLU53A does not match expected count -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 -148: [00:36:26] Molecule does not have explicit Hs. Consider calling AddHs() +143: [09:33:16] cis-2,3-diphenylcyclopropan-1-one 206.852 +143: [09:33:16] 2,3-diphenylcyclopropa-2-en-1-one 20.0443 +143: [09:33:16] cyclopropylidencyclobutane 218.879 159: ----------------- Test 1 -126: .[00:36:26] DEPRECATION WARNING: please use MorganGenerator -126: .[00:36:26] DEPRECATION WARNING: please use MorganGenerator -126: ..[00:36:26] DEPRECATION WARNING: please use AtomPairGenerator -126: [00:36:26] DEPRECATION WARNING: please use AtomPairGenerator -126: [00:36:26] DEPRECATION WARNING: please use AtomPairGenerator -126: [00:36:26] DEPRECATION WARNING: please use AtomPairGenerator -126: [00:36:26] DEPRECATION WARNING: please use AtomPairGenerator -126: [00:36:26] DEPRECATION WARNING: please use AtomPairGenerator -126: .[00:36:26] DEPRECATION WARNING: please use TopologicalTorsionGenerator -126: [00:36:26] DEPRECATION WARNING: please use TopologicalTorsionGenerator -126: ...[00:36:26] DEPRECATION WARNING: please use MorganGenerator -126: [00:36:26] DEPRECATION WARNING: please use MorganGenerator -126: [00:36:26] DEPRECATION WARNING: please use MorganGenerator -126: [00:36:26] DEPRECATION WARNING: please use MorganGenerator -126: [00:36:26] DEPRECATION WARNING: please use MorganGenerator -126: [00:36:26] DEPRECATION WARNING: please use MorganGenerator -126: [00:36:26] DEPRECATION WARNING: please use MorganGenerator -126: [00:36:26] DEPRECATION WARNING: please use MorganGenerator -126: [00:36:26] DEPRECATION WARNING: please use MorganGenerator -126: [00:36:26] DEPRECATION WARNING: please use MorganGenerator -126: [00:36:26] DEPRECATION WARNING: please use MorganGenerator -126: [00:36:26] DEPRECATION WARNING: please use MorganGenerator -126: [00:36:26] DEPRECATION WARNING: please use MorganGenerator -126: [00:36:26] DEPRECATION WARNING: please use MorganGenerator -126: [00:36:26] DEPRECATION WARNING: please use MorganGenerator -126: [00:36:26] DEPRECATION WARNING: please use MorganGenerator -126: [00:36:26] DEPRECATION WARNING: please use MorganGenerator -126: [00:36:26] DEPRECATION WARNING: please use MorganGenerator -126: [00:36:26] DEPRECATION WARNING: please use MorganGenerator -126: [00:36:26] DEPRECATION WARNING: please use MorganGenerator -126: [00:36:26] DEPRECATION WARNING: please use MorganGenerator -126: [00:36:26] DEPRECATION WARNING: please use MorganGenerator -126: ....[00:36:26] DEPRECATION WARNING: please use AtomPairGenerator -126: [00:36:26] DEPRECATION WARNING: please use AtomPairGenerator -148/238 Test #156: pyShapeHelpers ......................... Passed 0.55 sec +143: [09:33:16] diphenylmethylidencyclobutane 79.6139 +143: [09:33:16] done +143: [09:33:16] ------------------------------------- +143: [09:33:16] Test Github Issue 613: UFF Atom type not properly assigned to lanthanides. +143: [09:33:16] done +143: [09:33:16] ------------------------------------- +143: [09:33:16] Test square planar complexes +143: [09:33:16] done +143: [09:33:16] ------------------------------------- +143: [09:33:16] Test octahedral complexes +143: [09:33:16] done +148/238 Test #143: testUFFForceFieldHelpers ............... Passed 2.55 sec test 160 Start 160: moldraw2DTestCatch 160: Test command: /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/MolDraw2D/moldraw2DTestCatch 160: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/MolDraw2D 160: Test timeout computed to be: 1500 -126: ....[00:36:26] DEPRECATION WARNING: please use AtomPairGenerator -126: [00:36:26] DEPRECATION WARNING: please use AtomPairGenerator -126: .[00:36:26] DEPRECATION WARNING: please use TopologicalTorsionGenerator -126: [00:36:26] DEPRECATION WARNING: please use TopologicalTorsionGenerator -126: [00:36:26] DEPRECATION WARNING: please use TopologicalTorsionGenerator -126: [00:36:26] DEPRECATION WARNING: please use TopologicalTorsionGenerator -126: [00:36:26] DEPRECATION WARNING: please use TopologicalTorsionGenerator -126: ..[00:36:26] DEPRECATION WARNING: please use TopologicalTorsionGenerator -126: [00:36:26] DEPRECATION WARNING: please use TopologicalTorsionGenerator -126: [00:36:26] DEPRECATION WARNING: please use TopologicalTorsionGenerator -126: [00:36:26] DEPRECATION WARNING: please use TopologicalTorsionGenerator -126: [00:36:26] DEPRECATION WARNING: please use TopologicalTorsionGenerator -126: [00:36:26] DEPRECATION WARNING: please use TopologicalTorsionGenerator -126: .[00:36:26] DEPRECATION WARNING: please use TopologicalTorsionGenerator -126: [00:36:26] DEPRECATION WARNING: please use TopologicalTorsionGenerator -126: ... -126: ---------------------------------------------------------------------- -126: Ran 31 tests in 6.517s -126: -126: OK -126: exactmw 78.046950192 -126: amw 78.11399999999999 -126: lipinskiHBA 0.0 -126: lipinskiHBD 0.0 -126: NumRotatableBonds 0.0 -126: NumHBD 0.0 -126: NumHBA 0.0 -126: NumHeavyAtoms 6.0 -126: NumAtoms 12.0 -126: NumHeteroatoms 0.0 -126: NumAmideBonds 0.0 -126: FractionCSP3 0.0 -126: NumRings 1.0 -126: NumAromaticRings 1.0 -126: NumAliphaticRings 0.0 -126: NumSaturatedRings 0.0 -126: NumHeterocycles 0.0 -126: NumAromaticHeterocycles 0.0 -126: NumSaturatedHeterocycles 0.0 -126: NumAliphaticHeterocycles 0.0 -126: NumSpiroAtoms 0.0 -126: NumBridgeheadAtoms 0.0 -126: NumAtomStereoCenters 0.0 -126: NumUnspecifiedAtomStereoCenters 0.0 -126: labuteASA 37.43140311949697 -126: tpsa 0.0 -126: CrippenClogP 1.6866 -126: CrippenMR 26.441999999999993 -126: chi0v 3.464101615137755 -126: chi1v 2.0000000000000004 -126: chi2v 0.6666666666666671 -126: chi3v 0.6666666666666671 -126: chi4v 0.38490017945975075 -126: chi0n 3.464101615137755 -126: chi1n 2.0000000000000004 -126: chi2n 0.6666666666666671 -126: chi3n 0.6666666666666671 -126: chi4n 0.38490017945975075 -126: hallKierAlpha -0.78 -126: kappa1 3.4115708812260532 -126: kappa2 1.6057694396735218 -126: kappa3 0.5823992601400448 -126: Phi 0.9130327103921437 -126: CustomNumAtoms 6.0 -126: exactmw 78.046950192 -126: lipinskiHBA 0.0 159: file test1_6.svg gave hash 1109656969U not the expected 2635907956U 159: Done 159: ----------------- Test 2 +158: . +158: ---------------------------------------------------------------------- +158: Ran 1 test in 0.016s +158: +158: OK 159: file test2_1.png gave hash 2467931916U not the expected 638584804U 159: file test2_2.png gave hash 3737953282U not the expected 610424244U 159: file test2_3.png gave hash 2294574389U not the expected 2179746375U +160: Randomness seeded to: 4038130040 +160: file contourMol_1.svg gave hash 4125787245U not the expected 3634867913U 159: Done 159: ----------------- Test 4 +160: file contourMol_2.svg gave hash 2761342533U not the expected 1815941817U 159: file test4_1.png gave hash 516573244U not the expected 3993974247U +160: file contourMol_3.svg gave hash 1333854566U not the expected 2579392727U 159: Done 159: ----------------- Test 5 +160: file contourMol_4.svg gave hash 4249475618U not the expected 2914799663U +160: file contourMol_5.svg gave hash 3376179346U not the expected 3792684719U 159: file test5_1.png gave hash 2590128341U not the expected 571291290U 159: file test5_2.png gave hash 2869651309U not the expected 97265124U +149/238 Test #158: pyMolCatalog ........................... Passed 0.29 sec +test 161 + Start 161: moldraw2DRxnTest1 + +161: Test command: /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/MolDraw2D/moldraw2DRxnTest1 +161: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/MolDraw2D +161: Test timeout computed to be: 1500 159: file test5_3.png gave hash 4285469383U not the expected 606188176U 159: Done 159: ----------------- Test 6 (atom labels) 159: Done 159: ----------------- Test 7 (backgrounds) +161: ----------------- Test 1 +160: file testGithub3226_1.png gave hash 632134109U not the expected 3165135374U 159: file test7_1.png gave hash 3445382333U not the expected 1322246680U +160: file testGithub3226_2.png gave hash 1790248804U not the expected 643975155U 159: file test7_2.png gave hash 4080486780U not the expected 1499012715U 159: Done 159: ----------------- Test8: PrepareMolDrawing 159: Done 159: ----------------- Test multi-threaded drawing 159: reading molecules -149/238 Test #126: pyMolDescriptors ....................... Passed 7.05 sec -test 161 - Start 161: moldraw2DRxnTest1 - -161: Test command: /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/MolDraw2D/moldraw2DRxnTest1 -161: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/MolDraw2D -161: Test timeout computed to be: 1500 -160: Randomness seeded to: 4223203912 -160: file contourMol_1.svg gave hash 4125787245U not the expected 3634867913U -160: file contourMol_2.svg gave hash 2761342533U not the expected 1815941817U -161: ----------------- Test 1 -160: file contourMol_3.svg gave hash 1333854566U not the expected 2579392727U -160: file contourMol_4.svg gave hash 4249475618U not the expected 2914799663U -159: generating reference drawings -146: validating reference data -160: file contourMol_5.svg gave hash 3376179346U not the expected 3792684719U +160: file testGithub3226_3.png gave hash 1296655029U not the expected 3119571946U +160: file testPNGMetadata_1.png gave hash 2053548476U not the expected 997629701U 161: file rxn_test1_1.png gave hash 2332294744U not the expected 801892091U +148: [09:33:16] Molecule does not have explicit Hs. Consider calling AddHs() 161: file rxn_test1_2.png gave hash 3186000742U not the expected 507435337U -158: . -158: ---------------------------------------------------------------------- -158: Ran 1 test in 0.014s -158: -158: OK +159: generating reference drawings +160: file testPNGMetadata_2.png gave hash 1147517534U not the expected 1797853056U 161: file rxn_test1_3.png gave hash 2120547110U not the expected 1590809137U 161: file rxn_test1_4.png gave hash 59268109U not the expected 1766700542U -159: processing -159: launch :0 -159: launch :1 -159: launch :2 -159: launch :3 161: file rxn_test1_5.png gave hash 3733738372U not the expected 2552100594U -150/238 Test #158: pyMolCatalog ........................... Passed 0.45 sec +146: validating reference data +161: file rxn_test1_6.png gave hash 2102224395U not the expected 3791582903U +160: [09:33:16] Font file /build/reproducible-path/rdkit-202503.1/Data/Fonts/ComicNeue-Regular.ttf not found. +160: [09:33:16] Falling back to original font file /build/reproducible-path/rdkit-202503.1/Data/Fonts/Telex-Regular.ttf. +151: 286105080 +151: =============================================================================== +151: All tests passed (73 assertions in 3 test cases) +151: +150/238 Test #151: molAlignCatchTest ...................... Passed 1.65 sec +160: file testHandDrawn-1.svg gave hash 1143910631U not the expected 2253418236U +160: [09:33:16] Font file /build/reproducible-path/rdkit-202503.1/Data/Fonts/ComicNeue-Regular.ttf not found. +160: [09:33:16] Falling back to original font file /build/reproducible-path/rdkit-202503.1/Data/Fonts/Telex-Regular.ttf. test 162 Start 162: pyMolDraw2D 162: Test command: /usr/bin/python3 "/build/reproducible-path/rdkit-202503.1/Code/GraphMol/MolDraw2D/Wrap/testMolDraw2D.py" 162: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/MolDraw2D/Wrap 162: Test timeout computed to be: 1500 -161: file rxn_test1_6.png gave hash 2102224395U not the expected 3791582903U -160: file testGithub3226_1.png gave hash 632134109U not the expected 3165135374U -160: file testGithub3226_2.png gave hash 1790248804U not the expected 643975155U +148: [09:33:16] Molecule does not have explicit Hs. Consider calling AddHs() 161: file rxn_test1_7.png gave hash 3541821286U not the expected 1461397406U 161: Done 161: ----------------- Test 2: some examples that caused problems in testing -160: file testGithub3226_3.png gave hash 1296655029U not the expected 3119571946U -160: file testPNGMetadata_1.png gave hash 2053548476U not the expected 997629701U +159: processing +159: launch :0 +159: launch :1 +159: launch :2 +160: file testHandDrawn-1.png gave hash 1854123184U not the expected 3894611804U +159: launch :3 161: file rxn_test2_1.png gave hash 2631413446U not the expected 3551633840U -160: file testPNGMetadata_2.png gave hash 1147517534U not the expected 1797853056U 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 161: file rxn_test2_2_1.png gave hash 1629337085U not the expected 1268122583U 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 +160: [09:33:16] Font file /build/reproducible-path/rdkit-202503.1/Data/Fonts/ComicNeue-Regular.ttf not found. +160: [09:33:16] Falling back to original font file /build/reproducible-path/rdkit-202503.1/Data/Fonts/Telex-Regular.ttf. +160: file testHandDrawn-2.svg gave hash 700659102U not the expected 794717511U +160: [09:33:16] Font file /build/reproducible-path/rdkit-202503.1/Data/Fonts/ComicNeue-Regular.ttf not found. +160: [09:33:16] Falling back to original font file /build/reproducible-path/rdkit-202503.1/Data/Fonts/Telex-Regular.ttf. 161: file rxn_test2_2_2.png gave hash 4159784239U not the expected 82821108U 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 -160: [00:36:27] Font file /build/reproducible-path/rdkit-202503.1/Data/Fonts/ComicNeue-Regular.ttf not found. -160: [00:36:27] Falling back to original font file /build/reproducible-path/rdkit-202503.1/Data/Fonts/Telex-Regular.ttf. 161: file rxn_test2_2_3.png gave hash 351157945U not the expected 3828365604U +160: file testHandDrawn-2.png gave hash 3861646972U not the expected 1443443188U +160: [09:33:16] Font file /build/reproducible-path/rdkit-202503.1/Data/Fonts/ComicNeue-Regular.ttf not found. +160: [09:33:16] Falling back to original font file /build/reproducible-path/rdkit-202503.1/Data/Fonts/Telex-Regular.ttf. 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 -160: file testHandDrawn-1.svg gave hash 1143910631U not the expected 2253418236U -160: [00:36:27] Font file /build/reproducible-path/rdkit-202503.1/Data/Fonts/ComicNeue-Regular.ttf not found. -160: [00:36:27] 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: [09:33:16] Font file /build/reproducible-path/rdkit-202503.1/Data/Fonts/ComicNeue-Regular.ttf not found. +160: [09:33:16] Falling back to original font file /build/reproducible-path/rdkit-202503.1/Data/Fonts/Telex-Regular.ttf. 161: file rxn_test2_2_4.png gave hash 3038415749U not the expected 1230108677U +160: file testHandDrawn-3.png gave hash 2744546773U not the expected 865629432U 161: Done 161: ----------------- Test 3: test reactant highlighting -160: file testHandDrawn-1.png gave hash 1854123184U not the expected 3894611804U +160: [09:33:16] Font file /build/reproducible-path/rdkit-202503.1/Data/Fonts/ComicNeue-Regular.ttf not found. +160: [09:33:16] 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: [09:33:16] Font file /build/reproducible-path/rdkit-202503.1/Data/Fonts/ComicNeue-Regular.ttf not found. +160: [09:33:16] Falling back to original font file /build/reproducible-path/rdkit-202503.1/Data/Fonts/Telex-Regular.ttf. +160: file testHandDrawn-4.png gave hash 2378590163U not the expected 3919767093U 161: file rxn_test3_1.png gave hash 3254654119U not the expected 4189980366U 161: Done 161: ----------------- Test 4: some examples from SMARTS in testing 161: draw! -160: [00:36:27] Font file /build/reproducible-path/rdkit-202503.1/Data/Fonts/ComicNeue-Regular.ttf not found. -160: [00:36:27] Falling back to original font file /build/reproducible-path/rdkit-202503.1/Data/Fonts/Telex-Regular.ttf. -160: file testHandDrawn-2.svg gave hash 700659102U not the expected 794717511U -160: [00:36:27] Font file /build/reproducible-path/rdkit-202503.1/Data/Fonts/ComicNeue-Regular.ttf not found. -160: [00:36:27] Falling back to original font file /build/reproducible-path/rdkit-202503.1/Data/Fonts/Telex-Regular.ttf. 161: file rxn_test4_1.png gave hash 4262495936U not the expected 2745201873U 161: done -160: file testHandDrawn-2.png gave hash 3861646972U not the expected 1443443188U -160: [00:36:27] Font file /build/reproducible-path/rdkit-202503.1/Data/Fonts/ComicNeue-Regular.ttf not found. -160: [00:36:27] 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: [00:36:27] Font file /build/reproducible-path/rdkit-202503.1/Data/Fonts/ComicNeue-Regular.ttf not found. -160: [00:36:27] Falling back to original font file /build/reproducible-path/rdkit-202503.1/Data/Fonts/Telex-Regular.ttf. -160: file testHandDrawn-3.png gave hash 2744546773U not the expected 865629432U -160: [00:36:27] Font file /build/reproducible-path/rdkit-202503.1/Data/Fonts/ComicNeue-Regular.ttf not found. -160: [00:36:27] 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: [00:36:27] Font file /build/reproducible-path/rdkit-202503.1/Data/Fonts/ComicNeue-Regular.ttf not found. -160: [00:36:27] Falling back to original font file /build/reproducible-path/rdkit-202503.1/Data/Fonts/Telex-Regular.ttf. -160: file testHandDrawn-4.png gave hash 2378590163U not the expected 3919767093U 161: file rxn_test4_2.png gave hash 2281531937U not the expected 3094925886U 161: Done -151/238 Test #161: moldraw2DRxnTest1 ...................... Passed 0.51 sec +151/238 Test #161: moldraw2DRxnTest1 ...................... Passed 0.26 sec test 163 Start 163: testFMCS 163: Test command: /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FMCS/testFMCS 163: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FMCS 163: Test timeout computed to be: 1500 -148: [00:36:27] Molecule does not have explicit Hs. Consider calling AddHs() -162: ...[00:36:27] Font file /build/reproducible-path/rdkit-202503.1/Code/GraphMol/MolDraw2D/Amadeus.ttf not found. -162: [00:36:27] Falling back to original font file /build/reproducible-path/rdkit-202503.1/Data/Fonts/Telex-Regular.ttf. -162: ..........[00:36:27] +148: [09:33:16] Molecule does not have explicit Hs. Consider calling AddHs() +162: ...[09:33:17] Font file /build/reproducible-path/rdkit-202503.1/Code/GraphMol/MolDraw2D/Amadeus.ttf not found. +162: [09:33:17] Falling back to original font file /build/reproducible-path/rdkit-202503.1/Data/Fonts/Telex-Regular.ttf. +162: ..........[09:33:17] 162: 162: **** +148: [09:33:17] Molecule does not have explicit Hs. Consider calling AddHs() 162: Pre-condition Violation 162: molecule must not be None 162: Violation occurred on line 432 in file ./Code/GraphMol/MolDraw2D/Wrap/rdMolDraw2D.cpp @@ -27727,7 +27761,7 @@ 162: 2# RDKit::prepMolForDrawing(RDKit::ROMol const*, bool, bool, bool, bool, bool) in /build/reproducible-path/rdkit-202503.1/obj-aarch64-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-aarch64-linux-gnu/rdkit/Chem/Draw/rdMolDraw2D.so 162: 4# boost::python::objects::function::call(_object*, _object*) const in /lib/aarch64-linux-gnu/libboost_python313.so.1.83.0 -162: 5# 0x0000FFFF96522680 in /lib/aarch64-linux-gnu/libboost_python313.so.1.83.0 +162: 5# 0x0000FFFF98FF2680 in /lib/aarch64-linux-gnu/libboost_python313.so.1.83.0 162: 6# boost::python::detail::exception_handler::operator()(boost::function0 const&) const in /lib/aarch64-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-aarch64-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-aarch64-linux-gnu/rdkit/Chem/rdDepictor.so @@ -27738,17 +27772,17 @@ 162: 13# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202503.1/obj-aarch64-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-aarch64-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-aarch64-linux-gnu/rdkit/Chem/rdchem.so -162: 16# 0x0000FFFF95B2C320 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so -162: 17# 0x0000FFFF95B2C2B8 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so -162: 18# 0x0000FFFF95B2C248 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so -162: 19# 0x0000FFFF95B2C1E0 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so -162: 20# 0x0000FFFF95B2C178 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so +162: 16# 0x0000FFFF985FC320 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so +162: 17# 0x0000FFFF985FC2B8 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so +162: 18# 0x0000FFFF985FC248 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so +162: 19# 0x0000FFFF985FC1E0 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so +162: 20# 0x0000FFFF985FC178 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-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-aarch64-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-aarch64-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-aarch64-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-aarch64-linux-gnu/rdkit/rdBase.so 162: 25# boost::python::handle_exception_impl(boost::function0) in /lib/aarch64-linux-gnu/libboost_python313.so.1.83.0 -162: 26# 0x0000FFFF9651F25C in /lib/aarch64-linux-gnu/libboost_python313.so.1.83.0 +162: 26# 0x0000FFFF98FEF25C in /lib/aarch64-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# 0x000000000053D3B0 in /usr/bin/python3 @@ -27780,55 +27814,61 @@ 162: 55# 0x000000000065EE50 in /usr/bin/python3 162: 56# Py_RunMain in /usr/bin/python3 162: 57# Py_BytesMain in /usr/bin/python3 -162: 58# 0x0000FFFF97E8229C in /lib/aarch64-linux-gnu/libc.so.6 +162: 58# 0x0000FFFF9A95229C in /lib/aarch64-linux-gnu/libc.so.6 162: 59# __libc_start_main in /lib/aarch64-linux-gnu/libc.so.6 162: 60# _start in /usr/bin/python3 162: ---------- 162: **** 162: -148: [00:36:27] Molecule does not have explicit Hs. Consider calling AddHs() +148: [09:33:17] Molecule does not have explicit Hs. Consider calling AddHs() 162: ...................... 162: ---------------------------------------------------------------------- -162: Ran 35 tests in 0.262s +162: Ran 35 tests in 0.258s 162: 162: OK 162: json lasso -148: [00:36:27] Molecule does not have explicit Hs. Consider calling AddHs() -152/238 Test #162: pyMolDraw2D ............................ Passed 0.76 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-aarch64-linux-gnu/Code/GraphMol/FMCS/Wrap -164: Test timeout computed to be: 1500 29: Checking against /build/reproducible-path/rdkit-202503.1/Code/ForceField/MMFF/test_data/MMFF94_reference.log... -148: [00:36:27] Molecule does not have explicit Hs. Consider calling AddHs() 29: All 191 tests passed 29: done 29: ------------------------------------- 29: Unit tests for all MMFF constraint terms. +160: file testHandDrawn-5a.svg gave hash 2796249138U not the expected 1567781555U +160: [09:33:17] Font file /build/reproducible-path/rdkit-202503.1/Data/Fonts/ComicNeue-Regular.ttf not found. +160: [09:33:17] Falling back to original font file /build/reproducible-path/rdkit-202503.1/Data/Fonts/Telex-Regular.ttf. 29: 10.0003 +160: file testHandDrawn-5b.svg gave hash 4043231252U not the expected 66354106U +160: [09:33:17] Font file /build/reproducible-path/rdkit-202503.1/Data/Fonts/ComicNeue-Regular.ttf not found. +160: [09:33:17] Falling back to original font file /build/reproducible-path/rdkit-202503.1/Data/Fonts/Telex-Regular.ttf. 29: done 29: ------------------------------------- 29: Unit test for MMFF TorsionConstraint close to 0 degrees. 29: done 29: ------------------------------------- 29: Unit tests for copying MMFF ForceFields. +152/238 Test #162: pyMolDraw2D ............................ Passed 0.56 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-aarch64-linux-gnu/Code/GraphMol/FMCS/Wrap +164: Test timeout computed to be: 1500 29: done 29: ------------------------------------- 29: Unit test for MMFF butane scan. -51: Randomness seeded to: 3145280805 -51: =============================================================================== -51: All tests passed (14835 assertions in 14 test cases) -51: -153/238 Test #51: canonTestsCatch ........................ Passed 14.50 sec +160: file testHandDrawn-5.png gave hash 2095603616U not the expected 828378555U +160: file testBrackets-5a.svg gave hash 279553678U not the expected 1447240271U +148: [09:33:17] Molecule does not have explicit Hs. Consider calling AddHs() +160: file testPositionVariation-1b.svg gave hash 3055422087U not the expected 3269244452U +160: [09:33:17] unrecognized bond typefile testGithub4238_1.png gave hash 3445079665U not the expected 2623427676U +160: file testGithub4323_1.png gave hash 1102454531U not the expected 3075787867U +29: done +153/238 Test #29: testMMFFForceField ..................... Passed 9.97 sec test 165 Start 165: FMCStest 165: Test command: /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FMCS/Test/FMCStest 165: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FMCS/Test 165: Test timeout computed to be: 1500 -148: [00:36:27] 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 @@ -29801,59 +29841,244 @@ 166: Test command: /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/MolHash/molHashCatchTest 166: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/MolHash 166: 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 -166: Randomness seeded to: 496983755 +146: processing +146: launch :0 +146: launch :1 +146: launch :2 +146: launch :3 +166: Randomness seeded to: 2512736419 166: =============================================================================== 166: All tests passed (363 assertions in 14 test cases) 166: -155/238 Test #166: molHashCatchTest ....................... Passed 0.08 sec +155/238 Test #166: molHashCatchTest ....................... Passed 0.09 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-aarch64-linux-gnu/Code/GraphMol/MolHash/Wrap 167: Test timeout computed to be: 1500 -29: done -156/238 Test #29: testMMFFForceField ..................... Passed 15.26 sec +163: MCS: [#6]-[#6]1-[#6]-[#6]-[#6]-[#6]-[#6]-1 7 atoms, 7 bonds +163: Time elapsed 0.003 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 0.055 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 0.005 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 0.007 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 0.056 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 0.051 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 0.059 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 0.060 seconds +163: +163: testSegFault() +163: MCS: [#6]1:&@[#6]:&@[#6]:&@[#6]:&@[#6]:&@[#6]:&@1 6 atoms, 6 bonds +163: Time elapsed 0.005 seconds +163: MCS MatchFusedRings: [#6]1:&@[#6]:&@[#6]:&@[#6]:&@[#6]:&@[#6]:&@1 6 atoms, 6 bonds +163: Time elapsed 0.007 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 0.007 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 0.166 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 0.169 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 0.189 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 +160: file testGithub4323_3.png gave hash 2734641420U not the expected 381907253U +160: [09:33:17] FIELDDISP info not found for DAT SGroup which isn't associated with an atom. SGroup will not be rendered. +167: .... +167: ---------------------------------------------------------------------- +167: Ran 4 tests in 0.022s +167: +167: OK +163: Time elapsed 0.001 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 0.008 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 0.095 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 0.0008 seconds. bond[0]=6 +163: STATISTICS: +163: Total Growing Steps = 1, MCS found on 1 step, for 0.0008 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 +148: .[09:33:18] Molecule does not have explicit Hs. Consider calling AddHs() +156/238 Test #167: pyMolHash .............................. Passed 0.41 sec test 168 Start 168: testMMPA 168: Test command: /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/MMPA/testMMPA 168: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/MMPA 168: Test timeout computed to be: 1500 -148: [00:36:28] Molecule does not have explicit Hs. Consider calling AddHs() 168: 168: TEST mol: Case1 Cc1ccccc1NC(=O)[C:7](C)[NH+]1CCCC1 Case1 -168: Time elapsed 0.002339 seconds +168: Time elapsed 0.002311 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 @@ -29894,7 +30119,7 @@ 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 0.001945 seconds +168: Time elapsed 0.002027 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 @@ -29936,7 +30161,7 @@ 168: ----------------------------------- 168: 168: TEST mol: ZINC21984717 Cc1c(C(=O)NCCO)[n+](=O)c2ccccc2n1[O-] ZINC21984717 -168: Time elapsed 0.001951 seconds +168: Time elapsed 0.002962 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] @@ -29976,7 +30201,7 @@ 168: ----------------------------------- 168: 168: TEST mol: Case1-SIMPLE CC(N1CC1)C(=O) Case1-SIMPLE -168: Time elapsed 0.000548 seconds +168: Time elapsed 0.000546 seconds 168: 1: res= NULL,C[*:1].O=CC(N1CC1)[*:1] 168: 1: PASSED. matchedRefRes = 2 168: 2: res= O=CC([*:1])[*:2],C1CN1[*:2].C[*:1] @@ -29998,7 +30223,7 @@ 168: ----------------------------------- 168: 168: TEST mol: Case1 Cc1ccccc1NC(=O)[C:7](C)[NH+]1CCCC1 Case1 -168: Time elapsed 0.002151 seconds +168: Time elapsed 0.002191 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 @@ -30041,7 +30266,7 @@ 168: ----------------------------------- 168: 168: TEST mol: Case2 O=C(OCc1ccccc1)C(O)c1ccccc1 Case2 -168: Time elapsed 0.006530 seconds +168: Time elapsed 0.002364 seconds 168: 1: res= NULL,O=C(O[*:1])C(O)c1ccccc1.c1ccc(C[*:1])cc1 168: 1: NOREF. Reference data NOT LISTED in test case. 168: 2: res= C([*:1])[*:2],O=C(O[*:1])C(O)c1ccccc1.c1ccc([*:2])cc1 @@ -30076,273 +30301,62 @@ 168: 16: NOREF. Reference data NOT LISTED in test case. 168: 17: res= O=C(OCc1ccccc1)C([*:1])[*:2],O[*:1].c1ccc([*:2])cc1 168: 17: NOREF. Reference data NOT LISTED in test case. +51: Randomness seeded to: 3972342318 +51: =============================================================================== +51: All tests passed (14835 assertions in 14 test cases) +51: 168: 18: res= NULL,O=C(OCc1ccccc1)C(O)[*:1].c1ccc([*:1])cc1 168: 18: NOREF. Reference data NOT LISTED in test case. 168: 168: --- ALL PASSED --- 168: ----------------------------------- 168: 5 TEST CASES FAILED -157/238 Test #168: testMMPA ............................... Passed 0.14 sec +157/238 Test #168: testMMPA ............................... Passed 0.16 sec test 169 Start 169: pyMMPA 169: Test command: /usr/bin/python3 "/build/reproducible-path/rdkit-202503.1/Code/GraphMol/MMPA/Wrap/testMMPA.py" 169: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/MMPA/Wrap 169: Test timeout computed to be: 1500 -160: file testHandDrawn-5a.svg gave hash 2796249138U not the expected 1567781555U -160: [00:36:28] Font file /build/reproducible-path/rdkit-202503.1/Data/Fonts/ComicNeue-Regular.ttf not found. -160: [00:36:28] Falling back to original font file /build/reproducible-path/rdkit-202503.1/Data/Fonts/Telex-Regular.ttf. -146: processing -146: launch :0 -146: launch :1 -146: launch :2 -146: launch :3 -160: file testHandDrawn-5b.svg gave hash 4043231252U not the expected 66354106U -160: [00:36:28] Font file /build/reproducible-path/rdkit-202503.1/Data/Fonts/ComicNeue-Regular.ttf not found. -160: [00:36:28] Falling back to original font file /build/reproducible-path/rdkit-202503.1/Data/Fonts/Telex-Regular.ttf. -167: .... -167: ---------------------------------------------------------------------- -167: Ran 4 tests in 0.017s -167: -167: OK -160: file testHandDrawn-5.png gave hash 2095603616U not the expected 828378555U -158/238 Test #167: pyMolHash .............................. Passed 0.41 sec +158/238 Test #51: canonTestsCatch ........................ Passed 10.27 sec test 170 Start 170: testRascalMCES 170: Test command: /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/RascalMCES/testRascalMCES 170: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/RascalMCES 170: Test timeout computed to be: 1500 -160: file testBrackets-5a.svg gave hash 279553678U not the expected 1447240271U -160: file testPositionVariation-1b.svg gave hash 3055422087U not the expected 3269244452U -160: [00:36:28] unrecognized bond typefile testGithub4238_1.png gave hash 3445079665U not the expected 2623427676U -148: .[00:36:28] Molecule does not have explicit Hs. Consider calling AddHs() -160: file testGithub4323_1.png gave hash 1102454531U not the expected 3075787867U -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 0.063 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 0.020 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 0.112 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 0.083 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 0.066 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 0.115 seconds -163: -163: testSegFault() -163: MCS: [#6]1:&@[#6]:&@[#6]:&@[#6]:&@[#6]:&@[#6]:&@1 6 atoms, 6 bonds -163: Time elapsed 0.011 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 0.010 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 0.353 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 0.386 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 0.578 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 0.013 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 -160: file testGithub4323_3.png gave hash 2734641420U not the expected 381907253U -160: [00:36:29] FIELDDISP info not found for DAT SGroup which isn't associated with an atom. SGroup will not be rendered. -163: Time elapsed 0.001 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 0.012 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 0.144 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 0.046 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 0.0008 seconds. bond[0]=6 -163: STATISTICS: -163: Total Growing Steps = 1, MCS found on 1 step, for 0.0008 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 -150: processing -150: launch :0 -150: launch :1 -150: launch :2 -150: launch :3 -169: ......... -169: ---------------------------------------------------------------------- -169: Ran 9 tests in 1.172s -169: -169: OK +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.2a.png gave hash 1840424214U not the expected 2609920321U 160: file testFlexiCanvas.2b.png gave hash 3366044980U not the expected 3615599154U -159/238 Test #169: pyMMPA ................................. Passed 1.44 sec -test 171 - Start 171: testRascalCluster - -171: Test command: /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/RascalMCES/testRascalCluster -171: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/RascalMCES -171: Test timeout computed to be: 1500 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 @@ -30357,7 +30371,7 @@ 160: file acs1996_3.svg gave hash 510450189U not the expected 879041204U 160: file acs1996_8.svg gave hash 3359655656U not the expected 4110469272U 160: file acs1996_10.svg gave hash 1008047306U not the expected 2229333301U -160: [00:36:29] 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: [09:33:18] 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 197391689U not the expected 3119784980U 160: file test_github5947.svg gave hash 737562322U not the expected 3122633523U 160: file test_github6112.svg gave hash 3291975047U not the expected 3278777629U @@ -30367,39 +30381,56 @@ 160: file testHighlightHeteroAtoms_1.svg gave hash 4006401146U not the expected 1769258632U 160: file testHighlightHeteroAtoms_2.svg gave hash 1248188292U not the expected 893937335U 160: file testGithub_7739_1.svg gave hash 1295207536U not the expected 2615562225U -163: [00:36:31] The provided InitialSeed is not an MCS and will be ignored 160: file testGithub_7739_3.svg gave hash 3850267352U not the expected 1037942338U 160: file testGithub_7739_4.svg gave hash 1411616678U not the expected 3549083171U 160: file testSmallReactionCanvas.svg gave hash 3859901121U not the expected 2238356155U +163: [09:33:19] The provided InitialSeed is not an MCS and will be ignored +150: processing +150: launch :0 +150: launch :1 +150: launch :2 +150: launch :3 160: =============================================================================== 160: All tests passed (6857 assertions in 116 test cases) 160: -160/238 Test #160: moldraw2DTestCatch ..................... Passed 4.86 sec +159/238 Test #160: moldraw2DTestCatch ..................... Passed 2.77 sec +test 171 + Start 171: testRascalCluster + +171: Test command: /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/RascalMCES/testRascalCluster +171: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/RascalMCES +171: Test timeout computed to be: 1500 +164: ........................................[09:33:19] The provided InitialSeed is not an MCS and will be ignored +164: [09:33:19] The provided InitialSeed is not an MCS and will be ignored +164: [09:33:19] The provided InitialSeed is not an MCS and will be ignored +164: .[09:33:19] The provided InitialSeed is not an MCS and will be ignored +164: [09:33:19] The provided InitialSeed is not an MCS and will be ignored +164: [09:33:19] The provided InitialSeed is not an MCS and will be ignored +164: .[09:33:19] The provided InitialSeed is not an MCS and will be ignored +164: [09:33:19] The provided InitialSeed is not an MCS and will be ignored +164: [09:33:19] The provided InitialSeed is not an MCS and will be ignored +164: .[09:33:19] The provided InitialSeed is not an MCS and will be ignored +164: [09:33:19] The provided InitialSeed is not an MCS and will be ignored +164: [09:33:19] The provided InitialSeed is not an MCS and will be ignored +164: ................. +164: ---------------------------------------------------------------------- +164: Ran 60 tests in 1.837s +164: +164: OK +160/238 Test #164: pyFMCS ................................. Passed 2.14 sec test 172 Start 172: pyRascalMCES 172: Test command: /usr/bin/python3 "/build/reproducible-path/rdkit-202503.1/Code/GraphMol/RascalMCES/Wrap/testRascalMCES.py" 172: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/RascalMCES/Wrap 172: Test timeout computed to be: 1500 -172: ..........[00:36:32] Too many matching bond pairs (1032) so can't continue. -164: ........................................[00:36:33] The provided InitialSeed is not an MCS and will be ignored -164: [00:36:33] The provided InitialSeed is not an MCS and will be ignored -164: [00:36:33] The provided InitialSeed is not an MCS and will be ignored -164: .[00:36:33] The provided InitialSeed is not an MCS and will be ignored -164: [00:36:33] The provided InitialSeed is not an MCS and will be ignored -164: [00:36:33] The provided InitialSeed is not an MCS and will be ignored -164: .[00:36:33] The provided InitialSeed is not an MCS and will be ignored -164: [00:36:33] The provided InitialSeed is not an MCS and will be ignored -164: [00:36:33] The provided InitialSeed is not an MCS and will be ignored -164: .[00:36:33] The provided InitialSeed is not an MCS and will be ignored -164: [00:36:33] The provided InitialSeed is not an MCS and will be ignored -164: [00:36:33] The provided InitialSeed is not an MCS and will be ignored -164: ................. -164: ---------------------------------------------------------------------- -164: Ran 60 tests in 5.614s -164: -164: OK -161/238 Test #164: pyFMCS ................................. Passed 6.08 sec +169: ......... +169: ---------------------------------------------------------------------- +169: Ran 9 tests in 1.685s +169: +169: OK +172: ..........[09:33:20] Too many matching bond pairs (1032) so can't continue. +161/238 Test #169: pyMMPA ................................. Passed 2.11 sec test 173 Start 173: testSynthonSpaceSubstructureSearch @@ -30408,10 +30439,12 @@ 173: Test timeout computed to be: 1500 172: .... 172: ---------------------------------------------------------------------- -172: Ran 14 tests in 1.911s +172: Ran 14 tests in 1.686s 172: 172: OK -162/238 Test #172: pyRascalMCES ........................... Passed 2.52 sec +173: Randomness seeded to: 2897899173 +173: [09:33:21] Writing the enumerated file may take quite some time and result in a large file. +162/238 Test #172: pyRascalMCES ........................... Passed 2.18 sec test 174 Start 174: testSynthonSpaceRascalSearch @@ -30541,61 +30574,57 @@ 159: Done 159: ----------------- Test AND queries 159: Done -163/238 Test #159: moldraw2DTest1 ......................... Passed 8.66 sec +163/238 Test #159: moldraw2DTest1 ......................... Passed 6.37 sec test 175 Start 175: testCIPLabeler 175: Test command: /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/CIPLabeler/testCIPLabeler 175: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/CIPLabeler 175: Test timeout computed to be: 1500 -175: Randomness seeded to: 1593096844 -175: [00:36:35] non kekulizable aromatic bond being treated as bond order 1 -175: [00:36:35] non kekulizable aromatic bond being treated as bond order 1 -175: [00:36:35] non kekulizable aromatic bond being treated as bond order 1 -175: [00:36:35] non kekulizable aromatic bond being treated as bond order 1 -175: [00:36:35] non kekulizable aromatic bond being treated as bond order 1 -175: [00:36:35] non kekulizable aromatic bond being treated as bond order 1 -175: [00:36:35] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored -175: [00:36:35] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored +175: Randomness seeded to: 1822667884 +175: [09:33:22] non kekulizable aromatic bond being treated as bond order 1 +175: [09:33:22] non kekulizable aromatic bond being treated as bond order 1 +175: [09:33:22] non kekulizable aromatic bond being treated as bond order 1 +175: [09:33:22] non kekulizable aromatic bond being treated as bond order 1 +175: [09:33:22] non kekulizable aromatic bond being treated as bond order 1 +175: [09:33:22] non kekulizable aromatic bond being treated as bond order 1 +175: [09:33:22] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored +175: [09:33:22] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored 175: =============================================================================== 175: All tests passed (6577 assertions in 19 test cases) 175: -164/238 Test #175: testCIPLabeler ......................... Passed 0.20 sec +164/238 Test #175: testCIPLabeler ......................... Passed 0.11 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-aarch64-linux-gnu/Code/GraphMol/CIPLabeler/Wrap 176: Test timeout computed to be: 1500 -171: Randomness seeded to: 941517262 -171: /build/reproducible-path/rdkit-202503.1/Code/GraphMol/RascalMCES/data/chembl_1907596.smi -173: Randomness seeded to: 2652770057 -173: [00:36:35] Writing the enumerated file may take quite some time and result in a large file. 176: .... 176: ---------------------------------------------------------------------- -176: Ran 4 tests in 0.030s +176: Ran 4 tests in 0.022s 176: 176: OK -165/238 Test #176: pyCIPLabelsWrapTest .................... Passed 0.50 sec +165/238 Test #176: pyCIPLabelsWrapTest .................... Passed 0.35 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-aarch64-linux-gnu/Code/GraphMol/CIPLabeler/Wrap 177: Test timeout computed to be: 1500 -173: [00:36:38] Building the fingerprints may take some time. -152: .............[00:36:38] Molecule does not have explicit Hs. Consider calling AddHs() -152: [00:36:38] Molecule does not have explicit Hs. Consider calling AddHs() -152: [00:36:38] Molecule does not have explicit Hs. Consider calling AddHs() -152: [00:36:38] Molecule does not have explicit Hs. Consider calling AddHs() -152: [00:36:38] Molecule does not have explicit Hs. Consider calling AddHs() -152: [00:36:38] Molecule does not have explicit Hs. Consider calling AddHs() -152: [00:36:38] Molecule does not have explicit Hs. Consider calling AddHs() -152: [00:36:38] Molecule does not have explicit Hs. Consider calling AddHs() -152: [00:36:38] Molecule does not have explicit Hs. Consider calling AddHs() -152: [00:36:38] Molecule does not have explicit Hs. Consider calling AddHs() -152: [00:36:38] Molecule does not have explicit Hs. Consider calling AddHs() -173: [00:36:39] +173: [09:33:23] Building the fingerprints may take some time. +152: .............[09:33:23] Molecule does not have explicit Hs. Consider calling AddHs() +152: [09:33:23] Molecule does not have explicit Hs. Consider calling AddHs() +152: [09:33:23] Molecule does not have explicit Hs. Consider calling AddHs() +152: [09:33:23] Molecule does not have explicit Hs. Consider calling AddHs() +152: [09:33:23] Molecule does not have explicit Hs. Consider calling AddHs() +152: [09:33:23] Molecule does not have explicit Hs. Consider calling AddHs() +152: [09:33:23] Molecule does not have explicit Hs. Consider calling AddHs() +152: [09:33:23] Molecule does not have explicit Hs. Consider calling AddHs() +152: [09:33:23] Molecule does not have explicit Hs. Consider calling AddHs() +152: [09:33:23] Molecule does not have explicit Hs. Consider calling AddHs() +152: [09:33:23] Molecule does not have explicit Hs. Consider calling AddHs() +173: [09:33:23] 173: 173: **** 173: Invariant Violation @@ -30611,69 +30640,108 @@ 173: 4# RDKit::molzip(RDKit::ROMol const&, RDKit::MolzipParams const&) in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu//lib/libRDKitChemTransforms.so.1 173: 5# RDKit::SynthonSpaceSearch::SynthonSet::makeSynthonSearchMols() in /build/reproducible-path/rdkit-202503.1/obj-aarch64-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-aarch64-linux-gnu//lib/libRDKitSynthonSpaceSearch.so.1 -173: 7# 0x0000AAAABBD0DB50 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/SynthonSpaceSearch/testSynthonSpaceSubstructureSearch -173: 8# 0x0000AAAABBD5570C in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/SynthonSpaceSearch/testSynthonSpaceSubstructureSearch -173: 9# 0x0000AAAABBD560C0 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/SynthonSpaceSearch/testSynthonSpaceSubstructureSearch -173: 10# 0x0000AAAABBD564F4 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/SynthonSpaceSearch/testSynthonSpaceSubstructureSearch -173: 11# 0x0000AAAABBD2A978 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/SynthonSpaceSearch/testSynthonSpaceSubstructureSearch -173: 12# 0x0000AAAABBD2AEC4 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/SynthonSpaceSearch/testSynthonSpaceSubstructureSearch -173: 13# 0x0000AAAABBD0CC10 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/SynthonSpaceSearch/testSynthonSpaceSubstructureSearch -173: 14# 0x0000FFFFB42F229C in /lib/aarch64-linux-gnu/libc.so.6 +173: 7# 0x0000AAAABD38DB50 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/SynthonSpaceSearch/testSynthonSpaceSubstructureSearch +173: 8# 0x0000AAAABD3D570C in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/SynthonSpaceSearch/testSynthonSpaceSubstructureSearch +173: 9# 0x0000AAAABD3D60C0 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/SynthonSpaceSearch/testSynthonSpaceSubstructureSearch +173: 10# 0x0000AAAABD3D64F4 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/SynthonSpaceSearch/testSynthonSpaceSubstructureSearch +173: 11# 0x0000AAAABD3AA978 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/SynthonSpaceSearch/testSynthonSpaceSubstructureSearch +173: 12# 0x0000AAAABD3AAEC4 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/SynthonSpaceSearch/testSynthonSpaceSubstructureSearch +173: 13# 0x0000AAAABD38CC10 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/SynthonSpaceSearch/testSynthonSpaceSubstructureSearch +173: 14# 0x0000FFFF9229229C in /lib/aarch64-linux-gnu/libc.so.6 173: 15# __libc_start_main in /lib/aarch64-linux-gnu/libc.so.6 -173: 16# 0x0000AAAABBD0CCF0 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/SynthonSpaceSearch/testSynthonSpaceSubstructureSearch +173: 16# 0x0000AAAABD38CCF0 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/SynthonSpaceSearch/testSynthonSpaceSubstructureSearch 173: ---------- 173: **** 173: -173: [00:36:39] Error:: in reaction amide-1 :: building molecule from synthons : 1-1 (c1cc[1*]ccc1C(=O)[1*]) and 2-1 ([1*]N1CCCC1) +173: [09:33:23] 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: [00:36:39] Explicit valence for atom # 4 C, 5, is greater than permitted -173: [00:36:39] Error:: in reaction error-1 :: building molecule from synthons : 1-1 (C(=[2*])=CC=[1*]) and 2-1 (ClC([2*])=CN=[1*]) +173: [09:33:23] Explicit valence for atom # 4 C, 5, is greater than permitted +173: [09:33:23] 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: [00:36:39] Complex queries can be slow. -173: [00:36:39] Complex queries can be slow. -170: Randomness seeded to: 2055190247 -170: [00:36:39] Timed out after 11 seconds. -173: [00:36:39] Complex queries can be slow. -173: [00:36:39] Complex queries can be slow. -173: [00:36:40] Complex queries can be slow. -173: [00:36:40] Complex queries can be slow. -173: [00:36:40] Complex queries can be slow. -173: [00:36:40] Complex queries can be slow. -173: [00:36:40] Complex queries can be slow. -173: [00:36:41] Complex queries can be slow. -173: [00:36:41] Complex queries can be slow. -152: ...[00:36:41] Molecule does not have explicit Hs. Consider calling AddHs() -152: [00:36:41] Molecule does not have explicit Hs. Consider calling AddHs() -152: [00:36:41] Molecule does not have explicit Hs. Consider calling AddHs() -152: [00:36:41] Molecule does not have explicit Hs. Consider calling AddHs() -152: [00:36:41] Molecule does not have explicit Hs. Consider calling AddHs() +173: [09:33:23] Complex queries can be slow. +171: Randomness seeded to: 1591095040 +171: /build/reproducible-path/rdkit-202503.1/Code/GraphMol/RascalMCES/data/chembl_1907596.smi +173: [09:33:24] Complex queries can be slow. +173: [09:33:24] Complex queries can be slow. +173: [09:33:24] Complex queries can be slow. +173: [09:33:24] Complex queries can be slow. +173: [09:33:24] Complex queries can be slow. +173: [09:33:24] Complex queries can be slow. +173: [09:33:25] Complex queries can be slow. +173: [09:33:25] Complex queries can be slow. +173: [09:33:25] Complex queries can be slow. +173: [09:33:25] Complex queries can be slow. +152: ...[09:33:27] Molecule does not have explicit Hs. Consider calling AddHs() +152: [09:33:27] Molecule does not have explicit Hs. Consider calling AddHs() +152: [09:33:27] Molecule does not have explicit Hs. Consider calling AddHs() +152: [09:33:27] Molecule does not have explicit Hs. Consider calling AddHs() +152: [09:33:27] Molecule does not have explicit Hs. Consider calling AddHs() 152: ... 152: ---------------------------------------------------------------------- -152: Ran 19 tests in 15.876s +152: Ran 19 tests in 11.254s 152: 152: OK 152: Testing MolAlign Wrappers -166/238 Test #152: pyMolAlign ............................. Passed 16.24 sec +166/238 Test #152: pyMolAlign ............................. Passed 11.67 sec test 178 Start 178: deprotectTest 178: Test command: /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/Deprotect/deprotectTest 178: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/Deprotect 178: Test timeout computed to be: 1500 -178: Randomness seeded to: 352901392 +178: Randomness seeded to: 2756521574 178: =============================================================================== 178: All tests passed (111 assertions in 3 test cases) 178: -167/238 Test #178: deprotectTest .......................... Passed 0.17 sec +167/238 Test #178: deprotectTest .......................... Passed 0.13 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-aarch64-linux-gnu/Code/GraphMol/Deprotect/Wrap 179: Test timeout computed to be: 1500 +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 11.00 seconds +168/238 Test #163: testFMCS ............................... Passed 11.07 sec +test 180 + Start 180: testReducedGraphs + +180: Test command: /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/ReducedGraphs/testReducedGraphs +180: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/ReducedGraphs +180: Test timeout computed to be: 1500 +180: Size: 315 [ 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 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, 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Passed 0.05 sec +test 181 + Start 181: pyReducedGraphs + +181: Test command: /usr/bin/python3 "/build/reproducible-path/rdkit-202503.1/Code/GraphMol/ReducedGraphs/Wrap/testReducedGraphs.py" +181: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/ReducedGraphs/Wrap +181: Test timeout computed to be: 1500 179: ..... 179: ---------------------------------------------------------------------- -179: Ran 5 tests in 0.094s +179: Ran 5 tests in 0.068s 179: 179: OK 179: Testing tert-butyldimethylsilyl @@ -30726,80 +30794,68 @@ 179: Testing acetamide 179: Testing carbobenzyloxy 179: Testing Acetal/Ketal -168/238 Test #179: pyDeprotect ............................ Passed 1.20 sec -test 180 - Start 180: testReducedGraphs - -180: Test command: /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/ReducedGraphs/testReducedGraphs -180: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/ReducedGraphs -180: Test timeout computed to be: 1500 -180: Size: 315 [ 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0.3, 1, 0.3, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0.3, 1, 0.3, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 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0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0.3, 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: -169/238 Test #180: testReducedGraphs ...................... Passed 0.04 sec -test 181 - Start 181: pyReducedGraphs - -181: Test command: /usr/bin/python3 "/build/reproducible-path/rdkit-202503.1/Code/GraphMol/ReducedGraphs/Wrap/testReducedGraphs.py" -181: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/ReducedGraphs/Wrap -181: Test timeout computed to be: 1500 181: ..... 181: ---------------------------------------------------------------------- -181: Ran 5 tests in 0.019s +181: Ran 5 tests in 0.018s 181: 181: OK -170/238 Test #181: pyReducedGraphs ........................ Passed 0.49 sec +170/238 Test #179: pyDeprotect ............................ Passed 0.70 sec test 182 Start 182: trajectoryTest 182: Test command: /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/Trajectory/trajectoryTest 182: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/Trajectory 182: Test timeout computed to be: 1500 -171/238 Test #182: trajectoryTest ......................... Passed 0.28 sec +171/238 Test #181: pyReducedGraphs ........................ Passed 0.43 sec test 183 Start 183: substructLibraryTest 183: Test command: /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/SubstructLibrary/substructLibraryTest 183: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/SubstructLibrary 183: Test timeout computed to be: 1500 -183: [00:36:44] ------------------------------------- -183: [00:36:44] Test1 -183: [00:36:44] done -183: [00:36:44] ------------------------------------- -183: [00:36:44] Test2 -183: [00:36:44] done -183: [00:36:44] ------------------------------------- -183: [00:36:44] Test3 (stereo options) -183: [00:36:44] Done (stereo options) -183: [00:36:44] ------------------------------------- -183: [00:36:44] Test4 (trusted smiles) -183: [00:36:44] Done (trusted smiles) -183: [00:36:44] ------------------------------------- -183: [00:36:44] Testing C++ docs -183: [00:36:44] Done (C++ doc tests) -183: [00:36:44] ------------------------------------- -183: [00:36:44] Testing C++ ring query: PatternHolder -183: [00:36:44] Done (C++ ring query tests) -183: [00:36:44] ------------------------------------- -183: [00:36:44] Testing C++ ring query: TautomerPatternHolder -183: [00:36:44] Done (C++ ring query tests) -183: [00:36:44] ------------------------------------- -183: [00:36:44] Add Patterns +183: [09:33:28] ------------------------------------- +183: [09:33:28] Test1 +172/238 Test #182: trajectoryTest ......................... Passed 0.31 sec +test 184 + Start 184: substructLibraryCatchTest + +184: Test command: /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/SubstructLibrary/substructLibraryCatchTest +184: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/SubstructLibrary +184: Test timeout computed to be: 1500 +183: [09:33:28] done +183: [09:33:28] ------------------------------------- +183: [09:33:28] Test2 +183: [09:33:28] done +183: [09:33:28] ------------------------------------- +183: [09:33:28] Test3 (stereo options) +183: [09:33:29] Done (stereo options) +183: [09:33:29] ------------------------------------- +183: [09:33:29] Test4 (trusted smiles) +183: [09:33:29] Done (trusted smiles) +183: [09:33:29] ------------------------------------- +183: [09:33:29] Testing C++ docs +183: [09:33:29] Done (C++ doc tests) +183: [09:33:29] ------------------------------------- +183: [09:33:29] Testing C++ ring query: PatternHolder +183: [09:33:29] Done (C++ ring query tests) +183: [09:33:29] ------------------------------------- +183: [09:33:29] Testing C++ ring query: TautomerPatternHolder +183: [09:33:29] Done (C++ ring query tests) +183: [09:33:29] ------------------------------------- +183: [09:33:29] Add Patterns +184: Randomness seeded to: 4023640114 +184: =============================================================================== +184: All tests passed (171 assertions in 5 test cases) +184: +173/238 Test #184: substructLibraryCatchTest .............. Passed 0.56 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-aarch64-linux-gnu/Code/GraphMol/SubstructLibrary/Wrap +185: Test timeout computed to be: 1500 +170: Randomness seeded to: 1387815941 +170: [09:33:29] Timed out after 11 seconds. 177: VS001: PASSED 177: VS002: PASSED 177: VS003: PASSED @@ -31102,1069 +31158,1062 @@ 177: VS300: PASSED 177: Check finished: 0 molecules failed. 177: Failed: -172/238 Test #177: pyCIPLabelsValidation .................. Passed 12.03 sec -test 184 - Start 184: substructLibraryCatchTest - -184: Test command: /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/SubstructLibrary/substructLibraryCatchTest -184: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/SubstructLibrary -184: Test timeout computed to be: 1500 -183: [00:36:48] ------------------------------------- -183: [00:36:48] testing PatternHolder -183: [00:36:48] ------------------------------------- -183: [00:36:48] testing TautomerPatternHolder -184: Randomness seeded to: 3016088464 -184: =============================================================================== -184: All tests passed (171 assertions in 5 test cases) -184: -173/238 Test #184: substructLibraryCatchTest .............. Passed 0.59 sec -test 185 - Start 185: pySubstructLibrary +174/238 Test #177: pyCIPLabelsValidation .................. Passed 6.65 sec +test 186 + Start 186: testRGroupDecomp -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-aarch64-linux-gnu/Code/GraphMol/SubstructLibrary/Wrap -185: Test timeout computed to be: 1500 -183: [00:36:48] ------------------------------------- -183: [00:36:48] testSegFaultInHolder -183: [00:36:48] SMILES Parse Error: syntax error while parsing: dsafsdf -183: [00:36:48] SMILES Parse Error: check for mistakes around position 1: -183: [00:36:48] dsafsdf -183: [00:36:48] ^ -183: [00:36:48] SMILES Parse Error: syntax error while parsing: dsafsdf -183: [00:36:48] SMILES Parse Error: check for mistakes around position 1: -183: [00:36:48] dsafsdf -183: [00:36:48] ^ -183: [00:36:48] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -183: [00:36:48] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -183: [00:36:48] SMILES Parse Error: syntax error while parsing: dsafsdf -183: [00:36:48] SMILES Parse Error: check for mistakes around position [00:36:48] 1: -183: [00:36:48] dsafsdf -183: [00:36:48] ^ -183: [00:36:48] SMILES Parse Error: syntax error while parsing: dsafsdf -183: [00:36:48] SMILES Parse Error: check for mistakes around position 1: -183: [00:36:48] dsafsdf -183: [00:36:48] ^ -183: [00:36:48] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -183: [00:36:48] SMILES Parse Error: syntax error while parsing: dsafsdf -183: [00:36:48] SMILES Parse Error: check for mistakes around position 1: -183: [00:36:48] dsafsdf -183: [00:36:48] ^ -183: [00:36:48] SMILES Parse Error: syntax error while parsing: dsafsdf -183: [00:36:48] SMILES Parse Error: check for mistakes around position 1: -183: [00:36:48] dsafsdf[00:36:48] [00:36:48] SMILES Parse Error: syntax error while parsing: dsafsdf -183: [00:36:48] SMILES Parse Error: check for mistakes around position 1: -183: [00:36:48] [00:36:48] SMILES Parse Error: syntax error while parsing: dsafsdf -183: [00:36:48] SMILES Parse Error: check for mistakes around position 1:[00:36:48] SMILES Parse Error: syntax error while parsing: dsafsdf -183: [00:36:48] SMILES Parse Error: check for mistakes around position 1: -183: [00:36:48] dsafsdf -183: [00:36:48] ^ -183: [00:36:48] SMILES Parse Error: syntax error while parsing: dsafsdf -183: [00:36:48] SMILES Parse Error: check for mistakes around position 1:[00:36:48] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -183: [00:36:48] SMILES Parse Error: syntax error while parsing: dsafsdf -183: [00:36:48] SMILES Parse Error: check for mistakes around position 1: -183: [00:36:48] dsafsdf -183: [00:36:48] ^ -183: [00:36:48] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -183: [00:36:48] SMILES Parse Error: syntax error while parsing: dsafsdf -183: [00:36:48] SMILES Parse Error: check for mistakes around position 1: -183: [00:36:48] dsafsdf -183: [00:36:48] ^ -183: [00:36:48] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -183: [00:36:48] SMILES Parse Error: syntax error while parsing: dsafsdf -183: [00:36:48] SMILES Parse Error: check for mistakes around position 1: -183: [00:36:48] dsafsdf -183: [00:36:48] ^ -183: [00:36:48] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -183: [00:36:48] SMILES Parse Error: syntax error while parsing: dsafsdf -183: [00:36:48] SMILES Parse Error: check for mistakes around position 1: -183: [00:36:48] dsafsdf -183: [00:36:48] ^ -183: [00:36:48] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -183: [00:36:48] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -183: [00:36:48] SMILES Parse Error: syntax error while parsing: dsafsdf -183: [00:36:48] SMILES Parse Error: check for mistakes around position 1: -183: [00:36:48] dsafsdf -183: [00:36:48] ^ -183: [00:36:48] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -183: [00:36:48] SMILES Parse Error: syntax error while parsing: dsafsdf -183: [00:36:48] SMILES Parse Error: check for mistakes around position 1: -183: [00:36:48] dsafsdf -183: [00:36:48] ^ -183: [00:36:48] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -183: [00:36:48] SMILES Parse Error: syntax error while parsing: dsafsdf -183: [00:36:48] SMILES Parse Error: check for mistakes around position 1: -183: [00:36:48] dsafsdf -183: [00:36:48] ^ -183: [00:36:48] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -183: -183: [00:36:48] dsafsdf -183: [00:36:48] ^ -183: [00:36:48] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -183: [00:36:48] SMILES Parse Error: syntax error while parsing: dsafsdf -183: [00:36:48] SMILES Parse Error: check for mistakes around position 1: -183: [00:36:48] dsafsdf -183: [00:36:48] ^ -183: [00:36:48] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -183: [00:36:48] SMILES Parse Error: syntax error while parsing: dsafsdf -183: [00:36:48] SMILES Parse Error: check for mistakes around position 1: -183: [00:36:48] dsafsdf -183: [00:36:48] ^ -183: [00:36:48] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -183: [00:36:48] SMILES Parse Error: syntax error while parsing: dsafsdf -183: [00:36:48] SMILES Parse Error: check for mistakes around position 1: -183: [00:36:48] dsafsdf -183: [00:36:48] ^ -183: [00:36:48] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -183: [00:36:48] SMILES Parse Error: syntax error while parsing: dsafsdf -183: [00:36:48] SMILES Parse Error: check for mistakes around position 1: -183: [00:36:48] dsafsdfSMILES Parse Error: [00:36:48] -183: dsafsdf[00:36:48] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -183: +186: Test command: /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/RGroupDecomposition/testRGroupDecomp +186: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/RGroupDecomposition +186: Test timeout computed to be: 1500 +186: [09:33:30] Non terminal R group defined. To allow set allowNonTerminalRGroups in RGroupDecompositionParameters +186: [09:33:30] WARNING: not removing hydrogen atom with dummy atom neighbors +183: [09:33:30] ------------------------------------- +183: [09:33:30] testing PatternHolder +183: [09:33:31] ------------------------------------- +183: [09:33:31] testing TautomerPatternHolder +183: [09:33:31] ------------------------------------- +183: [09:33:31] testSegFaultInHolder +183: [09:33:31] SMILES Parse Error: syntax error while parsing: dsafsdf +183: [09:33:31] SMILES Parse Error: check for mistakes around position 1: +183: [09:33:31] dsafsdf +183: [09:33:31] ^ +183: [09:33:31] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +183: [09:33:31] SMILES Parse Error: syntax error while parsing: [09:33:31] SMILES Parse Error: syntax error while parsing: dsafsdf +183: [09:33:31] SMILES Parse Error: check for mistakes around position 1: +183: [09:33:31] dsafsdf +183: [09:33:31] ^ +183: [09:33:31] SMILES Parse Error: syntax error while parsing: dsafsdf +183: [09:33:31] SMILES Parse Error: check for mistakes around position 1: +183: [09:33:31] dsafsdf +183: [09:33:31] ^ +183: [09:33:31] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +183: [09:33:31] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +183: [09:33:31] SMILES Parse Error: syntax error while parsing: dsafsdf +183: [09:33:31] SMILES Parse Error: check for mistakes around position 1: +183: [09:33:31] dsafsdf +183: [09:33:31] ^ +183: [09:33:31] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +183: [09:33:31] SMILES Parse Error: syntax error while parsing: dsafsdf +183: [09:33:31] SMILES Parse Error: check for mistakes around position 1: +183: [09:33:31] dsafsdf +183: [09:33:31] ^ +183: [09:33:31] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +183: [09:33:31] SMILES Parse Error: syntax error while parsing: dsafsdf +183: [09:33:31] SMILES Parse Error: check for mistakes around position 1: +183: [09:33:31] dsafsdf +183: [09:33:31] ^ +183: [09:33:31] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +183: [09:33:31] SMILES Parse Error: syntax error while parsing: dsafsdf +183: [09:33:31] SMILES Parse Error: check for mistakes around position 1: +183: [09:33:31] dsafsdf +183: [09:33:31] ^ +183: [09:33:31] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +183: [09:33:31] SMILES Parse Error: syntax error while parsing: dsafsdf +183: [09:33:31] SMILES Parse Error: check for mistakes around position 1: +183: [09:33:31] dsafsdf +183: [09:33:31] ^ +183: [09:33:31] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +183: [09:33:31] SMILES Parse Error: syntax error while parsing: dsafsdf +183: [09:33:31] SMILES Parse Error: check for mistakes around position 1: +183: [09:33:31] dsafsdf +183: [09:33:31] ^ +183: [09:33:31] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +183: [09:33:31] SMILES Parse Error: syntax error while parsing: dsafsdf +183: [09:33:31] SMILES Parse Error: check for mistakes around position 1: +183: [09:33:31] dsafsdf +183: [09:33:31] ^ +183: [09:33:31] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +183: [09:33:31] SMILES Parse Error: syntax error while parsing: dsafsdf +183: [09:33:31] SMILES Parse Error: check for mistakes around position 1: +183: [09:33:31] dsafsdf +183: [09:33:31] ^ +183: [09:33:31] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +183: [09:33:31] SMILES Parse Error: syntax error while parsing: dsafsdf +183: [09:33:31] SMILES Parse Error: check for mistakes around position 1: +183: [09:33:31] dsafsdf +183: [09:33:31] ^ +183: [09:33:31] SMILES Parse Error: syntax error while parsing: dsafsdf +183: [09:33:31] dsafsdf +183: [09:33:31] SMILES Parse Error: check for mistakes around position 1: +183: [09:33:31] dsafsdf +183: [09:33:31] ^ +183: [09:33:31] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +183: [09:33:31] SMILES Parse Error: syntax error while parsing: dsafsdf +183: [09:33:31] SMILES Parse Error: syntax error while parsing: dsafsdf +183: [09:33:31] SMILES Parse Error: check for mistakes around position 1: +183: [09:33:31] dsafsdf +183: [09:33:31] SMILES Parse Error: syntax error while parsing: dsafsdf +183: [09:33:31] SMILES Parse Error: check for mistakes around position 1: +183: [09:33:31] SMILES Parse Error: syntax error while parsing: dsafsdfSMILES Parse Error: check for mistakes around position [09:33:31] SMILES Parse Error: syntax error while parsing: dsafsdf +183: [09:33:31] SMILES Parse Error: check for mistakes around position 1: +183: [09:33:31] dsafsdf +183: 1[09:33:31] ^ +183: : +183: [09:33:31] dsafsdf +183: [09:33:31] ^[09:33:31] +183: [09:33:31] +183: SMILES[09:33:31] [09:33:31] ^ +183: dsafsdf[09:33:31] [09:33:31] SMILES Parse Error: [09:33:31] [09:33:31] [09:33:31] [09:33:31] SMILES Parse Error: Failed parsing SMILES 'dsafsdf'SMILES Parse Error: check for mistakes around position for input: '1: +183: dsafsdfSMILES Parse Error: check for mistakes around position ' +183: syntax error Parse Error: SMILES Parse Error: SMILESsyntax error +183: 1: +183: [09:33:31] while parsing: [09:33:31] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf'^dsafsdfdsafsdf 183: -183: [00:36:48] ^ -183: [00:36:48] dsafsdf -183: [00:36:48] ^ -183: [00:36:48] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -183: [00:36:48] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -183: [00:36:48] SMILES Parse Error: syntax error while parsing: dsafsdf -183: [00:36:48] SMILES Parse Error: check for mistakes around position 1: -183: [00:36:48] dsafsdf -183: [00:36:48] ^ -183: [00:36:48] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -183: [00:36:48] SMILES Parse Error: syntax error while parsing: dsafsdf -183: [00:36:48] SMILES Parse Error: check for mistakes around position 1: -183: [00:36:48] dsafsdf -183: [00:36:48] ^ -183: [00:36:48] [00:36:48] SMILES Parse Error: syntax error while parsing: dsafsdfSMILES Parse Error: [00:36:48] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -183: syntax error while parsing: dsafsdf -183: [00:36:48] SMILES Parse Error: check for mistakes around position 1: -183: [00:36:48] dsafsdf -183: [00:36:48] ^ -183: [00:36:48] SMILES Parse Error: syntax error while parsing: dsafsdf -183: [00:36:48] [00:36:48] -183: [00:36:48] SMILES Parse Error: check for mistakes around position 1: -183: [00:36:48] dsafsdf -183: [00:36:48] SMILESSMILES Parse Error: check for mistakes around position 1: Parse Error: ^ -183: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -183: [00:36:48] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -183: [00:36:48] SMILES Parse Error: syntax error while parsing: dsafsdf -183: [00:36:48] SMILES Parse Error: check for mistakes around position 1:[00:36:48] SMILES Parse Error: syntax error while parsing: dsafsdf -183: [00:36:48] SMILES Parse Error: check for mistakes around position +183: while parsing: Failed parsing SMILES 'dsafsdf' 183: -183: [00:36:48] dsafsdf -183: [00:36:48] [00:36:48] 1: -183: dsafsdf^ +183: [09:33:31] dsafsdf +183: [09:33:31] SMILES Parse Error: check for mistakes around position 1:SMILES Parse Error: check for mistakes around position 1: +183: [09:33:31] [09:33:31] [09:33:31] SMILES Parse Error: syntax error while parsing: [09:33:31] dsafsdf[09:33:31] Parse Error: ^Failed parsing SMILES 'dsafsdf' +183: for input: ' +183: dsafsdf'dsafsdfSMILESSMILES Parse Error: syntax error while parsing: dsafsdf Parse Error: [09:33:31] +183: dsafsdf 183: -183: [00:36:48] ^ -183: [00:36:48] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -183: [00:36:48] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -183: [00:36:48] SMILES Parse Error: syntax error while parsing: dsafsdf -183: [00:36:48] SMILES Parse Error: check for mistakes around position 1: -183: [00:36:48] dsafsdf -183: [00:36:48] ^ -183: [00:36:48] [00:36:48] dsafsdf -183: SMILES Parse Error: syntax error while parsing: dsafsdf -183: [00:36:48] SMILES Parse Error: check for mistakes around position 1: -183: [00:36:48] [00:36:48] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +183: [09:33:31] Failed parsing SMILES 'dsafsdf'SMILES for input: ' +183: dsafsdf[09:33:31] '[09:33:31] SMILES Parse Error: check for mistakes around position 1^ +183: Parse Error: :[09:33:31] 183: dsafsdf -183: [00:36:48] ^ -183: [00:36:48] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -183: [00:36:48] ^ -183: [00:36:48] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -183: [00:36:48] SMILES Parse Error: syntax error while parsing: dsafsdf -183: [00:36:48] SMILES Parse Error: check for mistakes around position 1: -183: [00:36:48] dsafsdf -183: [00:36:48] ^ -183: [00:36:48] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -183: [00:36:48] ^ -183: SMILES Parse Error: syntax error while parsing: dsafsdf -183: [00:36:48] SMILES Parse Error: [00:36:48] syntax error while parsing: dsafsdfSMILES Parse Error: syntax error while parsing: dsafsdfFailed parsing SMILES 'dsafsdf' for input: 'dsafsdf +183: [09:33:31] ^ +183: [09:33:31] Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +183: [09:33:31] SMILES Parse Error: +183: [09:33:31] [09:33:31] SMILES Parse Error: syntax error while parsing: dsafsdf +183: [09:33:31] [09:33:31] for input: 'SMILES Parse Error: SMILES^[09:33:31] syntax errorSMILES Parse Error: check for mistakes around position 1Failed parsing SMILES 'dsafsdf' Parse Error: for input: 'dsafsdfdsafsdfFailed parsing SMILES 'dsafsdf' for input: 'dsafsdf''SMILES Parse Error: check for mistakes around position 183: -183: [00:36:48] SMILES Parse Error: check for mistakes around position SMILES Parse Error: check for mistakes around position 1[00:36:48] SMILES Parse Error: check for mistakes around position 1:1: +183: 1: while parsing: 183: 183: : -183: [00:36:48] [00:36:48] [00:36:48] dsafsdf' +183: [09:33:31] [09:33:31] [09:33:31] dsafsdf' +183: [09:33:31] SMILES Parse Error: syntax error while parsing: dsafsdf +183: [09:33:31] SMILES Parse Error: check for mistakes around position dsafsdf +183: 1: 183: -183: dsafsdf -183: [00:36:48] dsafsdf -183: ^[00:36:48] -183: [00:36:48] ^ -183: [00:36:48] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -183: [00:36:48] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -183: [00:36:48] SMILES Parse Error: syntax error while parsing: dsafsdf -183: [00:36:48] SMILES Parse Error: check for mistakes around position 1: -183: [00:36:48] dsafsdf -183: [00:36:48] ^ -183: [00:36:48] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -183: [00:36:48] SMILES Parse Error: syntax error while parsing: dsafsdf -183: [00:36:48] SMILES Parse Error: check for mistakes around position 1: -183: [00:36:48] ^ -183: [00:36:48] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -183: [00:36:48] SMILES Parse Error: syntax error while parsing: dsafsdf -183: [00:36:48] SMILES Parse Error: check for mistakes around position 1: -183: [00:36:48] dsafsdf -183: [00:36:48] ^ -183: [00:36:48] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: '[00:36:48] SMILES Parse Error: syntax error while parsing: dsafsdfSMILES Parse Error: dsafsdf'[00:36:48] dsafsdf -183: [00:36:48] syntax error while parsing: SMILES Parse Error: check for mistakes around position -183: [00:36:48] ^1dsafsdf -183: : +183: [09:33:31] SMILES Parse Error: dsafsdf +183: [09:33:31] +183: syntax errordsafsdf[09:33:31] +183: SMILES Parse Error: [09:33:31] syntax error while parsing: [09:33:31] SMILES Parse Error: check for mistakes around position dsafsdfdsafsdf +183: 1[09:33:31] : +183: [09:33:31] ^ +183: while parsing: dsafsdf^ +183: [09:33:31] +183: SMILES Parse Error: check for mistakes around position [09:33:31] [09:33:31] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +183: ^1 183: -183: [00:36:48] dsafsdf -183: [00:36:48] ^ -183: [00:36:48] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -183: [00:36:48] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -183: [00:36:48] SMILES Parse Error: syntax error while parsing: dsafsdf -183: [00:36:48] SMILES Parse Error: check for mistakes around position 1: -183: [00:36:48] [00:36:48] [00:36:48] SMILES Parse Error: check for mistakes around position 1 -183: : -183: [00:36:48] dsafsdf -183: [00:36:48] ^ -183: [00:36:48] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -183: [00:36:48] SMILES Parse Error: syntax error while parsing: dsafsdf -183: [00:36:48] SMILES Parse Error: check for mistakes around position 1: -183: [00:36:48] dsafsdf -183: [00:36:48] ^ -183: [00:36:48] SMILES[00:36:48] SMILES Parse Error: syntax error while parsing: dsafsdfSMILES Parse Error: Parse Error: Failed parsing SMILES 'dsafsdf'dsafsdf -183: for input: 'syntax error while parsing: dsafsdf[00:36:48] -183: [00:36:48] ^' +183: [09:33:31] [09:33:31] dsafsdf:[09:33:31] [09:33:31] +183: [09:33:31] dsafsdfSMILES[09:33:31] Parse Error: SMILES Parse Error: SMILES Parse Error: SMILES Parse Error: check for mistakes around position syntax error while parsing: dsafsdf +183: Failed parsing SMILES 'dsafsdf' +183: [09:33:31] +183: SMILES[09:33:31] 1 for input: ': +183: dsafsdf[09:33:31] Parse Error: [09:33:31] ^Failed parsing SMILES 'dsafsdf'SMILES Parse Error: dsafsdfSMILES Parse Error: check for mistakes around position ' +183: [09:33:31] ^ for input: 'syntax errordsafsdf +183: Failed parsing SMILES 'dsafsdf' while parsing: for input: 'dsafsdf'[09:33:31] [09:33:31] +183: SMILES Parse Error: Failed parsing SMILES 'dsafsdf' +183: ^1 +183: for input: ': +183: [09:33:31] dsafsdfdsafsdf +183: ' +183: [09:33:31] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: ''[09:33:31] SMILES Parse Error: +183: [09:33:31] [09:33:31] Failed parsing SMILES 'dsafsdf' for input: 'dsafsdfSMILES Parse Error: SMILES Parse Error: syntax errordsafsdf while parsing: dsafsdf +183: [09:33:31] ' +183: syntax error' while parsing: dsafsdfdsafsdf +183: [09:33:31] +183: ^ +183: [09:33:31] SMILES Parse Error: check for mistakes around position [09:33:31] [09:33:31] ^ +183: [09:33:31] SMILES Parse Error: check for mistakes around position 1[09:33:31] 1SMILESSMILES Parse Error: syntax error: +183: SMILES Parse Error: syntax error while parsing: +183: Parse Error: [09:33:31] dsafsdf +183: [09:33:31] [09:33:31] :SMILES Parse Error: +183: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf +183: '[09:33:31] dsafsdfSMILES Parse Error: ^[09:33:31] +183: dsafsdfFailed parsing SMILES 'dsafsdf' 183: -183: SMILES Parse Error: check for mistakes around position 1: -183: dsafsdf -183: [00:36:48] [00:36:48] dsafsdf -183: [00:36:48] ^ -183: [00:36:48] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf'[00:36:48] SMILES Parse Error: check for mistakes around position 1: -183: [00:36:48] dsafsdf -183: [00:36:48] ^ -183: [00:36:48] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -183: [00:36:48] SMILES Parse Error: syntax error while parsing: dsafsdf -183: [00:36:48] SMILES Parse Error: check for mistakes around position 1: -183: [00:36:48] dsafsdf -183: [00:36:48] ^ -183: [00:36:48] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -183: SMILES Parse Error: syntax error while parsing: dsafsdf -183: [00:36:48] SMILES Parse Error: check for mistakes around position 1: -183: [00:36:48] dsafsdf -183: [00:36:48] ^ -183: [00:36:48] SMILES Parse Error: syntax error while parsing: [00:36:48] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: '[00:36:48] -183: SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +183: for input: 'dsafsdf' +183: syntax error[09:33:31] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' while parsing: [09:33:31] dsafsdf^ +183: [09:33:31] [09:33:31] SMILES Parse Error: syntax error while parsing: dsafsdf +183: [09:33:31] SMILES Parse Error: SMILES Parse Error: check for mistakes around position [09:33:31] syntax error while parsing: dsafsdf +183: SMILES +183: [09:33:31] +183: [09:33:31] Parse Error: SMILES Parse Error: check for mistakes around position 11[09:33:31] SMILES Parse Error: check for mistakes around position Failed parsing SMILES 'dsafsdf':SMILES Parse Error: check for mistakes around position 1:: for input: 'dsafsdf' +183: +183: [09:33:31] dsafsdf for input: 'dsafsdf' +183: +183: [09:33:31] dsafsdf +183: [09:33:31] ^ +183: [09:33:31] SMILES Parse Error: check for mistakes around position 1: +183: +183: [09:33:31] SMILES Parse Error: syntax error[09:33:31] +183: [09:33:31] 1: +183: [09:33:31] while parsing: [09:33:31] [09:33:31] SMILES Parse Error: syntax error while parsing: ^SMILES +183: [09:33:31] [09:33:31] dsafsdfdsafsdf +183: [09:33:31] SMILES Parse Error: check for mistakes around position 1: +183: [09:33:31] dsafsdf +183: [09:33:31] dsafsdf^ +183: +183: [09:33:31] SMILES Parse Error: SMILES Parse Error: check for mistakes around position 1:syntax error[09:33:31] +183: [09:33:31] SMILES while parsing: SMILES[09:33:31] dsafsdf Parse Error: Failed parsing SMILES 'dsafsdf' Parse Error: ^dsafsdf +183: Parse Error: for input: ' +183: dsafsdf[09:33:31] +183: [09:33:31] ^Failed parsing SMILES 'dsafsdf'' +183: [09:33:31] 183: dsafsdf -183: [00:36:48] SMILES Parse Error: check for mistakes around position 1: -183: dsafsdf' -183: [00:36:48] dsafsdf -183: [00:36:48] ^ +183: for input: 'SMILESdsafsdf' +183: Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf'dsafsdf +183: 183: -183: [00:36:48] ^ -183: [00:36:48] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -183: [00:36:48] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -183: [00:36:48] SMILES Parse Error: syntax error while parsing: dsafsdf -183: [00:36:48] SMILES Parse Error: check for mistakes around position 1: -183: [00:36:48] dsafsdf -183: [00:36:48] ^ -183: [00:36:48] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -183: [00:36:48] SMILES Parse Error: syntax error while parsing: dsafsdf -183: [00:36:48] SMILES Parse Error: check for mistakes around position 1: -183: [00:36:48] dsafsdf -183: [00:36:48] ^ -183: [00:36:48] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -183: [00:36:48] SMILES Parse Error: syntax error while parsing: dsafsdf -183: [00:36:48] SMILES Parse Error: check for mistakes around position 1: -183: [00:36:48] dsafsdf -183: [00:36:48] ^ -183: [00:36:48] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -183: [00:36:48] SMILES Parse Error: syntax error while parsing: dsafsdf -183: [00:36:48] SMILES Parse Error: check for mistakes around position 1: -183: [00:36:48] dsafsdf -183: [00:36:48] ^ -183: [00:36:48] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -183: [00:36:48] SMILES Parse Error: syntax error while parsing: dsafsdf -183: [00:36:48] SMILES Parse Error: check for mistakes around position 1: -183: [00:36:48] dsafsdf -183: [00:36:48] ^ -183: [00:36:48] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -183: [00:36:48] SMILES Parse Error: syntax error while parsing: dsafsdf -183: [00:36:48] SMILES Parse Error: check for mistakes around position 1: -183: [00:36:48] dsafsdf -183: [00:36:48] ^ -183: [00:36:48] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -183: [00:36:48] SMILES Parse Error: syntax error while parsing: dsafsdf -183: [00:36:48] SMILES Parse Error: check for mistakes around position 1: -183: [00:36:48] dsafsdf -183: [00:36:48] ^ -183: [00:36:48] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -183: [00:36:48] SMILES Parse Error: syntax error while parsing: dsafsdf -183: [00:36:48] SMILES Parse Error: check for mistakes around position [00:36:48] SMILES Parse Error: syntax error while parsing: dsafsdf -183: [00:36:48] SMILES Parse Error: check for mistakes around position 1: -183: [00:36:48] dsafsdf -183: [00:36:48] ^ -183: [00:36:48] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -183: [00:36:48] SMILES Parse Error: syntax error while parsing: dsafsdf -183: [00:36:48] SMILES Parse Error: check for mistakes around position 1: -183: [00:36:48] dsafsdf -183: [00:36:48] ^ -183: [00:36:48] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -183: [00:36:48] SMILES Parse Error: syntax error while parsing: dsafsdf -183: [00:36:48] SMILES Parse Error: check for mistakes around position 1: -183: [00:36:48] dsafsdf -183: [00:36:48] ^ -183: [00:36:48] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -183: [00:36:48] SMILES Parse Error: syntax error while parsing: dsafsdf -183: [00:36:48] SMILES Parse Error: check for mistakes around position 1: -183: [00:36:48] dsafsdf -183: [00:36:48] ^ -183: [00:36:48] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -183: [00:36:48] SMILES Parse Error: syntax error while parsing: dsafsdf -183: [00:36:48] [00:36:48] [00:36:48] SMILES Parse Error: syntax error while parsing: dsafsdf -183: [00:36:48] SMILES Parse Error: check for mistakes around position 1: -183: [00:36:48] dsafsdf -183: [00:36:48] ^ -183: [00:36:48] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -183: [00:36:48] SMILES Parse Error: syntax error while parsing: dsafsdf -183: [00:36:48] SMILES Parse Error: check for mistakes around position 1: -183: [00:36:48] dsafsdf -183: [00:36:48] ^ -183: [00:36:48] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -183: [00:36:48] SMILES Parse Error: syntax error while parsing: dsafsdf -183: [00:36:48] SMILES Parse Error: check for mistakes around position 1: -183: [00:36:48] dsafsdf -183: [00:36:48] ^ -183: [00:36:48] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -183: [00:36:48] SMILES Parse Error: syntax error while parsing: dsafsdf -183: [00:36:48] SMILES Parse Error: check for mistakes around position 1: -183: [00:36:48] dsafsdf -183: [00:36:48] ^ -183: [00:36:48] SMILES Parse Error: syntax error while parsing: dsafsdf -183: [00:36:48] SMILES Parse Error: check for mistakes around position [00:36:48] SMILES Parse Error: Failed parsing SMILES 'dsafsdf'SMILES Parse Error: syntax error while parsing: dsafsdf -183: [00:36:48] SMILES Parse Error: check for mistakes around position 1: -183: [00:36:48] dsafsdf -183: [00:36:48] ^ -183: [00:36:48] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -183: [00:36:48] SMILES Parse Error: syntax error while parsing: dsafsdf -183: [00:36:48] SMILES Parse Error: check for mistakes around position 1: -183: [00:36:48] dsafsdf -183: [00:36:48] ^ -183: [00:36:48] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -183: [00:36:48] SMILES Parse Error: syntax error while parsing: dsafsdf -183: [00:36:48] SMILES Parse Error: check for mistakes around position 1: -183: [00:36:48] dsafsdf -183: [00:36:48] ^ -183: [00:36:48] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -183: [00:36:48] SMILES Parse Error: syntax error while parsing: dsafsdf -183: [00:36:48] SMILES Parse Error: check for mistakes around position 1: -183: [00:36:48] dsafsdf -183: [00:36:48] ^ -183: [00:36:48] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -183: [00:36:48] SMILES Parse Error: syntax error while parsing: dsafsdf -183: [00:36:48] SMILES Parse Error: check for mistakes around position 1: -183: [00:36:48] dsafsdf -183: [00:36:48] ^ -183: [00:36:48] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -183: [00:36:48] SMILES Parse Error: syntax error while parsing: dsafsdf -183: [00:36:48] SMILES Parse Error: check for mistakes around position 1: -183: [00:36:48] dsafsdf -183: [00:36:48] ^ -183: [00:36:48] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -183: [00:36:48] SMILES Parse Error: syntax error while parsing: dsafsdf -183: [00:36:48] SMILES Parse Error: check for mistakes around position 1: -183: [00:36:48] dsafsdf -183: [00:36:48] ^ -183: [00:36:48] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -183: [00:36:48] SMILES Parse Error: syntax error while parsing: dsafsdf -183: [00:36:48] SMILES Parse Error: check for mistakes around position 1: -183: [00:36:48] [00:36:48] dsafsdf -183: SMILES Parse Error: syntax error while parsing: [00:36:48] for input: 'dsafsdf' +183: [09:33:31] ^ +183: [09:33:31] SMILES Parse Error: syntax error while parsing: dsafsdf +183: [09:33:31] [09:33:31] Failed parsing SMILES 'dsafsdf'[09:33:31] SMILES Parse Error: check for mistakes around position SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +183: for input: 'SMILES Parse Error: dsafsdf[09:33:31] ^'Failed parsing SMILES 'dsafsdf' +183: for input: 'dsafsdf' +183: [09:33:31] SMILES Parse Error: check for mistakes around position 1: +183: [09:33:31] dsafsdf +183: [09:33:31] ^ +183: [09:33:31] SMILES Parse Error: syntax error while parsing: dsafsdf +183: [09:33:31] SMILES Parse Error: check for mistakes around position [09:33:31] 1: +183: SMILES[09:33:31] Parse Error: Failed parsing SMILES 'dsafsdf' for input: '[09:33:31] SMILES Parse Error: syntax error while parsing: dsafsdf +183: [09:33:31] SMILES Parse Error: check for mistakes around position 11: +183: [09:33:31] dsafsdf +183: [09:33:31] ^ +183: :dsafsdf +183: +183: [09:33:31] dsafsdf +183: [09:33:31] ^ +183: ' +183: [09:33:31] [09:33:31] dsafsdf +183: [09:33:31] ^ +183: [09:33:31] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf[09:33:31] SMILES Parse Error: Failed parsing SMILES 'dsafsdf'SMILES' +183: Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +183: [09:33:31] SMILES Parse Error: syntax error while parsing: dsafsdf +183: [09:33:31] SMILES Parse Error: check for mistakes around position [09:33:31] SMILES Parse Error: syntax error while parsing: dsafsdf +183: [09:33:31] SMILES Parse Error: check for mistakes around position 1 for input: 'dsafsdf' +183: : +183: [09:33:31] dsafsdf +183: [09:33:31] ^ +183: SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +183: [09:33:31] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +183: [09:33:31] SMILES Parse Error: syntax error while parsing: dsafsdf +183: [09:33:31] SMILES Parse Error: check for mistakes around position 1: +183: [09:33:31] dsafsdf +183: [09:33:31] ^ +183: [09:33:31] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +183: [09:33:31] SMILES Parse Error: syntax error while parsing: dsafsdf +183: [09:33:31] SMILES Parse Error: check for mistakes around position 1: +183: [09:33:31] dsafsdf +183: [09:33:31] ^ +183: [09:33:31] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' 183: 1: -183: [00:36:48] dsafsdf -183: [00:36:48] ^ -183: [00:36:48] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -183: [00:36:48] SMILES Parse Error: syntax error while parsing: dsafsdf -183: [00:36:48] SMILES Parse Error: check for mistakes around position 1: -183: [00:36:48] dsafsdf -183: [00:36:48] ^ -183: [00:36:48] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -183: [00:36:48] SMILES Parse Error: syntax error while parsing: dsafsdf -183: [00:36:48] SMILES Parse Error: check for mistakes around position 1: -183: [00:36:48] dsafsdf -183: [00:36:48] ^ -183: [00:36:48] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -183: [00:36:48] SMILES Parse Error: syntax error while parsing: dsafsdf -183: [00:36:48] SMILES Parse Error: check for mistakes around position 1: -183: [00:36:48] dsafsdf -183: [00:36:48] ^ -183: [00:36:48] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -183: [00:36:48] SMILES Parse Error: syntax error while parsing: dsafsdf -183: [00:36:48] SMILES Parse Error: check for mistakes around position 1: -183: [00:36:48] dsafsdf -183: [00:36:48] ^ -183: [00:36:48] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +183: [09:33:31] dsafsdf +183: [09:33:31] ^ +183: [09:33:31] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +183: while parsing: dsafsdf +183: [09:33:31] SMILES Parse Error: check for mistakes around position 1: +183: [09:33:31] dsafsdf +183: [09:33:31] ^ +183: [09:33:31] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +183: [09:33:31] SMILES Parse Error: syntax error while parsing: dsafsdf +183: [09:33:31] SMILES Parse Error: check for mistakes around position 1: +183: [09:33:31] dsafsdf +183: [09:33:31] ^ +183: [09:33:31] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +183: [09:33:31] SMILES Parse Error: syntax error while parsing: dsafsdf +183: [09:33:31] SMILES Parse Error: check for mistakes around position 1: +183: [09:33:31] dsafsdf +183: [09:33:31] ^ +183: [09:33:31] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +183: [09:33:31] SMILES Parse Error: syntax error while parsing: dsafsdf +183: [09:33:31] SMILES Parse Error: check for mistakes around position 1: +183: [09:33:31] dsafsdf +183: [09:33:31] ^ +183: [09:33:31] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +183: [09:33:31] SMILES Parse Error: syntax error while parsing: dsafsdf +183: [09:33:31] SMILES Parse Error: check for mistakes around position 1: +183: [09:33:31] dsafsdf +183: [09:33:31] ^ +183: [09:33:31] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +183: [09:33:31] SMILES Parse Error: syntax error while parsing: dsafsdf +183: [09:33:31] SMILES Parse Error: check for mistakes around position 1: +183: [09:33:31] dsafsdf +183: [09:33:31] ^ +183: [09:33:31] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +183: [09:33:31] SMILES Parse Error: syntax error while parsing: dsafsdf +183: [09:33:31] SMILES Parse Error: check for mistakes around position 1: +183: [09:33:31] [09:33:31] SMILES Parse Error: syntax error while parsing: dsafsdf +183: [09:33:31] SMILES Parse Error: check for mistakes around position 1: +183: [09:33:31] dsafsdf +183: [09:33:31] ^ +183: [09:33:31] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +183: [09:33:31] SMILES Parse Error: syntax error while parsing: dsafsdf +183: [09:33:31] SMILES Parse Error: check for mistakes around position 1: +183: [09:33:31] dsafsdf +183: [09:33:31] ^ +183: dsafsdf +183: [09:33:31] [09:33:31] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf[09:33:31] SMILES Parse Error: syntax error while parsing: dsafsdf +183: [09:33:31] SMILES Parse Error: check for mistakes around position 1: +183: [09:33:31] SMILES Parse Error: syntax error while parsing: dsafsdf +183: [09:33:31] SMILES Parse Error: check for mistakes around position 1: +183: [09:33:31] dsafsdf +183: [09:33:31] ^ +183: [09:33:31] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +183: [09:33:31] SMILES Parse Error: syntax error while parsing: dsafsdf +183: [09:33:31] SMILES Parse Error: check for mistakes around position 1: +183: [09:33:31] dsafsdf +183: [09:33:31] ^ +183: [09:33:31] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +183: [09:33:31] SMILES Parse Error: syntax error while parsing: dsafsdf +183: [09:33:31] SMILES Parse Error: check for mistakes around position 1: +183: [09:33:31] dsafsdf +183: [09:33:31] ^ +183: [09:33:31] [09:33:31] SMILES Parse Error: syntax error while parsing: dsafsdf +183: [09:33:31] SMILES Parse Error: check for mistakes around position 1: +183: [09:33:31] dsafsdf +183: [09:33:31] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' 183: ^ -183: [00:36:48] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -183: [00:36:48] SMILES Parse Error: syntax error while parsing: dsafsdf -183: [00:36:48] SMILES Parse Error: check for mistakes around position 1: -183: [00:36:48] dsafsdf -183: [00:36:48] ^ -183: [00:36:48] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +183: [09:33:31] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +183: [09:33:31] SMILES Parse Error: syntax error while parsing: dsafsdf +183: [09:33:31] SMILES Parse Error: check for mistakes around position 1: +183: [09:33:31] dsafsdf +183: [09:33:31] SMILES Parse Error: syntax error while parsing: dsafsdf +183: [09:33:31] SMILES Parse Error: check for mistakes around position [09:33:31] ^ +183: [09:33:31] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +183: [09:33:31] SMILES Parse Error: syntax error while parsing: dsafsdf +183: [09:33:31] SMILES Parse Error: check for mistakes around position 1: +183: [09:33:31] dsafsdf +183: [09:33:31] ^ +183: [09:33:31] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +183: [09:33:31] SMILES Parse Error: syntax error while parsing: dsafsdf +183: [09:33:31] SMILES Parse Error: check for mistakes around position 1: +183: [09:33:31] dsafsdf +183: [09:33:31] ^ +183: [09:33:31] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +183: [09:33:31] ^ +183: [09:33:31] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +183: [09:33:31] SMILES Parse Error: syntax error while parsing: dsafsdf +183: [09:33:31] SMILES Parse Error: check for mistakes around position 1: +183: [09:33:31] dsafsdf +183: [09:33:31] ^ +183: [09:33:31] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +183: [09:33:31] SMILES Parse Error: syntax error while parsing: dsafsdf +183: [09:33:31] SMILES Parse Error: check for mistakes around position 1: +183: [09:33:31] dsafsdf +183: [09:33:31] ^ +183: [09:33:31] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +183: [09:33:31] SMILES Parse Error: syntax error while parsing: dsafsdf +183: [09:33:31] SMILES Parse Error: check for mistakes around position 1: +183: [09:33:31] dsafsdf +183: [09:33:31] ^ +183: [09:33:31] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' 183: dsafsdf -183: [00:36:48] SMILES Parse Error: check for mistakes around position 1: -183: [00:36:48] dsafsdf -183: [00:36:48] ^ -183: [00:36:48] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -183: [00:36:48] SMILES Parse Error: syntax error while parsing: dsafsdf -183: [00:36:48] SMILES Parse Error: check for mistakes around position 1: -183: [00:36:48] dsafsdf -183: [00:36:48] ^ -183: [00:36:48] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -183: [00:36:48] SMILES Parse Error: syntax error while parsing: dsafsdf -183: [00:36:48] SMILES Parse Error: check for mistakes around position 1: -183: [00:36:48] dsafsdf -183: [00:36:48] ^ -183: [00:36:48] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -183: [00:36:48] SMILES Parse Error: syntax error while parsing: dsafsdf -183: [00:36:48] SMILES Parse Error: check for mistakes around position 1: -183: [00:36:48] dsafsdf -183: [00:36:48] ^ -183: [00:36:48] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +183: [09:33:31] ^ 183: 1: -183: [00:36:48] dsafsdf -183: [00:36:48] ^ -183: [00:36:48] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -183: [00:36:48] SMILES Parse Error: syntax error while parsing: dsafsdf -183: [00:36:48] SMILES Parse Error: check for mistakes around position 1: -183: [00:36:48] dsafsdf -183: [00:36:48] ^ -183: [00:36:48] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +183: [09:33:31] [09:33:31] [09:33:31] dsafsdf +183: [09:33:31] SMILES Parse Error: syntax error while parsing: dsafsdf +183: [09:33:31] SMILES Parse Error: check for mistakes around position 1: +183: [09:33:31] dsafsdf +183: [09:33:31] ^ +183: [09:33:31] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +183: [09:33:31] SMILES Parse Error: syntax error while parsing: dsafsdf +183: [09:33:31] SMILES Parse Error: check for mistakes around position 1: +183: [09:33:31] dsafsdf +183: [09:33:31] ^ +183: [09:33:31] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +183: [09:33:31] SMILES Parse Error: syntax error while parsing: dsafsdf +183: [09:33:31] SMILES Parse Error: check for mistakes around position 1[09:33:31] SMILES Parse Error: syntax error while parsing: dsafsdf +183: [09:33:31] SMILES Parse Error: check for mistakes around position 1: +183: [09:33:31] dsafsdf +183: [09:33:31] ^ +183: [09:33:31] ^ +183: SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf[09:33:31] [09:33:31] SMILES Parse Error: Failed parsing SMILES 'dsafsdf': +183: SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: '[09:33:31] ' +183: dsafsdf +183: [09:33:31] ^ +183: [09:33:31] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +183: for input: 'dsafsdf' +183: [09:33:31] SMILES Parse Error: syntax error while parsing: dsafsdf +183: [09:33:31] SMILES Parse Error: check for mistakes around position 1[09:33:31] SMILES Parse Error: syntax error while parsing: dsafsdf +183: [09:33:31] SMILES Parse Error: check for mistakes around position 1: +183: [09:33:31] dsafsdf +183: [09:33:31] ^ +183: [09:33:31] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +183: [09:33:31] SMILES Parse Error: syntax error while parsing: dsafsdf +183: [09:33:31] SMILES Parse Error: check for mistakes around position 1: +183: [09:33:31] dsafsdf +183: [09:33:31] ^ +183: [09:33:31] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +183: : +183: [09:33:31] dsafsdf +183: [09:33:31] ^ +183: [09:33:31] SMILES Parse Error: syntax error while parsing: dsafsdf +183: [09:33:31] SMILES Parse Error: check for mistakes around position 1[09:33:31] SMILESdsafsdf' +183: Parse Error: : +183: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +183: [09:33:31] SMILES Parse Error: syntax error while parsing: dsafsdf +183: [09:33:31] SMILES Parse Error: check for mistakes around position 1: +183: [09:33:31] dsafsdf +183: [09:33:31] ^ +183: [09:33:31] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +183: [09:33:31] SMILES Parse Error: syntax error while parsing: dsafsdf +183: [09:33:31] SMILES Parse Error: check for mistakes around position 1: +183: [09:33:31] dsafsdf +183: [09:33:31] ^ +183: [09:33:31] SMILES Parse Error: syntax error while parsing: dsafsdf +183: [09:33:31] SMILES Parse Error: check for mistakes around position 1: +183: [09:33:31] dsafsdf +183: [09:33:31] ^ +183: [09:33:31] dsafsdf +183: [09:33:31] ^ +183: [09:33:31] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +183: [09:33:31] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +183: [09:33:31] SMILES Parse Error: syntax error while parsing: dsafsdf +183: [09:33:31] SMILES Parse Error: check for mistakes around position 1: +183: [09:33:31] dsafsdf +183: [09:33:31] ^ +183: [09:33:31] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +183: [09:33:31] SMILES Parse Error: syntax error while parsing: dsafsdf +183: [09:33:31] SMILES Parse Error: check for mistakes around position 1: +183: [09:33:31] dsafsdf +183: [09:33:31] ^ +183: [09:33:31] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +183: [09:33:31] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +183: [09:33:31] SMILES Parse Error: syntax error while parsing: dsafsdf +183: [09:33:31] SMILES Parse Error: check for mistakes around position 1: +183: [09:33:31] dsafsdf +183: [09:33:31] ^ +183: [09:33:31] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' 183: SMILES Parse Error: syntax error while parsing: dsafsdf -183: [00:36:48] SMILES Parse Error: check for mistakes around position 1: -183: [00:36:48] dsafsdf -183: [00:36:48] ^ -183: [00:36:48] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -183: [00:36:48] SMILES Parse Error: syntax error while parsing: dsafsdf -183: [00:36:48] SMILES Parse Error: check for mistakes around position 1: -183: [00:36:48] dsafsdf -183: [00:36:48] ^ -183: [00:36:48] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -183: [00:36:48] SMILES Parse Error: syntax error while parsing: dsafsdf -183: [00:36:48] SMILES Parse Error: check for mistakes around position 1: -183: [00:36:48] dsafsdf -183: [00:36:48] ^ -183: [00:36:48] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -183: [00:36:48] SMILES Parse Error: syntax error while parsing: dsafsdf -183: [00:36:48] SMILES Parse Error: check for mistakes around position 1: -183: [00:36:48] dsafsdf -183: [00:36:48] ^ -183: [00:36:48] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -183: [00:36:48] SMILES Parse Error: syntax error while parsing: dsafsdf -183: [00:36:48] SMILES Parse Error: check for mistakes around position 1: -183: [00:36:48] dsafsdf -183: [00:36:48] ^ -183: [00:36:48] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -183: [00:36:48] SMILES Parse Error: syntax error while parsing: dsafsdf -183: [00:36:48] SMILES Parse Error: check for mistakes around position 1: -183: [00:36:48] dsafsdf -183: [00:36:48] ^ -183: [00:36:48] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -183: [00:36:48] SMILES Parse Error: syntax error while parsing: dsafsdf -183: [00:36:48] SMILES Parse Error: check for mistakes around position 1: -183: [00:36:48] dsafsdf -183: [00:36:48] ^ -183: [00:36:48] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -183: [00:36:48] SMILES Parse Error: syntax error while parsing: dsafsdf -183: [00:36:48] SMILES Parse Error: check for mistakes around position 1: -183: [00:36:48] dsafsdf -183: [00:36:48] ^ -183: [00:36:48] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -183: [00:36:48] SMILES Parse Error: syntax error while parsing: dsafsdf -183: [00:36:48] SMILES Parse Error: check for mistakes around position 1: -183: [00:36:48] dsafsdf -183: [00:36:48] ^ -183: [00:36:48] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -183: [00:36:48] SMILES Parse Error: syntax error while parsing: dsafsdf -183: [00:36:48] SMILES Parse Error: check for mistakes around position 1: -183: [00:36:48] dsafsdf -183: [00:36:48] ^ -183: [00:36:48] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -183: [00:36:48] SMILES Parse Error: syntax error while parsing: dsafsdf -183: [00:36:48] SMILES Parse Error: check for mistakes around position 1: -183: [00:36:48] dsafsdf -183: [00:36:48] ^ -183: [00:36:48] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -183: [00:36:48] SMILES Parse Error: syntax error while parsing: dsafsdf -183: [00:36:48] SMILES Parse Error: check for mistakes around position 1: -183: [00:36:48] dsafsdf -183: [00:36:48] ^ -183: [00:36:48] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -183: [00:36:48] SMILES Parse Error: syntax error while parsing: dsafsdf -183: [00:36:48] SMILES Parse Error: check for mistakes around position 1: -183: [00:36:48] dsafsdf -183: [00:36:48] ^ -183: [00:36:48] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -183: [00:36:48] SMILES Parse Error: syntax error while parsing: dsafsdf -183: [00:36:48] SMILES Parse Error: check for mistakes around position 1: -183: [00:36:48] dsafsdf -183: [00:36:48] ^ -183: [00:36:48] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -183: [00:36:48] SMILES Parse Error: syntax error while parsing: dsafsdf -183: [00:36:48] SMILES Parse Error: check for mistakes around position 1: -183: [00:36:48] dsafsdf -183: [00:36:48] ^ -183: [00:36:48] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -183: [00:36:48] SMILES Parse Error: check for mistakes around position 1: -183: [00:36:48] dsafsdf -183: [00:36:48] ^ -183: [00:36:48] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -183: [00:36:48] SMILES Parse Error: syntax error while parsing: dsafsdf -183: [00:36:48] SMILES Parse Error: check for mistakes around position 1: -183: [00:36:48] dsafsdf -183: [00:36:48] ^ -183: [00:36:48] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -183: [00:36:48] SMILES Parse Error: syntax error while parsing: dsafsdf -183: [00:36:48] SMILES Parse Error: check for mistakes around position 1: -183: [00:36:48] dsafsdf -183: [00:36:48] ^ -183: [00:36:48] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -183: [00:36:48] SMILES Parse Error: syntax error while parsing: dsafsdf -183: [00:36:48] SMILES Parse Error: check for mistakes around position 1: -183: [00:36:48] dsafsdf -183: [00:36:48] ^ -183: [00:36:48] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -183: [00:36:48] SMILES Parse Error: syntax error while parsing: dsafsdf -183: [00:36:48] SMILES Parse Error: check for mistakes around position 1: -183: [00:36:48] dsafsdf -183: [00:36:48] ^ -183: [00:36:48] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -183: [00:36:48] SMILES Parse Error: syntax error while parsing: dsafsdf -183: [00:36:48] SMILES Parse Error: check for mistakes around position 1: -183: [00:36:48] dsafsdf -183: [00:36:48] ^ -183: [00:36:48] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -183: [00:36:48] SMILES Parse Error: syntax error while parsing: dsafsdf -183: [00:36:48] SMILES Parse Error: check for mistakes around position 1: -183: [00:36:48] dsafsdf -183: [00:36:48] ^ -183: [00:36:48] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -183: [00:36:48] SMILES Parse Error: syntax error while parsing: dsafsdf -183: [00:36:48] SMILES Parse Error: check for mistakes around position 1: -183: [00:36:48] dsafsdf -183: [00:36:48] ^ -183: [00:36:48] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -183: [00:36:48] SMILES Parse Error: syntax error while parsing: dsafsdf -183: [00:36:48] SMILES Parse Error: check for mistakes around position 1: -183: [00:36:48] dsafsdf -183: [00:36:48] ^ -183: [00:36:48] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -183: [00:36:48] SMILES Parse Error: syntax error while parsing: dsafsdf -183: [00:36:48] SMILES Parse Error: check for mistakes around position 1: -183: [00:36:48] dsafsdf -183: [00:36:48] ^ -183: [00:36:48] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -183: [00:36:48] SMILES Parse Error: syntax error while parsing: dsafsdf -183: [00:36:48] SMILES Parse Error: check for mistakes around position 1: -183: [00:36:48] dsafsdf -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 21.30 seconds -183: [00:36:48] ^ -183: [00:36:48] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -183: [00:36:48] SMILES Parse Error: syntax error while parsing: dsafsdf -183: [00:36:48] SMILES Parse Error: check for mistakes around position 1: -183: [00:36:48] dsafsdf -183: [00:36:48] ^ -183: [00:36:48] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -183: [00:36:48] SMILES Parse Error: syntax error while parsing: dsafsdf -183: [00:36:48] SMILES Parse Error: check for mistakes around position 1: -183: [00:36:48] dsafsdf -183: [00:36:48] ^ -183: [00:36:48] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -183: [00:36:48] SMILES Parse Error: syntax error while parsing: dsafsdf -183: [00:36:48] SMILES Parse Error: check for mistakes around position 1: -183: [00:36:48] dsafsdf -183: [00:36:48] ^ -183: [00:36:48] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -183: [00:36:48] SMILES Parse Error: syntax error while parsing: dsafsdf -183: [00:36:48] SMILES Parse Error: check for mistakes around position 1: -183: [00:36:48] dsafsdf -183: [00:36:48] ^ -183: [00:36:48] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -183: [00:36:48] SMILES Parse Error: syntax error while parsing: dsafsdf -183: [00:36:48] SMILES Parse Error: check for mistakes around position 1: -183: [00:36:48] dsafsdf -183: [00:36:48] ^ -183: [00:36:48] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -183: [00:36:48] SMILES Parse Error: syntax error while parsing: dsafsdf -183: [00:36:48] SMILES Parse Error: check for mistakes around position 1: -183: [00:36:48] dsafsdf -183: [00:36:48] ^ -183: [00:36:48] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -183: [00:36:48] SMILES Parse Error: syntax error while parsing: dsafsdf -183: [00:36:48] SMILES Parse Error: check for mistakes around position 1: -183: [00:36:48] dsafsdf -183: [00:36:48] ^ -183: [00:36:48] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -183: [00:36:48] SMILES Parse Error: syntax error while parsing: dsafsdf -183: [00:36:48] SMILES Parse Error: check for mistakes around position 1: -183: [00:36:48] dsafsdf -183: [00:36:48] ^ -183: [00:36:48] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -183: [00:36:48] SMILES Parse Error: syntax error while parsing: dsafsdf -183: [00:36:48] SMILES Parse Error: check for mistakes around position 1: -183: [00:36:48] dsafsdf -183: [00:36:48] ^ -183: [00:36:48] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -183: [00:36:48] SMILES Parse Error: syntax error while parsing: dsafsdf -183: [00:36:48] SMILES Parse Error: check for mistakes around position 1: -183: [00:36:48] dsafsdf -183: [00:36:48] ^ -183: [00:36:48] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -183: [00:36:48] SMILES Parse Error: syntax error while parsing: dsafsdf -183: [00:36:48] SMILES Parse Error: check for mistakes around position 1: -183: [00:36:48] dsafsdf -183: [00:36:48] ^ -183: [00:36:48] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -183: [00:36:48] SMILES Parse Error: syntax error while parsing: dsafsdf -183: [00:36:48] SMILES Parse Error: check for mistakes around position 1: -183: [00:36:48] dsafsdf -183: [00:36:48] ^ -183: [00:36:48] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -183: [00:36:48] SMILES Parse Error: syntax error while parsing: dsafsdf -183: [00:36:48] SMILES Parse Error: check for mistakes around position 1: -183: [00:36:48] dsafsdf -183: [00:36:48] ^ -183: [00:36:48] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -183: [00:36:48] SMILES Parse Error: syntax error while parsing: dsafsdf -183: [00:36:48] SMILES Parse Error: check for mistakes around position 1: -183: [00:36:48] dsafsdf -183: [00:36:48] ^ -183: [00:36:48] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -183: [00:36:48] SMILES Parse Error: syntax error while parsing: dsafsdf -183: [00:36:48] SMILES Parse Error: check for mistakes around position 1: -183: [00:36:48] dsafsdf -183: [00:36:48] ^ -183: [00:36:48] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -183: [00:36:48] SMILES Parse Error: syntax error while parsing: dsafsdf -183: [00:36:48] SMILES Parse Error: check for mistakes around position 1: -183: [00:36:48] dsafsdf -183: [00:36:48] ^ -183: [00:36:48] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -183: [00:36:48] SMILES Parse Error: syntax error while parsing: dsafsdf -183: [00:36:48] SMILES Parse Error: check for mistakes around position 1: -183: [00:36:48] dsafsdf -183: [00:36:48] ^ -183: [00:36:48] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -183: [00:36:48] SMILES Parse Error: syntax error while parsing: dsafsdf -183: [00:36:48] SMILES Parse Error: check for mistakes around position 1: -183: [00:36:48] dsafsdf -183: [00:36:48] ^ -183: [00:36:48] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -183: [00:36:48] SMILES Parse Error: syntax error while parsing: dsafsdf -183: [00:36:48] SMILES Parse Error: check for mistakes around position 1: -183: [00:36:48] dsafsdf -183: [00:36:48] ^ -183: [00:36:48] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -183: [00:36:48] SMILES Parse Error: syntax error while parsing: dsafsdf -183: [00:36:48] SMILES Parse Error: check for mistakes around position 1: -183: [00:36:48] dsafsdf -183: [00:36:48] ^ -183: [00:36:48] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -183: [00:36:48] SMILES Parse Error: syntax error while parsing: dsafsdf -183: [00:36:48] SMILES Parse Error: check for mistakes around position 1: -183: [00:36:48] dsafsdf -183: [00:36:48] ^ -183: [00:36:48] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -183: [00:36:48] SMILES Parse Error: syntax error while parsing: dsafsdf -183: [00:36:48] SMILES Parse Error: check for mistakes around position 1: -183: [00:36:48] dsafsdf -183: [00:36:48] ^ -183: [00:36:48] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -183: [00:36:48] SMILES Parse Error: syntax error while parsing: dsafsdf -183: [00:36:48] SMILES Parse Error: check for mistakes around position 1: -183: [00:36:48] dsafsdf -183: [00:36:48] ^ -183: [00:36:48] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -183: [00:36:48] SMILES Parse Error: syntax error while parsing: dsafsdf -183: [00:36:48] SMILES Parse Error: check for mistakes around position 1: -183: [00:36:48] dsafsdf -183: [00:36:48] ^ -183: [00:36:48] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -183: [00:36:48] SMILES Parse Error: syntax error while parsing: dsafsdf -183: [00:36:48] SMILES Parse Error: check for mistakes around position 1: -183: [00:36:48] dsafsdf -183: [00:36:48] ^ -183: [00:36:48] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -183: [00:36:48] SMILES Parse Error: syntax error while parsing: dsafsdf -183: [00:36:48] SMILES Parse Error: check for mistakes around position 1: -183: [00:36:48] dsafsdf -183: [00:36:48] ^ -183: [00:36:48] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -183: [00:36:48] SMILES Parse Error: syntax error while parsing: dsafsdf -183: [00:36:48] SMILES Parse Error: check for mistakes around position 1: -183: [00:36:48] dsafsdf -183: [00:36:48] ^ -183: [00:36:48] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -183: [00:36:48] SMILES Parse Error: syntax error while parsing: dsafsdf -183: [00:36:48] SMILES Parse Error: check for mistakes around position 1: -183: [00:36:48] dsafsdf -183: [00:36:48] ^ -183: [00:36:48] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -183: [00:36:48] SMILES Parse Error: syntax error while parsing: dsafsdf -183: [00:36:48] SMILES Parse Error: check for mistakes around position 1: -183: [00:36:48] dsafsdf -183: [00:36:48] ^ -183: [00:36:48] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -183: [00:36:48] SMILES Parse Error: syntax error while parsing: dsafsdf -183: [00:36:48] SMILES Parse Error: check for mistakes around position 1: -183: [00:36:48] dsafsdf -183: [00:36:48] ^ -183: [00:36:48] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -183: [00:36:48] SMILES Parse Error: syntax error while parsing: dsafsdf -183: [00:36:48] SMILES Parse Error: check for mistakes around position 1: -183: [00:36:48] dsafsdf -183: [00:36:48] ^ -183: [00:36:48] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -183: [00:36:48] SMILES Parse Error: syntax error while parsing: dsafsdf -183: [00:36:48] SMILES Parse Error: check for mistakes around position 1: -183: [00:36:48] dsafsdf -183: [00:36:48] ^ -183: [00:36:48] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -183: [00:36:48] SMILES Parse Error: syntax error while parsing: dsafsdf -183: [00:36:48] SMILES Parse Error: check for mistakes around position 1: -183: [00:36:48] dsafsdf -183: [00:36:48] ^ -183: [00:36:48] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -183: [00:36:48] SMILES Parse Error: syntax error while parsing: dsafsdf -183: [00:36:48] SMILES Parse Error: check for mistakes around position 1: -183: [00:36:48] dsafsdf -183: [00:36:48] ^ -183: [00:36:48] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -183: [00:36:48] SMILES Parse Error: syntax error while parsing: dsafsdf -183: [00:36:48] SMILES Parse Error: check for mistakes around position 1: -183: [00:36:48] dsafsdf -183: [00:36:48] ^ -183: [00:36:48] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -183: [00:36:48] SMILES Parse Error: syntax error while parsing: dsafsdf -183: [00:36:48] SMILES Parse Error: check for mistakes around position 1: -183: [00:36:48] dsafsdf -183: [00:36:48] ^ -183: [00:36:48] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -183: [00:36:48] SMILES Parse Error: syntax error while parsing: dsafsdf -183: [00:36:48] SMILES Parse Error: check for mistakes around position 1: -183: [00:36:48] dsafsdf -183: [00:36:48] ^ -183: [00:36:48] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -183: [00:36:48] SMILES Parse Error: syntax error while parsing: dsafsdf -183: [00:36:48] SMILES Parse Error: check for mistakes around position 1: -183: [00:36:48] dsafsdf -183: [00:36:48] ^ -183: [00:36:48] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -183: [00:36:48] SMILES Parse Error: syntax error while parsing: dsafsdf -183: [00:36:48] SMILES Parse Error: check for mistakes around position 1: -183: [00:36:48] dsafsdf -183: [00:36:48] ^ -183: [00:36:48] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -183: [00:36:48] SMILES Parse Error: syntax error while parsing: dsafsdf -183: [00:36:48] SMILES Parse Error: check for mistakes around position 1: -183: [00:36:48] dsafsdf -183: [00:36:48] ^ -183: [00:36:48] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -183: [00:36:48] SMILES Parse Error: syntax error while parsing: dsafsdf -183: [00:36:48] SMILES Parse Error: check for mistakes around position 1: -183: [00:36:48] dsafsdf -183: [00:36:48] ^ -183: [00:36:48] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -183: [00:36:48] SMILES Parse Error: syntax error while parsing: dsafsdf -183: [00:36:48] SMILES Parse Error: check for mistakes around position 1: -183: [00:36:48] dsafsdf -183: [00:36:48] ^ -183: [00:36:48] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -183: [00:36:48] SMILES Parse Error: syntax error while parsing: dsafsdf -183: [00:36:48] SMILES Parse Error: check for mistakes around position 1: -183: [00:36:48] dsafsdf -183: [00:36:48] ^ -183: [00:36:48] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -183: [00:36:48] SMILES Parse Error: syntax error while parsing: dsafsdf -183: [00:36:48] SMILES Parse Error: check for mistakes around position 1: -183: [00:36:48] dsafsdf -183: [00:36:48] ^ -183: [00:36:48] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -183: [00:36:48] SMILES Parse Error: syntax error while parsing: dsafsdf -183: [00:36:48] SMILES Parse Error: check for mistakes around position 1: -183: [00:36:48] dsafsdf -183: [00:36:48] ^ -183: [00:36:48] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -183: [00:36:48] SMILES Parse Error: syntax error while parsing: dsafsdf -183: [00:36:48] SMILES Parse Error: check for mistakes around position 1: -183: [00:36:48] dsafsdf -183: [00:36:48] ^ -183: [00:36:48] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -183: [00:36:48] SMILES Parse Error: syntax error while parsing: dsafsdf -183: [00:36:48] SMILES Parse Error: check for mistakes around position 1: -183: [00:36:48] dsafsdf -183: [00:36:48] ^ -183: [00:36:48] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -183: [00:36:48] SMILES Parse Error: syntax error while parsing: dsafsdf -183: [00:36:48] SMILES Parse Error: check for mistakes around position 1: -183: [00:36:48] dsafsdf -183: [00:36:48] ^ -183: [00:36:48] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -183: [00:36:48] SMILES Parse Error: syntax error while parsing: dsafsdf -183: [00:36:48] SMILES Parse Error: check for mistakes around position 1: -183: [00:36:48] dsafsdf -183: [00:36:48] ^ -183: [00:36:48] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -183: [00:36:48] SMILES Parse Error: syntax error while parsing: dsafsdf -183: [00:36:48] SMILES Parse Error: check for mistakes around position 1: -183: [00:36:48] dsafsdf -183: [00:36:48] ^ -183: [00:36:48] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -183: [00:36:48] SMILES Parse Error: syntax error while parsing: dsafsdf -183: [00:36:48] SMILES Parse Error: check for mistakes around position 1: -183: [00:36:48] dsafsdf -183: [00:36:48] ^ -183: [00:36:48] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -183: [00:36:48] SMILES Parse Error: syntax error while parsing: dsafsdf -183: [00:36:48] SMILES Parse Error: check for mistakes around position 1: -183: [00:36:48] dsafsdf -183: [00:36:48] ^ -183: [00:36:48] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -183: [00:36:48] SMILES Parse Error: syntax error while parsing: dsafsdf -183: [00:36:48] SMILES Parse Error: check for mistakes around position 1: -183: [00:36:48] dsafsdf -183: [00:36:48] ^ -183: [00:36:48] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -183: [00:36:48] SMILES Parse Error: syntax error while parsing: dsafsdf -183: [00:36:48] SMILES Parse Error: check for mistakes around position 1: -183: [00:36:48] dsafsdf -183: [00:36:48] ^ -183: [00:36:48] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -183: [00:36:48] SMILES Parse Error: syntax error while parsing: dsafsdf -183: [00:36:48] SMILES Parse Error: check for mistakes around position 1: -183: [00:36:48] dsafsdf -183: [00:36:48] ^ -183: [00:36:48] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -183: [00:36:48] SMILES Parse Error: syntax error while parsing: dsafsdf -183: [00:36:48] SMILES Parse Error: check for mistakes around position 1: -183: [00:36:48] dsafsdf -183: [00:36:48] ^ -183: [00:36:48] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -183: [00:36:48] SMILES Parse Error: syntax error while parsing: dsafsdf -183: [00:36:48] SMILES Parse Error: check for mistakes around position 1: -183: [00:36:48] dsafsdf -183: [00:36:48] ^ -183: [00:36:48] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -183: [00:36:48] SMILES Parse Error: syntax error while parsing: dsafsdf -183: [00:36:48] SMILES Parse Error: check for mistakes around position 1: -183: [00:36:48] dsafsdf -183: [00:36:48] ^ -183: [00:36:48] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -183: [00:36:48] SMILES Parse Error: syntax error while parsing: dsafsdf -183: [00:36:48] SMILES Parse Error: check for mistakes around position 1: -183: [00:36:48] dsafsdf -183: [00:36:48] ^ -183: [00:36:48] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -183: [00:36:48] SMILES Parse Error: syntax error while parsing: dsafsdf -183: [00:36:48] SMILES Parse Error: check for mistakes around position 1: -183: [00:36:48] dsafsdf -183: [00:36:48] ^ -183: [00:36:48] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -183: [00:36:48] SMILES Parse Error: syntax error while parsing: dsafsdf -183: [00:36:48] SMILES Parse Error: check for mistakes around position 1: -183: [00:36:48] dsafsdf -183: [00:36:48] ^ -183: [00:36:48] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -183: [00:36:48] SMILES Parse Error: syntax error while parsing: dsafsdf -183: [00:36:48] SMILES Parse Error: check for mistakes around position 1: -183: [00:36:48] dsafsdf -183: [00:36:48] ^ -183: [00:36:48] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -183: [00:36:48] SMILES Parse Error: syntax error while parsing: dsafsdf -183: [00:36:48] SMILES Parse Error: check for mistakes around position 1: -183: [00:36:48] dsafsdf -183: [00:36:48] ^ -183: [00:36:48] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -183: [00:36:48] SMILES Parse Error: syntax error while parsing: dsafsdf -183: [00:36:48] SMILES Parse Error: check for mistakes around position 1: -183: [00:36:48] dsafsdf -183: [00:36:48] ^ -183: [00:36:48] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -183: [00:36:48] SMILES Parse Error: syntax error while parsing: dsafsdf -183: [00:36:48] SMILES Parse Error: check for mistakes around position 1: -183: [00:36:48] dsafsdf -183: [00:36:48] ^ -183: [00:36:48] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -183: [00:36:48] SMILES Parse Error: syntax error while parsing: dsafsdf -183: [00:36:48] SMILES Parse Error: check for mistakes around position 1: -183: [00:36:48] dsafsdf -183: [00:36:48] ^ -183: [00:36:48] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -183: [00:36:48] SMILES Parse Error: syntax error while parsing: dsafsdf -183: [00:36:48] SMILES Parse Error: check for mistakes around position 1: -183: [00:36:48] dsafsdf -183: [00:36:48] ^ -183: [00:36:48] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -183: [00:36:48] SMILES Parse Error: syntax error while parsing: dsafsdf -183: [00:36:48] SMILES Parse Error: check for mistakes around position 1: -183: [00:36:48] dsafsdf -183: [00:36:48] ^ -183: [00:36:48] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -183: [00:36:48] SMILES Parse Error: syntax error while parsing: dsafsdf -183: [00:36:48] SMILES Parse Error: check for mistakes around position 1: -183: [00:36:48] dsafsdf -183: [00:36:48] ^ -183: [00:36:48] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -183: [00:36:48] SMILES Parse Error: syntax error while parsing: dsafsdf -183: [00:36:48] SMILES Parse Error: check for mistakes around position 1: -183: [00:36:48] dsafsdf -183: [00:36:48] ^ -183: [00:36:48] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -183: [00:36:48] SMILES Parse Error: syntax error while parsing: dsafsdf -183: [00:36:48] SMILES Parse Error: check for mistakes around position 1: -183: [00:36:48] dsafsdf -183: [00:36:48] ^ -183: [00:36:48] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -183: [00:36:48] SMILES Parse Error: syntax error while parsing: dsafsdf -183: [00:36:48] SMILES Parse Error: check for mistakes around position 1: -183: [00:36:48] dsafsdf -183: [00:36:48] ^ -183: [00:36:48] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -183: [00:36:48] SMILES Parse Error: syntax error while parsing: dsafsdf -183: [00:36:48] SMILES Parse Error: check for mistakes around position 1: -183: [00:36:48] dsafsdf -183: [00:36:48] ^ -183: [00:36:48] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -183: [00:36:48] SMILES Parse Error: syntax error while parsing: dsafsdf -183: [00:36:48] SMILES Parse Error: check for mistakes around position 1: -183: [00:36:48] dsafsdf -183: [00:36:48] ^ -183: [00:36:48] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -183: [00:36:48] SMILES Parse Error: syntax error while parsing: dsafsdf -183: [00:36:48] SMILES Parse Error: check for mistakes around position 1: -183: [00:36:48] dsafsdf -183: [00:36:48] ^ -183: [00:36:48] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -183: [00:36:48] SMILES Parse Error: syntax error while parsing: dsafsdf -183: [00:36:48] SMILES Parse Error: check for mistakes around position 1: -183: [00:36:48] dsafsdf -183: [00:36:48] ^ -183: [00:36:48] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -183: [00:36:48] SMILES Parse Error: syntax error while parsing: dsafsdf -183: [00:36:48] SMILES Parse Error: check for mistakes around position 1: -183: [00:36:48] dsafsdf -183: [00:36:48] ^ -183: [00:36:48] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -183: [00:36:48] SMILES Parse Error: syntax error while parsing: dsafsdf -183: [00:36:48] SMILES Parse Error: check for mistakes around position 1: -183: [00:36:48] dsafsdf -183: [00:36:48] ^ -183: [00:36:48] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -183: [00:36:48] SMILES Parse Error: syntax error while parsing: dsafsdf -183: [00:36:48] SMILES Parse Error: check for mistakes around position 1: -183: [00:36:48] dsafsdf -183: [00:36:48] ^ -183: [00:36:48] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -183: [00:36:48] SMILES Parse Error: syntax error while parsing: dsafsdf -183: [00:36:48] SMILES Parse Error: check for mistakes around position 1: -183: [00:36:48] dsafsdf -183: [00:36:48] ^ -183: [00:36:48] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -183: [00:36:48] SMILES Parse Error: syntax error while parsing: dsafsdf -183: [00:36:48] SMILES Parse Error: check for mistakes around position 1: -183: [00:36:48] dsafsdf -183: [00:36:48] ^ -183: [00:36:48] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -183: [00:36:48] SMILES Parse Error: syntax error while parsing: dsafsdf -183: [00:36:48] SMILES Parse Error: check for mistakes around position 1: -183: [00:36:48] dsafsdf -183: [00:36:48] ^ -183: [00:36:48] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -183: [00:36:48] SMILES Parse Error: syntax error while parsing: dsafsdf -183: [00:36:48] SMILES Parse Error: check for mistakes around position 1: -183: [00:36:48] dsafsdf -183: [00:36:48] ^ -183: [00:36:48] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -183: [00:36:48] SMILES Parse Error: syntax error while parsing: dsafsdf -183: [00:36:48] SMILES Parse Error: check for mistakes around position 1: -183: [00:36:48] dsafsdf -183: [00:36:48] ^ -183: [00:36:48] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -183: [00:36:48] SMILES Parse Error: syntax error while parsing: dsafsdf -183: [00:36:48] SMILES Parse Error: check for mistakes around position 1: -183: [00:36:48] dsafsdf -183: [00:36:48] ^ -183: [00:36:48] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -183: [00:36:48] SMILES Parse Error: syntax error while parsing: dsafsdf -183: [00:36:48] SMILES Parse Error: check for mistakes around position 1: -183: [00:36:48] dsafsdf -183: [00:36:48] ^ -183: [00:36:48] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -183: [00:36:48] SMILES Parse Error: syntax error while parsing: dsafsdf -183: [00:36:48] SMILES Parse Error: check for mistakes around position 1: -183: [00:36:48] dsafsdf -183: [00:36:48] ^ -183: [00:36:48] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -183: [00:36:48] SMILES Parse Error: syntax error while parsing: dsafsdf -183: [00:36:48] SMILES Parse Error: check for mistakes around position 1: -183: [00:36:48] dsafsdf -183: [00:36:48] ^ -183: [00:36:48] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -183: [00:36:48] SMILES Parse Error: syntax error while parsing: dsafsdf -183: [00:36:48] SMILES Parse Error: check for mistakes around position 1: -183: [00:36:48] dsafsdf -183: [00:36:48] ^ -183: [00:36:48] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -183: [00:36:48] SMILES Parse Error: syntax error while parsing: dsafsdf -183: [00:36:48] SMILES Parse Error: check for mistakes around position 1: -183: [00:36:48] dsafsdf -183: [00:36:48] ^ -183: [00:36:48] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -183: [00:36:48] SMILES Parse Error: syntax error while parsing: dsafsdf -183: [00:36:48] SMILES Parse Error: check for mistakes around position 1: -183: [00:36:48] dsafsdf -183: [00:36:48] ^ -183: [00:36:48] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -183: [00:36:48] SMILES Parse Error: syntax error while parsing: dsafsdf -183: [00:36:48] SMILES Parse Error: check for mistakes around position 1: -183: [00:36:48] dsafsdf -183: [00:36:48] ^ -183: [00:36:48] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -183: [00:36:48] SMILES Parse Error: syntax error while parsing: dsafsdf -183: [00:36:48] SMILES Parse Error: check for mistakes around position 1: -183: [00:36:48] dsafsdf -183: [00:36:48] ^ -183: [00:36:48] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -183: [00:36:48] ------------------------------------- -183: [00:36:48] Results do not depend on numThreads -174/238 Test #163: testFMCS ............................... Passed 21.40 sec -test 186 - Start 186: testRGroupDecomp - -186: Test command: /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/RGroupDecomposition/testRGroupDecomp -186: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/RGroupDecomposition -186: Test timeout computed to be: 1500 -148: .........[00:36:48] Molecule does not have explicit Hs. Consider calling AddHs() -148: .[00:36:48] Molecule does not have explicit Hs. Consider calling AddHs() -148: [00:36:48] Molecule does not have explicit Hs. Consider calling AddHs() -148: [00:36:48] Molecule does not have explicit Hs. Consider calling AddHs() -148: [00:36:48] Molecule does not have explicit Hs. Consider calling AddHs() -148: [00:36:48] Molecule does not have explicit Hs. Consider calling AddHs() -148: [00:36:48] Molecule does not have explicit Hs. Consider calling AddHs() -148: [00:36:48] Molecule does not have explicit Hs. Consider calling AddHs() -148: [00:36:48] Molecule does not have explicit Hs. Consider calling AddHs() -148: [00:36:48] Molecule does not have explicit Hs. Consider calling AddHs() -148: [00:36:48] Molecule does not have explicit Hs. Consider calling AddHs() -148: .[00:36:48] Molecule does not have explicit Hs. Consider calling AddHs() -148: [00:36:48] Molecule does not have explicit Hs. Consider calling AddHs() -148: [00:36:48] Molecule does not have explicit Hs. Consider calling AddHs() -148: [00:36:48] Molecule does not have explicit Hs. Consider calling AddHs() -148: [00:36:48] Molecule does not have explicit Hs. Consider calling AddHs() -148: [00:36:48] Molecule does not have explicit Hs. Consider calling AddHs() -148: [00:36:48] Molecule does not have explicit Hs. Consider calling AddHs() -148: [00:36:48] Molecule does not have explicit Hs. Consider calling AddHs() -148: [00:36:48] Molecule does not have explicit Hs. Consider calling AddHs() -148: [00:36:48] Molecule does not have explicit Hs. Consider calling AddHs() -186: [00:36:49] Non terminal R group defined. To allow set allowNonTerminalRGroups in RGroupDecompositionParameters -186: [00:36:49] WARNING: not removing hydrogen atom with dummy atom neighbors +183: [09:33:31] SMILES Parse Error: check for mistakes around position 1: +183: [09:33:31] dsafsdf +183: [09:33:31] ^ +183: [09:33:31] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +183: [09:33:31] SMILES Parse Error: syntax error while parsing: dsafsdf +183: [09:33:31] SMILES Parse Error: check for mistakes around position 1: +183: [09:33:31] dsafsdf +183: [09:33:31] ^ +183: [09:33:31] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +183: [09:33:31] SMILES Parse Error: syntax error while parsing: dsafsdf +183: [09:33:31] SMILES Parse Error: check for mistakes around position 1: +183: [09:33:31] dsafsdf +183: [09:33:31] ^ +183: [09:33:31] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf'' +183: +183: [09:33:31] SMILES Parse Error: syntax error while parsing: dsafsdf +183: [09:33:31] SMILES Parse Error: check for mistakes around position 1: +183: [09:33:31] dsafsdf +183: [09:33:31] ^ +183: [09:33:31] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +183: [09:33:31] SMILES Parse Error: syntax error while parsing: dsafsdf +183: [09:33:31] SMILES Parse Error: check for mistakes around position 1: +183: [09:33:31] dsafsdf +183: [09:33:31] ^ +183: [09:33:31] [09:33:31] [09:33:31] SMILES Parse Error: Failed parsing SMILES 'dsafsdf'SMILES Parse Error: SMILES Parse Error: syntax error while parsing: dsafsdf +183: [09:33:31] SMILES Parse Error: check for mistakes around position syntax error while parsing: dsafsdf +183: [09:33:31] 1: +183: [09:33:31] dsafsdf +183: [09:33:31] ^ +183: SMILES Parse Error: check for mistakes around position 1: +183: [09:33:31] dsafsdf +183: [09:33:31] ^ +183: [09:33:31] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +183: [09:33:31] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +183: [09:33:31] SMILES Parse Error: syntax error[09:33:31] SMILES Parse Error: syntax error while parsing: dsafsdf +183: [09:33:31] SMILES Parse Error: check for mistakes around position 1: +183: [09:33:31] dsafsdf +183: [09:33:31] ^ +183: while parsing: dsafsdf +183: [09:33:31] SMILES Parse Error: check for mistakes around position [09:33:31] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +183: 1: +183: [09:33:31] dsafsdf +183: [09:33:31] ^ +183: for input: 'dsafsdf' +183: [09:33:31] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +183: [09:33:31] SMILES Parse Error: syntax error while parsing: dsafsdf +183: [09:33:31] SMILES Parse Error: check for mistakes around position 1: +183: [09:33:31] dsafsdf +183: [09:33:31] ^ +183: [09:33:31] [09:33:31] [09:33:31] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +183: SMILES Parse Error: syntax error while parsing: dsafsdf +183: [09:33:31] SMILES Parse Error: check for mistakes around position 1SMILES Parse Error: syntax error while parsing: dsafsdf +183: [09:33:31] SMILES Parse Error: check for mistakes around position : +183: [09:33:31] dsafsdf +183: 1: +183: [09:33:31] dsafsdf +183: [09:33:31] ^ +183: [09:33:31] ^ +183: [09:33:31] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +183: [09:33:31] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +183: [09:33:31] SMILES Parse Error: syntax error while parsing: dsafsdf +183: [09:33:31] SMILES Parse Error: check for mistakes around position 1: +183: [09:33:31] dsafsdf +183: [09:33:31] ^ +183: [09:33:31] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +183: [09:33:31] SMILES Parse Error: syntax error while parsing: dsafsdf +183: [09:33:31] SMILES Parse Error: check for mistakes around position 1: +183: [09:33:31] dsafsdf +183: [09:33:31] ^ +183: [09:33:31] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +183: [09:33:31] SMILES Parse Error: syntax error while parsing: dsafsdf +183: [09:33:31] SMILES Parse Error: check for mistakes around position 1: +183: [09:33:31] dsafsdf +183: [09:33:31] ^ +183: [09:33:31] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +183: [09:33:31] SMILES Parse Error: syntax error while parsing: dsafsdf +183: [09:33:31] SMILES Parse Error: check for mistakes around position 1: +183: [09:33:31] dsafsdf +183: [09:33:31] ^ +183: [09:33:31] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +183: [09:33:31] SMILES Parse Error: syntax error while parsing: dsafsdf +183: [09:33:31] SMILES Parse Error: check for mistakes around position 1: +183: [09:33:31] dsafsdf +183: [09:33:31] ^ +183: [09:33:31] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +183: [09:33:31] SMILES Parse Error: syntax error while parsing: dsafsdf +183: [09:33:31] SMILES Parse Error: check for mistakes around position 1: +183: [09:33:31] dsafsdf +183: [09:33:31] ^ +183: [09:33:31] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +183: [09:33:31] SMILES Parse Error: syntax error while parsing: dsafsdf +183: [09:33:31] SMILES Parse Error: check for mistakes around position 1: +183: [09:33:31] dsafsdf +183: [09:33:31] ^ +183: [09:33:31] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +183: [09:33:31] SMILES Parse Error: syntax error while parsing: dsafsdf +183: [09:33:31] SMILES Parse Error: check for mistakes around position 1: +183: [09:33:31] dsafsdf +183: [09:33:31] ^ +183: [09:33:31] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +183: [09:33:31] SMILES Parse Error: syntax error while parsing: dsafsdf +183: [09:33:31] SMILES Parse Error: check for mistakes around position 1: +183: [09:33:31] dsafsdf +183: [09:33:31] ^ +183: [09:33:31] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +183: [09:33:31] SMILES Parse Error: syntax error while parsing: dsafsdf +183: [09:33:31] SMILES Parse Error: check for mistakes around position 1: +183: [09:33:31] dsafsdf +183: [09:33:31] ^ +183: [09:33:31] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +183: [09:33:31] SMILES Parse Error: syntax error while parsing: dsafsdf +183: [09:33:31] SMILES Parse Error: check for mistakes around position 1: +183: [09:33:31] dsafsdf +183: [09:33:31] ^ +183: [09:33:31] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +183: [09:33:31] SMILES Parse Error: syntax error while parsing: dsafsdf +183: [09:33:31] SMILES Parse Error: check for mistakes around position 1: +183: [09:33:31] dsafsdf +183: [09:33:31] ^ +183: [09:33:31] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +183: [09:33:31] SMILES Parse Error: syntax error while parsing: dsafsdf +183: [09:33:31] SMILES Parse Error: check for mistakes around position 1: +183: [09:33:31] dsafsdf +183: [09:33:31] ^ +183: [09:33:31] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +183: [09:33:31] SMILES Parse Error: syntax error while parsing: dsafsdf +183: [09:33:31] SMILES Parse Error: check for mistakes around position 1: +183: [09:33:31] dsafsdf +183: [09:33:31] ^ +183: [09:33:31] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +183: [09:33:31] SMILES Parse Error: syntax error while parsing: dsafsdf +183: [09:33:31] SMILES Parse Error: check for mistakes around position 1: +183: [09:33:31] dsafsdf +183: [09:33:31] ^ +183: [09:33:31] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +183: [09:33:31] SMILES Parse Error: syntax error while parsing: dsafsdf +183: [09:33:31] SMILES Parse Error: check for mistakes around position 1: +183: [09:33:31] dsafsdf +183: [09:33:31] ^ +183: [09:33:31] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +183: [09:33:31] SMILES Parse Error: syntax error while parsing: dsafsdf +183: [09:33:31] SMILES Parse Error: check for mistakes around position 1: +183: [09:33:31] dsafsdf +183: [09:33:31] ^ +183: [09:33:31] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +183: [09:33:31] SMILES Parse Error: syntax error while parsing: dsafsdf +183: [09:33:31] SMILES Parse Error: check for mistakes around position 1: +183: [09:33:31] dsafsdf +183: [09:33:31] ^ +183: [09:33:31] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +183: [09:33:31] SMILES Parse Error: syntax error while parsing: dsafsdf +183: [09:33:31] SMILES Parse Error: check for mistakes around position 1: +183: [09:33:31] dsafsdf +183: [09:33:31] ^ +183: [09:33:31] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +183: [09:33:31] SMILES Parse Error: syntax error while parsing: dsafsdf +183: [09:33:31] SMILES Parse Error: check for mistakes around position 1: +183: [09:33:31] dsafsdf +183: [09:33:31] ^ +183: [09:33:31] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +183: [09:33:31] SMILES Parse Error: syntax error while parsing: dsafsdf +183: [09:33:31] SMILES Parse Error: check for mistakes around position 1: +183: [09:33:31] dsafsdf +183: [09:33:31] ^ +183: [09:33:31] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +183: [09:33:31] SMILES Parse Error: syntax error while parsing: dsafsdf +183: [09:33:31] SMILES Parse Error: check for mistakes around position 1: +183: [09:33:31] dsafsdf +183: [09:33:31] ^ +183: [09:33:31] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +183: [09:33:31] SMILES Parse Error: syntax error while parsing: dsafsdf +183: [09:33:31] SMILES Parse Error: check for mistakes around position 1: +183: [09:33:31] dsafsdf +183: [09:33:31] ^ +183: [09:33:31] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +183: [09:33:31] SMILES Parse Error: syntax error while parsing: dsafsdf +183: [09:33:31] SMILES Parse Error: check for mistakes around position 1: +183: [09:33:31] dsafsdf +183: [09:33:31] ^ +183: [09:33:31] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +183: [09:33:31] SMILES Parse Error: syntax error while parsing: dsafsdf +183: [09:33:31] SMILES Parse Error: check for mistakes around position 1: +183: [09:33:31] dsafsdf +183: [09:33:31] ^ +183: [09:33:31] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +183: [09:33:31] SMILES Parse Error: syntax error while parsing: dsafsdf +183: [09:33:31] SMILES Parse Error: check for mistakes around position 1: +183: [09:33:31] dsafsdf +183: [09:33:31] ^ +183: [09:33:31] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +183: [09:33:31] SMILES Parse Error: syntax error while parsing: dsafsdf +183: [09:33:31] SMILES Parse Error: check for mistakes around position 1: +183: [09:33:31] dsafsdf +183: [09:33:31] ^ +183: [09:33:31] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +183: [09:33:31] SMILES Parse Error: syntax error while parsing: dsafsdf +183: [09:33:31] SMILES Parse Error: check for mistakes around position 1: +183: [09:33:31] dsafsdf +183: [09:33:31] ^ +183: [09:33:31] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +183: [09:33:31] SMILES Parse Error: syntax error while parsing: dsafsdf +183: [09:33:31] SMILES Parse Error: check for mistakes around position 1: +183: [09:33:31] dsafsdf +183: [09:33:31] ^ +183: [09:33:31] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +183: [09:33:31] SMILES Parse Error: syntax error while parsing: dsafsdf +183: [09:33:31] SMILES Parse Error: check for mistakes around position 1: +183: [09:33:31] dsafsdf +183: [09:33:31] ^ +183: [09:33:31] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +183: [09:33:31] SMILES Parse Error: syntax error while parsing: dsafsdf +183: [09:33:31] SMILES Parse Error: check for mistakes around position 1: +183: [09:33:31] dsafsdf +183: [09:33:31] ^ +183: [09:33:31] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +183: [09:33:31] SMILES Parse Error: syntax error while parsing: dsafsdf +183: [09:33:31] SMILES Parse Error: check for mistakes around position 1: +183: [09:33:31] dsafsdf +183: [09:33:31] ^ +183: [09:33:31] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +183: [09:33:31] SMILES Parse Error: syntax error while parsing: dsafsdf +183: [09:33:31] SMILES Parse Error: check for mistakes around position 1: +183: [09:33:31] dsafsdf +183: [09:33:31] ^ +183: [09:33:31] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +183: [09:33:31] SMILES Parse Error: syntax error while parsing: dsafsdf +183: [09:33:31] SMILES Parse Error: check for mistakes around position 1: +183: [09:33:31] dsafsdf +183: [09:33:31] ^ +183: [09:33:31] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +183: [09:33:31] SMILES Parse Error: syntax error while parsing: dsafsdf +183: [09:33:31] SMILES Parse Error: check for mistakes around position 1: +183: [09:33:31] dsafsdf +183: [09:33:31] ^ +183: [09:33:31] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +183: [09:33:31] SMILES Parse Error: syntax error while parsing: dsafsdf +183: [09:33:31] SMILES Parse Error: check for mistakes around position 1: +183: [09:33:31] dsafsdf +183: [09:33:31] ^ +183: [09:33:31] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +183: [09:33:31] SMILES Parse Error: syntax error while parsing: dsafsdf +183: [09:33:31] SMILES Parse Error: check for mistakes around position 1: +183: [09:33:31] dsafsdf +183: [09:33:31] ^ +183: [09:33:31] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +183: [09:33:31] SMILES Parse Error: syntax error while parsing: dsafsdf +183: [09:33:31] SMILES Parse Error: check for mistakes around position 1: +183: [09:33:31] dsafsdf +183: [09:33:31] ^ +183: [09:33:31] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +183: [09:33:31] SMILES Parse Error: syntax error while parsing: dsafsdf +183: [09:33:31] SMILES Parse Error: check for mistakes around position 1: +183: [09:33:31] dsafsdf +183: [09:33:31] ^ +183: [09:33:31] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +183: [09:33:31] SMILES Parse Error: syntax error while parsing: dsafsdf +183: [09:33:31] SMILES Parse Error: check for mistakes around position 1: +183: [09:33:31] dsafsdf +183: [09:33:31] ^ +183: [09:33:31] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +183: [09:33:31] SMILES Parse Error: syntax error while parsing: dsafsdf +183: [09:33:31] SMILES Parse Error: check for mistakes around position 1: +183: [09:33:31] dsafsdf +183: [09:33:31] ^ +183: [09:33:31] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +183: [09:33:31] SMILES Parse Error: syntax error while parsing: dsafsdf +183: [09:33:31] SMILES Parse Error: check for mistakes around position 1: +183: [09:33:31] dsafsdf +183: [09:33:31] ^ +183: [09:33:31] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +183: [09:33:31] SMILES Parse Error: syntax error while parsing: dsafsdf +183: [09:33:31] SMILES Parse Error: check for mistakes around position 1: +183: [09:33:31] dsafsdf +183: [09:33:31] ^ +183: [09:33:31] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +183: [09:33:31] SMILES Parse Error: syntax error while parsing: dsafsdf +183: [09:33:31] SMILES Parse Error: check for mistakes around position 1: +183: [09:33:31] dsafsdf +183: [09:33:31] ^ +183: [09:33:31] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +183: [09:33:31] SMILES Parse Error: syntax error while parsing: dsafsdf +183: [09:33:31] SMILES Parse Error: check for mistakes around position 1: +183: [09:33:31] dsafsdf +183: [09:33:31] ^ +183: [09:33:31] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +183: [09:33:31] SMILES Parse Error: syntax error while parsing: dsafsdf +183: [09:33:31] SMILES Parse Error: check for mistakes around position 1: +183: [09:33:31] dsafsdf +183: [09:33:31] ^ +183: [09:33:31] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +183: [09:33:31] SMILES Parse Error: syntax error while parsing: dsafsdf +183: [09:33:31] SMILES Parse Error: check for mistakes around position 1: +183: [09:33:31] dsafsdf +183: [09:33:31] ^ +183: [09:33:31] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +183: [09:33:31] SMILES Parse Error: syntax error while parsing: dsafsdf +183: [09:33:31] SMILES Parse Error: check for mistakes around position 1: +183: [09:33:31] dsafsdf +183: [09:33:31] ^ +183: [09:33:31] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +183: [09:33:31] SMILES Parse Error: syntax error while parsing: dsafsdf +183: [09:33:31] SMILES Parse Error: check for mistakes around position 1: +183: [09:33:31] dsafsdf +183: [09:33:31] ^ +183: [09:33:31] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +183: [09:33:31] SMILES Parse Error: syntax error while parsing: dsafsdf +183: [09:33:31] SMILES Parse Error: check for mistakes around position 1: +183: [09:33:31] dsafsdf +183: [09:33:31] ^ +183: [09:33:31] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +183: [09:33:31] SMILES Parse Error: syntax error while parsing: dsafsdf +183: [09:33:31] SMILES Parse Error: check for mistakes around position 1: +183: [09:33:31] dsafsdf +183: [09:33:31] ^ +183: [09:33:31] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +183: [09:33:31] SMILES Parse Error: syntax error while parsing: dsafsdf +183: [09:33:31] SMILES Parse Error: check for mistakes around position 1: +183: [09:33:31] dsafsdf +183: [09:33:31] ^ +183: [09:33:31] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +183: [09:33:31] SMILES Parse Error: syntax error while parsing: dsafsdf +183: [09:33:31] SMILES Parse Error: check for mistakes around position 1: +183: [09:33:31] dsafsdf +183: [09:33:31] ^ +183: [09:33:31] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +183: [09:33:31] SMILES Parse Error: syntax error while parsing: dsafsdf +183: [09:33:31] SMILES Parse Error: check for mistakes around position 1: +183: [09:33:31] dsafsdf +183: [09:33:31] ^ +183: [09:33:31] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +183: [09:33:31] SMILES Parse Error: syntax error while parsing: dsafsdf +183: [09:33:31] SMILES Parse Error: check for mistakes around position 1: +183: [09:33:31] dsafsdf +183: [09:33:31] ^ +183: [09:33:31] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +183: [09:33:31] SMILES Parse Error: syntax error while parsing: dsafsdf +183: [09:33:31] SMILES Parse Error: check for mistakes around position 1: +183: [09:33:31] dsafsdf +183: [09:33:31] ^ +183: [09:33:31] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +183: [09:33:31] SMILES Parse Error: syntax error while parsing: dsafsdf +183: [09:33:31] SMILES Parse Error: check for mistakes around position 1: +183: [09:33:31] dsafsdf +183: [09:33:31] ^ +183: [09:33:31] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +183: [09:33:31] SMILES Parse Error: syntax error while parsing: dsafsdf +183: [09:33:31] SMILES Parse Error: check for mistakes around position 1: +183: [09:33:31] dsafsdf +183: [09:33:31] ^ +183: [09:33:31] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +183: [09:33:31] SMILES Parse Error: syntax error while parsing: dsafsdf +183: [09:33:31] SMILES Parse Error: check for mistakes around position 1: +183: [09:33:31] dsafsdf +183: [09:33:31] ^ +183: [09:33:31] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +183: [09:33:31] SMILES Parse Error: syntax error while parsing: dsafsdf +183: [09:33:31] SMILES Parse Error: check for mistakes around position 1: +183: [09:33:31] dsafsdf +183: [09:33:31] ^ +183: [09:33:31] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +183: [09:33:31] SMILES Parse Error: syntax error while parsing: dsafsdf +183: [09:33:31] SMILES Parse Error: check for mistakes around position 1: +183: [09:33:31] dsafsdf +183: [09:33:31] ^ +183: [09:33:31] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +183: [09:33:31] SMILES Parse Error: syntax error while parsing: dsafsdf +183: [09:33:31] SMILES Parse Error: check for mistakes around position 1: +183: [09:33:31] dsafsdf +183: [09:33:31] ^ +183: [09:33:31] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +183: [09:33:31] SMILES Parse Error: syntax error while parsing: dsafsdf +183: [09:33:31] SMILES Parse Error: check for mistakes around position 1: +183: [09:33:31] dsafsdf +183: [09:33:31] ^ +183: [09:33:31] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +183: [09:33:31] SMILES Parse Error: syntax error while parsing: dsafsdf +183: [09:33:31] SMILES Parse Error: check for mistakes around position 1: +183: [09:33:31] dsafsdf +183: [09:33:31] ^ +183: [09:33:31] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +183: [09:33:31] SMILES Parse Error: syntax error while parsing: dsafsdf +183: [09:33:31] SMILES Parse Error: check for mistakes around position 1: +183: [09:33:31] dsafsdf +183: [09:33:31] ^ +183: [09:33:31] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +183: [09:33:31] SMILES Parse Error: syntax error while parsing: dsafsdf +183: [09:33:31] SMILES Parse Error: check for mistakes around position 1: +183: [09:33:31] dsafsdf +183: [09:33:31] ^ +183: [09:33:31] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +183: [09:33:31] SMILES Parse Error: syntax error while parsing: dsafsdf +183: [09:33:31] SMILES Parse Error: check for mistakes around position 1: +183: [09:33:31] dsafsdf +183: [09:33:31] ^ +183: [09:33:31] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +183: [09:33:31] SMILES Parse Error: syntax error while parsing: dsafsdf +183: [09:33:31] SMILES Parse Error: check for mistakes around position 1: +183: [09:33:31] dsafsdf +183: [09:33:31] ^ +183: [09:33:31] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +183: [09:33:31] SMILES Parse Error: syntax error while parsing: dsafsdf +183: [09:33:31] SMILES Parse Error: check for mistakes around position 1: +183: [09:33:31] dsafsdf +183: [09:33:31] ^ +183: [09:33:31] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +183: [09:33:31] SMILES Parse Error: syntax error while parsing: dsafsdf +183: [09:33:31] SMILES Parse Error: check for mistakes around position 1: +183: [09:33:31] dsafsdf +183: [09:33:31] ^ +183: [09:33:31] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +183: [09:33:31] SMILES Parse Error: syntax error while parsing: dsafsdf +183: [09:33:31] SMILES Parse Error: check for mistakes around position 1: +183: [09:33:31] dsafsdf +183: [09:33:31] ^ +183: [09:33:31] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +183: [09:33:31] SMILES Parse Error: syntax error while parsing: dsafsdf +183: [09:33:31] SMILES Parse Error: check for mistakes around position 1: +183: [09:33:31] dsafsdf +183: [09:33:31] ^ +183: [09:33:31] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +183: [09:33:31] SMILES Parse Error: syntax error while parsing: dsafsdf +183: [09:33:31] SMILES Parse Error: check for mistakes around position 1: +183: [09:33:31] dsafsdf +183: [09:33:31] ^ +183: [09:33:31] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +183: [09:33:31] SMILES Parse Error: syntax error while parsing: dsafsdf +183: [09:33:31] SMILES Parse Error: check for mistakes around position 1: +183: [09:33:31] dsafsdf +183: [09:33:31] ^ +183: [09:33:31] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +183: [09:33:31] SMILES Parse Error: syntax error while parsing: dsafsdf +183: [09:33:31] SMILES Parse Error: check for mistakes around position 1: +183: [09:33:31] dsafsdf +183: [09:33:31] ^ +183: [09:33:31] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +183: [09:33:31] SMILES Parse Error: syntax error while parsing: dsafsdf +183: [09:33:31] SMILES Parse Error: check for mistakes around position 1: +183: [09:33:31] dsafsdf +183: [09:33:31] ^ +183: [09:33:31] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +183: [09:33:31] SMILES Parse Error: syntax error while parsing: dsafsdf +183: [09:33:31] SMILES Parse Error: check for mistakes around position 1: +183: [09:33:31] dsafsdf +183: [09:33:31] ^ +183: [09:33:31] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +183: [09:33:31] SMILES Parse Error: syntax error while parsing: dsafsdf +183: [09:33:31] SMILES Parse Error: check for mistakes around position 1: +183: [09:33:31] dsafsdf +183: [09:33:31] ^ +183: [09:33:31] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +183: [09:33:31] SMILES Parse Error: syntax error while parsing: dsafsdf +183: [09:33:31] SMILES Parse Error: check for mistakes around position 1: +183: [09:33:31] dsafsdf +183: [09:33:31] ^ +183: [09:33:31] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +183: [09:33:31] SMILES Parse Error: syntax error while parsing: dsafsdf +183: [09:33:31] SMILES Parse Error: check for mistakes around position 1: +183: [09:33:31] dsafsdf +183: [09:33:31] ^ +183: [09:33:31] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +183: [09:33:31] SMILES Parse Error: syntax error while parsing: dsafsdf +183: [09:33:31] SMILES Parse Error: check for mistakes around position 1: +183: [09:33:31] dsafsdf +183: [09:33:31] ^ +183: [09:33:31] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +183: [09:33:31] SMILES Parse Error: syntax error while parsing: dsafsdf +183: [09:33:31] SMILES Parse Error: check for mistakes around position 1: +183: [09:33:31] dsafsdf +183: [09:33:31] ^ +183: [09:33:31] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +183: [09:33:31] SMILES Parse Error: syntax error while parsing: dsafsdf +183: [09:33:31] SMILES Parse Error: check for mistakes around position 1: +183: [09:33:31] dsafsdf +183: [09:33:31] ^ +183: [09:33:31] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +183: [09:33:31] SMILES Parse Error: syntax error while parsing: dsafsdf +183: [09:33:31] SMILES Parse Error: check for mistakes around position 1: +183: [09:33:31] dsafsdf +183: [09:33:31] ^ +183: [09:33:31] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +183: [09:33:31] SMILES Parse Error: syntax error while parsing: dsafsdf +183: [09:33:31] SMILES Parse Error: check for mistakes around position 1: +183: [09:33:31] dsafsdf +183: [09:33:31] ^ +183: [09:33:31] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +183: [09:33:31] SMILES Parse Error: syntax error while parsing: dsafsdf +183: [09:33:31] SMILES Parse Error: check for mistakes around position 1: +183: [09:33:31] dsafsdf +183: [09:33:31] ^ +183: [09:33:31] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +183: [09:33:31] SMILES Parse Error: syntax error while parsing: dsafsdf +183: [09:33:31] SMILES Parse Error: check for mistakes around position 1: +183: [09:33:31] dsafsdf +183: [09:33:31] ^ +183: [09:33:31] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +183: [09:33:31] SMILES Parse Error: syntax error while parsing: dsafsdf +183: [09:33:31] SMILES Parse Error: check for mistakes around position 1: +183: [09:33:31] dsafsdf +183: [09:33:31] ^ +183: [09:33:31] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +183: [09:33:31] SMILES Parse Error: syntax error while parsing: dsafsdf +183: [09:33:31] SMILES Parse Error: check for mistakes around position 1: +183: [09:33:31] dsafsdf +183: [09:33:31] ^ +183: [09:33:31] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +183: [09:33:31] SMILES Parse Error: syntax error while parsing: dsafsdf +183: [09:33:31] SMILES Parse Error: check for mistakes around position 1: +183: [09:33:31] dsafsdf +183: [09:33:31] ^ +183: [09:33:31] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +183: [09:33:31] SMILES Parse Error: syntax error while parsing: dsafsdf +183: [09:33:31] SMILES Parse Error: check for mistakes around position 1: +183: [09:33:31] dsafsdf +183: [09:33:31] ^ +183: [09:33:31] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +183: [09:33:31] SMILES Parse Error: syntax error while parsing: dsafsdf +183: [09:33:31] SMILES Parse Error: check for mistakes around position 1: +183: [09:33:31] dsafsdf +183: [09:33:31] ^ +183: [09:33:31] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +183: [09:33:31] SMILES Parse Error: syntax error while parsing: dsafsdf +183: [09:33:31] SMILES Parse Error: check for mistakes around position 1: +183: [09:33:31] dsafsdf +183: [09:33:31] ^ +183: [09:33:31] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +183: [09:33:31] SMILES Parse Error: syntax error while parsing: dsafsdf +183: [09:33:31] SMILES Parse Error: check for mistakes around position 1: +183: [09:33:31] dsafsdf +183: [09:33:31] ^ +183: [09:33:31] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +183: [09:33:31] SMILES Parse Error: syntax error while parsing: dsafsdf +183: [09:33:31] SMILES Parse Error: check for mistakes around position 1: +183: [09:33:31] dsafsdf +183: [09:33:31] ^ +183: [09:33:31] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +183: [09:33:31] SMILES Parse Error: syntax error while parsing: dsafsdf +183: [09:33:31] SMILES Parse Error: check for mistakes around position 1: +183: [09:33:31] dsafsdf +183: [09:33:31] ^ +183: [09:33:31] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +183: [09:33:31] SMILES Parse Error: syntax error while parsing: dsafsdf +183: [09:33:31] SMILES Parse Error: check for mistakes around position 1: +183: [09:33:31] dsafsdf +183: [09:33:31] ^ +183: [09:33:31] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +183: [09:33:31] SMILES Parse Error: syntax error while parsing: dsafsdf +183: [09:33:31] SMILES Parse Error: check for mistakes around position 1: +183: [09:33:31] dsafsdf +183: [09:33:31] ^ +183: [09:33:31] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +183: [09:33:31] SMILES Parse Error: syntax error while parsing: dsafsdf +183: [09:33:31] SMILES Parse Error: check for mistakes around position 1: +183: [09:33:31] dsafsdf +183: [09:33:31] ^ +183: [09:33:31] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +183: [09:33:31] SMILES Parse Error: syntax error while parsing: dsafsdf +183: [09:33:31] SMILES Parse Error: check for mistakes around position 1: +183: [09:33:31] dsafsdf +183: [09:33:31] ^ +183: [09:33:31] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +183: [09:33:31] SMILES Parse Error: syntax error while parsing: dsafsdf +183: [09:33:31] SMILES Parse Error: check for mistakes around position 1: +183: [09:33:31] dsafsdf +183: [09:33:31] ^ +183: [09:33:31] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +183: [09:33:31] SMILES Parse Error: syntax error while parsing: dsafsdf +183: [09:33:31] SMILES Parse Error: check for mistakes around position 1: +183: [09:33:31] dsafsdf +183: [09:33:31] ^ +183: [09:33:31] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +183: [09:33:31] SMILES Parse Error: syntax error while parsing: dsafsdf +183: [09:33:31] SMILES Parse Error: check for mistakes around position 1: +183: [09:33:31] dsafsdf +183: [09:33:31] ^ +183: [09:33:31] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +183: [09:33:31] SMILES Parse Error: syntax error while parsing: dsafsdf +183: [09:33:31] SMILES Parse Error: check for mistakes around position 1: +183: [09:33:31] dsafsdf +183: [09:33:31] ^ +183: [09:33:31] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +183: [09:33:31] SMILES Parse Error: syntax error while parsing: dsafsdf +183: [09:33:31] SMILES Parse Error: check for mistakes around position 1: +183: [09:33:31] dsafsdf +183: [09:33:31] ^ +183: [09:33:31] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +183: [09:33:31] SMILES Parse Error: syntax error while parsing: dsafsdf +183: [09:33:31] SMILES Parse Error: check for mistakes around position 1: +183: [09:33:31] dsafsdf +183: [09:33:31] ^ +183: [09:33:31] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +183: [09:33:31] SMILES Parse Error: syntax error while parsing: dsafsdf +183: [09:33:31] SMILES Parse Error: check for mistakes around position 1: +183: [09:33:31] dsafsdf +183: [09:33:31] ^ +183: [09:33:31] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +183: [09:33:31] ------------------------------------- +183: [09:33:31] Results do not depend on numThreads +186: iterative +173: [09:33:32] Complex queries can be slow. +173: [09:33:32] Complex queries can be slow. +173: [09:33:32] Complex queries can be slow. +173: [09:33:32] Complex queries can be slow. +186: bulk +173: [09:33:32] Complex queries can be slow. +173: [09:33:32] Complex queries can be slow. +173: [09:33:32] Complex queries can be slow. +148: .........[09:33:32] Molecule does not have explicit Hs. Consider calling AddHs() +148: .[09:33:32] Molecule does not have explicit Hs. Consider calling AddHs() +148: [09:33:32] Molecule does not have explicit Hs. Consider calling AddHs() +148: [09:33:32] Molecule does not have explicit Hs. Consider calling AddHs() +148: [09:33:32] Molecule does not have explicit Hs. Consider calling AddHs() +148: [09:33:32] Molecule does not have explicit Hs. Consider calling AddHs() +148: [09:33:32] Molecule does not have explicit Hs. Consider calling AddHs() +148: [09:33:32] Molecule does not have explicit Hs. Consider calling AddHs() +148: [09:33:32] Molecule does not have explicit Hs. Consider calling AddHs() +148: [09:33:32] Molecule does not have explicit Hs. Consider calling AddHs() +148: [09:33:32] Molecule does not have explicit Hs. Consider calling AddHs() +148: .[09:33:32] Molecule does not have explicit Hs. Consider calling AddHs() +148: [09:33:32] Molecule does not have explicit Hs. Consider calling AddHs() +148: [09:33:32] Molecule does not have explicit Hs. Consider calling AddHs() +148: [09:33:32] Molecule does not have explicit Hs. Consider calling AddHs() +148: [09:33:32] Molecule does not have explicit Hs. Consider calling AddHs() +148: [09:33:32] Molecule does not have explicit Hs. Consider calling AddHs() +148: [09:33:32] Molecule does not have explicit Hs. Consider calling AddHs() +148: [09:33:32] Molecule does not have explicit Hs. Consider calling AddHs() +148: [09:33:32] Molecule does not have explicit Hs. Consider calling AddHs() +148: [09:33:32] Molecule does not have explicit Hs. Consider calling AddHs() +173: [09:33:32] Complex queries can be slow. +173: [09:33:33] Complex queries can be slow. +173: [09:33:33] Complex queries can be slow. +173: [09:33:33] Complex queries can be slow. +173: [09:33:33] Complex queries can be slow. +173: [09:33:33] Complex queries can be slow. +173: [09:33:33] Complex queries can be slow. +173: [09:33:33] Complex queries can be slow. +173: [09:33:33] Complex queries can be slow. 150: --------------------------------- 150: test O3A multithreading bug 150: @@ -32172,45 +32221,40 @@ 150: testCrippenO3A multithreading 150: 150: generating reference data -150: processing -150: launch :0 -150: launch :1 -150: launch :2 -150: launch :3 -186: iterative -148: ... -148: ---------------------------------------------------------------------- -148: Ran 22 tests in 27.280s -148: -148: OK -175/238 Test #148: pyDistGeomHelpers ...................... Passed 27.95 sec +173: [09:33:33] Complex queries can be slow. +173: [09:33:33] Complex queries can be slow. +173: [09:33:34] Complex queries can be slow. +173: =============================================================================== +173: All tests passed (121 assertions in 17 test cases) +173: +175/238 Test #173: testSynthonSpaceSubstructureSearch ..... Passed 13.86 sec test 187 Start 187: testRGroupDecompInternals 187: Test command: /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/RGroupDecomposition/testRGroupDecompInternals 187: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/RGroupDecomposition 187: Test timeout computed to be: 1500 -187: [00:36:52] WARNING: not removing hydrogen atom with dummy atom neighbors -187: [00:36:52] WARNING: not removing hydrogen atom with dummy atom neighbors -187: [00:36:52] WARNING: not removing hydrogen atom with dummy atom neighbors -187: [00:36:52] WARNING: not removing hydrogen atom with dummy atom neighbors -187: [00:36:52] WARNING: not removing hydrogen atom with dummy atom neighbors -187: [00:36:52] WARNING: not removing hydrogen atom with dummy atom neighbors -187: [00:36:52] WARNING: not removing hydrogen atom with dummy atom neighbors -187: [00:36:52] WARNING: not removing hydrogen atom with dummy atom neighbors -187: [00:36:52] WARNING: not removing hydrogen atom with dummy atom neighbors -187: [00:36:52] WARNING: not removing hydrogen atom with dummy atom neighbors -187: [00:36:52] WARNING: not removing hydrogen atom with dummy atom neighbors -187: [00:36:52] WARNING: not removing hydrogen atom with dummy atom neighbors -187: [00:36:52] WARNING: not removing hydrogen atom with dummy atom neighbors -187: [00:36:52] WARNING: not removing hydrogen atom with dummy atom neighbors -187: [00:36:52] WARNING: not removing hydrogen atom with dummy atom neighbors -187: [00:36:52] WARNING: not removing hydrogen atom with dummy atom neighbors -187: [00:36:52] WARNING: not removing hydrogen atom with dummy atom neighbors -187: [00:36:52] WARNING: not removing hydrogen atom with dummy atom neighbors -187: [00:36:52] WARNING: not removing hydrogen atom with dummy atom neighbors -187: [00:36:52] WARNING: not removing hydrogen atom with dummy atom neighbors -187: [00:36:52] WARNING: not removing hydrogen atom with dummy atom neighbors +187: [09:33:34] WARNING: not removing hydrogen atom with dummy atom neighbors +187: [09:33:34] WARNING: not removing hydrogen atom with dummy atom neighbors +187: [09:33:34] WARNING: not removing hydrogen atom with dummy atom neighbors +187: [09:33:34] WARNING: not removing hydrogen atom with dummy atom neighbors +187: [09:33:34] WARNING: not removing hydrogen atom with dummy atom neighbors +187: [09:33:34] WARNING: not removing hydrogen atom with dummy atom neighbors +187: [09:33:34] WARNING: not removing hydrogen atom with dummy atom neighbors +187: [09:33:34] WARNING: not removing hydrogen atom with dummy atom neighbors +187: [09:33:34] WARNING: not removing hydrogen atom with dummy atom neighbors +187: [09:33:34] WARNING: not removing hydrogen atom with dummy atom neighbors +187: [09:33:34] WARNING: not removing hydrogen atom with dummy atom neighbors +187: [09:33:34] WARNING: not removing hydrogen atom with dummy atom neighbors +187: [09:33:34] WARNING: not removing hydrogen atom with dummy atom neighbors +187: [09:33:34] WARNING: not removing hydrogen atom with dummy atom neighbors +187: [09:33:34] WARNING: not removing hydrogen atom with dummy atom neighbors +187: [09:33:34] WARNING: not removing hydrogen atom with dummy atom neighbors +187: [09:33:34] WARNING: not removing hydrogen atom with dummy atom neighbors +187: [09:33:34] WARNING: not removing hydrogen atom with dummy atom neighbors +187: [09:33:34] WARNING: not removing hydrogen atom with dummy atom neighbors +187: [09:33:34] WARNING: not removing hydrogen atom with dummy atom neighbors +187: [09:33:34] WARNING: not removing hydrogen atom with dummy atom neighbors 176/238 Test #187: testRGroupDecompInternals .............. Passed 0.06 sec test 188 Start 188: rgroupCatchTests @@ -32218,174 +32262,37 @@ 188: Test command: /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/RGroupDecomposition/rgroupCatchTests 188: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/RGroupDecomposition 188: Test timeout computed to be: 1500 -173: [00:36:52] Complex queries can be slow. -173: [00:36:52] Complex queries can be slow. -188: Randomness seeded to: 1214982583 +150: processing +150: launch :0 +150: launch :1 +150: launch :2 +150: launch :3 +183: [09:33:34] ------------------------------------- +183: [09:33:34] Results do not depend on numThreads (all same) +188: Randomness seeded to: 875519242 188: =============================================================================== 188: All tests passed (1475 assertions in 14 test cases) 188: -186: bulk -177/238 Test #188: rgroupCatchTests ....................... Passed 0.33 sec +177/238 Test #188: rgroupCatchTests ....................... Passed 0.34 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-aarch64-linux-gnu/Code/GraphMol/RGroupDecomposition/Wrap 189: Test timeout computed to be: 1500 -173: [00:36:52] Complex queries can be slow. -183: [00:36:52] ------------------------------------- -183: [00:36:52] Results do not depend on numThreads (all same) -173: [00:36:52] Complex queries can be slow. -183: [00:36:52] ------------------------------------- -183: [00:36:52] testTautomerQueries -183: [00:36:52] Pattern fingerprints for tautomersearch aren't tautomer fingerprints, ignoring... -183: [00:36:52] ------------------------------------- -183: [00:36:52] github3881 recursive smarts with rings -178/238 Test #183: substructLibraryTest ................... Passed 8.77 sec +183: [09:33:34] ------------------------------------- +183: [09:33:34] testTautomerQueries +183: [09:33:34] Pattern fingerprints for tautomersearch aren't tautomer fingerprints, ignoring... +183: [09:33:34] ------------------------------------- +183: [09:33:34] github3881 recursive smarts with rings +178/238 Test #183: substructLibraryTest ................... Passed 6.16 sec test 190 Start 190: determineBondsCatchTest 190: Test command: /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/DetermineBonds/determineBondsCatchTest 190: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/DetermineBonds 190: Test timeout computed to be: 1500 -173: [00:36:52] Complex queries can be slow. -173: [00:36:53] Complex queries can be slow. -173: [00:36:53] Complex queries can be slow. -190: Randomness seeded to: 3690466822 -190: =============================================================================== -190: All tests passed (5174 assertions in 7 test cases) -190: -179/238 Test #190: determineBondsCatchTest ................ Passed 0.83 sec -test 191 - Start 191: pyDetermineBonds - -191: Test command: /usr/bin/python3 "/build/reproducible-path/rdkit-202503.1/Code/GraphMol/DetermineBonds/Wrap/testDetermineBonds.py" -191: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/DetermineBonds/Wrap -191: Test timeout computed to be: 1500 -173: [00:36:53] Complex queries can be slow. -173: [00:36:53] Complex queries can be slow. -173: [00:36:54] Complex queries can be slow. -191: .s.. -191: ---------------------------------------------------------------------- -191: Ran 4 tests in 0.326s -191: -191: OK (skipped=1) -180/238 Test #191: pyDetermineBonds ....................... Passed 0.73 sec -test 192 - Start 192: molInterchangeTest1 - -192: Test command: /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/MolInterchange/molInterchangeTest1 -192: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/MolInterchange -192: Test timeout computed to be: 1500 -192: [00:36:54] test1: basics -192: [00:36:54] done -192: [00:36:54] test2: basic writing -192: {"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]}]}]} -192: {"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"]]}]}]} -192: {"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]]}]}]} -192: {"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]]}]}]} -192: [00:36:54] done -192: [00:36:54] test3: writing conformers -192: {"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]}]}]} -192: [00:36:54] done -192: [00:36:54] test4: writing properties -192: {"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]}]}]} -192: [00:36:54] done -192: [00:36:54] test5: writing partial charges -192: {"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]}]}]} -192: [00:36:54] testing parse options -192: [00:36:54] done -192: [00:36:54] testing github #2046: CIPRank values from JSONDataToMols are not unsigned -192: {"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]]}]}]} -192: [00:36:54] done -192: [00:36:54] testing 'either' stereochemistry -192: [00:36:54] done -181/238 Test #192: molInterchangeTest1 .................... Passed 0.04 sec -test 193 - Start 193: molInterchangeCatchTest - -193: Test command: /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/MolInterchange/molInterchangeCatchTest -193: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/MolInterchange -193: Test timeout computed to be: 1500 -173: [00:36:54] Complex queries can be slow. -193: Randomness seeded to: 3566905169 -193: [00:36:54] unrecognized bond type 12 set to zero while writing -193: [00:36:54] unrecognized bond type 0 set to zero while writing -193: =============================================================================== -193: All tests passed (125 assertions in 7 test cases) -193: -182/238 Test #193: molInterchangeCatchTest ................ Passed 0.05 sec -test 194 - Start 194: pyMolInterchange - -194: Test command: /usr/bin/python3 "/build/reproducible-path/rdkit-202503.1/Code/GraphMol/MolInterchange/Wrap/testMolInterchange.py" -194: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/MolInterchange/Wrap -194: Test timeout computed to be: 1500 -173: [00:36:54] Complex queries can be slow. -186: bulk, no symmetry -194: .. -194: ---------------------------------------------------------------------- -194: Ran 2 tests in 0.020s -194: -194: OK -183/238 Test #194: pyMolInterchange ....................... Passed 0.40 sec -test 195 - Start 195: testSLNParse - -195: Test command: /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/SLNParse/testSLNParse -195: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/SLNParse -195: Test timeout computed to be: 1500 -195: Atoms: -195: 0 6 C chg: 1 deg: 5 exp: N/A imp: 0 hyb: -195: 1 1 H chg: 0 deg: 1 exp: N/A imp: N/A hyb: -195: 2 1 H chg: 0 deg: 1 exp: N/A imp: N/A hyb: -195: 3 1 H chg: 0 deg: 1 exp: N/A imp: N/A hyb: -195: 4 1 H chg: 0 deg: 1 exp: N/A imp: N/A hyb: -195: 5 1 H chg: 0 deg: 1 exp: N/A imp: N/A hyb: -195: Bonds: -195: 0 0->1 order: 1 -195: 1 0->2 order: 1 -195: 2 0->3 order: 1 -195: 3 0->4 order: 1 -195: 4 0->5 order: 1 -195: [00:36:54] SLN Parse Error: syntax error while parsing: CH4[I=13] -195: [00:36:54] Failed parsing SLN 'CH4[I=13]' -195: [00:36:54] SLN Parser error: Atom ID 1 appears *after* its ring closure. -195: [00:36:54] SLN Parser error: Ring closure 1 does not have a corresponding opener. -195: [00:36:54] SLN Parse Error: syntax error while parsing: CH2(C@1H2)CH2(CH2CH2C[1]H2) -195: [00:36:54] Failed parsing SLN 'CH2(C@1H2)CH2(CH2CH2C[1]H2)' -195: [00:36:54] SLN Parse Error: syntax error while parsing: CH2(CH2[1])CH2(CH2CH2CH2@1) -195: [00:36:54] Failed parsing SLN 'CH2(CH2[1])CH2(CH2CH2CH2@1)' -195: [00:36:54] SLN Parse Error: syntax error while parsing: CH4 fff -195: [00:36:54] Failed parsing SLN 'CH4 fff' -195: [00:36:54] SLN Parse Error: syntax error while parsing: C[charge=+1] foo -195: [00:36:54] Failed parsing SLN 'C[charge=+1] foo' -195: [00:36:54] Query property 'is' ignored on non-query atom -195: [00:36:54] Query property 'is' ignored on non-query atom -184/238 Test #195: testSLNParse ........................... Passed 0.04 sec -test 196 - Start 196: pySLNParse - -196: Test command: /usr/bin/python3 "/build/reproducible-path/rdkit-202503.1/Code/GraphMol/SLNParse/Wrap/testSLN.py" -196: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/SLNParse/Wrap -196: Test timeout computed to be: 1500 -173: [00:36:54] Complex queries can be slow. -196: .. -196: ---------------------------------------------------------------------- -196: Ran 2 tests in 0.022s -196: -196: OK -173: [00:36:55] Complex queries can be slow. -185/238 Test #196: pySLNParse ............................. Passed 0.45 sec -test 197 - Start 197: pyGraphMolWrap - -197: Test command: /usr/bin/python3 "/build/reproducible-path/rdkit-202503.1/Code/GraphMol/Wrap/rough_test.py" -197: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/Wrap -197: Test timeout computed to be: 1500 -186: [00:36:55] Relabelling existing label -173: [00:36:55] Complex queries can be slow. -185: ......[00:36:55] +185: ......[09:33:34] 185: 185: **** 185: Pre-condition Violation @@ -32406,25 +32313,25 @@ 185: 9# RDKit::SubstructMatch(RDKit::ROMol const&, RDKit::ROMol const&, RDKit::SubstructMatchParameters const&) in /build/reproducible-path/rdkit-202503.1/obj-aarch64-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-aarch64-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-aarch64-linux-gnu/rdkit/Chem/rdchem.so -185: 12# 0x0000FFFF92091550 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so +185: 12# 0x0000FFFF861E1550 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so 185: 13# boost::python::objects::function::call(_object*, _object*) const in /lib/aarch64-linux-gnu/libboost_python313.so.1.83.0 -185: 14# 0x0000FFFF93B42680 in /lib/aarch64-linux-gnu/libboost_python313.so.1.83.0 +185: 14# 0x0000FFFF87C92680 in /lib/aarch64-linux-gnu/libboost_python313.so.1.83.0 185: 15# boost::python::detail::exception_handler::operator()(boost::function0 const&) const in /lib/aarch64-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-aarch64-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-aarch64-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-aarch64-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-aarch64-linux-gnu/rdkit/Chem/rdchem.so -185: 20# 0x0000FFFF91FEC320 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so -185: 21# 0x0000FFFF91FEC2B8 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so -185: 22# 0x0000FFFF91FEC248 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so -185: 23# 0x0000FFFF91FEC1E0 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so -185: 24# 0x0000FFFF91FEC178 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so +185: 20# 0x0000FFFF8613C320 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so +185: 21# 0x0000FFFF8613C2B8 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so +185: 22# 0x0000FFFF8613C248 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so +185: 23# 0x0000FFFF8613C1E0 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so +185: 24# 0x0000FFFF8613C178 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-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-aarch64-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-aarch64-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-aarch64-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-aarch64-linux-gnu/rdkit/rdBase.so 185: 29# boost::python::handle_exception_impl(boost::function0) in /lib/aarch64-linux-gnu/libboost_python313.so.1.83.0 -185: 30# 0x0000FFFF93B3F25C in /lib/aarch64-linux-gnu/libboost_python313.so.1.83.0 +185: 30# 0x0000FFFF87C8F25C in /lib/aarch64-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# 0x000000000053D3B0 in /usr/bin/python3 @@ -32456,13 +32363,13 @@ 185: 59# 0x000000000065EE50 in /usr/bin/python3 185: 60# Py_RunMain in /usr/bin/python3 185: 61# Py_BytesMain in /usr/bin/python3 -185: 62# 0x0000FFFF9452229C in /lib/aarch64-linux-gnu/libc.so.6 +185: 62# 0x0000FFFF8867229C in /lib/aarch64-linux-gnu/libc.so.6 185: 63# __libc_start_main in /lib/aarch64-linux-gnu/libc.so.6 185: 64# _start in /usr/bin/python3 185: ---------- 185: **** 185: -185: [00:36:55] +185: [09:33:34] 185: 185: **** 185: Pre-condition Violation @@ -32474,7 +32381,7 @@ 185: 0# Invar::Invariant::toString[abi:cxx11]() const in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu//lib/libRDKitRDGeneral.so.1 185: 1# Invar::operator<<(std::ostream&, Invar::Invariant const&) in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu//lib/libRDKitRDGeneral.so.1 185: 2# RDKit::RingInfo::numBondRings(unsigned int) const in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu//lib/libRDKitGraphMol.so.1 -185: 3# 0x0000FFFF91B41BC8 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu//lib/libRDKitGraphMol.so.1 +185: 3# 0x0000FFFF85C91BC8 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu//lib/libRDKitGraphMol.so.1 185: 4# Queries::EqualityQuery::Match(RDKit::Bond const*) const in /build/reproducible-path/rdkit-202503.1/obj-aarch64-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-aarch64-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-aarch64-linux-gnu//lib/libRDKitSubstructMatch.so.1 @@ -32484,25 +32391,25 @@ 185: 10# RDKit::SubstructMatch(RDKit::ROMol const&, RDKit::ROMol const&, RDKit::SubstructMatchParameters const&) in /build/reproducible-path/rdkit-202503.1/obj-aarch64-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-aarch64-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-aarch64-linux-gnu/rdkit/Chem/rdchem.so -185: 13# 0x0000FFFF92091550 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so +185: 13# 0x0000FFFF861E1550 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so 185: 14# boost::python::objects::function::call(_object*, _object*) const in /lib/aarch64-linux-gnu/libboost_python313.so.1.83.0 -185: 15# 0x0000FFFF93B42680 in /lib/aarch64-linux-gnu/libboost_python313.so.1.83.0 +185: 15# 0x0000FFFF87C92680 in /lib/aarch64-linux-gnu/libboost_python313.so.1.83.0 185: 16# boost::python::detail::exception_handler::operator()(boost::function0 const&) const in /lib/aarch64-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-aarch64-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-aarch64-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-aarch64-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-aarch64-linux-gnu/rdkit/Chem/rdchem.so -185: 21# 0x0000FFFF91FEC320 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so -185: 22# 0x0000FFFF91FEC2B8 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so -185: 23# 0x0000FFFF91FEC248 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so -185: 24# 0x0000FFFF91FEC1E0 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so -185: 25# 0x0000FFFF91FEC178 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so +185: 21# 0x0000FFFF8613C320 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so +185: 22# 0x0000FFFF8613C2B8 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so +185: 23# 0x0000FFFF8613C248 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so +185: 24# 0x0000FFFF8613C1E0 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so +185: 25# 0x0000FFFF8613C178 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-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-aarch64-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-aarch64-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-aarch64-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-aarch64-linux-gnu/rdkit/rdBase.so 185: 30# boost::python::handle_exception_impl(boost::function0) in /lib/aarch64-linux-gnu/libboost_python313.so.1.83.0 -185: 31# 0x0000FFFF93B3F25C in /lib/aarch64-linux-gnu/libboost_python313.so.1.83.0 +185: 31# 0x0000FFFF87C8F25C in /lib/aarch64-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# 0x000000000053D3B0 in /usr/bin/python3 @@ -32534,243 +32441,209 @@ 185: 60# 0x000000000065EE50 in /usr/bin/python3 185: 61# Py_RunMain in /usr/bin/python3 185: 62# Py_BytesMain in /usr/bin/python3 -185: 63# 0x0000FFFF9452229C in /lib/aarch64-linux-gnu/libc.so.6 +185: 63# 0x0000FFFF8867229C in /lib/aarch64-linux-gnu/libc.so.6 185: 64# __libc_start_main in /lib/aarch64-linux-gnu/libc.so.6 185: 65# _start in /usr/bin/python3 185: ---------- 185: **** 185: -189: .................... -189: ---------------------------------------------------------------------- -189: Ran 20 tests in 2.618s -189: -189: OK -173: [00:36:55] Complex queries can be slow. -186/238 Test #189: pyRGroupDecomposition .................. Passed 3.24 sec +186: bulk, no symmetry +190: Randomness seeded to: 2730457404 +190: =============================================================================== +190: All tests passed (5174 assertions in 7 test cases) +190: +179/238 Test #190: determineBondsCatchTest ................ Passed 0.68 sec +test 191 + Start 191: pyDetermineBonds + +191: Test command: /usr/bin/python3 "/build/reproducible-path/rdkit-202503.1/Code/GraphMol/DetermineBonds/Wrap/testDetermineBonds.py" +191: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/DetermineBonds/Wrap +191: Test timeout computed to be: 1500 +148: ... +148: ---------------------------------------------------------------------- +148: Ran 22 tests in 20.302s +148: +148: OK +180/238 Test #148: pyDistGeomHelpers ...................... Passed 20.79 sec +test 192 + Start 192: molInterchangeTest1 + +192: Test command: /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/MolInterchange/molInterchangeTest1 +192: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/MolInterchange +192: Test timeout computed to be: 1500 +192: [09:33:35] test1: basics +192: [09:33:35] done +192: [09:33:35] test2: basic writing +192: {"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]}]}]} +192: {"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"]]}]}]} +192: {"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]]}]}]} +192: {"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]]}]}]} +192: [09:33:35] done +192: [09:33:35] test3: writing conformers +192: {"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]}]}]} +192: [09:33:35] done +192: [09:33:35] test4: writing properties +192: {"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]}]}]} +192: [09:33:35] done +192: [09:33:35] test5: writing partial charges +192: {"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]}]}]} +192: [09:33:35] testing parse options +192: [09:33:35] done +192: [09:33:35] testing github #2046: CIPRank values from JSONDataToMols are not unsigned +192: {"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]]}]}]} +192: [09:33:35] done +192: [09:33:35] testing 'either' stereochemistry +192: [09:33:35] done +181/238 Test #192: molInterchangeTest1 .................... Passed 0.06 sec +test 193 + Start 193: molInterchangeCatchTest + +193: Test command: /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/MolInterchange/molInterchangeCatchTest +193: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/MolInterchange +193: Test timeout computed to be: 1500 +193: Randomness seeded to: 517237923 +193: [09:33:35] unrecognized bond type 12 set to zero while writing +193: [09:33:35] unrecognized bond type 0 set to zero while writing +193: =============================================================================== +193: All tests passed (125 assertions in 7 test cases) +193: +182/238 Test #193: molInterchangeCatchTest ................ Passed 0.07 sec +test 194 + Start 194: pyMolInterchange + +194: Test command: /usr/bin/python3 "/build/reproducible-path/rdkit-202503.1/Code/GraphMol/MolInterchange/Wrap/testMolInterchange.py" +194: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/MolInterchange/Wrap +194: Test timeout computed to be: 1500 +186: [09:33:35] Relabelling existing label +194: .. +194: ---------------------------------------------------------------------- +194: Ran 2 tests in 0.018s +194: +194: OK +186: Best mapping +191: .s.. +191: ---------------------------------------------------------------------- +191: Ran 4 tests in 0.320s +191: +191: OK (skipped=1) +183/238 Test #191: pyDetermineBonds ....................... Passed 0.70 sec +test 195 + Start 195: testSLNParse + +195: Test command: /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/SLNParse/testSLNParse +195: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/SLNParse +195: Test timeout computed to be: 1500 +184/238 Test #194: pyMolInterchange ....................... Passed 0.44 sec +test 196 + Start 196: pySLNParse + +196: Test command: /usr/bin/python3 "/build/reproducible-path/rdkit-202503.1/Code/GraphMol/SLNParse/Wrap/testSLN.py" +196: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/SLNParse/Wrap +196: Test timeout computed to be: 1500 +195: Atoms: +195: 0 6 C chg: 1 deg: 5 exp: N/A imp: 0 hyb: +195: 1 1 H chg: 0 deg: 1 exp: N/A imp: N/A hyb: +195: 2 1 H chg: 0 deg: 1 exp: N/A imp: N/A hyb: +195: 3 1 H chg: 0 deg: 1 exp: N/A imp: N/A hyb: +195: 4 1 H chg: 0 deg: 1 exp: N/A imp: N/A hyb: +195: 5 1 H chg: 0 deg: 1 exp: N/A imp: N/A hyb: +195: Bonds: +195: 0 0->1 order: 1 +195: 1 0->2 order: 1 +195: 2 0->3 order: 1 +195: 3 0->4 order: 1 +195: 4 0->5 order: 1 +195: [09:33:36] SLN Parse Error: syntax error while parsing: CH4[I=13] +195: [09:33:36] Failed parsing SLN 'CH4[I=13]' +195: [09:33:36] SLN Parser error: Atom ID 1 appears *after* its ring closure. +195: [09:33:36] SLN Parser error: Ring closure 1 does not have a corresponding opener. +195: [09:33:36] SLN Parse Error: syntax error while parsing: CH2(C@1H2)CH2(CH2CH2C[1]H2) +195: [09:33:36] Failed parsing SLN 'CH2(C@1H2)CH2(CH2CH2C[1]H2)' +195: [09:33:36] SLN Parse Error: syntax error while parsing: CH2(CH2[1])CH2(CH2CH2CH2@1) +195: [09:33:36] Failed parsing SLN 'CH2(CH2[1])CH2(CH2CH2CH2@1)' +195: [09:33:36] SLN Parse Error: syntax error while parsing: CH4 fff +195: [09:33:36] Failed parsing SLN 'CH4 fff' +195: [09:33:36] SLN Parse Error: syntax error while parsing: C[charge=+1] foo +195: [09:33:36] Failed parsing SLN 'C[charge=+1] foo' +195: [09:33:36] Query property 'is' ignored on non-query atom +195: [09:33:36] Query property 'is' ignored on non-query atom +185/238 Test #195: testSLNParse ........................... Passed 0.06 sec +test 197 + Start 197: pyGraphMolWrap + +197: Test command: /usr/bin/python3 "/build/reproducible-path/rdkit-202503.1/Code/GraphMol/Wrap/rough_test.py" +197: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/Wrap +197: Test timeout computed to be: 1500 +186/238 Test #186: testRGroupDecomp ....................... Passed 6.17 sec test 198 Start 198: pyTestConformerWrap 198: Test command: /usr/bin/python3 "/build/reproducible-path/rdkit-202503.1/Code/GraphMol/Wrap/testConformer.py" 198: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/Wrap 198: Test timeout computed to be: 1500 -186: Best mapping -197: ..............[00:36:55] SMARTS Parse Error: syntax error while parsing: fiib -197: [00:36:55] SMARTS Parse Error: Failed parsing SMARTS 'fiib' for input: 'fiib' -197: ....[00:36:55] ERROR: Problems encountered parsing data fields -197: [00:36:55] ERROR: moving to the beginning of the next molecule -197: [00:36:55] ERROR: Problems encountered parsing data fields -197: [00:36:55] ERROR: moving to the beginning of the next molecule -197: [00:36:55] Spurious data before the first property will be ignored -197: [00:36:55] Property will be truncated after the first blank line -197: [00:36:55] Property will be truncated after the first blank line -197: [00:36:55] Property will be truncated after the first blank line -197: [00:36:55] ERROR: Problems encountered parsing data fields -197: [00:36:55] ERROR: moving to the beginning of the next molecule -197: [00:36:55] ERROR: Problems encountered parsing data fields -197: [00:36:55] ERROR: moving to the beginning of the next molecule -197: [00:36:55] Spurious data before the first property will be ignored -197: [00:36:55] Property will be truncated after the first blank line -197: [00:36:55] Property will be truncated after the first blank line -197: [00:36:55] Property will be truncated after the first blank line -197: [00:36:55] ERROR: Problems encountered parsing data fields -197: [00:36:55] ERROR: moving to the beginning of the next molecule -197: [00:36:55] Property will be truncated after the first blank line -197: [00:36:55] ERROR: Problems encountered parsing data fields -197: [00:36:55] ERROR: moving to the beginning of the next molecule -197: [00:36:55] Property will be truncated after the first blank line -197: .[00:36:55] SMILES Parse Error: syntax error while parsing: fail -197: [00:36:55] SMILES Parse Error: check for mistakes around position 1: -197: [00:36:55] fail -197: [00:36:55] ^ -197: [00:36:55] SMILES Parse Error: Failed parsing SMILES 'fail' for input: 'fail' -197: [00:36:55] ERROR: Smiles parse error on line 2 -197: [00:36:55] ERROR: Cannot create molecule from : 'fail' -197: >>> This may result in an infinite loop. It should finish almost instantly -197: <<< OK, it finished. -197: ............[00:36:55] Explicit valence for atom # 1 C, 5, is greater than permitted -197: ......[00:36:55] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -197: [00:36:55] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -197: [00:36:55] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -197: [00:36:55] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -197: .inWedges: [H]C12C3([H])C4([H])C1([H])C1([H])C2([H])C3([H])C41[H] |(-0.612,-0.6446,0.635;0.0021,-0.0041,0.002;-0.0187,1.5258,0.0104;-0.6498,2.1424,0.6504;1.5111,1.5466,-0.0041;2.1372,2.1804,0.624;1.5319,0.0168,-0.0125;2.175,-0.6067,0.6086;1.5173,0.025,-1.5424;2.1484,-0.5936,-2.1805;-0.0125,0.0041,-1.5279;-0.6405,-0.6297,-2.154;-0.0333,1.534,-1.5195;-0.6783,2.1574,-2.1387;1.4965,1.5548,-1.534;2.1106,2.1972,-2.1651)| -197: ........[00:36:56] non-ring atom 0 marked aromatic -197: [00:36:56] non-ring atom 0 marked aromatic -197: [00:36:56] -197: -197: **** -197: Range Error -197: idx -197: Violation occurred on line 209 in file ./Code/GraphMol/ROMol.cpp -197: Failed Expression: 12 < 6 -197: ---------- -197: Stacktrace: -197: 0# Invar::Invariant::toString[abi:cxx11]() const in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu//lib/libRDKitRDGeneral.so.1 -197: 1# Invar::operator<<(std::ostream&, Invar::Invariant const&) in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu//lib/libRDKitRDGeneral.so.1 -197: 2# RDKit::ROMol::getAtomWithIdx(unsigned int) in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu//lib/libRDKitGraphMol.so.1 -197: 3# RDKit::RWMol::removeAtom(unsigned int) in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu//lib/libRDKitGraphMol.so.1 -197: 4# 0x0000FFFF9F0E9610 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so -197: 5# boost::python::objects::function::call(_object*, _object*) const in /lib/aarch64-linux-gnu/libboost_python313.so.1.83.0 -197: 6# 0x0000FFFFA0B32680 in /lib/aarch64-linux-gnu/libboost_python313.so.1.83.0 -197: 7# boost::python::detail::exception_handler::operator()(boost::function0 const&) const in /lib/aarch64-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-aarch64-linux-gnu/rdkit/Chem/rdSLNParse.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-aarch64-linux-gnu/rdkit/Chem/rdChemReactions.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-aarch64-linux-gnu/rdkit/Chem/rdChemReactions.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-aarch64-linux-gnu/rdkit/Chem/rdMolChemicalFeatures.so -197: 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-aarch64-linux-gnu/rdkit/Chem/rdDepictor.so -197: 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-aarch64-linux-gnu/rdkit/Chem/rdmolfiles.so -197: 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-aarch64-linux-gnu/rdkit/Chem/rdmolfiles.so -197: 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-aarch64-linux-gnu/rdkit/Chem/rdCIPLabeler.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-aarch64-linux-gnu/rdkit/Chem/rdchem.so -197: 17# 0x0000FFFF9F01C320 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so -197: 18# 0x0000FFFF9F01C2B8 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so -197: 19# 0x0000FFFF9F01C248 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so -197: 20# 0x0000FFFF9F01C1E0 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so -197: 21# 0x0000FFFF9F01C178 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so -197: 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-aarch64-linux-gnu/rdkit/rdBase.so -197: 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-aarch64-linux-gnu/rdkit/rdBase.so -197: 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-aarch64-linux-gnu/rdkit/rdBase.so -197: 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-aarch64-linux-gnu/rdkit/rdBase.so -197: 26# boost::python::handle_exception_impl(boost::function0) in /lib/aarch64-linux-gnu/libboost_python313.so.1.83.0 -197: 27# 0x0000FFFFA0B2F25C in /lib/aarch64-linux-gnu/libboost_python313.so.1.83.0 -197: 28# _PyObject_MakeTpCall in /usr/bin/python3 -197: 29# _PyEval_EvalFrameDefault in /usr/bin/python3 -197: 30# 0x000000000053D3B0 in /usr/bin/python3 -197: 31# _PyEval_EvalFrameDefault in /usr/bin/python3 -197: 32# 0x000000000061C8E0 in /usr/bin/python3 -197: 33# 0x00000000005A787C in /usr/bin/python3 -197: 34# _PyObject_MakeTpCall in /usr/bin/python3 -197: 35# _PyEval_EvalFrameDefault in /usr/bin/python3 -197: 36# 0x000000000053D3B0 in /usr/bin/python3 -197: 37# _PyEval_EvalFrameDefault in /usr/bin/python3 -197: 38# 0x000000000061C8E0 in /usr/bin/python3 -197: 39# 0x00000000005A787C in /usr/bin/python3 -197: 40# _PyObject_MakeTpCall in /usr/bin/python3 -197: 41# _PyEval_EvalFrameDefault in /usr/bin/python3 -197: 42# 0x000000000053D3B0 in /usr/bin/python3 -197: 43# _PyEval_EvalFrameDefault in /usr/bin/python3 -197: 44# 0x000000000061C8E0 in /usr/bin/python3 -197: 45# 0x00000000005A787C in /usr/bin/python3 -197: 46# _PyObject_MakeTpCall in /usr/bin/python3 -197: 47# _PyEval_EvalFrameDefault in /usr/bin/python3 -197: 48# 0x000000000050B030 in /usr/bin/python3 -197: 49# _PyObject_MakeTpCall in /usr/bin/python3 -197: 50# _PyEval_EvalFrameDefault in /usr/bin/python3 -197: 51# PyEval_EvalCode in /usr/bin/python3 -197: 52# 0x000000000064023C in /usr/bin/python3 -197: 53# 0x000000000063BC30 in /usr/bin/python3 -197: 54# 0x000000000065F810 in /usr/bin/python3 -197: 55# 0x000000000065F0B4 in /usr/bin/python3 -197: 56# 0x000000000065EE50 in /usr/bin/python3 -197: 57# Py_RunMain in /usr/bin/python3 -197: 58# Py_BytesMain in /usr/bin/python3 -197: 59# 0x0000FFFFA187229C in /lib/aarch64-linux-gnu/libc.so.6 -197: 60# __libc_start_main in /lib/aarch64-linux-gnu/libc.so.6 -197: 61# _start in /usr/bin/python3 -197: ---------- -197: **** -197: -197: [00:36:56] non-ring atom 0 marked aromatic -197: [00:36:56] non-ring atom 0 marked aromatic -197: [00:36:56] -197: -197: **** -197: Range Error -197: idx -197: Violation occurred on line 209 in file ./Code/GraphMol/ROMol.cpp -197: Failed Expression: 12 < 6 -197: ---------- -197: Stacktrace: -197: 0# Invar::Invariant::toString[abi:cxx11]() const in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu//lib/libRDKitRDGeneral.so.1 -197: 1# Invar::operator<<(std::ostream&, Invar::Invariant const&) in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu//lib/libRDKitRDGeneral.so.1 -197: 2# RDKit::ROMol::getAtomWithIdx(unsigned int) in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu//lib/libRDKitGraphMol.so.1 -197: 3# RDKit::RWMol::removeAtom(unsigned int) in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu//lib/libRDKitGraphMol.so.1 -197: 4# 0x0000FFFF9F0E9610 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so -197: 5# boost::python::objects::function::call(_object*, _object*) const in /lib/aarch64-linux-gnu/libboost_python313.so.1.83.0 -197: 6# 0x0000FFFFA0B32680 in /lib/aarch64-linux-gnu/libboost_python313.so.1.83.0 -197: 7# boost::python::detail::exception_handler::operator()(boost::function0 const&) const in /lib/aarch64-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-aarch64-linux-gnu/rdkit/Chem/rdSLNParse.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-aarch64-linux-gnu/rdkit/Chem/rdChemReactions.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-aarch64-linux-gnu/rdkit/Chem/rdChemReactions.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-aarch64-linux-gnu/rdkit/Chem/rdMolChemicalFeatures.so -197: 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-aarch64-linux-gnu/rdkit/Chem/rdDepictor.so -197: 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-aarch64-linux-gnu/rdkit/Chem/rdmolfiles.so -197: 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-aarch64-linux-gnu/rdkit/Chem/rdmolfiles.so -197: 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-aarch64-linux-gnu/rdkit/Chem/rdCIPLabeler.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-aarch64-linux-gnu/rdkit/Chem/rdchem.so -197: 17# 0x0000FFFF9F01C320 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so -197: 18# 0x0000FFFF9F01C2B8 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so -197: 19# 0x0000FFFF9F01C248 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so -197: 20# 0x0000FFFF9F01C1E0 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so -197: 21# 0x0000FFFF9F01C178 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so -197: 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-aarch64-linux-gnu/rdkit/rdBase.so -197: 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-aarch64-linux-gnu/rdkit/rdBase.so -197: 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-aarch64-linux-gnu/rdkit/rdBase.so -197: 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-aarch64-linux-gnu/rdkit/rdBase.so -197: 26# boost::python::handle_exception_impl(boost::function0) in /lib/aarch64-linux-gnu/libboost_python313.so.1.83.0 -197: 27# 0x0000FFFFA0B2F25C in /lib/aarch64-linux-gnu/libboost_python313.so.1.83.0 -197: 28# _PyObject_MakeTpCall in /usr/bin/python3 -197: 29# _PyEval_EvalFrameDefault in /usr/bin/python3 -197: 30# 0x000000000053D3B0 in /usr/bin/python3 -197: 31# _PyEval_EvalFrameDefault in /usr/bin/python3 -197: 32# 0x000000000061C8E0 in /usr/bin/python3 -197: 33# 0x00000000005A787C in /usr/bin/python3 -197: 34# _PyObject_MakeTpCall in /usr/bin/python3 -197: 35# _PyEval_EvalFrameDefault in /usr/bin/python3 -197: 36# 0x000000000053D3B0 in /usr/bin/python3 -197: 37# _PyEval_EvalFrameDefault in /usr/bin/python3 -197: 38# 0x000000000061C8E0 in /usr/bin/python3 -197: 39# 0x00000000005A787C in /usr/bin/python3 -197: 40# _PyObject_MakeTpCall in /usr/bin/python3 -197: 41# _PyEval_EvalFrameDefault in /usr/bin/python3 -197: 42# 0x000000000053D3B0 in /usr/bin/python3 -197: 43# _PyEval_EvalFrameDefault in /usr/bin/python3 -197: 44# 0x000000000061C8E0 in /usr/bin/python3 -197: 45# 0x00000000005A787C in /usr/bin/python3 -197: 46# _PyObject_MakeTpCall in /usr/bin/python3 -197: 47# _PyEval_EvalFrameDefault in /usr/bin/python3 -197: 48# 0x000000000050B030 in /usr/bin/python3 -197: 49# _PyObject_MakeTpCall in /usr/bin/python3 -197: 50# _PyEval_EvalFrameDefault in /usr/bin/python3 -197: 51# PyEval_EvalCode in /usr/bin/python3 -197: 52# 0x000000000064023C in /usr/bin/python3 -197: 53# 0x000000000063BC30 in /usr/bin/python3 -197: 54# 0x000000000065F810 in /usr/bin/python3 -197: 55# 0x000000000065F0B4 in /usr/bin/python3 -197: 56# 0x000000000065EE50 in /usr/bin/python3 -197: 57# Py_RunMain in /usr/bin/python3 -197: 58# Py_BytesMain in /usr/bin/python3 -197: 59# 0x0000FFFFA187229C in /lib/aarch64-linux-gnu/libc.so.6 -197: 60# __libc_start_main in /lib/aarch64-linux-gnu/libc.so.6 -197: 61# _start in /usr/bin/python3 -197: ---------- -197: **** -197: -187/238 Test #186: testRGroupDecomp ....................... Passed 7.45 sec +196: .. +196: ---------------------------------------------------------------------- +196: Ran 2 tests in 0.007s +196: +196: OK +187/238 Test #196: pySLNParse ............................. Passed 0.33 sec test 199 Start 199: pyTestTrajectory 199: Test command: /usr/bin/python3 "/build/reproducible-path/rdkit-202503.1/Code/GraphMol/Wrap/testTrajectory.py" 199: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/Wrap 199: Test timeout computed to be: 1500 -197: ...............[00:36:56] 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. -197: [00:36:56] 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. -197: ..............[00:36:56] Can't kekulize mol. Unkekulized atoms: 0 1 2 3 4 -197: [00:36:56] Explicit valence for atom # 1 C, 5, is greater than permitted -173: [00:36:56] Complex queries can be slow. 198: ...... 198: ---------------------------------------------------------------------- -198: Ran 6 tests in 0.018s +198: Ran 6 tests in 0.023s 198: 198: OK -188/238 Test #198: pyTestConformerWrap .................... Passed 0.42 sec +188/238 Test #198: pyTestConformerWrap .................... Passed 0.45 sec test 200 Start 200: pyTestSGroups 200: Test command: /usr/bin/python3 "/build/reproducible-path/rdkit-202503.1/Code/GraphMol/Wrap/testSGroups.py" 200: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/Wrap 200: Test timeout computed to be: 1500 -173: [00:36:56] Complex queries can be slow. -199: [00:36:56] +197: ..............[09:33:36] SMARTS Parse Error: syntax error while parsing: fiib +197: [09:33:36] SMARTS Parse Error: Failed parsing SMARTS 'fiib' for input: 'fiib' +197: ....[09:33:36] ERROR: Problems encountered parsing data fields +197: [09:33:36] ERROR: moving to the beginning of the next molecule +197: [09:33:36] ERROR: Problems encountered parsing data fields +197: [09:33:36] ERROR: moving to the beginning of the next molecule +197: [09:33:36] Spurious data before the first property will be ignored +197: [09:33:36] Property will be truncated after the first blank line +197: [09:33:36] Property will be truncated after the first blank line +197: [09:33:36] Property will be truncated after the first blank line +197: [09:33:36] ERROR: Problems encountered parsing data fields +197: [09:33:36] ERROR: moving to the beginning of the next molecule +197: [09:33:36] ERROR: Problems encountered parsing data fields +197: [09:33:36] ERROR: moving to the beginning of the next molecule +197: [09:33:36] Spurious data before the first property will be ignored +197: [09:33:36] Property will be truncated after the first blank line +197: [09:33:36] Property will be truncated after the first blank line +197: [09:33:36] Property will be truncated after the first blank line +189: .................... +189: ---------------------------------------------------------------------- +189: Ran 20 tests in 1.746s +189: +189: OK +197: [09:33:36] ERROR: Problems encountered parsing data fields +197: [09:33:36] ERROR: moving to the beginning of the next molecule +197: [09:33:36] Property will be truncated after the first blank line +197: [09:33:36] ERROR: Problems encountered parsing data fields +197: [09:33:36] ERROR: moving to the beginning of the next molecule +197: [09:33:36] Property will be truncated after the first blank line +197: .[09:33:36] SMILES Parse Error: syntax error while parsing: fail +197: [09:33:36] SMILES Parse Error: check for mistakes around position 1: +197: [09:33:36] fail +197: [09:33:36] ^ +197: [09:33:36] SMILES Parse Error: Failed parsing SMILES 'fail' for input: 'fail' +197: [09:33:36] ERROR: Smiles parse error on line 2 +197: [09:33:36] ERROR: Cannot create molecule from : 'fail' +197: >>> This may result in an infinite loop. It should finish almost instantly +197: <<< OK, it finished. +199: [09:33:36] 199: 199: **** 199: Pre-condition Violation @@ -32784,23 +32657,23 @@ 199: 2# RDKit::Trajectory::addConformersToMol(RDKit::ROMol&, int, int) in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu//lib/libRDKitTrajectory.so.1 199: 3# boost::python::objects::caller_py_function_impl > >::operator()(_object*, _object*) in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdtrajectory.so 199: 4# boost::python::objects::function::call(_object*, _object*) const in /lib/aarch64-linux-gnu/libboost_python313.so.1.83.0 -199: 5# 0x0000FFFF7F5A2680 in /lib/aarch64-linux-gnu/libboost_python313.so.1.83.0 +199: 5# 0x0000FFFFAC042680 in /lib/aarch64-linux-gnu/libboost_python313.so.1.83.0 199: 6# boost::python::detail::exception_handler::operator()(boost::function0 const&) const in /lib/aarch64-linux-gnu/libboost_python313.so.1.83.0 199: 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-aarch64-linux-gnu/rdkit/Chem/rdmolfiles.so 199: 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-aarch64-linux-gnu/rdkit/Chem/rdmolfiles.so 199: 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-aarch64-linux-gnu/rdkit/Chem/rdCIPLabeler.so 199: 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-aarch64-linux-gnu/rdkit/Chem/rdchem.so -199: 11# 0x0000FFFF7DB2C320 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so -199: 12# 0x0000FFFF7DB2C2B8 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so -199: 13# 0x0000FFFF7DB2C248 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so -199: 14# 0x0000FFFF7DB2C1E0 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so -199: 15# 0x0000FFFF7DB2C178 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so +199: 11# 0x0000FFFFAA5CC320 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so +199: 12# 0x0000FFFFAA5CC2B8 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so +199: 13# 0x0000FFFFAA5CC248 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so +199: 14# 0x0000FFFFAA5CC1E0 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so +199: 15# 0x0000FFFFAA5CC178 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so 199: 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-aarch64-linux-gnu/rdkit/rdBase.so 199: 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-aarch64-linux-gnu/rdkit/rdBase.so 199: 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-aarch64-linux-gnu/rdkit/rdBase.so 199: 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-aarch64-linux-gnu/rdkit/rdBase.so 199: 20# boost::python::handle_exception_impl(boost::function0) in /lib/aarch64-linux-gnu/libboost_python313.so.1.83.0 -199: 21# 0x0000FFFF7F59F25C in /lib/aarch64-linux-gnu/libboost_python313.so.1.83.0 +199: 21# 0x0000FFFFAC03F25C in /lib/aarch64-linux-gnu/libboost_python313.so.1.83.0 199: 22# _PyObject_MakeTpCall in /usr/bin/python3 199: 23# _PyEval_EvalFrameDefault in /usr/bin/python3 199: 24# 0x000000000053D3B0 in /usr/bin/python3 @@ -32832,13 +32705,13 @@ 199: 50# 0x000000000065EE50 in /usr/bin/python3 199: 51# Py_RunMain in /usr/bin/python3 199: 52# Py_BytesMain in /usr/bin/python3 -199: 53# 0x0000FFFF7FD8229C in /lib/aarch64-linux-gnu/libc.so.6 +199: 53# 0x0000FFFFAC82229C in /lib/aarch64-linux-gnu/libc.so.6 199: 54# __libc_start_main in /lib/aarch64-linux-gnu/libc.so.6 199: 55# _start in /usr/bin/python3 199: ---------- 199: **** 199: -199: .[00:36:56] +199: .[09:33:36] 199: 199: **** 199: Pre-condition Violation @@ -32852,23 +32725,23 @@ 199: 2# RDKit::Trajectory::addConformersToMol(RDKit::ROMol&, int, int) in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu//lib/libRDKitTrajectory.so.1 199: 3# boost::python::objects::caller_py_function_impl > >::operator()(_object*, _object*) in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdtrajectory.so 199: 4# boost::python::objects::function::call(_object*, _object*) const in /lib/aarch64-linux-gnu/libboost_python313.so.1.83.0 -199: 5# 0x0000FFFF7F5A2680 in /lib/aarch64-linux-gnu/libboost_python313.so.1.83.0 +199: 5# 0x0000FFFFAC042680 in /lib/aarch64-linux-gnu/libboost_python313.so.1.83.0 199: 6# boost::python::detail::exception_handler::operator()(boost::function0 const&) const in /lib/aarch64-linux-gnu/libboost_python313.so.1.83.0 199: 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-aarch64-linux-gnu/rdkit/Chem/rdmolfiles.so 199: 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-aarch64-linux-gnu/rdkit/Chem/rdmolfiles.so 199: 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-aarch64-linux-gnu/rdkit/Chem/rdCIPLabeler.so 199: 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-aarch64-linux-gnu/rdkit/Chem/rdchem.so -199: 11# 0x0000FFFF7DB2C320 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so -199: 12# 0x0000FFFF7DB2C2B8 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so -199: 13# 0x0000FFFF7DB2C248 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so -199: 14# 0x0000FFFF7DB2C1E0 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so -199: 15# 0x0000FFFF7DB2C178 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so +199: 11# 0x0000FFFFAA5CC320 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so +199: 12# 0x0000FFFFAA5CC2B8 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so +199: 13# 0x0000FFFFAA5CC248 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so +199: 14# 0x0000FFFFAA5CC1E0 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so +199: 15# 0x0000FFFFAA5CC178 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so 199: 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-aarch64-linux-gnu/rdkit/rdBase.so 199: 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-aarch64-linux-gnu/rdkit/rdBase.so 199: 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-aarch64-linux-gnu/rdkit/rdBase.so 199: 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-aarch64-linux-gnu/rdkit/rdBase.so 199: 20# boost::python::handle_exception_impl(boost::function0) in /lib/aarch64-linux-gnu/libboost_python313.so.1.83.0 -199: 21# 0x0000FFFF7F59F25C in /lib/aarch64-linux-gnu/libboost_python313.so.1.83.0 +199: 21# 0x0000FFFFAC03F25C in /lib/aarch64-linux-gnu/libboost_python313.so.1.83.0 199: 22# _PyObject_MakeTpCall in /usr/bin/python3 199: 23# _PyEval_EvalFrameDefault in /usr/bin/python3 199: 24# 0x000000000053D3B0 in /usr/bin/python3 @@ -32900,35 +32773,43 @@ 199: 50# 0x000000000065EE50 in /usr/bin/python3 199: 51# Py_RunMain in /usr/bin/python3 199: 52# Py_BytesMain in /usr/bin/python3 -199: 53# 0x0000FFFF7FD8229C in /lib/aarch64-linux-gnu/libc.so.6 +199: 53# 0x0000FFFFAC82229C in /lib/aarch64-linux-gnu/libc.so.6 199: 54# __libc_start_main in /lib/aarch64-linux-gnu/libc.so.6 199: 55# _start in /usr/bin/python3 199: ---------- 199: **** 199: -197: ............................[00:36:56] unable to set wavy bonds for double bonds: 3 -200: ............. -200: ---------------------------------------------------------------------- -200: Ran 13 tests in 0.039s -200: -200: OK -200: Testing SubstanceGroups wrapper -197: .............[00:36:56] +197: ............[09:33:36] Explicit valence for atom # 1 C, 5, is greater than permitted +189/238 Test #189: pyRGroupDecomposition .................. Passed 2.14 sec +test 201 + Start 201: pyTestThreads + +201: Test command: /usr/bin/python3 "/build/reproducible-path/rdkit-202503.1/Code/GraphMol/Wrap/testThreads.py" +201: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/Wrap +201: Test timeout computed to be: 1500 +197: ......[09:33:36] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +197: [09:33:36] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +197: [09:33:36] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +197: [09:33:36] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +197: .inWedges: [H]C12C3([H])C4([H])C1([H])C1([H])C2([H])C3([H])C41[H] |(-0.612,-0.6446,0.635;0.0021,-0.0041,0.002;-0.0187,1.5258,0.0104;-0.6498,2.1424,0.6504;1.5111,1.5466,-0.0041;2.1372,2.1804,0.624;1.5319,0.0168,-0.0125;2.175,-0.6067,0.6086;1.5173,0.025,-1.5424;2.1484,-0.5936,-2.1805;-0.0125,0.0041,-1.5279;-0.6405,-0.6297,-2.154;-0.0333,1.534,-1.5195;-0.6783,2.1574,-2.1387;1.4965,1.5548,-1.534;2.1106,2.1972,-2.1651)| +197: ........[09:33:36] non-ring atom 0 marked aromatic +197: [09:33:36] non-ring atom 0 marked aromatic +197: [09:33:36] 197: 197: **** 197: Range Error 197: idx 197: Violation occurred on line 209 in file ./Code/GraphMol/ROMol.cpp -197: Failed Expression: 6 < 5 +197: Failed Expression: 12 < 6 197: ---------- 197: Stacktrace: 197: 0# Invar::Invariant::toString[abi:cxx11]() const in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu//lib/libRDKitRDGeneral.so.1 197: 1# Invar::operator<<(std::ostream&, Invar::Invariant const&) in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu//lib/libRDKitRDGeneral.so.1 197: 2# RDKit::ROMol::getAtomWithIdx(unsigned int) in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu//lib/libRDKitGraphMol.so.1 197: 3# RDKit::RWMol::removeAtom(unsigned int) in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu//lib/libRDKitGraphMol.so.1 -197: 4# boost::python::objects::caller_py_function_impl > >::operator()(_object*, _object*) in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so +197: 4# 0x0000FFFFB8059610 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so 197: 5# boost::python::objects::function::call(_object*, _object*) const in /lib/aarch64-linux-gnu/libboost_python313.so.1.83.0 -197: 6# 0x0000FFFFA0B32680 in /lib/aarch64-linux-gnu/libboost_python313.so.1.83.0 +197: 6# 0x0000FFFFB9AA2680 in /lib/aarch64-linux-gnu/libboost_python313.so.1.83.0 197: 7# boost::python::detail::exception_handler::operator()(boost::function0 const&) const in /lib/aarch64-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-aarch64-linux-gnu/rdkit/Chem/rdSLNParse.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-aarch64-linux-gnu/rdkit/Chem/rdChemReactions.so @@ -32939,17 +32820,17 @@ 197: 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-aarch64-linux-gnu/rdkit/Chem/rdmolfiles.so 197: 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-aarch64-linux-gnu/rdkit/Chem/rdCIPLabeler.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-aarch64-linux-gnu/rdkit/Chem/rdchem.so -197: 17# 0x0000FFFF9F01C320 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so -197: 18# 0x0000FFFF9F01C2B8 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so -197: 19# 0x0000FFFF9F01C248 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so -197: 20# 0x0000FFFF9F01C1E0 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so -197: 21# 0x0000FFFF9F01C178 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so +197: 17# 0x0000FFFFB7F8C320 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so +197: 18# 0x0000FFFFB7F8C2B8 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so +197: 19# 0x0000FFFFB7F8C248 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so +197: 20# 0x0000FFFFB7F8C1E0 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so +197: 21# 0x0000FFFFB7F8C178 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so 197: 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-aarch64-linux-gnu/rdkit/rdBase.so 197: 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-aarch64-linux-gnu/rdkit/rdBase.so 197: 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-aarch64-linux-gnu/rdkit/rdBase.so 197: 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-aarch64-linux-gnu/rdkit/rdBase.so 197: 26# boost::python::handle_exception_impl(boost::function0) in /lib/aarch64-linux-gnu/libboost_python313.so.1.83.0 -197: 27# 0x0000FFFFA0B2F25C in /lib/aarch64-linux-gnu/libboost_python313.so.1.83.0 +197: 27# 0x0000FFFFB9A9F25C in /lib/aarch64-linux-gnu/libboost_python313.so.1.83.0 197: 28# _PyObject_MakeTpCall in /usr/bin/python3 197: 29# _PyEval_EvalFrameDefault in /usr/bin/python3 197: 30# 0x000000000053D3B0 in /usr/bin/python3 @@ -32981,31 +32862,93 @@ 197: 56# 0x000000000065EE50 in /usr/bin/python3 197: 57# Py_RunMain in /usr/bin/python3 197: 58# Py_BytesMain in /usr/bin/python3 -197: 59# 0x0000FFFFA187229C in /lib/aarch64-linux-gnu/libc.so.6 +197: 59# 0x0000FFFFBA7E229C in /lib/aarch64-linux-gnu/libc.so.6 197: 60# __libc_start_main in /lib/aarch64-linux-gnu/libc.so.6 197: 61# _start in /usr/bin/python3 197: ---------- 197: **** 197: -189/238 Test #200: pyTestSGroups .......................... Passed 0.45 sec -test 201 - Start 201: pyTestThreads - -201: Test command: /usr/bin/python3 "/build/reproducible-path/rdkit-202503.1/Code/GraphMol/Wrap/testThreads.py" -201: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/Wrap -201: Test timeout computed to be: 1500 -173: [00:36:56] Complex queries can be slow. -173: =============================================================================== -173: All tests passed (121 assertions in 17 test cases) -173: -190/238 Test #173: testSynthonSpaceSubstructureSearch ..... Passed 23.19 sec -test 202 - Start 202: pyTestMultithreadedMolSupplier - -202: Test command: /usr/bin/python3 "/build/reproducible-path/rdkit-202503.1/Code/GraphMol/Wrap/testMultithreadedMolSupplier.py" -202: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/Wrap -202: Test timeout computed to be: 1500 -199: .[00:36:56] +197: [09:33:36] non-ring atom 0 marked aromatic +197: [09:33:36] non-ring atom 0 marked aromatic +197: [09:33:36] +197: +197: **** +197: Range Error +197: idx +197: Violation occurred on line 209 in file ./Code/GraphMol/ROMol.cpp +197: Failed Expression: 12 < 6 +197: ---------- +197: Stacktrace: +197: 0# Invar::Invariant::toString[abi:cxx11]() const in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu//lib/libRDKitRDGeneral.so.1 +197: 1# Invar::operator<<(std::ostream&, Invar::Invariant const&) in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu//lib/libRDKitRDGeneral.so.1 +197: 2# RDKit::ROMol::getAtomWithIdx(unsigned int) in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu//lib/libRDKitGraphMol.so.1 +197: 3# RDKit::RWMol::removeAtom(unsigned int) in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu//lib/libRDKitGraphMol.so.1 +197: 4# 0x0000FFFFB8059610 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so +197: 5# boost::python::objects::function::call(_object*, _object*) const in /lib/aarch64-linux-gnu/libboost_python313.so.1.83.0 +197: 6# 0x0000FFFFB9AA2680 in /lib/aarch64-linux-gnu/libboost_python313.so.1.83.0 +197: 7# boost::python::detail::exception_handler::operator()(boost::function0 const&) const in /lib/aarch64-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-aarch64-linux-gnu/rdkit/Chem/rdSLNParse.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-aarch64-linux-gnu/rdkit/Chem/rdChemReactions.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-aarch64-linux-gnu/rdkit/Chem/rdChemReactions.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-aarch64-linux-gnu/rdkit/Chem/rdMolChemicalFeatures.so +197: 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-aarch64-linux-gnu/rdkit/Chem/rdDepictor.so +197: 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-aarch64-linux-gnu/rdkit/Chem/rdmolfiles.so +197: 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-aarch64-linux-gnu/rdkit/Chem/rdmolfiles.so +197: 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-aarch64-linux-gnu/rdkit/Chem/rdCIPLabeler.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-aarch64-linux-gnu/rdkit/Chem/rdchem.so +197: 17# 0x0000FFFFB7F8C320 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so +197: 18# 0x0000FFFFB7F8C2B8 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so +197: 19# 0x0000FFFFB7F8C248 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so +197: 20# 0x0000FFFFB7F8C1E0 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so +197: 21# 0x0000FFFFB7F8C178 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so +197: 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-aarch64-linux-gnu/rdkit/rdBase.so +197: 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-aarch64-linux-gnu/rdkit/rdBase.so +197: 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-aarch64-linux-gnu/rdkit/rdBase.so +197: 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-aarch64-linux-gnu/rdkit/rdBase.so +197: 26# boost::python::handle_exception_impl(boost::function0) in /lib/aarch64-linux-gnu/libboost_python313.so.1.83.0 +197: 27# 0x0000FFFFB9A9F25C in /lib/aarch64-linux-gnu/libboost_python313.so.1.83.0 +197: 28# _PyObject_MakeTpCall in /usr/bin/python3 +197: 29# _PyEval_EvalFrameDefault in /usr/bin/python3 +197: 30# 0x000000000053D3B0 in /usr/bin/python3 +197: 31# _PyEval_EvalFrameDefault in /usr/bin/python3 +197: 32# 0x000000000061C8E0 in /usr/bin/python3 +197: 33# 0x00000000005A787C in /usr/bin/python3 +197: 34# _PyObject_MakeTpCall in /usr/bin/python3 +197: 35# _PyEval_EvalFrameDefault in /usr/bin/python3 +197: 36# 0x000000000053D3B0 in /usr/bin/python3 +197: 37# _PyEval_EvalFrameDefault in /usr/bin/python3 +197: 38# 0x000000000061C8E0 in /usr/bin/python3 +197: 39# 0x00000000005A787C in /usr/bin/python3 +197: 40# _PyObject_MakeTpCall in /usr/bin/python3 +197: 41# _PyEval_EvalFrameDefault in /usr/bin/python3 +197: 42# 0x000000000053D3B0 in /usr/bin/python3 +197: 43# _PyEval_EvalFrameDefault in /usr/bin/python3 +197: 44# 0x000000000061C8E0 in /usr/bin/python3 +197: 45# 0x00000000005A787C in /usr/bin/python3 +197: 46# _PyObject_MakeTpCall in /usr/bin/python3 +197: 47# _PyEval_EvalFrameDefault in /usr/bin/python3 +197: 48# 0x000000000050B030 in /usr/bin/python3 +197: 49# _PyObject_MakeTpCall in /usr/bin/python3 +197: 50# _PyEval_EvalFrameDefault in /usr/bin/python3 +197: 51# PyEval_EvalCode in /usr/bin/python3 +197: 52# 0x000000000064023C in /usr/bin/python3 +197: 53# 0x000000000063BC30 in /usr/bin/python3 +197: 54# 0x000000000065F810 in /usr/bin/python3 +197: 55# 0x000000000065F0B4 in /usr/bin/python3 +197: 56# 0x000000000065EE50 in /usr/bin/python3 +197: 57# Py_RunMain in /usr/bin/python3 +197: 58# Py_BytesMain in /usr/bin/python3 +197: 59# 0x0000FFFFBA7E229C in /lib/aarch64-linux-gnu/libc.so.6 +197: 60# __libc_start_main in /lib/aarch64-linux-gnu/libc.so.6 +197: 61# _start in /usr/bin/python3 +197: ---------- +197: **** +197: +197: ...............[09:33:36] 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. +197: [09:33:36] 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. +197: ..............[09:33:36] Can't kekulize mol. Unkekulized atoms: 0 1 2 3 4 +197: [09:33:36] Explicit valence for atom # 1 C, 5, is greater than permitted +199: .[09:33:36] 199: 199: **** 199: Range Error @@ -33020,23 +32963,23 @@ 199: 3# RDKit::getSnapshot_wrap(RDKit::Trajectory*, unsigned int) in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdtrajectory.so 199: 4# boost::python::objects::caller_py_function_impl, boost::mpl::vector3 > >::operator()(_object*, _object*) in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdtrajectory.so 199: 5# boost::python::objects::function::call(_object*, _object*) const in /lib/aarch64-linux-gnu/libboost_python313.so.1.83.0 -199: 6# 0x0000FFFF7F5A2680 in /lib/aarch64-linux-gnu/libboost_python313.so.1.83.0 +199: 6# 0x0000FFFFAC042680 in /lib/aarch64-linux-gnu/libboost_python313.so.1.83.0 199: 7# boost::python::detail::exception_handler::operator()(boost::function0 const&) const in /lib/aarch64-linux-gnu/libboost_python313.so.1.83.0 199: 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-aarch64-linux-gnu/rdkit/Chem/rdmolfiles.so 199: 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-aarch64-linux-gnu/rdkit/Chem/rdmolfiles.so 199: 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-aarch64-linux-gnu/rdkit/Chem/rdCIPLabeler.so 199: 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-aarch64-linux-gnu/rdkit/Chem/rdchem.so -199: 12# 0x0000FFFF7DB2C320 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so -199: 13# 0x0000FFFF7DB2C2B8 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so -199: 14# 0x0000FFFF7DB2C248 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so -199: 15# 0x0000FFFF7DB2C1E0 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so -199: 16# 0x0000FFFF7DB2C178 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so +199: 12# 0x0000FFFFAA5CC320 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so +199: 13# 0x0000FFFFAA5CC2B8 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so +199: 14# 0x0000FFFFAA5CC248 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so +199: 15# 0x0000FFFFAA5CC1E0 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so +199: 16# 0x0000FFFFAA5CC178 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so 199: 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-aarch64-linux-gnu/rdkit/rdBase.so 199: 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-aarch64-linux-gnu/rdkit/rdBase.so 199: 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-aarch64-linux-gnu/rdkit/rdBase.so 199: 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-aarch64-linux-gnu/rdkit/rdBase.so 199: 21# boost::python::handle_exception_impl(boost::function0) in /lib/aarch64-linux-gnu/libboost_python313.so.1.83.0 -199: 22# 0x0000FFFF7F59F25C in /lib/aarch64-linux-gnu/libboost_python313.so.1.83.0 +199: 22# 0x0000FFFFAC03F25C in /lib/aarch64-linux-gnu/libboost_python313.so.1.83.0 199: 23# _PyObject_MakeTpCall in /usr/bin/python3 199: 24# _PyEval_EvalFrameDefault in /usr/bin/python3 199: 25# 0x000000000053D3B0 in /usr/bin/python3 @@ -33068,13 +33011,13 @@ 199: 51# 0x000000000065EE50 in /usr/bin/python3 199: 52# Py_RunMain in /usr/bin/python3 199: 53# Py_BytesMain in /usr/bin/python3 -199: 54# 0x0000FFFF7FD8229C in /lib/aarch64-linux-gnu/libc.so.6 +199: 54# 0x0000FFFFAC82229C in /lib/aarch64-linux-gnu/libc.so.6 199: 55# __libc_start_main in /lib/aarch64-linux-gnu/libc.so.6 199: 56# _start in /usr/bin/python3 199: ---------- 199: **** 199: -199: .[00:36:56] +199: .[09:33:36] 199: 199: **** 199: Pre-condition Violation @@ -33088,23 +33031,23 @@ 199: 2# RDKit::readAmberTrajectory(std::__cxx11::basic_string, std::allocator > const&, RDKit::Trajectory&) in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu//lib/libRDKitTrajectory.so.1 199: 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-aarch64-linux-gnu/rdkit/Chem/rdtrajectory.so 199: 4# boost::python::objects::function::call(_object*, _object*) const in /lib/aarch64-linux-gnu/libboost_python313.so.1.83.0 -199: 5# 0x0000FFFF7F5A2680 in /lib/aarch64-linux-gnu/libboost_python313.so.1.83.0 +199: 5# 0x0000FFFFAC042680 in /lib/aarch64-linux-gnu/libboost_python313.so.1.83.0 199: 6# boost::python::detail::exception_handler::operator()(boost::function0 const&) const in /lib/aarch64-linux-gnu/libboost_python313.so.1.83.0 199: 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-aarch64-linux-gnu/rdkit/Chem/rdmolfiles.so 199: 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-aarch64-linux-gnu/rdkit/Chem/rdmolfiles.so 199: 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-aarch64-linux-gnu/rdkit/Chem/rdCIPLabeler.so 199: 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-aarch64-linux-gnu/rdkit/Chem/rdchem.so -199: 11# 0x0000FFFF7DB2C320 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so -199: 12# 0x0000FFFF7DB2C2B8 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so -199: 13# 0x0000FFFF7DB2C248 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so -199: 14# 0x0000FFFF7DB2C1E0 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so -199: 15# 0x0000FFFF7DB2C178 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so +199: 11# 0x0000FFFFAA5CC320 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so +199: 12# 0x0000FFFFAA5CC2B8 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so +199: 13# 0x0000FFFFAA5CC248 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so +199: 14# 0x0000FFFFAA5CC1E0 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so +199: 15# 0x0000FFFFAA5CC178 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so 199: 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-aarch64-linux-gnu/rdkit/rdBase.so 199: 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-aarch64-linux-gnu/rdkit/rdBase.so 199: 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-aarch64-linux-gnu/rdkit/rdBase.so 199: 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-aarch64-linux-gnu/rdkit/rdBase.so 199: 20# boost::python::handle_exception_impl(boost::function0) in /lib/aarch64-linux-gnu/libboost_python313.so.1.83.0 -199: 21# 0x0000FFFF7F59F25C in /lib/aarch64-linux-gnu/libboost_python313.so.1.83.0 +199: 21# 0x0000FFFFAC03F25C in /lib/aarch64-linux-gnu/libboost_python313.so.1.83.0 199: 22# _PyObject_MakeTpCall in /usr/bin/python3 199: 23# _PyEval_EvalFrameDefault in /usr/bin/python3 199: 24# 0x000000000053D3B0 in /usr/bin/python3 @@ -33136,13 +33079,13 @@ 199: 50# 0x000000000065EE50 in /usr/bin/python3 199: 51# Py_RunMain in /usr/bin/python3 199: 52# Py_BytesMain in /usr/bin/python3 -199: 53# 0x0000FFFF7FD8229C in /lib/aarch64-linux-gnu/libc.so.6 +199: 53# 0x0000FFFFAC82229C in /lib/aarch64-linux-gnu/libc.so.6 199: 54# __libc_start_main in /lib/aarch64-linux-gnu/libc.so.6 199: 55# _start in /usr/bin/python3 199: ---------- 199: **** 199: -199: ..[00:36:56] +199: ..[09:33:36] 199: 199: **** 199: Pre-condition Violation @@ -33156,23 +33099,23 @@ 199: 2# RDKit::readGromosTrajectory(std::__cxx11::basic_string, std::allocator > const&, RDKit::Trajectory&) in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu//lib/libRDKitTrajectory.so.1 199: 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-aarch64-linux-gnu/rdkit/Chem/rdtrajectory.so 199: 4# boost::python::objects::function::call(_object*, _object*) const in /lib/aarch64-linux-gnu/libboost_python313.so.1.83.0 -199: 5# 0x0000FFFF7F5A2680 in /lib/aarch64-linux-gnu/libboost_python313.so.1.83.0 +199: 5# 0x0000FFFFAC042680 in /lib/aarch64-linux-gnu/libboost_python313.so.1.83.0 199: 6# boost::python::detail::exception_handler::operator()(boost::function0 const&) const in /lib/aarch64-linux-gnu/libboost_python313.so.1.83.0 199: 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-aarch64-linux-gnu/rdkit/Chem/rdmolfiles.so 199: 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-aarch64-linux-gnu/rdkit/Chem/rdmolfiles.so 199: 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-aarch64-linux-gnu/rdkit/Chem/rdCIPLabeler.so 199: 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-aarch64-linux-gnu/rdkit/Chem/rdchem.so -199: 11# 0x0000FFFF7DB2C320 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so -199: 12# 0x0000FFFF7DB2C2B8 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so -199: 13# 0x0000FFFF7DB2C248 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so -199: 14# 0x0000FFFF7DB2C1E0 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so -199: 15# 0x0000FFFF7DB2C178 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so +199: 11# 0x0000FFFFAA5CC320 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so +199: 12# 0x0000FFFFAA5CC2B8 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so +199: 13# 0x0000FFFFAA5CC248 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so +199: 14# 0x0000FFFFAA5CC1E0 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so +199: 15# 0x0000FFFFAA5CC178 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so 199: 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-aarch64-linux-gnu/rdkit/rdBase.so 199: 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-aarch64-linux-gnu/rdkit/rdBase.so 199: 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-aarch64-linux-gnu/rdkit/rdBase.so 199: 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-aarch64-linux-gnu/rdkit/rdBase.so 199: 20# boost::python::handle_exception_impl(boost::function0) in /lib/aarch64-linux-gnu/libboost_python313.so.1.83.0 -199: 21# 0x0000FFFF7F59F25C in /lib/aarch64-linux-gnu/libboost_python313.so.1.83.0 +199: 21# 0x0000FFFFAC03F25C in /lib/aarch64-linux-gnu/libboost_python313.so.1.83.0 199: 22# _PyObject_MakeTpCall in /usr/bin/python3 199: 23# _PyEval_EvalFrameDefault in /usr/bin/python3 199: 24# 0x000000000053D3B0 in /usr/bin/python3 @@ -33204,13 +33147,13 @@ 199: 50# 0x000000000065EE50 in /usr/bin/python3 199: 51# Py_RunMain in /usr/bin/python3 199: 52# Py_BytesMain in /usr/bin/python3 -199: 53# 0x0000FFFF7FD8229C in /lib/aarch64-linux-gnu/libc.so.6 +199: 53# 0x0000FFFFAC82229C in /lib/aarch64-linux-gnu/libc.so.6 199: 54# __libc_start_main in /lib/aarch64-linux-gnu/libc.so.6 199: 55# _start in /usr/bin/python3 199: ---------- 199: **** 199: -199: .[00:36:56] +199: .[09:33:36] 199: 199: **** 199: Pre-condition Violation @@ -33224,23 +33167,23 @@ 199: 2# RDKit::Snapshot::getPoint2D(unsigned int) const in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu//lib/libRDKitTrajectory.so.1 199: 3# boost::python::objects::caller_py_function_impl > >::operator()(_object*, _object*) in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdtrajectory.so 199: 4# boost::python::objects::function::call(_object*, _object*) const in /lib/aarch64-linux-gnu/libboost_python313.so.1.83.0 -199: 5# 0x0000FFFF7F5A2680 in /lib/aarch64-linux-gnu/libboost_python313.so.1.83.0 +199: 5# 0x0000FFFFAC042680 in /lib/aarch64-linux-gnu/libboost_python313.so.1.83.0 199: 6# boost::python::detail::exception_handler::operator()(boost::function0 const&) const in /lib/aarch64-linux-gnu/libboost_python313.so.1.83.0 199: 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-aarch64-linux-gnu/rdkit/Chem/rdmolfiles.so 199: 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-aarch64-linux-gnu/rdkit/Chem/rdmolfiles.so 199: 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-aarch64-linux-gnu/rdkit/Chem/rdCIPLabeler.so 199: 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-aarch64-linux-gnu/rdkit/Chem/rdchem.so -199: 11# 0x0000FFFF7DB2C320 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so -199: 12# 0x0000FFFF7DB2C2B8 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so -199: 13# 0x0000FFFF7DB2C248 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so -199: 14# 0x0000FFFF7DB2C1E0 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so -199: 15# 0x0000FFFF7DB2C178 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so +199: 11# 0x0000FFFFAA5CC320 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so +199: 12# 0x0000FFFFAA5CC2B8 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so +199: 13# 0x0000FFFFAA5CC248 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so +199: 14# 0x0000FFFFAA5CC1E0 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so +199: 15# 0x0000FFFFAA5CC178 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so 199: 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-aarch64-linux-gnu/rdkit/rdBase.so 199: 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-aarch64-linux-gnu/rdkit/rdBase.so 199: 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-aarch64-linux-gnu/rdkit/rdBase.so 199: 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-aarch64-linux-gnu/rdkit/rdBase.so 199: 20# boost::python::handle_exception_impl(boost::function0) in /lib/aarch64-linux-gnu/libboost_python313.so.1.83.0 -199: 21# 0x0000FFFF7F59F25C in /lib/aarch64-linux-gnu/libboost_python313.so.1.83.0 +199: 21# 0x0000FFFFAC03F25C in /lib/aarch64-linux-gnu/libboost_python313.so.1.83.0 199: 22# _PyObject_MakeTpCall in /usr/bin/python3 199: 23# _PyEval_EvalFrameDefault in /usr/bin/python3 199: 24# 0x000000000053D3B0 in /usr/bin/python3 @@ -33272,13 +33215,13 @@ 199: 50# 0x000000000065EE50 in /usr/bin/python3 199: 51# Py_RunMain in /usr/bin/python3 199: 52# Py_BytesMain in /usr/bin/python3 -199: 53# 0x0000FFFF7FD8229C in /lib/aarch64-linux-gnu/libc.so.6 +199: 53# 0x0000FFFFAC82229C in /lib/aarch64-linux-gnu/libc.so.6 199: 54# __libc_start_main in /lib/aarch64-linux-gnu/libc.so.6 199: 55# _start in /usr/bin/python3 199: ---------- 199: **** 199: -199: [00:36:56] +199: [09:33:36] 199: 199: **** 199: Pre-condition Violation @@ -33292,23 +33235,23 @@ 199: 2# RDKit::Snapshot::getPoint2D(unsigned int) const in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu//lib/libRDKitTrajectory.so.1 199: 3# boost::python::objects::caller_py_function_impl > >::operator()(_object*, _object*) in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdtrajectory.so 199: 4# boost::python::objects::function::call(_object*, _object*) const in /lib/aarch64-linux-gnu/libboost_python313.so.1.83.0 -199: 5# 0x0000FFFF7F5A2680 in /lib/aarch64-linux-gnu/libboost_python313.so.1.83.0 +199: 5# 0x0000FFFFAC042680 in /lib/aarch64-linux-gnu/libboost_python313.so.1.83.0 199: 6# boost::python::detail::exception_handler::operator()(boost::function0 const&) const in /lib/aarch64-linux-gnu/libboost_python313.so.1.83.0 199: 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-aarch64-linux-gnu/rdkit/Chem/rdmolfiles.so 199: 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-aarch64-linux-gnu/rdkit/Chem/rdmolfiles.so 199: 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-aarch64-linux-gnu/rdkit/Chem/rdCIPLabeler.so 199: 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-aarch64-linux-gnu/rdkit/Chem/rdchem.so -199: 11# 0x0000FFFF7DB2C320 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so -199: 12# 0x0000FFFF7DB2C2B8 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so -199: 13# 0x0000FFFF7DB2C248 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so -199: 14# 0x0000FFFF7DB2C1E0 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so -199: 15# 0x0000FFFF7DB2C178 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so +199: 11# 0x0000FFFFAA5CC320 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so +199: 12# 0x0000FFFFAA5CC2B8 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so +199: 13# 0x0000FFFFAA5CC248 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so +199: 14# 0x0000FFFFAA5CC1E0 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so +199: 15# 0x0000FFFFAA5CC178 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so 199: 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-aarch64-linux-gnu/rdkit/rdBase.so 199: 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-aarch64-linux-gnu/rdkit/rdBase.so 199: 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-aarch64-linux-gnu/rdkit/rdBase.so 199: 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-aarch64-linux-gnu/rdkit/rdBase.so 199: 20# boost::python::handle_exception_impl(boost::function0) in /lib/aarch64-linux-gnu/libboost_python313.so.1.83.0 -199: 21# 0x0000FFFF7F59F25C in /lib/aarch64-linux-gnu/libboost_python313.so.1.83.0 +199: 21# 0x0000FFFFAC03F25C in /lib/aarch64-linux-gnu/libboost_python313.so.1.83.0 199: 22# _PyObject_MakeTpCall in /usr/bin/python3 199: 23# _PyEval_EvalFrameDefault in /usr/bin/python3 199: 24# 0x000000000053D3B0 in /usr/bin/python3 @@ -33340,13 +33283,13 @@ 199: 50# 0x000000000065EE50 in /usr/bin/python3 199: 51# Py_RunMain in /usr/bin/python3 199: 52# Py_BytesMain in /usr/bin/python3 -199: 53# 0x0000FFFF7FD8229C in /lib/aarch64-linux-gnu/libc.so.6 +199: 53# 0x0000FFFFAC82229C in /lib/aarch64-linux-gnu/libc.so.6 199: 54# __libc_start_main in /lib/aarch64-linux-gnu/libc.so.6 199: 55# _start in /usr/bin/python3 199: ---------- 199: **** 199: -199: .[00:36:56] +199: .[09:33:36] 199: 199: **** 199: Range Error @@ -33361,23 +33304,23 @@ 199: 3# RDKit::getSnapshot_wrap(RDKit::Trajectory*, unsigned int) in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdtrajectory.so 199: 4# boost::python::objects::caller_py_function_impl, boost::mpl::vector3 > >::operator()(_object*, _object*) in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdtrajectory.so 199: 5# boost::python::objects::function::call(_object*, _object*) const in /lib/aarch64-linux-gnu/libboost_python313.so.1.83.0 -199: 6# 0x0000FFFF7F5A2680 in /lib/aarch64-linux-gnu/libboost_python313.so.1.83.0 +199: 6# 0x0000FFFFAC042680 in /lib/aarch64-linux-gnu/libboost_python313.so.1.83.0 199: 7# boost::python::detail::exception_handler::operator()(boost::function0 const&) const in /lib/aarch64-linux-gnu/libboost_python313.so.1.83.0 199: 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-aarch64-linux-gnu/rdkit/Chem/rdmolfiles.so 199: 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-aarch64-linux-gnu/rdkit/Chem/rdmolfiles.so 199: 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-aarch64-linux-gnu/rdkit/Chem/rdCIPLabeler.so 199: 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-aarch64-linux-gnu/rdkit/Chem/rdchem.so -199: 12# 0x0000FFFF7DB2C320 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so -199: 13# 0x0000FFFF7DB2C2B8 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so -199: 14# 0x0000FFFF7DB2C248 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so -199: 15# 0x0000FFFF7DB2C1E0 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so -199: 16# 0x0000FFFF7DB2C178 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so +199: 12# 0x0000FFFFAA5CC320 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so +199: 13# 0x0000FFFFAA5CC2B8 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so +199: 14# 0x0000FFFFAA5CC248 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so +199: 15# 0x0000FFFFAA5CC1E0 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so +199: 16# 0x0000FFFFAA5CC178 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so 199: 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-aarch64-linux-gnu/rdkit/rdBase.so 199: 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-aarch64-linux-gnu/rdkit/rdBase.so 199: 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-aarch64-linux-gnu/rdkit/rdBase.so 199: 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-aarch64-linux-gnu/rdkit/rdBase.so 199: 21# boost::python::handle_exception_impl(boost::function0) in /lib/aarch64-linux-gnu/libboost_python313.so.1.83.0 -199: 22# 0x0000FFFF7F59F25C in /lib/aarch64-linux-gnu/libboost_python313.so.1.83.0 +199: 22# 0x0000FFFFAC03F25C in /lib/aarch64-linux-gnu/libboost_python313.so.1.83.0 199: 23# _PyObject_MakeTpCall in /usr/bin/python3 199: 24# _PyEval_EvalFrameDefault in /usr/bin/python3 199: 25# 0x000000000053D3B0 in /usr/bin/python3 @@ -33409,13 +33352,13 @@ 199: 51# 0x000000000065EE50 in /usr/bin/python3 199: 52# Py_RunMain in /usr/bin/python3 199: 53# Py_BytesMain in /usr/bin/python3 -199: 54# 0x0000FFFF7FD8229C in /lib/aarch64-linux-gnu/libc.so.6 +199: 54# 0x0000FFFFAC82229C in /lib/aarch64-linux-gnu/libc.so.6 199: 55# __libc_start_main in /lib/aarch64-linux-gnu/libc.so.6 199: 56# _start in /usr/bin/python3 199: ---------- 199: **** 199: -199: [00:36:56] +199: [09:33:36] 199: 199: **** 199: Range Error @@ -33429,23 +33372,23 @@ 199: 2# RDKit::Snapshot::getPoint2D(unsigned int) const in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu//lib/libRDKitTrajectory.so.1 199: 3# boost::python::objects::caller_py_function_impl > >::operator()(_object*, _object*) in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdtrajectory.so 199: 4# boost::python::objects::function::call(_object*, _object*) const in /lib/aarch64-linux-gnu/libboost_python313.so.1.83.0 -199: 5# 0x0000FFFF7F5A2680 in /lib/aarch64-linux-gnu/libboost_python313.so.1.83.0 +199: 5# 0x0000FFFFAC042680 in /lib/aarch64-linux-gnu/libboost_python313.so.1.83.0 199: 6# boost::python::detail::exception_handler::operator()(boost::function0 const&) const in /lib/aarch64-linux-gnu/libboost_python313.so.1.83.0 199: 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-aarch64-linux-gnu/rdkit/Chem/rdmolfiles.so 199: 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-aarch64-linux-gnu/rdkit/Chem/rdmolfiles.so 199: 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-aarch64-linux-gnu/rdkit/Chem/rdCIPLabeler.so 199: 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-aarch64-linux-gnu/rdkit/Chem/rdchem.so -199: 11# 0x0000FFFF7DB2C320 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so -199: 12# 0x0000FFFF7DB2C2B8 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so -199: 13# 0x0000FFFF7DB2C248 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so -199: 14# 0x0000FFFF7DB2C1E0 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so -199: 15# 0x0000FFFF7DB2C178 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so +199: 11# 0x0000FFFFAA5CC320 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so +199: 12# 0x0000FFFFAA5CC2B8 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so +199: 13# 0x0000FFFFAA5CC248 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so +199: 14# 0x0000FFFFAA5CC1E0 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so +199: 15# 0x0000FFFFAA5CC178 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so 199: 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-aarch64-linux-gnu/rdkit/rdBase.so 199: 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-aarch64-linux-gnu/rdkit/rdBase.so 199: 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-aarch64-linux-gnu/rdkit/rdBase.so 199: 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-aarch64-linux-gnu/rdkit/rdBase.so 199: 20# boost::python::handle_exception_impl(boost::function0) in /lib/aarch64-linux-gnu/libboost_python313.so.1.83.0 -199: 21# 0x0000FFFF7F59F25C in /lib/aarch64-linux-gnu/libboost_python313.so.1.83.0 +199: 21# 0x0000FFFFAC03F25C in /lib/aarch64-linux-gnu/libboost_python313.so.1.83.0 199: 22# _PyObject_MakeTpCall in /usr/bin/python3 199: 23# _PyEval_EvalFrameDefault in /usr/bin/python3 199: 24# 0x000000000053D3B0 in /usr/bin/python3 @@ -33477,13 +33420,13 @@ 199: 50# 0x000000000065EE50 in /usr/bin/python3 199: 51# Py_RunMain in /usr/bin/python3 199: 52# Py_BytesMain in /usr/bin/python3 -199: 53# 0x0000FFFF7FD8229C in /lib/aarch64-linux-gnu/libc.so.6 +199: 53# 0x0000FFFFAC82229C in /lib/aarch64-linux-gnu/libc.so.6 199: 54# __libc_start_main in /lib/aarch64-linux-gnu/libc.so.6 199: 55# _start in /usr/bin/python3 199: ---------- 199: **** 199: -199: .[00:36:56] +199: .[09:33:36] 199: 199: **** 199: Range Error @@ -33498,23 +33441,23 @@ 199: 3# RDKit::getSnapshot_wrap(RDKit::Trajectory*, unsigned int) in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdtrajectory.so 199: 4# boost::python::objects::caller_py_function_impl, boost::mpl::vector3 > >::operator()(_object*, _object*) in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdtrajectory.so 199: 5# boost::python::objects::function::call(_object*, _object*) const in /lib/aarch64-linux-gnu/libboost_python313.so.1.83.0 -199: 6# 0x0000FFFF7F5A2680 in /lib/aarch64-linux-gnu/libboost_python313.so.1.83.0 +199: 6# 0x0000FFFFAC042680 in /lib/aarch64-linux-gnu/libboost_python313.so.1.83.0 199: 7# boost::python::detail::exception_handler::operator()(boost::function0 const&) const in /lib/aarch64-linux-gnu/libboost_python313.so.1.83.0 199: 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-aarch64-linux-gnu/rdkit/Chem/rdmolfiles.so 199: 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-aarch64-linux-gnu/rdkit/Chem/rdmolfiles.so 199: 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-aarch64-linux-gnu/rdkit/Chem/rdCIPLabeler.so 199: 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-aarch64-linux-gnu/rdkit/Chem/rdchem.so -199: 12# 0x0000FFFF7DB2C320 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so -199: 13# 0x0000FFFF7DB2C2B8 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so -199: 14# 0x0000FFFF7DB2C248 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so -199: 15# 0x0000FFFF7DB2C1E0 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so -199: 16# 0x0000FFFF7DB2C178 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so +199: 12# 0x0000FFFFAA5CC320 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so +199: 13# 0x0000FFFFAA5CC2B8 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so +199: 14# 0x0000FFFFAA5CC248 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so +199: 15# 0x0000FFFFAA5CC1E0 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so +199: 16# 0x0000FFFFAA5CC178 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so 199: 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-aarch64-linux-gnu/rdkit/rdBase.so 199: 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-aarch64-linux-gnu/rdkit/rdBase.so 199: 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-aarch64-linux-gnu/rdkit/rdBase.so 199: 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-aarch64-linux-gnu/rdkit/rdBase.so 199: 21# boost::python::handle_exception_impl(boost::function0) in /lib/aarch64-linux-gnu/libboost_python313.so.1.83.0 -199: 22# 0x0000FFFF7F59F25C in /lib/aarch64-linux-gnu/libboost_python313.so.1.83.0 +199: 22# 0x0000FFFFAC03F25C in /lib/aarch64-linux-gnu/libboost_python313.so.1.83.0 199: 23# _PyObject_MakeTpCall in /usr/bin/python3 199: 24# _PyEval_EvalFrameDefault in /usr/bin/python3 199: 25# 0x000000000053D3B0 in /usr/bin/python3 @@ -33546,13 +33489,13 @@ 199: 51# 0x000000000065EE50 in /usr/bin/python3 199: 52# Py_RunMain in /usr/bin/python3 199: 53# Py_BytesMain in /usr/bin/python3 -199: 54# 0x0000FFFF7FD8229C in /lib/aarch64-linux-gnu/libc.so.6 +199: 54# 0x0000FFFFAC82229C in /lib/aarch64-linux-gnu/libc.so.6 199: 55# __libc_start_main in /lib/aarch64-linux-gnu/libc.so.6 199: 56# _start in /usr/bin/python3 199: ---------- 199: **** 199: -199: [00:36:56] +199: [09:33:36] 199: 199: **** 199: Pre-condition Violation @@ -33566,23 +33509,23 @@ 199: 2# RDKit::Snapshot::getPoint2D(unsigned int) const in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu//lib/libRDKitTrajectory.so.1 199: 3# boost::python::objects::caller_py_function_impl > >::operator()(_object*, _object*) in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdtrajectory.so 199: 4# boost::python::objects::function::call(_object*, _object*) const in /lib/aarch64-linux-gnu/libboost_python313.so.1.83.0 -199: 5# 0x0000FFFF7F5A2680 in /lib/aarch64-linux-gnu/libboost_python313.so.1.83.0 +199: 5# 0x0000FFFFAC042680 in /lib/aarch64-linux-gnu/libboost_python313.so.1.83.0 199: 6# boost::python::detail::exception_handler::operator()(boost::function0 const&) const in /lib/aarch64-linux-gnu/libboost_python313.so.1.83.0 199: 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-aarch64-linux-gnu/rdkit/Chem/rdmolfiles.so 199: 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-aarch64-linux-gnu/rdkit/Chem/rdmolfiles.so 199: 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-aarch64-linux-gnu/rdkit/Chem/rdCIPLabeler.so 199: 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-aarch64-linux-gnu/rdkit/Chem/rdchem.so -199: 11# 0x0000FFFF7DB2C320 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so -199: 12# 0x0000FFFF7DB2C2B8 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so -199: 13# 0x0000FFFF7DB2C248 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so -199: 14# 0x0000FFFF7DB2C1E0 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so -199: 15# 0x0000FFFF7DB2C178 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so +199: 11# 0x0000FFFFAA5CC320 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so +199: 12# 0x0000FFFFAA5CC2B8 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so +199: 13# 0x0000FFFFAA5CC248 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so +199: 14# 0x0000FFFFAA5CC1E0 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so +199: 15# 0x0000FFFFAA5CC178 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so 199: 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-aarch64-linux-gnu/rdkit/rdBase.so 199: 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-aarch64-linux-gnu/rdkit/rdBase.so 199: 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-aarch64-linux-gnu/rdkit/rdBase.so 199: 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-aarch64-linux-gnu/rdkit/rdBase.so 199: 20# boost::python::handle_exception_impl(boost::function0) in /lib/aarch64-linux-gnu/libboost_python313.so.1.83.0 -199: 21# 0x0000FFFF7F59F25C in /lib/aarch64-linux-gnu/libboost_python313.so.1.83.0 +199: 21# 0x0000FFFFAC03F25C in /lib/aarch64-linux-gnu/libboost_python313.so.1.83.0 199: 22# _PyObject_MakeTpCall in /usr/bin/python3 199: 23# _PyEval_EvalFrameDefault in /usr/bin/python3 199: 24# 0x000000000053D3B0 in /usr/bin/python3 @@ -33614,13 +33557,13 @@ 199: 50# 0x000000000065EE50 in /usr/bin/python3 199: 51# Py_RunMain in /usr/bin/python3 199: 52# Py_BytesMain in /usr/bin/python3 -199: 53# 0x0000FFFF7FD8229C in /lib/aarch64-linux-gnu/libc.so.6 +199: 53# 0x0000FFFFAC82229C in /lib/aarch64-linux-gnu/libc.so.6 199: 54# __libc_start_main in /lib/aarch64-linux-gnu/libc.so.6 199: 55# _start in /usr/bin/python3 199: ---------- 199: **** 199: -199: [00:36:56] +199: [09:33:36] 199: 199: **** 199: Pre-condition Violation @@ -33634,23 +33577,23 @@ 199: 2# RDKit::Snapshot::getPoint2D(unsigned int) const in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu//lib/libRDKitTrajectory.so.1 199: 3# boost::python::objects::caller_py_function_impl > >::operator()(_object*, _object*) in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdtrajectory.so 199: 4# boost::python::objects::function::call(_object*, _object*) const in /lib/aarch64-linux-gnu/libboost_python313.so.1.83.0 -199: 5# 0x0000FFFF7F5A2680 in /lib/aarch64-linux-gnu/libboost_python313.so.1.83.0 +199: 5# 0x0000FFFFAC042680 in /lib/aarch64-linux-gnu/libboost_python313.so.1.83.0 199: 6# boost::python::detail::exception_handler::operator()(boost::function0 const&) const in /lib/aarch64-linux-gnu/libboost_python313.so.1.83.0 199: 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-aarch64-linux-gnu/rdkit/Chem/rdmolfiles.so 199: 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-aarch64-linux-gnu/rdkit/Chem/rdmolfiles.so 199: 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-aarch64-linux-gnu/rdkit/Chem/rdCIPLabeler.so 199: 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-aarch64-linux-gnu/rdkit/Chem/rdchem.so -199: 11# 0x0000FFFF7DB2C320 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so -199: 12# 0x0000FFFF7DB2C2B8 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so -199: 13# 0x0000FFFF7DB2C248 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so -199: 14# 0x0000FFFF7DB2C1E0 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so -199: 15# 0x0000FFFF7DB2C178 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so +199: 11# 0x0000FFFFAA5CC320 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so +199: 12# 0x0000FFFFAA5CC2B8 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so +199: 13# 0x0000FFFFAA5CC248 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so +199: 14# 0x0000FFFFAA5CC1E0 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so +199: 15# 0x0000FFFFAA5CC178 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so 199: 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-aarch64-linux-gnu/rdkit/rdBase.so 199: 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-aarch64-linux-gnu/rdkit/rdBase.so 199: 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-aarch64-linux-gnu/rdkit/rdBase.so 199: 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-aarch64-linux-gnu/rdkit/rdBase.so 199: 20# boost::python::handle_exception_impl(boost::function0) in /lib/aarch64-linux-gnu/libboost_python313.so.1.83.0 -199: 21# 0x0000FFFF7F59F25C in /lib/aarch64-linux-gnu/libboost_python313.so.1.83.0 +199: 21# 0x0000FFFFAC03F25C in /lib/aarch64-linux-gnu/libboost_python313.so.1.83.0 199: 22# _PyObject_MakeTpCall in /usr/bin/python3 199: 23# _PyEval_EvalFrameDefault in /usr/bin/python3 199: 24# 0x000000000053D3B0 in /usr/bin/python3 @@ -33682,7 +33625,7 @@ 199: 50# 0x000000000065EE50 in /usr/bin/python3 199: 51# Py_RunMain in /usr/bin/python3 199: 52# Py_BytesMain in /usr/bin/python3 -199: 53# 0x0000FFFF7FD8229C in /lib/aarch64-linux-gnu/libc.so.6 +199: 53# 0x0000FFFFAC82229C in /lib/aarch64-linux-gnu/libc.so.6 199: 54# __libc_start_main in /lib/aarch64-linux-gnu/libc.so.6 199: 55# _start in /usr/bin/python3 199: ---------- @@ -33690,45 +33633,133 @@ 199: 199: . 199: ---------------------------------------------------------------------- -199: Ran 9 tests in 0.512s +199: Ran 9 tests in 0.192s 199: 199: OK 199: Testing Trajectory wrapper -191/238 Test #199: pyTestTrajectory ....................... Passed 1.05 sec +190/238 Test #199: pyTestTrajectory ....................... Passed 0.55 sec +test 202 + Start 202: pyTestMultithreadedMolSupplier + +202: Test command: /usr/bin/python3 "/build/reproducible-path/rdkit-202503.1/Code/GraphMol/Wrap/testMultithreadedMolSupplier.py" +202: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/Wrap +202: Test timeout computed to be: 1500 +200: ............. +200: ---------------------------------------------------------------------- +200: Ran 13 tests in 0.028s +200: +200: OK +200: Testing SubstanceGroups wrapper +191/238 Test #200: pyTestSGroups .......................... Passed 0.45 sec test 203 Start 203: pyTestPropertyLists 203: Test command: /usr/bin/python3 "/build/reproducible-path/rdkit-202503.1/Code/GraphMol/Wrap/testPropertyLists.py" 203: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/Wrap 203: Test timeout computed to be: 1500 +197: ............................[09:33:37] unable to set wavy bonds for double bonds: 3 +197: .............[09:33:37] +197: +197: **** +197: Range Error +197: idx +197: Violation occurred on line 209 in file ./Code/GraphMol/ROMol.cpp +197: Failed Expression: 6 < 5 +197: ---------- +197: Stacktrace: +197: 0# Invar::Invariant::toString[abi:cxx11]() const in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu//lib/libRDKitRDGeneral.so.1 +197: 1# Invar::operator<<(std::ostream&, Invar::Invariant const&) in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu//lib/libRDKitRDGeneral.so.1 +197: 2# RDKit::ROMol::getAtomWithIdx(unsigned int) in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu//lib/libRDKitGraphMol.so.1 +197: 3# RDKit::RWMol::removeAtom(unsigned int) in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu//lib/libRDKitGraphMol.so.1 +197: 4# boost::python::objects::caller_py_function_impl > >::operator()(_object*, _object*) in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so +197: 5# boost::python::objects::function::call(_object*, _object*) const in /lib/aarch64-linux-gnu/libboost_python313.so.1.83.0 +197: 6# 0x0000FFFFB9AA2680 in /lib/aarch64-linux-gnu/libboost_python313.so.1.83.0 +197: 7# boost::python::detail::exception_handler::operator()(boost::function0 const&) const in /lib/aarch64-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-aarch64-linux-gnu/rdkit/Chem/rdSLNParse.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-aarch64-linux-gnu/rdkit/Chem/rdChemReactions.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-aarch64-linux-gnu/rdkit/Chem/rdChemReactions.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-aarch64-linux-gnu/rdkit/Chem/rdMolChemicalFeatures.so +197: 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-aarch64-linux-gnu/rdkit/Chem/rdDepictor.so +197: 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-aarch64-linux-gnu/rdkit/Chem/rdmolfiles.so +197: 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-aarch64-linux-gnu/rdkit/Chem/rdmolfiles.so +197: 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-aarch64-linux-gnu/rdkit/Chem/rdCIPLabeler.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-aarch64-linux-gnu/rdkit/Chem/rdchem.so +197: 17# 0x0000FFFFB7F8C320 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so +197: 18# 0x0000FFFFB7F8C2B8 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so +197: 19# 0x0000FFFFB7F8C248 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so +197: 20# 0x0000FFFFB7F8C1E0 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so +197: 21# 0x0000FFFFB7F8C178 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so +197: 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-aarch64-linux-gnu/rdkit/rdBase.so +197: 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-aarch64-linux-gnu/rdkit/rdBase.so +197: 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-aarch64-linux-gnu/rdkit/rdBase.so +197: 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-aarch64-linux-gnu/rdkit/rdBase.so +197: 26# boost::python::handle_exception_impl(boost::function0) in /lib/aarch64-linux-gnu/libboost_python313.so.1.83.0 +197: 27# 0x0000FFFFB9A9F25C in /lib/aarch64-linux-gnu/libboost_python313.so.1.83.0 +197: 28# _PyObject_MakeTpCall in /usr/bin/python3 +197: 29# _PyEval_EvalFrameDefault in /usr/bin/python3 +197: 30# 0x000000000053D3B0 in /usr/bin/python3 +197: 31# _PyEval_EvalFrameDefault in /usr/bin/python3 +197: 32# 0x000000000061C8E0 in /usr/bin/python3 +197: 33# 0x00000000005A787C in /usr/bin/python3 +197: 34# _PyObject_MakeTpCall in /usr/bin/python3 +197: 35# _PyEval_EvalFrameDefault in /usr/bin/python3 +197: 36# 0x000000000053D3B0 in /usr/bin/python3 +197: 37# _PyEval_EvalFrameDefault in /usr/bin/python3 +197: 38# 0x000000000061C8E0 in /usr/bin/python3 +197: 39# 0x00000000005A787C in /usr/bin/python3 +197: 40# _PyObject_MakeTpCall in /usr/bin/python3 +197: 41# _PyEval_EvalFrameDefault in /usr/bin/python3 +197: 42# 0x000000000053D3B0 in /usr/bin/python3 +197: 43# _PyEval_EvalFrameDefault in /usr/bin/python3 +197: 44# 0x000000000061C8E0 in /usr/bin/python3 +197: 45# 0x00000000005A787C in /usr/bin/python3 +197: 46# _PyObject_MakeTpCall in /usr/bin/python3 +197: 47# _PyEval_EvalFrameDefault in /usr/bin/python3 +197: 48# 0x000000000050B030 in /usr/bin/python3 +197: 49# _PyObject_MakeTpCall in /usr/bin/python3 +197: 50# _PyEval_EvalFrameDefault in /usr/bin/python3 +197: 51# PyEval_EvalCode in /usr/bin/python3 +197: 52# 0x000000000064023C in /usr/bin/python3 +197: 53# 0x000000000063BC30 in /usr/bin/python3 +197: 54# 0x000000000065F810 in /usr/bin/python3 +197: 55# 0x000000000065F0B4 in /usr/bin/python3 +197: 56# 0x000000000065EE50 in /usr/bin/python3 +197: 57# Py_RunMain in /usr/bin/python3 +197: 58# Py_BytesMain in /usr/bin/python3 +197: 59# 0x0000FFFFBA7E229C in /lib/aarch64-linux-gnu/libc.so.6 +197: 60# __libc_start_main in /lib/aarch64-linux-gnu/libc.so.6 +197: 61# _start in /usr/bin/python3 +197: ---------- +197: **** +197: 202: .s. 202: ---------------------------------------------------------------------- -202: Ran 3 tests in 0.178s +202: Ran 3 tests in 0.096s 202: 202: OK (skipped=1) 202: Testing Smiles and SD MultithreadedMolSupplier -203: [00:36:57] Value [?] for property atom.iprop.PartiallyMissingInt of atom 0 can not be parsed. Ignoring it. -203: [00:36:57] Value ? for property atom.iprop.PartiallyMissingInt of atom 3 can not be parsed. Ignoring it. -203: [00:36:57] Value $$$$ for property atom.iprop.PartiallyMissingInt of atom 4 can not be parsed. Ignoring it. -203: .[00:36:57] Value [?] for property atom.iprop.PartiallyMissingInt of atom 0 can not be parsed. Ignoring it. -203: [00:36:57] Value ? for property atom.iprop.PartiallyMissingInt of atom 3 can not be parsed. Ignoring it. -203: [00:36:57] Value $$$$ for property atom.iprop.PartiallyMissingInt of atom 4 can not be parsed. Ignoring it. -203: ...[00:36:57] Value [?] for property atom.iprop.PartiallyMissingInt of atom 0 can not be parsed. Ignoring it. -203: [00:36:57] Value ? for property atom.iprop.PartiallyMissingInt of atom 3 can not be parsed. Ignoring it. -203: [00:36:57] Value $$$$ for property atom.iprop.PartiallyMissingInt of atom 4 can not be parsed. Ignoring it. +203: [09:33:37] Value [?] for property atom.iprop.PartiallyMissingInt of atom 0 can not be parsed. Ignoring it. +203: [09:33:37] Value ? for property atom.iprop.PartiallyMissingInt of atom 3 can not be parsed. Ignoring it. +203: [09:33:37] Value $$$$ for property atom.iprop.PartiallyMissingInt of atom 4 can not be parsed. Ignoring it. +203: .[09:33:37] Value [?] for property atom.iprop.PartiallyMissingInt of atom 0 can not be parsed. Ignoring it. +203: [09:33:37] Value ? for property atom.iprop.PartiallyMissingInt of atom 3 can not be parsed. Ignoring it. +203: [09:33:37] Value $$$$ for property atom.iprop.PartiallyMissingInt of atom 4 can not be parsed. Ignoring it. +203: ...[09:33:37] Value [?] for property atom.iprop.PartiallyMissingInt of atom 0 can not be parsed. Ignoring it. +203: [09:33:37] Value ? for property atom.iprop.PartiallyMissingInt of atom 3 can not be parsed. Ignoring it. +203: [09:33:37] Value $$$$ for property atom.iprop.PartiallyMissingInt of atom 4 can not be parsed. Ignoring it. 203: . 203: ---------------------------------------------------------------------- -203: Ran 5 tests in 0.023s +203: Ran 5 tests in 0.011s 203: 203: OK -192/238 Test #202: pyTestMultithreadedMolSupplier ......... Passed 0.75 sec +192/238 Test #202: pyTestMultithreadedMolSupplier ......... Passed 0.35 sec test 204 Start 204: pyCDXMLTest 204: Test command: /usr/bin/python3 "/build/reproducible-path/rdkit-202503.1/Code/GraphMol/Wrap/test_cdxml.py" 204: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/Wrap 204: Test timeout computed to be: 1500 -193/238 Test #203: pyTestPropertyLists .................... Passed 0.56 sec +193/238 Test #203: pyTestPropertyLists .................... Passed 0.24 sec test 205 Start 205: molStandardizeTest @@ -33737,28 +33768,25 @@ 205: Test timeout computed to be: 1500 204: . 204: ---------------------------------------------------------------------- -204: Ran 1 test in 0.023s +204: Ran 1 test in 0.010s 204: 204: OK -194/238 Test #204: pyCDXMLTest ............................ Passed 0.59 sec +194/238 Test #204: pyCDXMLTest ............................ Passed 0.44 sec test 206 Start 206: molNormalizeTest 206: Test command: /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/MolStandardize/molNormalizeTest 206: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/MolStandardize 206: Test timeout computed to be: 1500 -206: [00:36:58] Can't kekulize mol. Unkekulized atoms: 3 7 8 9 -197: ....................[00:36:58] Explicit valence for atom # 1 F, 2, is greater than permitted -197: [00:36:58] Explicit valence for atom # 6 F, 2, is greater than permitted -197: [00:36:58] Can't kekulize mol. Unkekulized atoms: 3 4 5 -206: [00:36:58] Initializing Normalizer -206: [00:36:58] Running Normalizer -206: [00:36:58] Rule applied: BrokenazidetoN=N+=N- -206: [00:36:58] Initializing Normalizer -206: [00:36:58] Running Normalizer -206: [00:36:58] Initializing Normalizer -206: [00:36:58] Running Normalizer -195/238 Test #206: molNormalizeTest ....................... Passed 0.24 sec +206: [09:33:37] Can't kekulize mol. Unkekulized atoms: 3 7 8 9 +206: [09:33:37] Initializing Normalizer +206: [09:33:37] Running Normalizer +206: [09:33:37] Rule applied: BrokenazidetoN=N+=N- +206: [09:33:37] Initializing Normalizer +206: [09:33:37] Running Normalizer +206: [09:33:37] Initializing Normalizer +206: [09:33:37] Running Normalizer +195/238 Test #206: molNormalizeTest ....................... Passed 0.19 sec test 207 Start 207: molValidateTest @@ -33783,70 +33811,83 @@ 207: ERROR: [StereoValidation] Bond 3 has assigned stereo type, but unexpected bond order. 207: there 207: ERROR: [StereoValidation] Atom 0 has stereo bonds, but less than 3 explicit substituents. -196/238 Test #207: molValidateTest ........................ Passed 0.10 sec +196/238 Test #207: molValidateTest ........................ Passed 0.07 sec test 208 Start 208: molChargeTest 208: Test command: /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/MolStandardize/molChargeTest 208: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/MolStandardize 208: Test timeout computed to be: 1500 -197: .................[00:36:58] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -197/238 Test #208: molChargeTest .......................... Passed 0.13 sec +197/238 Test #208: molChargeTest .......................... Passed 0.06 sec test 209 Start 209: molTautomerTest 209: Test command: /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/MolStandardize/molTautomerTest 209: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/MolStandardize 209: Test timeout computed to be: 1500 -209: [00:36:59] Tautomer enumeration stopped at 292 tautomers: max transforms reached -198/238 Test #205: molStandardizeTest ..................... Passed 1.90 sec +197: ....................[09:33:38] Explicit valence for atom # 1 F, 2, is greater than permitted +197: [09:33:38] Explicit valence for atom # 6 F, 2, is greater than permitted +197: [09:33:38] Can't kekulize mol. Unkekulized atoms: 3 4 5 +197: .................[09:33:38] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +209: [09:33:38] Tautomer enumeration stopped at 292 tautomers: max transforms reached +198/238 Test #205: molStandardizeTest ..................... Passed 1.26 sec test 210 Start 210: molStandardizeSmallTest 210: Test command: /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/MolStandardize/molStandardizeSmallTest 210: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/MolStandardize 210: Test timeout computed to be: 1500 -199/238 Test #210: molStandardizeSmallTest ................ Passed 0.09 sec +199/238 Test #210: molStandardizeSmallTest ................ Passed 0.06 sec test 211 Start 211: molFragmentTest 211: Test command: /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/MolStandardize/molFragmentTest 211: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/MolStandardize 211: Test timeout computed to be: 1500 -211: [00:36:59] SMARTS Parse Error: syntax error while parsing: [Cl -211: [00:36:59] SMARTS Parse Error: Failed parsing SMARTS '[Cl' for input: '[Cl' -200/238 Test #211: molFragmentTest ........................ Passed 0.09 sec +211: [09:33:38] SMARTS Parse Error: syntax error while parsing: [Cl +211: [09:33:38] SMARTS Parse Error: Failed parsing SMARTS '[Cl' for input: '[Cl' +200/238 Test #211: molFragmentTest ........................ Passed 0.08 sec test 212 Start 212: molStandardizeCatchTest 212: Test command: /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/MolStandardize/molStandardizeCatchTest 212: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/MolStandardize 212: Test timeout computed to be: 1500 -209: [00:36:59] Tautomer enumeration stopped at 292 tautomers: max transforms reached -209: [00:36:59] Tautomer enumeration stopped at 50 tautomers: max tautomers reached -212: Randomness seeded to: 1793947438 +209: [09:33:38] Tautomer enumeration stopped at 292 tautomers: max transforms reached +209: [09:33:38] Tautomer enumeration stopped at 50 tautomers: max tautomers reached +212: Randomness seeded to: 1679854586 212: * - * - * - * m1 212: * - * - * - * m2 212: * - * - * - * m1 212: * - * - * - * m2 -212: [00:37:00] Can't kekulize mol. Unkekulized atoms: 3 7 -212: [00:37:00] Can't kekulize mol. Unkekulized atoms: 3 8 -212: [00:37:00] Can't kekulize mol. Unkekulized atoms: 2 3 4 -209: [00:37:00] Tautomer enumeration stopped at 86 tautomers: canceled +212: [09:33:39] Can't kekulize mol. Unkekulized atoms: 3 7 +212: [09:33:39] Can't kekulize mol. Unkekulized atoms: 3 8 +212: [09:33:39] Can't kekulize mol. Unkekulized atoms: 2 3 4 +209: [09:33:39] Tautomer enumeration stopped at 85 tautomers: canceled 209: Enumeration was canceled due to timeout (50 ms) -201/238 Test #201: pyTestThreads .......................... Passed 3.65 sec +185: ............. +185: ---------------------------------------------------------------------- +185: Ran 19 tests in 9.710s +185: +185: OK +185: Testing atom rings +185: testing bond rings +185: searching atom rings +185: searching bond rings +185: done +201/238 Test #185: pySubstructLibrary ..................... Passed 10.20 sec test 213 Start 213: molStandardizePipelineTest 213: Test command: /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/MolStandardize/molStandardizePipelineTest 213: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/MolStandardize 213: Test timeout computed to be: 1500 -213: Randomness seeded to: 4257349845 +213: Randomness seeded to: 3653587749 213: 1 Counts line too short: '' on line4 213: 1 Could not instantiate a valid molecule from input 213: 8 Molecule has no atoms -213: [00:37:00] Explicit valence for atom # 1 N, 4, is greater than permitted -213: [00:37:00] Explicit valence for atom # 1 N, 4, is greater than permitted +213: [09:33:39] Explicit valence for atom # 1 N, 4, is greater than permitted +213: [09:33:39] Explicit valence for atom # 1 N, 4, is greater than permitted 213: 8 Explicit valence for atom # 1 N, 4, is greater than permitted 213: 128 An error occurred while preparing the molecule for standardization. 213: 8 The molecule contains an unknown isotope: 3C @@ -33861,13 +33902,13 @@ 213: 4 Bond 3 of dative type is not allowed 213: 4 Enhanced stereochemistry features are not allowed 213: 8 The radical at atom 0 is not allowed -213: [00:37:00] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +213: [09:33:39] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 213: 16 The molecule includes non-null Z coordinates 213: 32 Atom 0 too close to bond 2 213: 32 The length of bond 3 between atoms 0 and 3 exceeds a configured limit 213: 64 Atom 0 has 3 explicit substituents and multiple stereo bonds 213: 64 Atom 0 has adjacent stereo bonds with like orientation -213: [00:37:00] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +213: [09:33:39] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 213: 16 The molecule includes non-null Z coordinates 213: 64 Atom 0 has adjacent stereo bonds with like orientation 213: 32 The length of bond 16 between atoms 16 and 1 exceeds a configured limit @@ -33913,11 +33954,11 @@ 213: 16777216 Double bond 2 was assigned an undefined/unknown stereochemical configuration 213: 16777216 The "wavy" style of bond 3 was removed 213: 16777216 The representation of some functional groups was adjusted. -213: [00:37:00] Can't kekulize mol. Unkekulized atoms: 2 3 5 +213: [09:33:39] Can't kekulize mol. Unkekulized atoms: 2 3 5 213: =============================================================================== 213: All tests passed (268 assertions in 5 test cases) 213: -202/238 Test #213: molStandardizePipelineTest ............. Passed 0.35 sec +202/238 Test #213: molStandardizePipelineTest ............. Passed 0.26 sec test 214 Start 214: pyMolStandardize @@ -33926,9 +33967,14 @@ 214: Test timeout computed to be: 1500 209: 375 209: Enumeration has completed -209: [00:37:01] Tautomer enumeration stopped at 61 tautomers: canceled -214: .....[00:37:01] Tautomer enumeration stopped at 292 tautomers: max transforms reached -214: [00:37:01] Tautomer enumeration stopped at 50 tautomers: max tautomers reached +209: [09:33:39] Tautomer enumeration stopped at 127 tautomers: canceled +203/238 Test #201: pyTestThreads .......................... Passed 3.20 sec +test 215 + Start 215: testScaffoldNetwork + +215: Test command: /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/ScaffoldNetwork/testScaffoldNetwork +215: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/ScaffoldNetwork +215: Test timeout computed to be: 1500 209: CN=c1cc[nH]cn1 209: CN=c1ccnc[nH]1 209: CNc1ccncn1 @@ -33936,159 +33982,150 @@ 209: CN=c1cccc[nH]1 209: CNc1ccccn1 209: res: CNc1ccccn1 -214: .[00:37:01] Tautomer enumeration stopped at 34 tautomers: canceled -214: Enumeration was canceled due to timeout (50 ms) -203/238 Test #209: molTautomerTest ........................ Passed 3.40 sec -test 215 - Start 215: testScaffoldNetwork - -215: Test command: /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/ScaffoldNetwork/testScaffoldNetwork -215: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/ScaffoldNetwork -215: Test timeout computed to be: 1500 -150: --------------------------------- -150: test getO3AForProbeConfs -150: -150: *********************************************************** -204/238 Test #150: testO3AAlign ........................... Passed 38.35 sec +204/238 Test #209: molTautomerTest ........................ Passed 2.29 sec test 216 Start 216: pyScaffoldNetwork 216: Test command: /usr/bin/python3 "/build/reproducible-path/rdkit-202503.1/Code/GraphMol/ScaffoldNetwork/Wrap/testScaffoldNetwork.py" 216: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/ScaffoldNetwork/Wrap 216: Test timeout computed to be: 1500 -185: ............. -185: ---------------------------------------------------------------------- -185: Ran 19 tests in 14.093s -185: -185: OK -185: Testing atom rings -185: testing bond rings -185: searching atom rings -185: searching bond rings -185: done -205/238 Test #185: pySubstructLibrary ..................... Passed 14.70 sec +214: .....[09:33:40] Tautomer enumeration stopped at 292 tautomers: max transforms reached +214: [09:33:40] Tautomer enumeration stopped at 50 tautomers: max tautomers reached +216: ....... +216: ---------------------------------------------------------------------- +216: Ran 7 tests in 0.054s +216: +216: OK +205/238 Test #216: pyScaffoldNetwork ...................... Passed 0.39 sec test 217 Start 217: pyScaffoldNetworkPickling 217: Test command: /usr/bin/python3 "/build/reproducible-path/rdkit-202503.1/Code/GraphMol/ScaffoldNetwork/Wrap/testPickleScaffoldNetwork.py" 217: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/ScaffoldNetwork/Wrap 217: Test timeout computed to be: 1500 -216: ....... -216: ---------------------------------------------------------------------- -216: Ran 7 tests in 0.046s -216: -216: OK -206/238 Test #216: pyScaffoldNetwork ...................... Passed 0.44 sec +214: .[09:33:40] Tautomer enumeration stopped at 71 tautomers: canceled +214: Enumeration was canceled due to timeout (50 ms) +217: . +217: ---------------------------------------------------------------------- +217: Ran 1 test in 0.016s +217: +217: OK +206/238 Test #217: pyScaffoldNetworkPickling .............. Passed 0.41 sec test 218 Start 218: testMolEnumerator 218: Test command: /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/MolEnumerator/testMolEnumerator 218: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/MolEnumerator 218: Test timeout computed to be: 1500 -218: Randomness seeded to: 442037947 -218: [00:37:03] can only enumerate SRUs with CONNECT=HT or CONNECT=HH -217: . -217: ---------------------------------------------------------------------- -217: Ran 1 test in 0.019s -217: -217: OK -218: =============================================================================== -218: All tests passed (321 assertions in 16 test cases) -218: -207/238 Test #218: testMolEnumerator ...................... Passed 0.10 sec +218: Randomness seeded to: 70515075 +218: [09:33:41] can only enumerate SRUs with CONNECT=HT or CONNECT=HH +215: Randomness seeded to: 4288885564 +215: =============================================================================== +215: All tests passed (273 assertions in 19 test cases) +215: +207/238 Test #215: testScaffoldNetwork .................... Passed 1.29 sec test 219 Start 219: pyMolEnumerator 219: Test command: /usr/bin/python3 "/build/reproducible-path/rdkit-202503.1/Code/GraphMol/MolEnumerator/Wrap/rough_test.py" 219: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/MolEnumerator/Wrap 219: Test timeout computed to be: 1500 -208/238 Test #217: pyScaffoldNetworkPickling .............. Passed 0.42 sec +218: =============================================================================== +218: All tests passed (321 assertions in 16 test cases) +218: +208/238 Test #218: testMolEnumerator ...................... Passed 0.10 sec test 220 Start 220: testAbbreviations 220: Test command: /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/Abbreviations/testAbbreviations 220: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/Abbreviations 220: Test timeout computed to be: 1500 -220: Randomness seeded to: 3013092340 -220: [00:37:03] SMARTS Parse Error: syntax error while parsing: *fail -220: [00:37:03] SMARTS Parse Error: Failed parsing SMARTS '*fail' for input: '*fail' -215: Randomness seeded to: 757071560 -215: =============================================================================== -215: All tests passed (273 assertions in 19 test cases) -215: -220: [00:37:03] no suitable SubstanceGroups found -209/238 Test #215: testScaffoldNetwork .................... Passed 1.50 sec +220: Randomness seeded to: 4087160680 +220: [09:33:41] SMARTS Parse Error: syntax error while parsing: *fail +220: [09:33:41] SMARTS Parse Error: Failed parsing SMARTS '*fail' for input: '*fail' +220: [09:33:41] no suitable SubstanceGroups found +220: =============================================================================== +220: All tests passed (195 assertions in 12 test cases) +220: +209/238 Test #220: testAbbreviations ...................... Passed 0.08 sec test 221 Start 221: pyAbbreviations 221: Test command: /usr/bin/python3 "/build/reproducible-path/rdkit-202503.1/Code/GraphMol/Abbreviations/Wrap/testAbbreviations.py" 221: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/Abbreviations/Wrap 221: Test timeout computed to be: 1500 -220: =============================================================================== -220: All tests passed (195 assertions in 12 test cases) -220: -210/238 Test #220: testAbbreviations ...................... Passed 0.05 sec +219: ... +219: ---------------------------------------------------------------------- +219: Ran 3 tests in 0.023s +219: +219: OK +221: ....... +221: ---------------------------------------------------------------------- +221: Ran 7 tests in 0.029s +221: +221: OK +210/238 Test #219: pyMolEnumerator ........................ Passed 0.39 sec test 222 Start 222: generalizedSubstructCatch 222: Test command: /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/GeneralizedSubstruct/generalizedSubstructCatch 222: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/GeneralizedSubstruct 222: Test timeout computed to be: 1500 -222: Randomness seeded to: 436605374 -222: =============================================================================== -222: All tests passed (486 assertions in 10 test cases) -222: -211/238 Test #222: generalizedSubstructCatch .............. Passed 0.40 sec +211/238 Test #221: pyAbbreviations ........................ Passed 0.36 sec test 223 Start 223: pyGeneralizedSubstruct 223: Test command: /usr/bin/python3 "/build/reproducible-path/rdkit-202503.1/Code/GraphMol/GeneralizedSubstruct/Wrap/testGeneralizedSubstruct.py" 223: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/GeneralizedSubstruct/Wrap 223: Test timeout computed to be: 1500 -221: ....... -221: ---------------------------------------------------------------------- -221: Ran 7 tests in 0.042s -221: -221: OK -219: ... -219: ---------------------------------------------------------------------- -219: Ran 3 tests in 0.021s -219: -219: OK -212/238 Test #219: pyMolEnumerator ........................ Passed 0.69 sec +214: Enumeration has completed +222: Randomness seeded to: 3069922279 +222: =============================================================================== +222: All tests passed (486 assertions in 10 test cases) +222: +212/238 Test #222: generalizedSubstructCatch .............. Passed 0.31 sec test 224 Start 224: testMolProcessing 224: Test command: /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/MolProcessing/testMolProcessing 224: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/MolProcessing 224: Test timeout computed to be: 1500 -213/238 Test #221: pyAbbreviations ........................ Passed 0.61 sec +214: [09:33:41] Tautomer enumeration stopped at 90 tautomers: canceled +223: ....... +223: ---------------------------------------------------------------------- +223: Ran 7 tests in 0.111s +223: +223: OK +213/238 Test #223: pyGeneralizedSubstruct ................. Passed 0.44 sec test 225 Start 225: pyMolProcessing 225: Test command: /usr/bin/python3 "/build/reproducible-path/rdkit-202503.1/Code/GraphMol/MolProcessing/Wrap/testMolProcessing.py" 225: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/MolProcessing/Wrap 225: Test timeout computed to be: 1500 -214: Enumeration has completed -223: ....... -223: ---------------------------------------------------------------------- -223: Ran 7 tests in 0.215s -223: -223: OK -214/238 Test #223: pyGeneralizedSubstruct ................. Passed 0.62 sec +214: ..........[09:33:42] Explicit valence for atom # 1 N, 4, is greater than permitted +214: [09:33:42] Explicit valence for atom # 1 N, 4, is greater than permitted +214: [09:33:42] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +214: [09:33:42] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +147: [09:33:42] UFFTYPER: Unrecognized atom type: S_6+6 (0) +147: [09:33:42] UFFTYPER: Warning: hybridization set to SP3 for atom 0 +147: [09:33:42] UFFTYPER: Unrecognized charge state for atom: 0 +225: .. +225: ---------------------------------------------------------------------- +225: Ran 2 tests in 0.208s +225: +225: OK +214/238 Test #225: pyMolProcessing ........................ Passed 0.62 sec test 226 Start 226: testMIF 226: Test command: /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/MolInteractionFields/testMIF 226: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/MolInteractionFields 226: Test timeout computed to be: 1500 -226: Randomness seeded to: 3535896579 +226: Randomness seeded to: 2573063959 226: =============================================================================== 226: All tests passed (27926 assertions in 8 test cases) 226: -214: ..........[00:37:04] Explicit valence for atom # 1 N, 4, is greater than permitted -214: [00:37:04] Explicit valence for atom # 1 N, 4, is greater than permitted -214: [00:37:04] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 215/238 Test #226: testMIF ................................ Passed 0.11 sec test 227 Start 227: pyMIF @@ -34096,13 +34133,16 @@ 227: Test command: /usr/bin/python3 "/build/reproducible-path/rdkit-202503.1/Code/GraphMol/MolInteractionFields/Wrap/testMIF.py" 227: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/MolInteractionFields/Wrap 227: Test timeout computed to be: 1500 -214: [00:37:04] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -225: .. -225: ---------------------------------------------------------------------- -225: Ran 2 tests in 0.234s -225: -225: OK -216/238 Test #225: pyMolProcessing ........................ Passed 0.96 sec +214: ............[09:33:43] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +214: [09:33:43] Warning: ambiguous stereochemistry - opposing bonds have opposite wedging - at atom 1 ignored. +214: [09:33:43] Warning: ambiguous stereochemistry - opposing bonds have opposite wedging - at atom 1 ignored. +227: ....... +227: ---------------------------------------------------------------------- +227: Ran 7 tests in 0.080s +227: +227: OK +227: Testing MIF wrapper +216/238 Test #227: pyMIF .................................. Passed 0.54 sec test 228 Start 228: testQuery @@ -34126,7 +34166,7 @@ 228: XOr 228: pointer and copy foo 228: Set2 -217/238 Test #228: testQuery .............................. Passed 0.08 sec +217/238 Test #228: testQuery .............................. Passed 0.01 sec test 229 Start 229: testBaseFeatures @@ -34194,32 +34234,37 @@ 230: 9.49496e+07 230: 2.25618e+08 230: 1.30219e+08 -219/238 Test #230: testMatCalc ............................ Passed 0.03 sec +219/238 Test #230: testMatCalc ............................ Passed 0.01 sec test 231 Start 231: pyMatCalc 231: Test command: /usr/bin/python3 "/build/reproducible-path/rdkit-202503.1/Code/DataManip/MetricMatrixCalc/Wrap/testMatricCalc.py" 231: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/DataManip/MetricMatrixCalc/Wrap 231: Test timeout computed to be: 1500 -227: ....... -227: ---------------------------------------------------------------------- -227: Ran 7 tests in 0.155s -227: -227: OK -227: Testing MIF wrapper -220/238 Test #227: pyMIF .................................. Passed 0.95 sec +214: ........[09:33:43] Explicit valence for atom # 1 O, 3, is greater than permitted +214: .. +214: ---------------------------------------------------------------------- +214: Ran 38 tests in 3.505s +214: +214: OK +214: done +150: --------------------------------- +150: test getO3AForProbeConfs +150: +150: *********************************************************** +220/238 Test #150: testO3AAlign ........................... Passed 28.60 sec test 232 Start 232: testSimDivPickers 232: Test command: /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/SimDivPickers/testSimDivPickers 232: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/SimDivPickers 232: Test timeout computed to be: 1500 -232: [00:37:05] ------------------------------------- -232: [00:37:05] Testing github issue 1421: MaxMinPicker picking non-existent element. -232: [00:37:05] Done -232: [00:37:05] ------------------------------------- -232: [00:37:05] Testing github issue 2245: MinMax Diversity picker seeding shows deterministic / non-random behaviour. -232: [00:37:05] Done +232: [09:33:43] ------------------------------------- +232: [09:33:43] Testing github issue 1421: MaxMinPicker picking non-existent element. +232: [09:33:43] Done +232: [09:33:43] ------------------------------------- +232: [09:33:43] Testing github issue 2245: MinMax Diversity picker seeding shows deterministic / non-random behaviour. +232: [09:33:43] Done 221/238 Test #232: testSimDivPickers ...................... Passed 0.01 sec test 233 Start 233: pickersTestsCatch @@ -34227,18 +34272,134 @@ 233: Test command: /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/SimDivPickers/pickersTestsCatch 233: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/SimDivPickers 233: Test timeout computed to be: 1500 -233: Randomness seeded to: 268285783 -233: =============================================================================== -233: All tests passed (21267 assertions in 1 test case) -233: -222/238 Test #233: pickersTestsCatch ...................... Passed 0.19 sec +222/238 Test #214: pyMolStandardize ....................... Passed 3.95 sec test 234 Start 234: pySimDivPickers 234: Test command: /usr/bin/python3 "/build/reproducible-path/rdkit-202503.1/Code/SimDivPickers/Wrap/testPickers.py" 234: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/SimDivPickers/Wrap 234: Test timeout computed to be: 1500 -197: ..[00:37:05] +233: Randomness seeded to: 764441085 +233: =============================================================================== +233: All tests passed (21267 assertions in 1 test case) +233: +223/238 Test #233: pickersTestsCatch ...................... Passed 0.13 sec +test 235 + Start 235: pyRanker + +235: Test command: /usr/bin/python3 "/build/reproducible-path/rdkit-202503.1/Code/ML/InfoTheory/Wrap/testRanker.py" +235: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/ML/InfoTheory/Wrap +235: Test timeout computed to be: 1500 +234: [09:33:43] the useCache argument is deprecated and ignored +235: ..[09:33:44] +235: +235: **** +235: Invariant Violation +235: Can't rank more bits than the ensemble size +235: Violation occurred on line 156 in file ./Code/ML/InfoTheory/InfoBitRanker.cpp +235: Failed Expression: num <= dp_maskBits->getNumOnBits() +235: ---------- +235: Stacktrace: +235: 0# Invar::Invariant::toString[abi:cxx11]() const in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu//lib/libRDKitRDGeneral.so.1 +235: 1# Invar::operator<<(std::ostream&, Invar::Invariant const&) in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu//lib/libRDKitRDGeneral.so.1 +235: 2# RDInfoTheory::InfoBitRanker::getTopN(unsigned int) in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu//lib/libRDKitInfoTheory.so.1 +235: 3# RDInfoTheory::getTopNbits(RDInfoTheory::InfoBitRanker*, int) in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/ML/InfoTheory/rdInfoTheory.so +235: 4# boost::python::objects::caller_py_function_impl > >::operator()(_object*, _object*) in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/ML/InfoTheory/rdInfoTheory.so +235: 5# boost::python::objects::function::call(_object*, _object*) const in /lib/aarch64-linux-gnu/libboost_python313.so.1.83.0 +235: 6# 0x0000FFFF95A82680 in /lib/aarch64-linux-gnu/libboost_python313.so.1.83.0 +235: 7# boost::python::detail::exception_handler::operator()(boost::function0 const&) const in /lib/aarch64-linux-gnu/libboost_python313.so.1.83.0 +235: 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-aarch64-linux-gnu/rdkit/rdBase.so +235: 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-aarch64-linux-gnu/rdkit/rdBase.so +235: 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-aarch64-linux-gnu/rdkit/rdBase.so +235: 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-aarch64-linux-gnu/rdkit/rdBase.so +235: 12# boost::python::handle_exception_impl(boost::function0) in /lib/aarch64-linux-gnu/libboost_python313.so.1.83.0 +235: 13# 0x0000FFFF95A7F25C in /lib/aarch64-linux-gnu/libboost_python313.so.1.83.0 +235: 14# _PyObject_MakeTpCall in /usr/bin/python3 +235: 15# _PyEval_EvalFrameDefault in /usr/bin/python3 +235: 16# 0x000000000053D3B0 in /usr/bin/python3 +235: 17# _PyEval_EvalFrameDefault in /usr/bin/python3 +235: 18# 0x000000000061C8E0 in /usr/bin/python3 +235: 19# 0x00000000005A787C in /usr/bin/python3 +235: 20# _PyObject_MakeTpCall in /usr/bin/python3 +235: 21# _PyEval_EvalFrameDefault in /usr/bin/python3 +235: 22# 0x000000000053D3B0 in /usr/bin/python3 +235: 23# _PyEval_EvalFrameDefault in /usr/bin/python3 +235: 24# 0x000000000061C8E0 in /usr/bin/python3 +235: 25# 0x00000000005A787C in /usr/bin/python3 +235: 26# _PyObject_MakeTpCall in /usr/bin/python3 +235: 27# _PyEval_EvalFrameDefault in /usr/bin/python3 +235: 28# 0x000000000053D3B0 in /usr/bin/python3 +235: 29# _PyEval_EvalFrameDefault in /usr/bin/python3 +235: 30# 0x000000000061C8E0 in /usr/bin/python3 +235: 31# 0x00000000005A787C in /usr/bin/python3 +235: 32# _PyObject_MakeTpCall in /usr/bin/python3 +235: 33# _PyEval_EvalFrameDefault in /usr/bin/python3 +235: 34# 0x000000000050B030 in /usr/bin/python3 +235: 35# _PyObject_MakeTpCall in /usr/bin/python3 +235: 36# _PyEval_EvalFrameDefault in /usr/bin/python3 +235: 37# PyEval_EvalCode in /usr/bin/python3 +235: 38# 0x000000000064023C in /usr/bin/python3 +235: 39# 0x000000000063BC30 in /usr/bin/python3 +235: 40# 0x000000000065F810 in /usr/bin/python3 +235: 41# 0x000000000065F0B4 in /usr/bin/python3 +235: 42# 0x000000000065EE50 in /usr/bin/python3 +235: 43# Py_RunMain in /usr/bin/python3 +235: 44# Py_BytesMain in /usr/bin/python3 +235: 45# 0x0000FFFF973E229C in /lib/aarch64-linux-gnu/libc.so.6 +235: 46# __libc_start_main in /lib/aarch64-linux-gnu/libc.so.6 +235: 47# _start in /usr/bin/python3 +235: ---------- +235: **** +235: +235: ... +235: ---------------------------------------------------------------------- +235: Ran 5 tests in 0.032s +235: +235: OK +224: Randomness seeded to: 353521545 +224: =============================================================================== +224: All tests passed (203 assertions in 1 test case) +224: +224/238 Test #224: testMolProcessing ...................... Passed 2.16 sec +test 236 + Start 236: testChemicalFeatures + +236: Test command: /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/ChemicalFeatures/testChemicalFeatures +236: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/ChemicalFeatures +236: Test timeout computed to be: 1500 +236: ----------------------------------------- +236: Test1 +236: Done +225/238 Test #236: testChemicalFeatures ................... Passed 0.00 sec +test 237 + Start 237: pyFeatures + +237: Test command: /usr/bin/python3 "/build/reproducible-path/rdkit-202503.1/Code/ChemicalFeatures/Wrap/testFeatures.py" +237: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/ChemicalFeatures/Wrap +237: Test timeout computed to be: 1500 +231: ..... +231: ---------------------------------------------------------------------- +231: Ran 5 tests in 0.432s +231: +231: OK +226/238 Test #235: pyRanker ............................... Passed 0.37 sec +test 238 + Start 238: pythonProjectTests + +238: Test command: /usr/bin/python3 "-m" "pytest" +238: Working Directory: /build/reproducible-path/rdkit-202503.1/Projects +238: Test timeout computed to be: 1500 +234: ...[09:33:44] the useCache argument is deprecated and ignored +234: [09:33:44] the useCache argument is deprecated and ignored +234: .[09:33:44] the useCache argument is deprecated and ignored +227/238 Test #231: pyMatCalc .............................. Passed 0.79 sec +237: .. +237: ---------------------------------------------------------------------- +237: Ran 2 tests in 0.007s +237: +237: OK +237: Testing ChemicalFeatures Wrapper code: +197: ..[09:33:44] 197: 197: **** 197: Pre-condition Violation @@ -34252,7 +34413,7 @@ 197: 2# RDKit::Atom::getOwningMol() const in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so 197: 3# boost::python::objects::caller_py_function_impl, boost::mpl::vector2 > >::operator()(_object*, _object*) in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so 197: 4# boost::python::objects::function::call(_object*, _object*) const in /lib/aarch64-linux-gnu/libboost_python313.so.1.83.0 -197: 5# 0x0000FFFFA0B32680 in /lib/aarch64-linux-gnu/libboost_python313.so.1.83.0 +197: 5# 0x0000FFFFB9AA2680 in /lib/aarch64-linux-gnu/libboost_python313.so.1.83.0 197: 6# boost::python::detail::exception_handler::operator()(boost::function0 const&) const in /lib/aarch64-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-aarch64-linux-gnu/rdkit/Chem/rdSLNParse.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-aarch64-linux-gnu/rdkit/Chem/rdChemReactions.so @@ -34263,17 +34424,17 @@ 197: 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-aarch64-linux-gnu/rdkit/Chem/rdmolfiles.so 197: 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-aarch64-linux-gnu/rdkit/Chem/rdCIPLabeler.so 197: 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-aarch64-linux-gnu/rdkit/Chem/rdchem.so -197: 16# 0x0000FFFF9F01C320 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so -197: 17# 0x0000FFFF9F01C2B8 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so -197: 18# 0x0000FFFF9F01C248 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so -197: 19# 0x0000FFFF9F01C1E0 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so -197: 20# 0x0000FFFF9F01C178 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so +197: 16# 0x0000FFFFB7F8C320 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so +197: 17# 0x0000FFFFB7F8C2B8 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so +197: 18# 0x0000FFFFB7F8C248 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so +197: 19# 0x0000FFFFB7F8C1E0 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so +197: 20# 0x0000FFFFB7F8C178 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so 197: 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-aarch64-linux-gnu/rdkit/rdBase.so 197: 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-aarch64-linux-gnu/rdkit/rdBase.so 197: 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-aarch64-linux-gnu/rdkit/rdBase.so 197: 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-aarch64-linux-gnu/rdkit/rdBase.so 197: 25# boost::python::handle_exception_impl(boost::function0) in /lib/aarch64-linux-gnu/libboost_python313.so.1.83.0 -197: 26# 0x0000FFFFA0B2F25C in /lib/aarch64-linux-gnu/libboost_python313.so.1.83.0 +197: 26# 0x0000FFFFB9A9F25C in /lib/aarch64-linux-gnu/libboost_python313.so.1.83.0 197: 27# _PyObject_MakeTpCall in /usr/bin/python3 197: 28# _PyEval_EvalFrameDefault in /usr/bin/python3 197: 29# 0x000000000053D3B0 in /usr/bin/python3 @@ -34305,13 +34466,13 @@ 197: 55# 0x000000000065EE50 in /usr/bin/python3 197: 56# Py_RunMain in /usr/bin/python3 197: 57# Py_BytesMain in /usr/bin/python3 -197: 58# 0x0000FFFFA187229C in /lib/aarch64-linux-gnu/libc.so.6 +197: 58# 0x0000FFFFBA7E229C in /lib/aarch64-linux-gnu/libc.so.6 197: 59# __libc_start_main in /lib/aarch64-linux-gnu/libc.so.6 197: 60# _start in /usr/bin/python3 197: ---------- 197: **** 197: -197: [00:37:05] +197: [09:33:44] 197: 197: **** 197: Pre-condition Violation @@ -34325,7 +34486,7 @@ 197: 2# RDKit::AtomGetNeighbors(RDKit::Atom*) in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so 197: 3# boost::python::objects::caller_py_function_impl > >::operator()(_object*, _object*) in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so 197: 4# boost::python::objects::function::call(_object*, _object*) const in /lib/aarch64-linux-gnu/libboost_python313.so.1.83.0 -197: 5# 0x0000FFFFA0B32680 in /lib/aarch64-linux-gnu/libboost_python313.so.1.83.0 +197: 5# 0x0000FFFFB9AA2680 in /lib/aarch64-linux-gnu/libboost_python313.so.1.83.0 197: 6# boost::python::detail::exception_handler::operator()(boost::function0 const&) const in /lib/aarch64-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-aarch64-linux-gnu/rdkit/Chem/rdSLNParse.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-aarch64-linux-gnu/rdkit/Chem/rdChemReactions.so @@ -34336,17 +34497,17 @@ 197: 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-aarch64-linux-gnu/rdkit/Chem/rdmolfiles.so 197: 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-aarch64-linux-gnu/rdkit/Chem/rdCIPLabeler.so 197: 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-aarch64-linux-gnu/rdkit/Chem/rdchem.so -197: 16# 0x0000FFFF9F01C320 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so -197: 17# 0x0000FFFF9F01C2B8 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so -197: 18# 0x0000FFFF9F01C248 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so -197: 19# 0x0000FFFF9F01C1E0 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so -197: 20# 0x0000FFFF9F01C178 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so +197: 16# 0x0000FFFFB7F8C320 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so +197: 17# 0x0000FFFFB7F8C2B8 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so +197: 18# 0x0000FFFFB7F8C248 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so +197: 19# 0x0000FFFFB7F8C1E0 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so +197: 20# 0x0000FFFFB7F8C178 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so 197: 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-aarch64-linux-gnu/rdkit/rdBase.so 197: 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-aarch64-linux-gnu/rdkit/rdBase.so 197: 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-aarch64-linux-gnu/rdkit/rdBase.so 197: 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-aarch64-linux-gnu/rdkit/rdBase.so 197: 25# boost::python::handle_exception_impl(boost::function0) in /lib/aarch64-linux-gnu/libboost_python313.so.1.83.0 -197: 26# 0x0000FFFFA0B2F25C in /lib/aarch64-linux-gnu/libboost_python313.so.1.83.0 +197: 26# 0x0000FFFFB9A9F25C in /lib/aarch64-linux-gnu/libboost_python313.so.1.83.0 197: 27# _PyObject_MakeTpCall in /usr/bin/python3 197: 28# _PyEval_EvalFrameDefault in /usr/bin/python3 197: 29# 0x000000000053D3B0 in /usr/bin/python3 @@ -34378,13 +34539,13 @@ 197: 55# 0x000000000065EE50 in /usr/bin/python3 197: 56# Py_RunMain in /usr/bin/python3 197: 57# Py_BytesMain in /usr/bin/python3 -197: 58# 0x0000FFFFA187229C in /lib/aarch64-linux-gnu/libc.so.6 +197: 58# 0x0000FFFFBA7E229C in /lib/aarch64-linux-gnu/libc.so.6 197: 59# __libc_start_main in /lib/aarch64-linux-gnu/libc.so.6 197: 60# _start in /usr/bin/python3 197: ---------- 197: **** 197: -197: [00:37:06] +197: [09:33:44] 197: 197: **** 197: Pre-condition Violation @@ -34398,7 +34559,7 @@ 197: 2# RDKit::AtomGetBonds(RDKit::Atom*) in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so 197: 3# boost::python::objects::caller_py_function_impl > >::operator()(_object*, _object*) in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so 197: 4# boost::python::objects::function::call(_object*, _object*) const in /lib/aarch64-linux-gnu/libboost_python313.so.1.83.0 -197: 5# 0x0000FFFFA0B32680 in /lib/aarch64-linux-gnu/libboost_python313.so.1.83.0 +197: 5# 0x0000FFFFB9AA2680 in /lib/aarch64-linux-gnu/libboost_python313.so.1.83.0 197: 6# boost::python::detail::exception_handler::operator()(boost::function0 const&) const in /lib/aarch64-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-aarch64-linux-gnu/rdkit/Chem/rdSLNParse.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-aarch64-linux-gnu/rdkit/Chem/rdChemReactions.so @@ -34409,17 +34570,17 @@ 197: 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-aarch64-linux-gnu/rdkit/Chem/rdmolfiles.so 197: 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-aarch64-linux-gnu/rdkit/Chem/rdCIPLabeler.so 197: 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-aarch64-linux-gnu/rdkit/Chem/rdchem.so -197: 16# 0x0000FFFF9F01C320 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so -197: 17# 0x0000FFFF9F01C2B8 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so -197: 18# 0x0000FFFF9F01C248 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so -197: 19# 0x0000FFFF9F01C1E0 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so -197: 20# 0x0000FFFF9F01C178 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so +197: 16# 0x0000FFFFB7F8C320 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so +197: 17# 0x0000FFFFB7F8C2B8 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so +197: 18# 0x0000FFFFB7F8C248 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so +197: 19# 0x0000FFFFB7F8C1E0 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so +197: 20# 0x0000FFFFB7F8C178 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so 197: 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-aarch64-linux-gnu/rdkit/rdBase.so 197: 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-aarch64-linux-gnu/rdkit/rdBase.so 197: 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-aarch64-linux-gnu/rdkit/rdBase.so 197: 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-aarch64-linux-gnu/rdkit/rdBase.so 197: 25# boost::python::handle_exception_impl(boost::function0) in /lib/aarch64-linux-gnu/libboost_python313.so.1.83.0 -197: 26# 0x0000FFFFA0B2F25C in /lib/aarch64-linux-gnu/libboost_python313.so.1.83.0 +197: 26# 0x0000FFFFB9A9F25C in /lib/aarch64-linux-gnu/libboost_python313.so.1.83.0 197: 27# _PyObject_MakeTpCall in /usr/bin/python3 197: 28# _PyEval_EvalFrameDefault in /usr/bin/python3 197: 29# 0x000000000053D3B0 in /usr/bin/python3 @@ -34451,13 +34612,13 @@ 197: 55# 0x000000000065EE50 in /usr/bin/python3 197: 56# Py_RunMain in /usr/bin/python3 197: 57# Py_BytesMain in /usr/bin/python3 -197: 58# 0x0000FFFFA187229C in /lib/aarch64-linux-gnu/libc.so.6 +197: 58# 0x0000FFFFBA7E229C in /lib/aarch64-linux-gnu/libc.so.6 197: 59# __libc_start_main in /lib/aarch64-linux-gnu/libc.so.6 197: 60# _start in /usr/bin/python3 197: ---------- 197: **** 197: -197: [00:37:06] +197: [09:33:44] 197: 197: **** 197: Pre-condition Violation @@ -34471,7 +34632,7 @@ 197: 2# RDKit::AtomIsInRing(RDKit::Atom const*) in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so 197: 3# boost::python::objects::caller_py_function_impl > >::operator()(_object*, _object*) in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so 197: 4# boost::python::objects::function::call(_object*, _object*) const in /lib/aarch64-linux-gnu/libboost_python313.so.1.83.0 -197: 5# 0x0000FFFFA0B32680 in /lib/aarch64-linux-gnu/libboost_python313.so.1.83.0 +197: 5# 0x0000FFFFB9AA2680 in /lib/aarch64-linux-gnu/libboost_python313.so.1.83.0 197: 6# boost::python::detail::exception_handler::operator()(boost::function0 const&) const in /lib/aarch64-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-aarch64-linux-gnu/rdkit/Chem/rdSLNParse.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-aarch64-linux-gnu/rdkit/Chem/rdChemReactions.so @@ -34482,17 +34643,17 @@ 197: 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-aarch64-linux-gnu/rdkit/Chem/rdmolfiles.so 197: 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-aarch64-linux-gnu/rdkit/Chem/rdCIPLabeler.so 197: 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-aarch64-linux-gnu/rdkit/Chem/rdchem.so -197: 16# 0x0000FFFF9F01C320 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so -197: 17# 0x0000FFFF9F01C2B8 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so -197: 18# 0x0000FFFF9F01C248 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so -197: 19# 0x0000FFFF9F01C1E0 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so -197: 20# 0x0000FFFF9F01C178 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so +197: 16# 0x0000FFFFB7F8C320 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so +197: 17# 0x0000FFFFB7F8C2B8 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so +197: 18# 0x0000FFFFB7F8C248 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so +197: 19# 0x0000FFFFB7F8C1E0 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so +197: 20# 0x0000FFFFB7F8C178 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so 197: 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-aarch64-linux-gnu/rdkit/rdBase.so 197: 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-aarch64-linux-gnu/rdkit/rdBase.so 197: 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-aarch64-linux-gnu/rdkit/rdBase.so 197: 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-aarch64-linux-gnu/rdkit/rdBase.so 197: 25# boost::python::handle_exception_impl(boost::function0) in /lib/aarch64-linux-gnu/libboost_python313.so.1.83.0 -197: 26# 0x0000FFFFA0B2F25C in /lib/aarch64-linux-gnu/libboost_python313.so.1.83.0 +197: 26# 0x0000FFFFB9A9F25C in /lib/aarch64-linux-gnu/libboost_python313.so.1.83.0 197: 27# _PyObject_MakeTpCall in /usr/bin/python3 197: 28# _PyEval_EvalFrameDefault in /usr/bin/python3 197: 29# 0x000000000053D3B0 in /usr/bin/python3 @@ -34524,13 +34685,13 @@ 197: 55# 0x000000000065EE50 in /usr/bin/python3 197: 56# Py_RunMain in /usr/bin/python3 197: 57# Py_BytesMain in /usr/bin/python3 -197: 58# 0x0000FFFFA187229C in /lib/aarch64-linux-gnu/libc.so.6 +197: 58# 0x0000FFFFBA7E229C in /lib/aarch64-linux-gnu/libc.so.6 197: 59# __libc_start_main in /lib/aarch64-linux-gnu/libc.so.6 197: 60# _start in /usr/bin/python3 197: ---------- 197: **** 197: -197: [00:37:06] +197: [09:33:44] 197: 197: **** 197: Pre-condition Violation @@ -34544,7 +34705,7 @@ 197: 2# RDKit::AtomIsInRingSize(RDKit::Atom const*, int) in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so 197: 3# boost::python::objects::caller_py_function_impl > >::operator()(_object*, _object*) in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so 197: 4# boost::python::objects::function::call(_object*, _object*) const in /lib/aarch64-linux-gnu/libboost_python313.so.1.83.0 -197: 5# 0x0000FFFFA0B32680 in /lib/aarch64-linux-gnu/libboost_python313.so.1.83.0 +197: 5# 0x0000FFFFB9AA2680 in /lib/aarch64-linux-gnu/libboost_python313.so.1.83.0 197: 6# boost::python::detail::exception_handler::operator()(boost::function0 const&) const in /lib/aarch64-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-aarch64-linux-gnu/rdkit/Chem/rdSLNParse.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-aarch64-linux-gnu/rdkit/Chem/rdChemReactions.so @@ -34555,17 +34716,17 @@ 197: 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-aarch64-linux-gnu/rdkit/Chem/rdmolfiles.so 197: 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-aarch64-linux-gnu/rdkit/Chem/rdCIPLabeler.so 197: 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-aarch64-linux-gnu/rdkit/Chem/rdchem.so -197: 16# 0x0000FFFF9F01C320 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so -197: 17# 0x0000FFFF9F01C2B8 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so -197: 18# 0x0000FFFF9F01C248 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so -197: 19# 0x0000FFFF9F01C1E0 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so -197: 20# 0x0000FFFF9F01C178 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so +197: 16# 0x0000FFFFB7F8C320 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so +197: 17# 0x0000FFFFB7F8C2B8 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so +197: 18# 0x0000FFFFB7F8C248 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so +197: 19# 0x0000FFFFB7F8C1E0 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so +197: 20# 0x0000FFFFB7F8C178 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so 197: 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-aarch64-linux-gnu/rdkit/rdBase.so 197: 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-aarch64-linux-gnu/rdkit/rdBase.so 197: 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-aarch64-linux-gnu/rdkit/rdBase.so 197: 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-aarch64-linux-gnu/rdkit/rdBase.so 197: 25# boost::python::handle_exception_impl(boost::function0) in /lib/aarch64-linux-gnu/libboost_python313.so.1.83.0 -197: 26# 0x0000FFFFA0B2F25C in /lib/aarch64-linux-gnu/libboost_python313.so.1.83.0 +197: 26# 0x0000FFFFB9A9F25C in /lib/aarch64-linux-gnu/libboost_python313.so.1.83.0 197: 27# _PyObject_MakeTpCall in /usr/bin/python3 197: 28# _PyEval_EvalFrameDefault in /usr/bin/python3 197: 29# 0x000000000053D3B0 in /usr/bin/python3 @@ -34597,13 +34758,13 @@ 197: 55# 0x000000000065EE50 in /usr/bin/python3 197: 56# Py_RunMain in /usr/bin/python3 197: 57# Py_BytesMain in /usr/bin/python3 -197: 58# 0x0000FFFFA187229C in /lib/aarch64-linux-gnu/libc.so.6 +197: 58# 0x0000FFFFBA7E229C in /lib/aarch64-linux-gnu/libc.so.6 197: 59# __libc_start_main in /lib/aarch64-linux-gnu/libc.so.6 197: 60# _start in /usr/bin/python3 197: ---------- 197: **** 197: -197: .....[00:37:06] +197: .....[09:33:44] 197: 197: **** 197: Range Error @@ -34617,7 +34778,7 @@ 197: 2# RDKit::RWMol::addBond(unsigned int, unsigned int, RDKit::Bond::BondType) in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu//lib/libRDKitGraphMol.so.1 197: 3# boost::python::objects::caller_py_function_impl > >::operator()(_object*, _object*) in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so 197: 4# boost::python::objects::function::call(_object*, _object*) const in /lib/aarch64-linux-gnu/libboost_python313.so.1.83.0 -197: 5# 0x0000FFFFA0B32680 in /lib/aarch64-linux-gnu/libboost_python313.so.1.83.0 +197: 5# 0x0000FFFFB9AA2680 in /lib/aarch64-linux-gnu/libboost_python313.so.1.83.0 197: 6# boost::python::detail::exception_handler::operator()(boost::function0 const&) const in /lib/aarch64-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-aarch64-linux-gnu/rdkit/Chem/rdSLNParse.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-aarch64-linux-gnu/rdkit/Chem/rdChemReactions.so @@ -34628,17 +34789,17 @@ 197: 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-aarch64-linux-gnu/rdkit/Chem/rdmolfiles.so 197: 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-aarch64-linux-gnu/rdkit/Chem/rdCIPLabeler.so 197: 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-aarch64-linux-gnu/rdkit/Chem/rdchem.so -197: 16# 0x0000FFFF9F01C320 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so -197: 17# 0x0000FFFF9F01C2B8 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so -197: 18# 0x0000FFFF9F01C248 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so -197: 19# 0x0000FFFF9F01C1E0 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so -197: 20# 0x0000FFFF9F01C178 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so +197: 16# 0x0000FFFFB7F8C320 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so +197: 17# 0x0000FFFFB7F8C2B8 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so +197: 18# 0x0000FFFFB7F8C248 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so +197: 19# 0x0000FFFFB7F8C1E0 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so +197: 20# 0x0000FFFFB7F8C178 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so 197: 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-aarch64-linux-gnu/rdkit/rdBase.so 197: 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-aarch64-linux-gnu/rdkit/rdBase.so 197: 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-aarch64-linux-gnu/rdkit/rdBase.so 197: 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-aarch64-linux-gnu/rdkit/rdBase.so 197: 25# boost::python::handle_exception_impl(boost::function0) in /lib/aarch64-linux-gnu/libboost_python313.so.1.83.0 -197: 26# 0x0000FFFFA0B2F25C in /lib/aarch64-linux-gnu/libboost_python313.so.1.83.0 +197: 26# 0x0000FFFFB9A9F25C in /lib/aarch64-linux-gnu/libboost_python313.so.1.83.0 197: 27# _PyObject_MakeTpCall in /usr/bin/python3 197: 28# _PyEval_EvalFrameDefault in /usr/bin/python3 197: 29# 0x000000000053D3B0 in /usr/bin/python3 @@ -34670,49 +34831,50 @@ 197: 55# 0x000000000065EE50 in /usr/bin/python3 197: 56# Py_RunMain in /usr/bin/python3 197: 57# Py_BytesMain in /usr/bin/python3 -197: 58# 0x0000FFFFA187229C in /lib/aarch64-linux-gnu/libc.so.6 +197: 58# 0x0000FFFFBA7E229C in /lib/aarch64-linux-gnu/libc.so.6 197: 59# __libc_start_main in /lib/aarch64-linux-gnu/libc.so.6 197: 60# _start in /usr/bin/python3 197: ---------- 197: **** 197: -197: ......[00:37:06] SMILES Parse Error: unclosed ring for input: 'c1ccccc' -197: [00:37:06] ERROR: Smiles parse error on line 0 -197: [00:37:06] ERROR: Cannot create molecule from : 'c1ccccc' -197: [00:37:06] SMILES Parse Error: extra open parentheses while parsing: C(C -197: [00:37:06] SMILES Parse Error: check for mistakes around position 2: -197: [00:37:06] C(C -197: [00:37:06] ~^ -197: [00:37:06] SMILES Parse Error: Failed parsing SMILES 'C(C' for input: 'C(C' -197: [00:37:06] ERROR: Smiles parse error on line 3 -197: [00:37:06] ERROR: Cannot create molecule from : 'C(C' -197: [00:37:06] Explicit valence for atom # 1 C, 5, is greater than permitted -197: [00:37:06] ERROR: Could not sanitize molecule on line 6 -197: [00:37:06] ERROR: Explicit valence for atom # 1 C, 5, is greater than permitted -197: [00:37:06] SMILES Parse Error: unclosed ring for input: 'c1ccccc' -197: [00:37:06] ERROR: Smiles parse error on line 0 -197: [00:37:06] ERROR: Cannot create molecule from : 'c1ccccc' -197: [00:37:06] SMILES Parse Error: extra open parentheses while parsing: C(C -197: [00:37:06] SMILES Parse Error: check for mistakes around position 2: -197: [00:37:06] C(C -197: [00:37:06] ~^ -197: [00:37:06] SMILES Parse Error: Failed parsing SMILES 'C(C' for input: 'C(C' -197: [00:37:06] ERROR: Smiles parse error on line 3 -197: [00:37:06] ERROR: Cannot create molecule from : 'C(C' -197: [00:37:06] SMILES Parse Error: unclosed ring for input: 'C1C(Cl)CCCC' -197: [00:37:06] ERROR: Smiles parse error on line 6 -197: [00:37:06] ERROR: Cannot create molecule from : 'C1C(Cl)CCCC' -197: [00:37:06] Explicit valence for atom # 1 F, 2, is greater than permitted -197: [00:37:06] ERROR: Could not sanitize molecule ending on line 21 -197: [00:37:06] ERROR: Explicit valence for atom # 1 F, 2, is greater than permitted -197: [00:37:06] ERROR: EOF hit while reading atoms -197: [00:37:06] ERROR: moving to the beginning of the next molecule -197: [00:37:06] Explicit valence for atom # 1 F, 2, is greater than permitted -197: [00:37:06] ERROR: Could not sanitize molecule ending on line 21 -197: [00:37:06] ERROR: Explicit valence for atom # 1 F, 2, is greater than permitted -197: [00:37:06] ERROR: EOF hit while reading atoms -197: [00:37:06] ERROR: moving to the beginning of the next molecule -197: ....[00:37:06] +228/238 Test #237: pyFeatures ............................. Passed 0.41 sec +197: ......[09:33:44] SMILES Parse Error: unclosed ring for input: 'c1ccccc' +197: [09:33:44] ERROR: Smiles parse error on line 0 +197: [09:33:44] ERROR: Cannot create molecule from : 'c1ccccc' +197: [09:33:44] SMILES Parse Error: extra open parentheses while parsing: C(C +197: [09:33:44] SMILES Parse Error: check for mistakes around position 2: +197: [09:33:44] C(C +197: [09:33:44] ~^ +197: [09:33:44] SMILES Parse Error: Failed parsing SMILES 'C(C' for input: 'C(C' +197: [09:33:44] ERROR: Smiles parse error on line 3 +197: [09:33:44] ERROR: Cannot create molecule from : 'C(C' +197: [09:33:44] Explicit valence for atom # 1 C, 5, is greater than permitted +197: [09:33:44] ERROR: Could not sanitize molecule on line 6 +197: [09:33:44] ERROR: Explicit valence for atom # 1 C, 5, is greater than permitted +197: [09:33:44] SMILES Parse Error: unclosed ring for input: 'c1ccccc' +197: [09:33:44] ERROR: Smiles parse error on line 0 +197: [09:33:44] ERROR: Cannot create molecule from : 'c1ccccc' +197: [09:33:44] SMILES Parse Error: extra open parentheses while parsing: C(C +197: [09:33:44] SMILES Parse Error: check for mistakes around position 2: +197: [09:33:44] C(C +197: [09:33:44] ~^ +197: [09:33:44] SMILES Parse Error: Failed parsing SMILES 'C(C' for input: 'C(C' +197: [09:33:44] ERROR: Smiles parse error on line 3 +197: [09:33:44] ERROR: Cannot create molecule from : 'C(C' +197: [09:33:44] SMILES Parse Error: unclosed ring for input: 'C1C(Cl)CCCC' +197: [09:33:44] ERROR: Smiles parse error on line 6 +197: [09:33:44] ERROR: Cannot create molecule from : 'C1C(Cl)CCCC' +197: [09:33:44] Explicit valence for atom # 1 F, 2, is greater than permitted +197: [09:33:44] ERROR: Could not sanitize molecule ending on line 21 +197: [09:33:44] ERROR: Explicit valence for atom # 1 F, 2, is greater than permitted +197: [09:33:44] ERROR: EOF hit while reading atoms +197: [09:33:44] ERROR: moving to the beginning of the next molecule +197: [09:33:44] Explicit valence for atom # 1 F, 2, is greater than permitted +197: [09:33:44] ERROR: Could not sanitize molecule ending on line 21 +197: [09:33:44] ERROR: Explicit valence for atom # 1 F, 2, is greater than permitted +197: [09:33:44] ERROR: EOF hit while reading atoms +197: [09:33:44] ERROR: moving to the beginning of the next molecule +197: ....[09:33:44] 197: 197: **** 197: Pre-condition Violation @@ -34726,7 +34888,7 @@ 197: 2# RDKit::RingInfo::numRings() const in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu//lib/libRDKitGraphMol.so.1 197: 3# boost::python::objects::caller_py_function_impl > >::operator()(_object*, _object*) in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so 197: 4# boost::python::objects::function::call(_object*, _object*) const in /lib/aarch64-linux-gnu/libboost_python313.so.1.83.0 -197: 5# 0x0000FFFFA0B32680 in /lib/aarch64-linux-gnu/libboost_python313.so.1.83.0 +197: 5# 0x0000FFFFB9AA2680 in /lib/aarch64-linux-gnu/libboost_python313.so.1.83.0 197: 6# boost::python::detail::exception_handler::operator()(boost::function0 const&) const in /lib/aarch64-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-aarch64-linux-gnu/rdkit/Chem/rdSLNParse.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-aarch64-linux-gnu/rdkit/Chem/rdChemReactions.so @@ -34737,17 +34899,17 @@ 197: 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-aarch64-linux-gnu/rdkit/Chem/rdmolfiles.so 197: 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-aarch64-linux-gnu/rdkit/Chem/rdCIPLabeler.so 197: 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-aarch64-linux-gnu/rdkit/Chem/rdchem.so -197: 16# 0x0000FFFF9F01C320 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so -197: 17# 0x0000FFFF9F01C2B8 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so -197: 18# 0x0000FFFF9F01C248 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so -197: 19# 0x0000FFFF9F01C1E0 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so -197: 20# 0x0000FFFF9F01C178 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so +197: 16# 0x0000FFFFB7F8C320 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so +197: 17# 0x0000FFFFB7F8C2B8 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so +197: 18# 0x0000FFFFB7F8C248 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so +197: 19# 0x0000FFFFB7F8C1E0 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so +197: 20# 0x0000FFFFB7F8C178 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so 197: 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-aarch64-linux-gnu/rdkit/rdBase.so 197: 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-aarch64-linux-gnu/rdkit/rdBase.so 197: 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-aarch64-linux-gnu/rdkit/rdBase.so 197: 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-aarch64-linux-gnu/rdkit/rdBase.so 197: 25# boost::python::handle_exception_impl(boost::function0) in /lib/aarch64-linux-gnu/libboost_python313.so.1.83.0 -197: 26# 0x0000FFFFA0B2F25C in /lib/aarch64-linux-gnu/libboost_python313.so.1.83.0 +197: 26# 0x0000FFFFB9A9F25C in /lib/aarch64-linux-gnu/libboost_python313.so.1.83.0 197: 27# _PyObject_MakeTpCall in /usr/bin/python3 197: 28# _PyEval_EvalFrameDefault in /usr/bin/python3 197: 29# 0x000000000053D3B0 in /usr/bin/python3 @@ -34779,13 +34941,13 @@ 197: 55# 0x000000000065EE50 in /usr/bin/python3 197: 56# Py_RunMain in /usr/bin/python3 197: 57# Py_BytesMain in /usr/bin/python3 -197: 58# 0x0000FFFFA187229C in /lib/aarch64-linux-gnu/libc.so.6 +197: 58# 0x0000FFFFBA7E229C in /lib/aarch64-linux-gnu/libc.so.6 197: 59# __libc_start_main in /lib/aarch64-linux-gnu/libc.so.6 197: 60# _start in /usr/bin/python3 197: ---------- 197: **** 197: -197: .............[00:37:06] +197: .............[09:33:44] 197: 197: **** 197: Range Error @@ -34799,7 +34961,7 @@ 197: 2# RDKit::ROMol::getAtomWithIdx(unsigned int) in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu//lib/libRDKitGraphMol.so.1 197: 3# boost::python::objects::caller_py_function_impl >, boost::mpl::vector3 > >::operator()(_object*, _object*) in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so 197: 4# boost::python::objects::function::call(_object*, _object*) const in /lib/aarch64-linux-gnu/libboost_python313.so.1.83.0 -197: 5# 0x0000FFFFA0B32680 in /lib/aarch64-linux-gnu/libboost_python313.so.1.83.0 +197: 5# 0x0000FFFFB9AA2680 in /lib/aarch64-linux-gnu/libboost_python313.so.1.83.0 197: 6# boost::python::detail::exception_handler::operator()(boost::function0 const&) const in /lib/aarch64-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-aarch64-linux-gnu/rdkit/Chem/rdSLNParse.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-aarch64-linux-gnu/rdkit/Chem/rdChemReactions.so @@ -34810,17 +34972,17 @@ 197: 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-aarch64-linux-gnu/rdkit/Chem/rdmolfiles.so 197: 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-aarch64-linux-gnu/rdkit/Chem/rdCIPLabeler.so 197: 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-aarch64-linux-gnu/rdkit/Chem/rdchem.so -197: 16# 0x0000FFFF9F01C320 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so -197: 17# 0x0000FFFF9F01C2B8 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so -197: 18# 0x0000FFFF9F01C248 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so -197: 19# 0x0000FFFF9F01C1E0 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so -197: 20# 0x0000FFFF9F01C178 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so +197: 16# 0x0000FFFFB7F8C320 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so +197: 17# 0x0000FFFFB7F8C2B8 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so +197: 18# 0x0000FFFFB7F8C248 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so +197: 19# 0x0000FFFFB7F8C1E0 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so +197: 20# 0x0000FFFFB7F8C178 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so 197: 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-aarch64-linux-gnu/rdkit/rdBase.so 197: 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-aarch64-linux-gnu/rdkit/rdBase.so 197: 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-aarch64-linux-gnu/rdkit/rdBase.so 197: 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-aarch64-linux-gnu/rdkit/rdBase.so 197: 25# boost::python::handle_exception_impl(boost::function0) in /lib/aarch64-linux-gnu/libboost_python313.so.1.83.0 -197: 26# 0x0000FFFFA0B2F25C in /lib/aarch64-linux-gnu/libboost_python313.so.1.83.0 +197: 26# 0x0000FFFFB9A9F25C in /lib/aarch64-linux-gnu/libboost_python313.so.1.83.0 197: 27# _PyObject_MakeTpCall in /usr/bin/python3 197: 28# _PyEval_EvalFrameDefault in /usr/bin/python3 197: 29# 0x000000000053D3B0 in /usr/bin/python3 @@ -34852,231 +35014,101 @@ 197: 55# 0x000000000065EE50 in /usr/bin/python3 197: 56# Py_RunMain in /usr/bin/python3 197: 57# Py_BytesMain in /usr/bin/python3 -197: 58# 0x0000FFFFA187229C in /lib/aarch64-linux-gnu/libc.so.6 +197: 58# 0x0000FFFFBA7E229C in /lib/aarch64-linux-gnu/libc.so.6 197: 59# __libc_start_main in /lib/aarch64-linux-gnu/libc.so.6 197: 60# _start in /usr/bin/python3 197: ---------- 197: **** 197: -197: ...[00:37:06] Can't kekulize mol. Unkekulized atoms: 0 1 2 3 4 -231: ..... -231: ---------------------------------------------------------------------- -231: Ran 5 tests in 0.674s -231: -231: OK -234: [00:37:06] the useCache argument is deprecated and ignored -214: ............[00:37:06] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -214: [00:37:06] Warning: ambiguous stereochemistry - opposing bonds have opposite wedging - at atom 1 ignored. -214: [00:37:06] Warning: ambiguous stereochemistry - opposing bonds have opposite wedging - at atom 1 ignored. -197: ............................[00:37:06] SMILES Parse Error: unclosed ring for input: 'C1CC' +197: ...[09:33:44] Can't kekulize mol. Unkekulized atoms: 0 1 2 3 4 +197: ............................[09:33:44] SMILES Parse Error: unclosed ring for input: 'C1CC' 197: ......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| -197: 336 -197: ..[00:37:06] WARNING: not removing hydrogen atom without neighbors -197: [00:37:06] WARNING: not removing hydrogen atom with dummy atom neighbors -197: [00:37:06] WARNING: not removing hydrogen atom with wedged bond -197: [00:37:06] WARNING: not removing hydrogen atom without neighbors -197: [00:37:06] WARNING: not removing hydrogen atom with dummy atom neighbors -223/238 Test #231: pyMatCalc .............................. Passed 1.05 sec -test 235 - Start 235: pyRanker - -235: Test command: /usr/bin/python3 "/build/reproducible-path/rdkit-202503.1/Code/ML/InfoTheory/Wrap/testRanker.py" -235: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/ML/InfoTheory/Wrap -235: Test timeout computed to be: 1500 -234: ...[00:37:06] the useCache argument is deprecated and ignored -234: [00:37:06] the useCache argument is deprecated and ignored -234: .[00:37:06] the useCache argument is deprecated and ignored -214: ........[00:37:06] Explicit valence for atom # 1 O, 3, is greater than permitted -214: .. -214: ---------------------------------------------------------------------- -214: Ran 38 tests in 5.529s -214: -214: OK -214: done -197: ......[00:37:06] Explicit valence for atom # 1 F, 2, is greater than permitted -197: [00:37:06] Can't kekulize mol. Unkekulized atoms: 0 1 2 -197: .[00:37:06] Explicit valence for atom # 1 F, 2, is greater than permitted -197: [00:37:06] Explicit valence for atom # 1 F, 2, is greater than permitted -197: [00:37:06] Explicit valence for atom # 1 F, 2, is greater than permitted -197: [00:37:06] Explicit valence for atom # 1 F, 2, is greater than permitted -197: [00:37:06] Can't kekulize mol. Unkekulized atoms: 0 1 2 -197: [00:37:06] Can't kekulize mol. Unkekulized atoms: 0 1 2 -197: [00:37:06] Can't kekulize mol. Unkekulized atoms: 0 1 2 -224/238 Test #214: pyMolStandardize ....................... Passed 6.04 sec -test 236 - Start 236: testChemicalFeatures - -236: Test command: /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/ChemicalFeatures/testChemicalFeatures -236: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/ChemicalFeatures -236: Test timeout computed to be: 1500 -236: ----------------------------------------- -236: Test1 -236: Done -225/238 Test #236: testChemicalFeatures ................... Passed 0.00 sec -test 237 - Start 237: pyFeatures - -237: Test command: /usr/bin/python3 "/build/reproducible-path/rdkit-202503.1/Code/ChemicalFeatures/Wrap/testFeatures.py" -237: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/ChemicalFeatures/Wrap -237: Test timeout computed to be: 1500 -197: ..........[00:37:06] SMARTS Parse Error: syntax error while parsing: CCC |$foo;;bar$| ourname -197: [00:37:06] SMARTS Parse Error: Failed parsing SMARTS 'CCC |$foo;;bar$| ourname' for input: 'CCC |$foo;;bar$| ourname' -197: .[00:37:06] SMILES Parse Error: syntax error while parsing: CCC |$foo;;bar$| ourname -197: [00:37:06] SMILES Parse Error: check for mistakes around position 4: -197: [00:37:06] CCC |$foo;;bar$| ourname -197: [00:37:06] ~~~^ -197: [00:37:06] SMILES Parse Error: Failed parsing SMILES 'CCC |$foo;;bar$| ourname' for input: 'CCC |$foo;;bar$| ourname' -197: ..[00:37:06] SMILES Parse Error: syntax error while parsing: error -197: [00:37:06] SMILES Parse Error: check for mistakes around position 1: -197: [00:37:06] error -197: [00:37:06] ^ -197: [00:37:06] SMILES Parse Error: Failed parsing SMILES 'error' for input: 'error' -197: [00:37:06] SMILES Parse Error: Failed parsing SMILES 'd' for input: 'd' -197: [00:37:06] SMARTS Parse Error: Failed parsing SMARTS 'error' for input: 'error' -197: [00:37:06] SMARTS Parse Error: Failed parsing SMARTS 'd' for input: 'd' -235: ..[00:37:06] -235: -235: **** -235: Invariant Violation -235: Can't rank more bits than the ensemble size -235: Violation occurred on line 156 in file ./Code/ML/InfoTheory/InfoBitRanker.cpp -235: Failed Expression: num <= dp_maskBits->getNumOnBits() -235: ---------- -235: Stacktrace: -235: 0# Invar::Invariant::toString[abi:cxx11]() const in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu//lib/libRDKitRDGeneral.so.1 -235: 1# Invar::operator<<(std::ostream&, Invar::Invariant const&) in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu//lib/libRDKitRDGeneral.so.1 -235: 2# RDInfoTheory::InfoBitRanker::getTopN(unsigned int) in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu//lib/libRDKitInfoTheory.so.1 -235: 3# RDInfoTheory::getTopNbits(RDInfoTheory::InfoBitRanker*, int) in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/ML/InfoTheory/rdInfoTheory.so -235: 4# boost::python::objects::caller_py_function_impl > >::operator()(_object*, _object*) in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/ML/InfoTheory/rdInfoTheory.so -235: 5# boost::python::objects::function::call(_object*, _object*) const in /lib/aarch64-linux-gnu/libboost_python313.so.1.83.0 -235: 6# 0x0000FFFF93BD2680 in /lib/aarch64-linux-gnu/libboost_python313.so.1.83.0 -235: 7# boost::python::detail::exception_handler::operator()(boost::function0 const&) const in /lib/aarch64-linux-gnu/libboost_python313.so.1.83.0 -235: 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-aarch64-linux-gnu/rdkit/rdBase.so -235: 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-aarch64-linux-gnu/rdkit/rdBase.so -235: 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-aarch64-linux-gnu/rdkit/rdBase.so -235: 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-aarch64-linux-gnu/rdkit/rdBase.so -235: 12# boost::python::handle_exception_impl(boost::function0) in /lib/aarch64-linux-gnu/libboost_python313.so.1.83.0 -235: 13# 0x0000FFFF93BCF25C in /lib/aarch64-linux-gnu/libboost_python313.so.1.83.0 -235: 14# _PyObject_MakeTpCall in /usr/bin/python3 -235: 15# _PyEval_EvalFrameDefault in /usr/bin/python3 -235: 16# 0x000000000053D3B0 in /usr/bin/python3 -235: 17# _PyEval_EvalFrameDefault in /usr/bin/python3 -235: 18# 0x000000000061C8E0 in /usr/bin/python3 -235: 19# 0x00000000005A787C in /usr/bin/python3 -235: 20# _PyObject_MakeTpCall in /usr/bin/python3 -235: 21# _PyEval_EvalFrameDefault in /usr/bin/python3 -235: 22# 0x000000000053D3B0 in /usr/bin/python3 -235: 23# _PyEval_EvalFrameDefault in /usr/bin/python3 -235: 24# 0x000000000061C8E0 in /usr/bin/python3 -235: 25# 0x00000000005A787C in /usr/bin/python3 -235: 26# _PyObject_MakeTpCall in /usr/bin/python3 -235: 27# _PyEval_EvalFrameDefault in /usr/bin/python3 -235: 28# 0x000000000053D3B0 in /usr/bin/python3 -235: 29# _PyEval_EvalFrameDefault in /usr/bin/python3 -235: 30# 0x000000000061C8E0 in /usr/bin/python3 -235: 31# 0x00000000005A787C in /usr/bin/python3 -235: 32# _PyObject_MakeTpCall in /usr/bin/python3 -235: 33# _PyEval_EvalFrameDefault in /usr/bin/python3 -235: 34# 0x000000000050B030 in /usr/bin/python3 -235: 35# _PyObject_MakeTpCall in /usr/bin/python3 -235: 36# _PyEval_EvalFrameDefault in /usr/bin/python3 -235: 37# PyEval_EvalCode in /usr/bin/python3 -235: 38# 0x000000000064023C in /usr/bin/python3 -235: 39# 0x000000000063BC30 in /usr/bin/python3 -235: 40# 0x000000000065F810 in /usr/bin/python3 -235: 41# 0x000000000065F0B4 in /usr/bin/python3 -235: 42# 0x000000000065EE50 in /usr/bin/python3 -235: 43# Py_RunMain in /usr/bin/python3 -235: 44# Py_BytesMain in /usr/bin/python3 -235: 45# 0x0000FFFF9553229C in /lib/aarch64-linux-gnu/libc.so.6 -235: 46# __libc_start_main in /lib/aarch64-linux-gnu/libc.so.6 -235: 47# _start in /usr/bin/python3 -235: ---------- -235: **** -235: -235: ... -235: ---------------------------------------------------------------------- -235: Ran 5 tests in 0.034s -235: -235: OK -197: .........................[00:37:06] SMILES Parse Error: syntax error while parsing: garbage_0 -197: [00:37:06] SMILES Parse Error: check for mistakes around position 1: -197: [00:37:06] garbage_0 -197: [00:37:06] ^ -197: [00:37:06] SMILES Parse Error: Failed parsing SMILES 'garbage_0' for input: 'garbage_0' -197: [00:37:06] SMILES Parse Error: syntax error while parsing: garbage_2 -197: [00:37:06] SMILES Parse Error: check for mistakes around position 1: -197: [00:37:06] garbage_2 -197: [00:37:06] ^ -197: [00:37:06] SMILES Parse Error: Failed parsing SMILES 'garbage_2' for input: 'garbage_2' -197: [00:37:06] SMILES Parse Error: syntax error while parsing: garbage_4 -197: [00:37:06] SMILES Parse Error: check for mistakes around position 1: -197: [00:37:06] garbage_4 -197: [00:37:06] ^ -197: [00:37:06] SMILES Parse Error: Failed parsing SMILES 'garbage_4' for input: 'garbage_4' -226/238 Test #235: pyRanker ............................... Passed 0.50 sec -test 238 - Start 238: pythonProjectTests - -238: Test command: /usr/bin/python3 "-m" "pytest" -238: Working Directory: /build/reproducible-path/rdkit-202503.1/Projects -238: Test timeout computed to be: 1500 +197: 643 +197: ..[09:33:44] WARNING: not removing hydrogen atom without neighbors +197: [09:33:44] WARNING: not removing hydrogen atom with dummy atom neighbors +197: [09:33:44] WARNING: not removing hydrogen atom with wedged bond +197: [09:33:44] WARNING: not removing hydrogen atom without neighbors +197: [09:33:44] WARNING: not removing hydrogen atom with dummy atom neighbors +197: ......[09:33:44] Explicit valence for atom # 1 F, 2, is greater than permitted +197: [09:33:44] Can't kekulize mol. Unkekulized atoms: 0 1 2 +197: .[09:33:44] Explicit valence for atom # 1 F, 2, is greater than permitted +197: [09:33:44] Explicit valence for atom # 1 F, 2, is greater than permitted +197: [09:33:44] Explicit valence for atom # 1 F, 2, is greater than permitted +197: [09:33:44] Explicit valence for atom # 1 F, 2, is greater than permitted +197: [09:33:44] Can't kekulize mol. Unkekulized atoms: 0 1 2 +197: [09:33:44] Can't kekulize mol. Unkekulized atoms: 0 1 2 +197: [09:33:44] Can't kekulize mol. Unkekulized atoms: 0 1 2 +197: ..........[09:33:44] SMARTS Parse Error: syntax error while parsing: CCC |$foo;;bar$| ourname +197: [09:33:44] SMARTS Parse Error: Failed parsing SMARTS 'CCC |$foo;;bar$| ourname' for input: 'CCC |$foo;;bar$| ourname' +197: .[09:33:44] SMILES Parse Error: syntax error while parsing: CCC |$foo;;bar$| ourname +197: [09:33:44] SMILES Parse Error: check for mistakes around position 4: +197: [09:33:44] CCC |$foo;;bar$| ourname +197: [09:33:44] ~~~^ +197: [09:33:44] SMILES Parse Error: Failed parsing SMILES 'CCC |$foo;;bar$| ourname' for input: 'CCC |$foo;;bar$| ourname' +197: ..[09:33:44] SMILES Parse Error: syntax error while parsing: error +197: [09:33:44] SMILES Parse Error: check for mistakes around position 1: +197: [09:33:44] error +197: [09:33:44] ^ +197: [09:33:44] SMILES Parse Error: Failed parsing SMILES 'error' for input: 'error' +197: [09:33:44] SMILES Parse Error: Failed parsing SMILES 'd' for input: 'd' +197: [09:33:44] SMARTS Parse Error: Failed parsing SMARTS 'error' for input: 'error' +197: [09:33:44] SMARTS Parse Error: Failed parsing SMARTS 'd' for input: 'd' +234: ....... +234: ---------------------------------------------------------------------- +234: Ran 11 tests in 0.947s +234: +234: OK +197: .........................[09:33:44] SMILES Parse Error: syntax error while parsing: garbage_0 +197: [09:33:44] SMILES Parse Error: check for mistakes around position 1: +197: [09:33:44] garbage_0 +197: [09:33:44] ^ +197: [09:33:44] SMILES Parse Error: Failed parsing SMILES 'garbage_0' for input: 'garbage_0' +197: [09:33:44] SMILES Parse Error: syntax error while parsing: garbage_2 +197: [09:33:44] SMILES Parse Error: check for mistakes around position 1: +197: [09:33:44] garbage_2 +197: [09:33:44] ^ +197: [09:33:44] SMILES Parse Error: Failed parsing SMILES 'garbage_2' for input: 'garbage_2' +197: [09:33:44] SMILES Parse Error: syntax error while parsing: garbage_4 +197: [09:33:44] SMILES Parse Error: check for mistakes around position 1: +197: [09:33:44] garbage_4 +197: [09:33:44] ^ +197: [09:33:44] SMILES Parse Error: Failed parsing SMILES 'garbage_4' for input: 'garbage_4' +229/238 Test #234: pySimDivPickers ........................ Passed 1.26 sec 197: ............ 197: ---------------------------------------------------------------------- -197: Ran 279 tests in 10.974s +197: Ran 279 tests in 8.372s 197: 197: OK 197: supplier: 197: supplier: 197: supplier: -227/238 Test #197: pyGraphMolWrap ......................... Passed 11.61 sec -224: Randomness seeded to: 3104490251 -224: =============================================================================== -224: All tests passed (203 assertions in 1 test case) -224: -228/238 Test #224: testMolProcessing ...................... Passed 2.78 sec -237: .. -237: ---------------------------------------------------------------------- -237: Ran 2 tests in 0.005s -237: -237: OK -237: Testing ChemicalFeatures Wrapper code: -229/238 Test #237: pyFeatures ............................. Passed 0.40 sec -234: ....... -234: ---------------------------------------------------------------------- -234: Ran 11 tests in 1.864s -234: -234: OK -230/238 Test #234: pySimDivPickers ........................ Passed 2.23 sec +230/238 Test #197: pyGraphMolWrap ......................... Passed 9.01 sec 238: ============================= test session starts ============================== 238: platform linux -- Python 3.13.6, pytest-8.4.1, pluggy-1.6.0 238: rootdir: /build/reproducible-path/rdkit-202503.1/Projects 238: configfile: pytest.ini 238: collected 12 items 238: -147: [00:37:09] UFFTYPER: Unrecognized atom type: S_6+6 (0) -147: [00:37:09] UFFTYPER: Warning: hybridization set to SP3 for atom 0 -147: [00:37:09] UFFTYPER: Unrecognized charge state for atom: 0 -212: [00:37:19] Explicit valence for atom # 0 Br, 1, is greater than permitted -212: =============================================================================== -212: All tests passed (38344 assertions in 51 test cases) -212: -231/238 Test #212: molStandardizeCatchTest ................ Passed 20.17 sec -146: [00:37:20] done -146: [00:37:20] --------------------------------- -146: [00:37:20] test github issue 256: handling of zero-atom molecules +146: [09:33:49] done +146: [09:33:49] --------------------------------- +146: [09:33:49] test github issue 256: handling of zero-atom molecules 146: -146: [00:37:20] --------------------------------- -146: [00:37:20] test embedder callback function -146: [00:37:20] --------------------------------- -146: [00:37:20] test multi-threaded multi-conf embedding +146: [09:33:49] --------------------------------- +146: [09:33:49] test embedder callback function +146: [09:33:49] --------------------------------- +146: [09:33:49] test multi-threaded multi-conf embedding 146: -146: [00:37:23] --------------------------------- -146: [00:37:23] test github issue 563: Incorrect ring stereochemistry after embedding +146: [09:33:54] --------------------------------- +146: [09:33:54] test github issue 563: Incorrect ring stereochemistry after embedding 146: 146: CNC[C@H]1CC[C@H](C[NH3+])CC1 -146: [00:37:25] --------------------------------- -146: [00:37:25] test github issue 568: Incorrect stereochemistry after embedding +212: [09:33:54] Explicit valence for atom # 0 Br, 1, is greater than permitted +212: =============================================================================== +212: All tests passed (38344 assertions in 51 test cases) +212: +231/238 Test #212: molStandardizeCatchTest ................ Passed 15.47 sec +146: [09:33:54] --------------------------------- +146: [09:33:54] 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 @@ -35088,16 +35120,6 @@ 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 -238: DbCLI/UnitTestDbCLI.py ............ [100%] -238: -238: =============================== warnings summary =============================== -238: ../obj-aarch64-linux-gnu/rdkit/Chem/MolDb/Loader_sa.py:20 -238: /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/MolDb/Loader_sa.py:20: MovedIn20Warning: The ``declarative_base()`` function is now available as sqlalchemy.orm.declarative_base(). (deprecated since: 2.0) (Background on SQLAlchemy 2.0 at: https://sqlalche.me/e/b8d9) -238: decBase = declarative_base() -238: -238: -- Docs: https://docs.pytest.org/en/stable/how-to/capture-warnings.html -238: ======================== 12 passed, 1 warning in 22.11s ======================== -232/238 Test #238: pythonProjectTests ..................... Passed 23.21 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 @@ -35107,13 +35129,20 @@ 146: Oc1ccc2c(c1)OC[C@@H](N1CCC(Cc3ccccc3)CC1)[C@H]2O 146: Oc1ccc2c(c1)OC[C@H](N1CCC(O)(c3ccccc3)CC1)[C@@H]2O 146: CC(=O)c1ccc2c(c1)[C@@]13CCCC[C@H]1[C@@H](C2)N(CC1CC1)CC3 +146: CC(=O)O[C@@H]1CC[C@@H]2CN3CCc4cc5c(cc4[C@@H]3C[C@@H]2C1)OCO5 +146: COc1cc2c(cc1OC)[C@@H]1C[C@@H]3C[C@H](O)CC[C@@H]3CN1CC2 +146: N#C[C@@H]1C[C@@H]2CN3CCc4cc5c(cc4[C@@H]3C[C@@H]2C[C@@H]1O)OCO5 +146: COC(=O)[C@@H]1C[C@](C)(C(=O)O)NC(=O)N1 +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 171: =============================================================================== 171: All tests passed (93 assertions in 5 test cases) 171: -233/238 Test #171: testRascalCluster ...................... Passed 65.73 sec -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 -147: [00:37:36] Interrupted, cancelling conformer generation +232/238 Test #171: testRascalCluster ...................... Passed 47.36 sec +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-] +147: [09:34:07] 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] @@ -35146,67 +35175,70 @@ 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: N#C[C@@H]1C[C@@H]2CN3CCc4cc5c(cc4[C@@H]3C[C@@H]2C[C@@H]1O)OCO5 147: =============================================================================== 147: All tests passed (12742 assertions in 21 test cases) 147: -234/238 Test #147: distGeomHelpersCatch ................... Passed 73.57 sec -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-] +233/238 Test #147: distGeomHelpersCatch ................... Passed 53.93 sec +238: DbCLI/UnitTestDbCLI.py ............ [100%] +238: +238: =============================== warnings summary =============================== +238: ../obj-aarch64-linux-gnu/rdkit/Chem/MolDb/Loader_sa.py:20 +238: /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/MolDb/Loader_sa.py:20: MovedIn20Warning: The ``declarative_base()`` function is now available as sqlalchemy.orm.declarative_base(). (deprecated since: 2.0) (Background on SQLAlchemy 2.0 at: https://sqlalche.me/e/b8d9) +238: decBase = declarative_base() +238: +238: -- Docs: https://docs.pytest.org/en/stable/how-to/capture-warnings.html +238: ======================== 12 passed, 1 warning in 25.50s ======================== +234/238 Test #238: pythonProjectTests ..................... Passed 26.83 sec +146: [09:34:14] Molecule does not have explicit Hs. Consider calling AddHs() +146: [09:34:08] --------------------------------- +146: [09:34:08] test github issue 696: Bad 1-4 bounds matrix elements in highly constrained system +146: [09:34:08] --------------------------------- +146: [09:34:08] More ChEMBL molecules failing bounds smoothing. +146: [09:34:08] --------------------------------- +146: [09:34:08] ugly conformations can be generated for highly constrained ring systems. +146: [09:34:08] --------------------------------- +146: [09:34:08] test embed parameters structure. +146: [09:34:08] --------------------------------- +146: [09:34:08] test github 1227: Hs being used in RMSD filtering. +146: [09:34:08] --------------------------------- +146: [09:34:08] Failure to embed larger aromatic rings. +146: [09:34:10] --------------------------------- +146: [09:34:10] Deterministic with large random seeds +146: [09:34:13] --------------------------------- +146: [09:34:13] Github #1990: seg fault after RemoveHs +146: [09:34:13] --------------------------------- +146: [09:34:13] Github #2246: Use coordMap when starting embedding from random coords +146: [09:34:14] --------------------------------- +146: [09:34:14] Providing a distance bounds matrix. +146: [09:34:14] --------------------------------- +146: [09:34:14] Disabling fragmentation. +146: [09:34:14] --------------------------------- +146: [09:34:14] Using symmetry in conformation pruning. +146: [09:34:14] --------------------------------- +146: [09:34:14] Force trans amides. +146: [09:34:14] --------------------------------- +146: [09:34:14] test missing Hs warning. +146: [09:34:14] --------------------------------- +146: [09:34:14] basic H bond support. +146: [09:34:14] ******************************************************* +235/238 Test #146: testDistGeomHelpers .................... Passed 60.45 sec 170: =============================================================================== 170: All tests passed (3590 assertions in 35 test cases) 170: -235/238 Test #170: testRascalMCES ......................... Passed 73.68 sec -146: [00:37:45] Molecule does not have explicit Hs. Consider calling AddHs() -146: [00:37:41] --------------------------------- -146: [00:37:41] test github issue 696: Bad 1-4 bounds matrix elements in highly constrained system -146: [00:37:41] --------------------------------- -146: [00:37:41] More ChEMBL molecules failing bounds smoothing. -146: [00:37:41] --------------------------------- -146: [00:37:41] ugly conformations can be generated for highly constrained ring systems. -146: [00:37:41] --------------------------------- -146: [00:37:41] test embed parameters structure. -146: [00:37:41] --------------------------------- -146: [00:37:41] test github 1227: Hs being used in RMSD filtering. -146: [00:37:41] --------------------------------- -146: [00:37:41] Failure to embed larger aromatic rings. -146: [00:37:42] --------------------------------- -146: [00:37:42] Deterministic with large random seeds -146: [00:37:43] --------------------------------- -146: [00:37:43] Github #1990: seg fault after RemoveHs -146: [00:37:43] --------------------------------- -146: [00:37:43] Github #2246: Use coordMap when starting embedding from random coords -146: [00:37:44] --------------------------------- -146: [00:37:44] Providing a distance bounds matrix. -146: [00:37:44] --------------------------------- -146: [00:37:44] Disabling fragmentation. -146: [00:37:44] --------------------------------- -146: [00:37:44] Using symmetry in conformation pruning. -146: [00:37:45] --------------------------------- -146: [00:37:45] Force trans amides. -146: [00:37:45] --------------------------------- -146: [00:37:45] test missing Hs warning. -146: [00:37:45] --------------------------------- -146: [00:37:45] basic H bond support. -146: [00:37:45] ******************************************************* -236/238 Test #146: testDistGeomHelpers .................... Passed 82.49 sec -174: Randomness seeded to: 2023853055 +236/238 Test #170: testRascalMCES ......................... Passed 63.09 sec +5: [09:34:37] Finished: testMultipleTimes() +5: [09:34:37] +5: ----------------------------------------- +237/238 Test #5: testConcurrentQueue .................... Passed 90.34 sec +174: Randomness seeded to: 3373958121 174: =============================================================================== 174: All tests passed (28 assertions in 2 test cases) 174: -237/238 Test #174: testSynthonSpaceRascalSearch ........... Passed 96.37 sec -5: [00:40:38] Finished: testMultipleTimes() -5: [00:40:38] -5: ----------------------------------------- -238/238 Test #5: testConcurrentQueue .................... Passed 266.01 sec +238/238 Test #174: testSynthonSpaceRascalSearch ........... Passed 79.20 sec 100% tests passed, 0 tests failed out of 238 -Total Test time (real) = 266.09 sec +Total Test time (real) = 93.61 sec make[2]: Leaving directory '/build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu' make[1]: Leaving directory '/build/reproducible-path/rdkit-202503.1' create-stamp debian/debhelper-build-stamp @@ -37867,37 +37899,37 @@ diversion by libc6 from: /lib/ld-linux-aarch64.so.1 dpkg-shlibdeps: warning: diversions involved - output may be incorrect diversion by libc6 to: /lib/ld-linux-aarch64.so.1.usr-is-merged -dpkg-shlibdeps: warning: debian/postgresql-17-rdkit/usr/lib/postgresql/17/lib/rdkit.so contains an unresolvable reference to symbol AggCheckCallContext: 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 DefineCustomIntVariable: it's probably a plugin dpkg-shlibdeps: warning: 24 other similar warnings have been skipped (use -v to see them all) +dpkg-shlibdeps: warning: symbol 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_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 PyExc_KeyError 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 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_Dealloc used by debian/librdkit1t64/usr/lib/libRDKitRDBoost.so.1.2025.03.1 found in none of the libraries -dpkg-shlibdeps: warning: symbol PyExc_ValueError used by debian/librdkit1t64/usr/lib/libRDKitRDBoost.so.1.2025.03.1 found in none of the libraries -dpkg-shlibdeps: warning: symbol PyObject_CallFunction used by debian/librdkit1t64/usr/lib/libRDKitRDBoost.so.1.2025.03.1 found in none of the libraries dpkg-shlibdeps: warning: symbol 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_IndexError 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_ValueError 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 PyObject_IsTrue 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) dh_installdeb -O--buildsystem=cmake dh_gencontrol -O--buildsystem=cmake dpkg-gencontrol: warning: Depends field of package rdkit-data: substitution variable ${shlibs:Depends} used, but is not defined -dpkg-gencontrol: warning: Depends field of package 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: Provides field of package python3-rdkit: substitution variable ${python3:Provides} used, but is not defined +dpkg-gencontrol: warning: Depends field of package rdkit-doc: substitution variable ${shlibs:Depends} used, but is not defined +dpkg-gencontrol: warning: 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_202503.1-5_arm64.deb'. dpkg-deb: building package 'postgresql-17-rdkit-dbgsym' in '../postgresql-17-rdkit-dbgsym_202503.1-5_arm64.deb'. +dpkg-deb: building package 'rdkit-data' in '../rdkit-data_202503.1-5_all.deb'. dpkg-deb: building package 'librdkit1t64' in '../librdkit1t64_202503.1-5_arm64.deb'. +dpkg-deb: building package 'rdkit-doc' in '../rdkit-doc_202503.1-5_all.deb'. dpkg-deb: building package 'python3-rdkit' in '../python3-rdkit_202503.1-5_arm64.deb'. -dpkg-deb: building package 'rdkit-data' in '../rdkit-data_202503.1-5_all.deb'. +dpkg-deb: building package 'postgresql-17-rdkit' in '../postgresql-17-rdkit_202503.1-5_arm64.deb'. dpkg-deb: building package 'python3-rdkit-dbgsym' in '../python3-rdkit-dbgsym_202503.1-5_arm64.deb'. +dpkg-deb: building package 'librdkit-dev' in '../librdkit-dev_202503.1-5_arm64.deb'. dpkg-deb: building package 'librdkit1t64-dbgsym' in '../librdkit1t64-dbgsym_202503.1-5_arm64.deb'. -dpkg-deb: building package 'postgresql-17-rdkit' in '../postgresql-17-rdkit_202503.1-5_arm64.deb'. -dpkg-deb: building package 'rdkit-doc' in '../rdkit-doc_202503.1-5_all.deb'. dpkg-genbuildinfo --build=binary -O../rdkit_202503.1-5_arm64.buildinfo dpkg-genchanges --build=binary -O../rdkit_202503.1-5_arm64.changes dpkg-genchanges: info: binary-only upload (no source code included) @@ -37905,12 +37937,14 @@ 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/3072577/tmp/hooks/B01_cleanup starting +I: user script /srv/workspace/pbuilder/3072577/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/3735765 and its subdirectories -I: Current time: Thu Aug 14 00:44:20 -12 2025 -I: pbuilder-time-stamp: 1755175460 +I: removing directory /srv/workspace/pbuilder/3072577 and its subdirectories +I: Current time: Thu Sep 17 09:37:46 +14 2026 +I: pbuilder-time-stamp: 1789587466