Diff of the two buildlogs: -- --- b1/build.log 2025-07-23 21:51:12.055251619 +0000 +++ b2/build.log 2025-07-23 23:02:12.928375356 +0000 @@ -1,7 +1,6 @@ -W: cgroups are not available on the host, not using them. I: pbuilder: network access will be disabled during build -I: Current time: Tue Aug 25 15:31:51 -12 2026 -I: pbuilder-time-stamp: 1787715111 +I: Current time: Thu Jul 24 11:51:20 +14 2025 +I: pbuilder-time-stamp: 1753307480 I: Building the build Environment I: extracting base tarball [/var/cache/pbuilder/unstable-reproducible-base.tgz] I: copying local configuration @@ -37,51 +36,84 @@ dpkg-source: info: applying better_enums.patch I: Not using root during the build. I: Installing the build-deps -I: user script /srv/workspace/pbuilder/4014508/tmp/hooks/D02_print_environment starting +I: user script /srv/workspace/pbuilder/1849633/tmp/hooks/D01_modify_environment starting +debug: Running on codethink04-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 Jul 23 21:51 /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/1849633/tmp/hooks/D01_modify_environment finished +I: user script /srv/workspace/pbuilder/1849633/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=' ' - 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='4014508' - PS1='# ' - PS2='> ' + INVOCATION_ID=70c9c177d64948e5af6c922ca8e1b787 + 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=1849633 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.xyecyvbX/pbuilderrc_ibFM --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.xyecyvbX/b1 --logfile b1/build.log rdkit_202503.1-4.dsc' - SUDO_GID='109' - SUDO_UID='104' - SUDO_USER='jenkins' - TERM='unknown' - TZ='/usr/share/zoneinfo/Etc/GMT+12' - USER='root' - _='/usr/sbin/chroot' - 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.xyecyvbX/pbuilderrc_xJom --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.xyecyvbX/b2 --logfile b2/build.log rdkit_202503.1-4.dsc' + SUDO_GID=109 + SUDO_UID=104 + SUDO_USER=jenkins + TERM=unknown + TZ=/usr/share/zoneinfo/Etc/GMT-14 + UID=0 + USER=root + _='I: set' + http_proxy=http://192.168.101.4:3128 I: uname -a - Linux codethink03-arm64 6.1.0-37-cloud-arm64 #1 SMP Debian 6.1.140-1 (2025-05-22) aarch64 GNU/Linux + Linux i-capture-the-hostname 6.1.0-37-cloud-arm64 #1 SMP Debian 6.1.140-1 (2025-05-22) aarch64 GNU/Linux I: ls -l /bin - lrwxrwxrwx 1 root root 7 May 12 2025 /bin -> usr/bin -I: user script /srv/workspace/pbuilder/4014508/tmp/hooks/D02_print_environment finished + lrwxrwxrwx 1 root root 7 May 12 19:25 /bin -> usr/bin +I: user script /srv/workspace/pbuilder/1849633/tmp/hooks/D02_print_environment finished -> Attempting to satisfy build-dependencies -> Creating pbuilder-satisfydepends-dummy package Package: pbuilder-satisfydepends-dummy @@ -573,7 +605,7 @@ Get: 367 http://deb.debian.org/debian unstable/main arm64 texlive-latex-recommended all 2024.20250309-1 [8745 kB] Get: 368 http://deb.debian.org/debian unstable/main arm64 texlive-pictures all 2024.20250309-1 [17.0 MB] Get: 369 http://deb.debian.org/debian unstable/main arm64 texlive-latex-extra all 2024.20250309-2 [25.2 MB] -Fetched 398 MB in 2s (192 MB/s) +Fetched 398 MB in 1s (314 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 ... 19963 files and directories currently installed.) @@ -1758,8 +1790,8 @@ Setting up tzdata (2025b-4) ... Current default time zone: 'Etc/UTC' -Local time is now: Wed Aug 26 03:33:24 UTC 2026. -Universal Time is now: Wed Aug 26 03:33:24 UTC 2026. +Local time is now: Wed Jul 23 21:52:21 UTC 2025. +Universal Time is now: Wed Jul 23 21:52:21 UTC 2025. Run 'dpkg-reconfigure tzdata' if you wish to change it. Setting up libboost-atomic1.83.0:arm64 (1.83.0-4.2) ... @@ -1923,11 +1955,6 @@ Setting up pandoc (3.1.11.1+ds-2) ... 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 'codethink03-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) ... @@ -2149,7 +2176,11 @@ Building tag database... -> Finished parsing the build-deps I: Building the package -I: Running cd /build/reproducible-path/rdkit-202503.1/ && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games" HOME="/nonexistent/first-build" dpkg-buildpackage -us -uc -b && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games" HOME="/nonexistent/first-build" dpkg-genchanges -S > ../rdkit_202503.1-4_source.changes +I: user script /srv/workspace/pbuilder/1849633/tmp/hooks/A99_set_merged_usr starting +Not re-configuring usrmerge for unstable +I: user script /srv/workspace/pbuilder/1849633/tmp/hooks/A99_set_merged_usr finished +hostname: Name or service not known +I: Running cd /build/reproducible-path/rdkit-202503.1/ && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/i/capture/the/path" HOME="/nonexistent/second-build" dpkg-buildpackage -us -uc -b && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/i/capture/the/path" HOME="/nonexistent/second-build" dpkg-genchanges -S > ../rdkit_202503.1-4_source.changes dpkg-buildpackage: info: source package rdkit dpkg-buildpackage: info: source version 202503.1-4 dpkg-buildpackage: info: source distribution unstable @@ -2273,8 +2304,8 @@ command to set the policy and suppress this warning. This warning is for project developers. Use -Wno-dev to suppress it. --- Configuring done (6.2s) --- Generating done (1.0s) +-- Configuring done (3.2s) +-- Generating done (0.8s) CMake Warning: Manually-specified variables were not used by the project: @@ -2335,7 +2366,7 @@ command to set the policy and suppress this warning. This warning is for project developers. Use -Wno-dev to suppress it. --- Configuring done (1.0s) +-- Configuring done (1.1s) -- Generating done (0.0s) -- Build files have been written to: /build/reproducible-path/rdkit-202503.1/Code/PgSQL/rdkit/build-17 make[1]: Leaving directory '/build/reproducible-path/rdkit-202503.1' @@ -2350,107 +2381,101 @@ 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 -f External/CoordGen/CMakeFiles/coordgen_support.dir/build.make External/CoordGen/CMakeFiles/coordgen_support.dir/depend +make -f External/RingFamilies/CMakeFiles/ringdecomposerlib_support.dir/build.make External/RingFamilies/CMakeFiles/ringdecomposerlib_support.dir/depend +make -f External/GA/CMakeFiles/ga.dir/build.make External/GA/CMakeFiles/ga.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 /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/External/INCHI-API /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/External/INCHI-API/CMakeFiles/inchi_support.dir/DependInfo.cmake "--color=" -make -f External/CoordGen/CMakeFiles/coordgen_support.dir/build.make External/CoordGen/CMakeFiles/coordgen_support.dir/depend +make -f Code/RDGeneral/CMakeFiles/rdkitCatch.dir/build.make Code/RDGeneral/CMakeFiles/rdkitCatch.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 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/build/reproducible-path/rdkit-202503.1/Code/ML/Cluster/Murtagh/hcdriver.c [ 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 /usr/bin/cc -fPIC -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -fPIC -Wl,--dependency-file=CMakeFiles/hc.dir/link.d -Wl,-z,relro -Wl,-z,now -shared -Wl,-soname,libRDKithc.so.1 -o ../../../../lib/libRDKithc.so.1.2025.03.1 CMakeFiles/hc.dir/hc.c.o CMakeFiles/hc.dir/hcdriver.c.o /usr/lib/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/ML/Cluster/Murtagh && /usr/bin/cmake -E cmake_symlink_library ../../../../lib/libRDKithc.so.1.2025.03.1 ../../../../lib/libRDKithc.so.1 ../../../../lib/libRDKithc.so make[4]: Leaving directory '/build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu' +[ 2%] Building CXX object External/GA/CMakeFiles/ga.dir/ga/BinaryStringChromosomePolicy.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 -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -Dga_EXPORTS -I/build/reproducible-path/rdkit-202503.1/External -I/build/reproducible-path/rdkit-202503.1/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=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/BinaryStringChromosomePolicy.cpp.o -MF CMakeFiles/ga.dir/ga/BinaryStringChromosomePolicy.cpp.o.d -o CMakeFiles/ga.dir/ga/BinaryStringChromosomePolicy.cpp.o -c /build/reproducible-path/rdkit-202503.1/External/GA/ga/BinaryStringChromosomePolicy.cpp [ 2%] Built target hc -[ 2%] Linking CXX shared library ../../lib/libRDKitga.so -cd /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/External/GA && /usr/bin/cmake -E cmake_link_script 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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/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 +[ 2%] 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_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/versions.cpp.o -MF CMakeFiles/RDGeneral.dir/versions.cpp.o.d -o CMakeFiles/RDGeneral.dir/versions.cpp.o -c /build/reproducible-path/rdkit-202503.1/Code/RDGeneral/versions.cpp +[ 2%] 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 -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -Dga_EXPORTS -I/build/reproducible-path/rdkit-202503.1/External -I/build/reproducible-path/rdkit-202503.1/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=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/Util.cpp.o -MF CMakeFiles/ga.dir/util/Util.cpp.o.d -o CMakeFiles/ga.dir/util/Util.cpp.o -c /build/reproducible-path/rdkit-202503.1/External/GA/util/Util.cpp [ 2%] Linking CXX static library librdkitCatch.a cd /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/RDGeneral && /usr/bin/cmake -P CMakeFiles/rdkitCatch.dir/cmake_clean_target.cmake cd /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/RDGeneral && /usr/bin/cmake -E cmake_link_script CMakeFiles/rdkitCatch.dir/link.txt --verbose=1 @@ -2458,6 +2483,12 @@ /usr/bin/ranlib librdkitCatch.a make[4]: Leaving directory '/build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu' [ 2%] Built target rdkitCatch +[ 2%] Linking CXX shared library ../../lib/libRDKitga.so +cd 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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 +cd /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/External/GA && /usr/bin/cmake -E cmake_symlink_library ../../lib/libRDKitga.so.1.2025.03.1 ../../lib/libRDKitga.so.1 ../../lib/libRDKitga.so +make[4]: Leaving directory '/build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu' +[ 2%] Built target ga [ 2%] Linking CXX shared library ../../lib/libRDKitRDStreams.so cd /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/RDStreams && /usr/bin/cmake -E cmake_link_script CMakeFiles/RDStreams.dir/link.txt --verbose=1 /usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=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/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 @@ -2472,209 +2503,209 @@ [ 2%] Built target RDGeneral make -f Code/DataStructs/CMakeFiles/DataStructs.dir/build.make Code/DataStructs/CMakeFiles/DataStructs.dir/depend make -f Code/Numerics/EigenSolvers/CMakeFiles/EigenSolvers.dir/build.make Code/Numerics/EigenSolvers/CMakeFiles/EigenSolvers.dir/depend +make -f Code/RDBoost/CMakeFiles/RDBoost.dir/build.make Code/RDBoost/CMakeFiles/RDBoost.dir/depend +make -f Code/RDGeneral/CMakeFiles/testDict.dir/build.make Code/RDGeneral/CMakeFiles/testDict.dir/depend +make -f Code/RDGeneral/CMakeFiles/testRDValue.dir/build.make Code/RDGeneral/CMakeFiles/testRDValue.dir/depend +make -f Code/RDGeneral/CMakeFiles/testConcurrentQueue.dir/build.make Code/RDGeneral/CMakeFiles/testConcurrentQueue.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-202503.1/obj-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/DataStructs /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/DataStructs /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/DataStructs/CMakeFiles/DataStructs.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 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-f Code/RDGeneral/CMakeFiles/testRDValue.dir/build.make Code/RDGeneral/CMakeFiles/testRDValue.dir/depend -make[4]: Leaving directory '/build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu' +make -f Code/Numerics/CMakeFiles/testMatrices.dir/build.make Code/Numerics/CMakeFiles/testMatrices.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/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/DataStructs/CMakeFiles/DataStructs.dir/build.make Code/DataStructs/CMakeFiles/DataStructs.dir/build 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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 -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/dictTestsCatch.dir/link.d CMakeFiles/dictTestsCatch.dir/catch_dict.cpp.o -o dictTestsCatch librdkitCatch.a ../../lib/libRDKitRDGeneral.so.1.2025.03.1 /usr/lib/libCatch2.a /usr/lib/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 dictTestsCatch [ 8%] Linking CXX shared library ../../lib/libRDKitSimDivPickers.so cd /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/SimDivPickers && /usr/bin/cmake -E cmake_link_script CMakeFiles/SimDivPickers.dir/link.txt --verbose=1 /usr/bin/c++ -fPIC -g -O2 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shared library ../../lib/libRDKitDataStructs.so cd /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/DataStructs && /usr/bin/cmake -E cmake_link_script CMakeFiles/DataStructs.dir/link.txt --verbose=1 +[ 9%] Linking CXX executable testDict +cd /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/RDGeneral && /usr/bin/cmake -E cmake_link_script CMakeFiles/testDict.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/DataStructs.dir/link.d -Wl,-z,relro -Wl,-z,now -shared -Wl,-soname,libRDKitDataStructs.so.1 -o ../../lib/libRDKitDataStructs.so.1.2025.03.1 CMakeFiles/DataStructs.dir/BitVect.cpp.o 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'/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[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' 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/DataManip/MetricMatrixCalc/Wrap /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/DataManip/MetricMatrixCalc/Wrap /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/DataManip/MetricMatrixCalc/Wrap/CMakeFiles/rdMetricMatrixCalc.dir/DependInfo.cmake "--color=" make -f Code/Geometry/CMakeFiles/RDGeometryLib.dir/build.make 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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/DataStructs/CMakeFiles/testMultiFPB.dir/testMultiFPB.cpp.o -MF CMakeFiles/testMultiFPB.dir/testMultiFPB.cpp.o.d -o CMakeFiles/testMultiFPB.dir/testMultiFPB.cpp.o -c /build/reproducible-path/rdkit-202503.1/Code/DataStructs/testMultiFPB.cpp make[4]: Entering directory '/build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu' +[ 10%] Building CXX object Code/DataStructs/CMakeFiles/testDataStructs.dir/testDatastructs.cpp.o +[ 10%] Building CXX object Code/Geometry/CMakeFiles/RDGeometryLib.dir/Transform2D.cpp.o make -f 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-I/build/reproducible-path/rdkit-202503.1/External -I/build/reproducible-path/rdkit-202503.1/Code -I/usr/lib/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/DataStructs/Wrap/CMakeFiles/cDataStructs.dir/DataStructs.cpp.o -MF CMakeFiles/cDataStructs.dir/DataStructs.cpp.o.d -o CMakeFiles/cDataStructs.dir/DataStructs.cpp.o -c /build/reproducible-path/rdkit-202503.1/Code/DataStructs/Wrap/DataStructs.cpp -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 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-DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202503.1/External -I/build/reproducible-path/rdkit-202503.1/Code -isystem /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/GridUtils.cpp.o -MF CMakeFiles/RDGeometryLib.dir/GridUtils.cpp.o.d -o CMakeFiles/RDGeometryLib.dir/GridUtils.cpp.o -c /build/reproducible-path/rdkit-202503.1/Code/Geometry/GridUtils.cpp [ 12%] Linking CXX executable catchDataStructs cd 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Code/Numerics/Alignment/Wrap/CMakeFiles/rdAlignment.dir/rdAlignment.cpp.o +[ 15%] 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_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 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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/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 -[ 17%] Linking CXX executable testAlignment -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 +[ 17%] Building CXX object Code/GraphMol/CMakeFiles/GraphMol.dir/FindRings.cpp.o +cd 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Code/GraphMol/CMakeFiles/GraphMol.dir/atomic_data.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_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_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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target ChemicalFeatures +[ 17%] 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_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 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/usr/bin/cmake -E cmake_link_script CMakeFiles/cQuantize.dir/link.txt --verbose=1 /build/reproducible-path/rdkit-202503.1/Code/GraphMol/FindRings.cpp: In function 'void RDKit::MolOps::findRingFamilies(const RDKit::ROMol&)': /build/reproducible-path/rdkit-202503.1/Code/GraphMol/FindRings.cpp:1292:36: warning: unused parameter 'mol' [-Wunused-parameter] 1292 | void findRingFamilies(const ROMol &mol) { | ~~~~~~~~~~~~~^~~ +/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/cQuantize.dir/link.d -Wl,-z,relro -Wl,-z,now -shared -o ../../../rdkit/ML/Data/cQuantize.so CMakeFiles/cQuantize.dir/cQuantize.cpp.o 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-I/build/reproducible-path/rdkit-202503.1/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-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 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, @@ -3082,37 +3099,38 @@ /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, 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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/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 [ 18%] Building CXX object Code/GraphMol/CMakeFiles/GraphMol.dir/Aromaticity.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 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/build/reproducible-path/rdkit-202503.1/Code/GraphMol/Aromaticity.cpp [ 18%] Building CXX object Code/GraphMol/CMakeFiles/GraphMol.dir/Kekulize.cpp.o @@ -3125,16 +3143,28 @@ 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_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_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 [ 19%] 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_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_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 +[ 19%] 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 -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -g -fwrapv -O2 -Wl,--dependency-file=CMakeFiles/rdGeometry.dir/link.d -Wl,-z,relro -Wl,-z,now -shared -o ../../../rdkit/Geometry/rdGeometry.so CMakeFiles/rdGeometry.dir/Point.cpp.o CMakeFiles/rdGeometry.dir/UniformGrid3D.cpp.o CMakeFiles/rdGeometry.dir/UniformRealValueGrid3D.cpp.o CMakeFiles/rdGeometry.dir/rdGeometry.cpp.o ../../../lib/libRDKitRDGeometryLib.so.1.2025.03.1 ../../../lib/libRDKitRDBoost.so.1.2025.03.1 ../../../lib/libRDKitDataStructs.so.1.2025.03.1 /usr/lib/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' +[ 19%] Built target rdGeometry [ 19%] 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_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS 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-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 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/DataStructs/Wrap/CMakeFiles/cDataStructs.dir/wrap_SparseBV.cpp.o -MF CMakeFiles/cDataStructs.dir/wrap_SparseBV.cpp.o.d -o CMakeFiles/cDataStructs.dir/wrap_SparseBV.cpp.o -c /build/reproducible-path/rdkit-202503.1/Code/DataStructs/Wrap/wrap_SparseBV.cpp +[ 19%] Building CXX object Code/DataStructs/Wrap/CMakeFiles/cDataStructs.dir/wrap_ExplicitBV.cpp.o +cd 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-Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/DataStructs/Wrap/CMakeFiles/cDataStructs.dir/wrap_ExplicitBV.cpp.o -MF CMakeFiles/cDataStructs.dir/wrap_ExplicitBV.cpp.o.d -o CMakeFiles/cDataStructs.dir/wrap_ExplicitBV.cpp.o -c /build/reproducible-path/rdkit-202503.1/Code/DataStructs/Wrap/wrap_ExplicitBV.cpp [ 19%] Building CXX object Code/GraphMol/CMakeFiles/GraphMol.dir/Conformer.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_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_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/Conformer.cpp.o -MF CMakeFiles/GraphMol.dir/Conformer.cpp.o.d -o CMakeFiles/GraphMol.dir/Conformer.cpp.o -c /build/reproducible-path/rdkit-202503.1/Code/GraphMol/Conformer.cpp [ 19%] Building CXX object Code/GraphMol/CMakeFiles/GraphMol.dir/Renumber.cpp.o cd 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-I/build/reproducible-path/rdkit-202503.1/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-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/AdjustQuery.cpp.o -MF CMakeFiles/GraphMol.dir/AdjustQuery.cpp.o.d -o CMakeFiles/GraphMol.dir/AdjustQuery.cpp.o -c /build/reproducible-path/rdkit-202503.1/Code/GraphMol/AdjustQuery.cpp +[ 19%] 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 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Code/GraphMol/CMakeFiles/GraphMol.dir/Resonance.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_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_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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/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 [ 20%] Building CXX object Code/GraphMol/CMakeFiles/GraphMol.dir/Atropisomers.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 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/build/reproducible-path/rdkit-202503.1/Code/GraphMol/Atropisomers.cpp [ 20%] Building CXX object Code/GraphMol/CMakeFiles/GraphMol.dir/WedgeBonds.cpp.o cd /build/reproducible-path/rdkit-202503.1/obj-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_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_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 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-DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202503.1/External -I/build/reproducible-path/rdkit-202503.1/Code -isystem /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/MolProps.cpp.o -MF CMakeFiles/GraphMol.dir/MolProps.cpp.o.d -o CMakeFiles/GraphMol.dir/MolProps.cpp.o -c /build/reproducible-path/rdkit-202503.1/Code/GraphMol/MolProps.cpp -[ 20%] Linking CXX shared module ../../../rdkit/rdBase.so -cd /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/RDBoost/Wrap && /usr/bin/cmake -E cmake_link_script 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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/DataStructs/Wrap/CMakeFiles/cDataStructs.dir/wrap_Utils.cpp.o -MF CMakeFiles/cDataStructs.dir/wrap_Utils.cpp.o.d -o CMakeFiles/cDataStructs.dir/wrap_Utils.cpp.o -c /build/reproducible-path/rdkit-202503.1/Code/DataStructs/Wrap/wrap_Utils.cpp [ 20%] Linking CXX shared library ../../lib/libRDKitGraphMol.so cd /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol && /usr/bin/cmake -E cmake_link_script CMakeFiles/GraphMol.dir/link.txt --verbose=1 /usr/bin/c++ -fPIC -g -O2 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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/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 make[4]: Entering directory '/build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu' +make -f Code/GraphMol/CMakeFiles/tableTestsCatch.dir/build.make Code/GraphMol/CMakeFiles/tableTestsCatch.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu' -make -f 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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/SmilesParse/CMakeFiles/SmilesParse.dir/SmilesParse.cpp.o -MF CMakeFiles/SmilesParse.dir/SmilesParse.cpp.o.d -o CMakeFiles/SmilesParse.dir/SmilesParse.cpp.o -c /build/reproducible-path/rdkit-202503.1/Code/GraphMol/SmilesParse/SmilesParse.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/MolTransforms/CMakeFiles/MolTransforms.dir/MolTransforms.cpp.o -MF CMakeFiles/MolTransforms.dir/MolTransforms.cpp.o.d -o CMakeFiles/MolTransforms.dir/MolTransforms.cpp.o -c /build/reproducible-path/rdkit-202503.1/Code/GraphMol/MolTransforms/MolTransforms.cpp -[ 21%] Building CXX object Code/GraphMol/GenericGroups/CMakeFiles/GenericGroups.dir/GenericGroups.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 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-ldl +make[4]: Leaving directory '/build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu' +[ 22%] Built target cDataStructs +make -f Code/GraphMol/MolCatalog/CMakeFiles/MolCatalog.dir/build.make Code/GraphMol/MolCatalog/CMakeFiles/MolCatalog.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/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=" +[ 22%] Built target tableTestsCatch make -f Code/GraphMol/MolInterchange/CMakeFiles/MolInterchange.dir/build.make 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/usr/bin/cmake -E cmake_symlink_library ../../../lib/libRDKitTrajectory.so.1.2025.03.1 ../../../lib/libRDKitTrajectory.so.1 ../../../lib/libRDKitTrajectory.so +[ 22%] 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_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -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 make[4]: Leaving directory '/build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu' -[ 22%] Built target tableTestsCatch +[ 22%] Built target Trajectory make -f Code/GraphMol/SLNParse/CMakeFiles/SLNParse.dir/build.make Code/GraphMol/SLNParse/CMakeFiles/SLNParse.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/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=" @@ -3282,14 +3313,12 @@ make[4]: Entering directory '/build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu' [ 22%] 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/SLNParse && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB 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/build/reproducible-path/rdkit-202503.1/Code/GraphMol/SLNParse/SLNParse.cpp -[ 22%] 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 -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DMolCatalog_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_MOLCATALOG_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_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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-D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,--dependency-file=CMakeFiles/MolCatalog.dir/link.d -Wl,-z,relro -Wl,-z,now -shared -Wl,-soname,libRDKitMolCatalog.so.1 -o ../../../lib/libRDKitMolCatalog.so.1.2025.03.1 CMakeFiles/MolCatalog.dir/MolCatalogEntry.cpp.o CMakeFiles/MolCatalog.dir/MolCatalogParams.cpp.o ../../../lib/libRDKitGraphMol.so.1.2025.03.1 ../../../lib/libRDKitCatalogs.so.1.2025.03.1 ../../../lib/libRDKitRDGeometryLib.so.1.2025.03.1 ../../../lib/libRDKitDataStructs.so.1.2025.03.1 ../../../lib/libRDKitRDGeneral.so.1.2025.03.1 /usr/lib/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/MolCatalog && /usr/bin/cmake -E cmake_symlink_library ../../../lib/libRDKitMolCatalog.so.1.2025.03.1 ../../../lib/libRDKitMolCatalog.so.1 ../../../lib/libRDKitMolCatalog.so +[ 22%] Linking CXX shared library ../../../lib/libRDKitSubgraphs.so +cd /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/Subgraphs && /usr/bin/cmake -E cmake_link_script CMakeFiles/Subgraphs.dir/link.txt --verbose=1 +/usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=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/Subgraphs.dir/link.d -Wl,-z,relro -Wl,-z,now -shared -Wl,-soname,libRDKitSubgraphs.so.1 -o ../../../lib/libRDKitSubgraphs.so.1.2025.03.1 CMakeFiles/Subgraphs.dir/Subgraphs.cpp.o CMakeFiles/Subgraphs.dir/SubgraphUtils.cpp.o ../../../lib/libRDKitGraphMol.so.1.2025.03.1 ../../../lib/libRDKitRDGeometryLib.so.1.2025.03.1 ../../../lib/libRDKitDataStructs.so.1.2025.03.1 ../../../lib/libRDKitRDGeneral.so.1.2025.03.1 /usr/lib/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/Subgraphs && /usr/bin/cmake -E cmake_symlink_library ../../../lib/libRDKitSubgraphs.so.1.2025.03.1 ../../../lib/libRDKitSubgraphs.so.1 ../../../lib/libRDKitSubgraphs.so make[4]: Leaving directory '/build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu' -[ 22%] Built target MolCatalog +[ 22%] Built target Subgraphs 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' 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 /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/Wrap/CMakeFiles/rdqueries.dir/DependInfo.cmake "--color=" @@ -3298,46 +3327,62 @@ make[4]: Entering directory '/build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu' [ 22%] Building CXX object Code/GraphMol/Wrap/CMakeFiles/rdqueries.dir/rdqueries.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 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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/SmilesParse/CMakeFiles/SmilesParse.dir/CXSmilesOps.cpp.o -MF CMakeFiles/SmilesParse.dir/CXSmilesOps.cpp.o.d -o CMakeFiles/SmilesParse.dir/CXSmilesOps.cpp.o -c /build/reproducible-path/rdkit-202503.1/Code/GraphMol/SmilesParse/CXSmilesOps.cpp -[ 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 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/build/reproducible-path/rdkit-202503.1/Code/GraphMol/SmilesParse/CanonicalizeStereoGroups.cpp -[ 22%] Building CXX object Code/GraphMol/SmilesParse/CMakeFiles/SmilesParse.dir/SmilesJSONParsers.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_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/SmilesJSONParsers.cpp.o -MF CMakeFiles/SmilesParse.dir/SmilesJSONParsers.cpp.o.d -o CMakeFiles/SmilesParse.dir/SmilesJSONParsers.cpp.o -c /build/reproducible-path/rdkit-202503.1/Code/GraphMol/SmilesParse/SmilesJSONParsers.cpp -[ 22%] 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 -Wall -Wextra -fPIC -Wl,--dependency-file=CMakeFiles/PartialCharges.dir/link.d -Wl,-z,relro -Wl,-z,now -shared -Wl,-soname,libRDKitPartialCharges.so.1 -o ../../../lib/libRDKitPartialCharges.so.1.2025.03.1 CMakeFiles/PartialCharges.dir/GasteigerCharges.cpp.o CMakeFiles/PartialCharges.dir/GasteigerParams.cpp.o ../../../lib/libRDKitGraphMol.so.1.2025.03.1 ../../../lib/libRDKitRDGeometryLib.so.1.2025.03.1 ../../../lib/libRDKitDataStructs.so.1.2025.03.1 ../../../lib/libRDKitRDGeneral.so.1.2025.03.1 /usr/lib/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/PartialCharges && /usr/bin/cmake -E cmake_symlink_library ../../../lib/libRDKitPartialCharges.so.1.2025.03.1 ../../../lib/libRDKitPartialCharges.so.1 ../../../lib/libRDKitPartialCharges.so +[ 22%] Building CXX object Code/GraphMol/SmilesParse/CMakeFiles/SmilesParse.dir/SmartsWrite.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_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/SmartsWrite.cpp.o -MF CMakeFiles/SmilesParse.dir/SmartsWrite.cpp.o.d -o CMakeFiles/SmilesParse.dir/SmartsWrite.cpp.o -c /build/reproducible-path/rdkit-202503.1/Code/GraphMol/SmilesParse/SmartsWrite.cpp +[ 22%] Linking CXX shared library ../../../lib/libRDKitGenericGroups.so +cd /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/GenericGroups && /usr/bin/cmake -E cmake_link_script CMakeFiles/GenericGroups.dir/link.txt --verbose=1 +[ 22%] Linking CXX shared library ../../../lib/libRDKitMolTransforms.so +cd 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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/GenericGroups && /usr/bin/cmake -E cmake_symlink_library ../../../lib/libRDKitGenericGroups.so.1.2025.03.1 ../../../lib/libRDKitGenericGroups.so.1 ../../../lib/libRDKitGenericGroups.so make[4]: Leaving directory '/build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu' -[ 22%] Built target PartialCharges +[ 22%] Built target GenericGroups make -f Code/GraphMol/Wrap/CMakeFiles/rdtrajectory.dir/build.make Code/GraphMol/Wrap/CMakeFiles/rdtrajectory.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-202503.1/obj-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 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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 -DBOOST_NUMPY_DYN_LINK -DBOOST_NUMPY_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -Drdtrajectory_EXPORTS -I/build/reproducible-path/rdkit-202503.1/External -I/build/reproducible-path/rdkit-202503.1/Code -I/usr/lib/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/Trajectory.cpp.o -MF CMakeFiles/rdtrajectory.dir/Trajectory.cpp.o.d -o CMakeFiles/rdtrajectory.dir/Trajectory.cpp.o -c /build/reproducible-path/rdkit-202503.1/Code/GraphMol/Wrap/Trajectory.cpp -[ 22%] 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 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,--dependency-file=CMakeFiles/MolTransforms.dir/link.d -Wl,-z,relro -Wl,-z,now -shared -Wl,-soname,libRDKitMolTransforms.so.1 -o ../../../lib/libRDKitMolTransforms.so.1.2025.03.1 CMakeFiles/MolTransforms.dir/MolTransforms.cpp.o ../../../lib/libRDKitGraphMol.so.1.2025.03.1 ../../../lib/libRDKitEigenSolvers.so.1.2025.03.1 ../../../lib/libRDKitRDGeometryLib.so.1.2025.03.1 ../../../lib/libRDKitDataStructs.so.1.2025.03.1 ../../../lib/libRDKitRDGeneral.so.1.2025.03.1 /usr/lib/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/MolTransforms && /usr/bin/cmake -E cmake_symlink_library 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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/rdtrajectory.dir/Trajectory.cpp.o -MF CMakeFiles/rdtrajectory.dir/Trajectory.cpp.o.d -o CMakeFiles/rdtrajectory.dir/Trajectory.cpp.o -c /build/reproducible-path/rdkit-202503.1/Code/GraphMol/Wrap/Trajectory.cpp 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 /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/ChemicalFeatures/Wrap /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/ChemicalFeatures/Wrap/CMakeFiles/rdChemicalFeatures.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu' make -f Code/ChemicalFeatures/Wrap/CMakeFiles/rdChemicalFeatures.dir/build.make Code/ChemicalFeatures/Wrap/CMakeFiles/rdChemicalFeatures.dir/build make[4]: Entering directory '/build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu' +[ 22%] Building CXX object Code/GraphMol/SmilesParse/CMakeFiles/SmilesParse.dir/CXSmilesOps.cpp.o +cd 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-DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DrdChemicalFeatures_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/ChemicalFeatures/Wrap/CMakeFiles/rdChemicalFeatures.dir/rdChemicalFeatures.cpp.o -MF CMakeFiles/rdChemicalFeatures.dir/rdChemicalFeatures.cpp.o.d -o CMakeFiles/rdChemicalFeatures.dir/rdChemicalFeatures.cpp.o -c /build/reproducible-path/rdkit-202503.1/Code/ChemicalFeatures/Wrap/rdChemicalFeatures.cpp -[ 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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 -cd /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/GenericGroups && /usr/bin/cmake -E cmake_symlink_library ../../../lib/libRDKitGenericGroups.so.1.2025.03.1 ../../../lib/libRDKitGenericGroups.so.1 ../../../lib/libRDKitGenericGroups.so +[ 22%] 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 -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DMolCatalog_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_MOLCATALOG_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_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/MolCatalog/CMakeFiles/MolCatalog.dir/MolCatalogParams.cpp.o -MF 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 +[ 22%] 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 -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DCIPLabeler_EXPORTS -DRDKIT_CIPLABELER_BUILD -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202503.1/External -I/build/reproducible-path/rdkit-202503.1/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-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 +[ 22%] 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 -Wall -Wextra -fPIC 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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/Numerics/Optimizer/CMakeFiles/Optimizer.dir/BFGSOpt.cpp.o -MF CMakeFiles/Optimizer.dir/BFGSOpt.cpp.o.d -o CMakeFiles/Optimizer.dir/BFGSOpt.cpp.o -c /build/reproducible-path/rdkit-202503.1/Code/Numerics/Optimizer/BFGSOpt.cpp -[ 22%] Building CXX object Code/GraphMol/SmilesParse/CMakeFiles/SmilesParse.dir/smarts.tab.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 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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/CIPLabeler/CMakeFiles/CIPLabeler.dir/Digraph.cpp.o -MF CMakeFiles/CIPLabeler.dir/Digraph.cpp.o.d -o CMakeFiles/CIPLabeler.dir/Digraph.cpp.o -c /build/reproducible-path/rdkit-202503.1/Code/GraphMol/CIPLabeler/Digraph.cpp [ 22%] 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 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC 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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/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 +[ 22%] Building CXX object Code/GraphMol/PartialCharges/Wrap/CMakeFiles/rdPartialCharges.dir/rdPartialCharges.cpp.o +cd /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/PartialCharges/Wrap && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK 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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' -[ 25%] Built target rdtrajectory +[ 25%] Building CXX object Code/GraphMol/ShapeHelpers/CMakeFiles/ShapeHelpers.dir/ShapeEncoder.cpp.o +cd /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/ShapeHelpers && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDKIT_SHAPEHELPERS_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DShapeHelpers_EXPORTS -I/build/reproducible-path/rdkit-202503.1/External -I/build/reproducible-path/rdkit-202503.1/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/ShapeHelpers/CMakeFiles/ShapeHelpers.dir/ShapeEncoder.cpp.o -MF CMakeFiles/ShapeHelpers.dir/ShapeEncoder.cpp.o.d -o CMakeFiles/ShapeHelpers.dir/ShapeEncoder.cpp.o -c /build/reproducible-path/rdkit-202503.1/Code/GraphMol/ShapeHelpers/ShapeEncoder.cpp +[ 25%] Built target rdPartialCharges make -f Code/GraphMol/MolCatalog/Wrap/CMakeFiles/rdMolCatalog.dir/build.make Code/GraphMol/MolCatalog/Wrap/CMakeFiles/rdMolCatalog.dir/depend make[4]: Entering directory 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Code/GraphMol/SmilesParse/CMakeFiles/SmilesParse.dir/smiles.tab.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_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 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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%] Building CXX object Code/GraphMol/Substruct/CMakeFiles/SubstructMatch.dir/SubstructUtils.cpp.o +cd 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-fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/Substruct/CMakeFiles/SubstructMatch.dir/SubstructUtils.cpp.o -MF CMakeFiles/SubstructMatch.dir/SubstructUtils.cpp.o.d -o CMakeFiles/SubstructMatch.dir/SubstructUtils.cpp.o -c /build/reproducible-path/rdkit-202503.1/Code/GraphMol/Substruct/SubstructUtils.cpp +[ 26%] Linking CXX shared module ../../../rdkit/Chem/rdtrajectory.so +cd /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/Wrap && /usr/bin/cmake -E cmake_link_script CMakeFiles/rdtrajectory.dir/link.txt --verbose=1 +/usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=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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-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/configs/Sp2Bond.cpp.o -MF CMakeFiles/CIPLabeler.dir/configs/Sp2Bond.cpp.o.d -o CMakeFiles/CIPLabeler.dir/configs/Sp2Bond.cpp.o -c /build/reproducible-path/rdkit-202503.1/Code/GraphMol/CIPLabeler/configs/Sp2Bond.cpp -[ 26%] Building CXX object Code/GraphMol/Substruct/CMakeFiles/SubstructMatch.dir/SubstructUtils.cpp.o -cd /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/Substruct && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK 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Code/GraphMol/Substruct/CMakeFiles/SubstructMatch.dir/SubstructUtils.cpp.o -MF CMakeFiles/SubstructMatch.dir/SubstructUtils.cpp.o.d -o CMakeFiles/SubstructMatch.dir/SubstructUtils.cpp.o -c /build/reproducible-path/rdkit-202503.1/Code/GraphMol/Substruct/SubstructUtils.cpp -[ 26%] 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 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Code/ForceField/CMakeFiles/ForceField.dir/build.make Code/ForceField/CMakeFiles/ForceField.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/ForceField /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/ForceField /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/ForceField/CMakeFiles/ForceField.dir/DependInfo.cmake "--color=" -[ 26%] Building CXX object Code/GraphMol/SLNParse/CMakeFiles/SLNParse.dir/sln.tab.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 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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 -fPIC -MD -MT Code/ForceField/CMakeFiles/ForceField.dir/ForceField.cpp.o -MF CMakeFiles/ForceField.dir/ForceField.cpp.o.d -o CMakeFiles/ForceField.dir/ForceField.cpp.o -c /build/reproducible-path/rdkit-202503.1/Code/ForceField/ForceField.cpp -[ 26%] Linking CXX shared module ../../../../rdkit/Chem/rdMolTransforms.so -cd /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/MolTransforms/Wrap && /usr/bin/cmake -E cmake_link_script CMakeFiles/rdMolTransforms.dir/link.txt 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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/ForceField/CMakeFiles/ForceField.dir/AngleConstraint.cpp.o -MF CMakeFiles/ForceField.dir/AngleConstraint.cpp.o.d -o CMakeFiles/ForceField.dir/AngleConstraint.cpp.o -c /build/reproducible-path/rdkit-202503.1/Code/ForceField/AngleConstraint.cpp +[ 26%] Building CXX object Code/ForceField/CMakeFiles/ForceField.dir/AngleConstraints.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 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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/CIPLabeler/CMakeFiles/CIPLabeler.dir/configs/Sp2Bond.cpp.o -MF CMakeFiles/CIPLabeler.dir/configs/Sp2Bond.cpp.o.d -o CMakeFiles/CIPLabeler.dir/configs/Sp2Bond.cpp.o -c /build/reproducible-path/rdkit-202503.1/Code/GraphMol/CIPLabeler/configs/Sp2Bond.cpp +[ 26%] 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 +[ 26%] Building CXX object Code/ForceField/CMakeFiles/ForceField.dir/DistanceConstraint.cpp.o +cd 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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/ShapeHelpers/Wrap/CMakeFiles/rdShapeHelpers.dir/build.make Code/GraphMol/ShapeHelpers/Wrap/CMakeFiles/rdShapeHelpers.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-202503.1/obj-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/ShapeHelpers/Wrap /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu 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'/build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu' +[ 31%] Building CXX object Code/GraphMol/CMakeFiles/moliteratorTestsCatch.dir/catch_moliterators.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_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_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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object Code/GraphMol/SmilesParse/CMakeFiles/smiTest2.dir/test2.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 -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_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 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+[ 31%] Built target ForceField make -f Code/GraphMol/SmilesParse/CMakeFiles/v2smiTestCatch.dir/build.make Code/GraphMol/SmilesParse/CMakeFiles/v2smiTestCatch.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-202503.1/obj-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/v2smiTestCatch.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu' make -f Code/GraphMol/SmilesParse/CMakeFiles/v2smiTestCatch.dir/build.make 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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' -[ 30%] Built target SLNParse +[ 31%] Built target graphmolMemTest1 make -f Code/GraphMol/FragCatalog/CMakeFiles/FragCatalog.dir/build.make Code/GraphMol/FragCatalog/CMakeFiles/FragCatalog.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/FragCatalog.dir/DependInfo.cmake "--color=" make[4]: Leaving directory 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/build/reproducible-path/rdkit-202503.1/Code/GraphMol/MolChemicalFeatures/MolChemicalFeature.cpp -[ 32%] Linking CXX executable molbundleTestsCatch -cd /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol && /usr/bin/cmake -E cmake_link_script CMakeFiles/molbundleTestsCatch.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/molbundleTestsCatch.dir/link.d CMakeFiles/molbundleTestsCatch.dir/catch_molbundle.cpp.o -o molbundleTestsCatch ../RDGeneral/librdkitCatch.a ../../lib/libRDKitSmilesParse.so.1.2025.03.1 ../../lib/libRDKitGraphMol.so.1.2025.03.1 /usr/lib/libCatch2.a 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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/MolChemicalFeatures/CMakeFiles/MolChemicalFeatures.dir/MolChemicalFeatureFactory.cpp.o -MF CMakeFiles/MolChemicalFeatures.dir/MolChemicalFeatureFactory.cpp.o.d -o CMakeFiles/MolChemicalFeatures.dir/MolChemicalFeatureFactory.cpp.o -c /build/reproducible-path/rdkit-202503.1/Code/GraphMol/MolChemicalFeatures/MolChemicalFeatureFactory.cpp -[ 35%] 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 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-DRDK_USE_BOOST_IOSTREAMS -DRDK_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/FilterMatchers.cpp.o -MF CMakeFiles/FilterCatalog.dir/FilterMatchers.cpp.o.d -o CMakeFiles/FilterCatalog.dir/FilterMatchers.cpp.o -c /build/reproducible-path/rdkit-202503.1/Code/GraphMol/FilterCatalog/FilterMatchers.cpp [ 36%] Linking CXX shared module ../../../../rdkit/Chem/rdSLNParse.so cd 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-I/build/reproducible-path/rdkit-202503.1/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/GraphMol/ReducedGraphs/CMakeFiles/testReducedGraphs.dir/test1.cpp.o -MF CMakeFiles/testReducedGraphs.dir/test1.cpp.o.d -o CMakeFiles/testReducedGraphs.dir/test1.cpp.o -c /build/reproducible-path/rdkit-202503.1/Code/GraphMol/ReducedGraphs/test1.cpp -[ 36%] Building CXX object Code/GraphMol/Fingerprints/CMakeFiles/Fingerprints.dir/PatternFingerprints.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 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Code/GraphMol/Fingerprints/CMakeFiles/Fingerprints.dir/PatternFingerprints.cpp.o -MF CMakeFiles/Fingerprints.dir/PatternFingerprints.cpp.o.d -o CMakeFiles/Fingerprints.dir/PatternFingerprints.cpp.o -c /build/reproducible-path/rdkit-202503.1/Code/GraphMol/Fingerprints/PatternFingerprints.cpp -[ 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 -[ 36%] Linking CXX shared library ../../../lib/libRDKitAbbreviations.so -cd /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/Abbreviations && /usr/bin/cmake -E cmake_link_script CMakeFiles/Abbreviations.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 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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 ../../../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 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/build/reproducible-path/rdkit-202503.1/Code/GraphMol/Depictor/RDDepictor.cpp -[ 36%] Linking CXX shared library ../../../lib/libRDKitFragCatalog.so -cd /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FragCatalog && /usr/bin/cmake -E cmake_link_script CMakeFiles/FragCatalog.dir/link.txt --verbose=1 -/usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=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/FragCatalog.dir/link.d -Wl,-z,relro -Wl,-z,now -shared -Wl,-soname,libRDKitFragCatalog.so.1 -o ../../../lib/libRDKitFragCatalog.so.1.2025.03.1 CMakeFiles/FragCatalog.dir/FragCatalogUtils.cpp.o CMakeFiles/FragCatalog.dir/FragCatGenerator.cpp.o CMakeFiles/FragCatalog.dir/FragCatalogEntry.cpp.o 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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/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 -[ 36%] Linking CXX executable testSLNParse -cd /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/SLNParse 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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/MolChemicalFeatures/Wrap/CMakeFiles/rdMolChemicalFeatures.dir/MolChemicalFeature.cpp.o -MF CMakeFiles/rdMolChemicalFeatures.dir/MolChemicalFeature.cpp.o.d -o CMakeFiles/rdMolChemicalFeatures.dir/MolChemicalFeature.cpp.o -c /build/reproducible-path/rdkit-202503.1/Code/GraphMol/MolChemicalFeatures/Wrap/MolChemicalFeature.cpp -[ 36%] Linking CXX executable testReducedGraphs -cd 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/usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/MolChemicalFeatures/Wrap/CMakeFiles/rdMolChemicalFeatures.dir/ChemicalFeatureUtils.cpp.o -MF CMakeFiles/rdMolChemicalFeatures.dir/ChemicalFeatureUtils.cpp.o.d -o CMakeFiles/rdMolChemicalFeatures.dir/ChemicalFeatureUtils.cpp.o -c /build/reproducible-path/rdkit-202503.1/Code/GraphMol/MolChemicalFeatures/Wrap/ChemicalFeatureUtils.cpp -[ 36%] Building CXX object Code/GraphMol/Fingerprints/CMakeFiles/Fingerprints.dir/AtomPairs.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 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-I/build/reproducible-path/rdkit-202503.1/External -I/build/reproducible-path/rdkit-202503.1/Code -I/build/reproducible-path/rdkit-202503.1/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-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/FilterCatalogEntry.cpp.o -MF CMakeFiles/FilterCatalog.dir/FilterCatalogEntry.cpp.o.d -o CMakeFiles/FilterCatalog.dir/FilterCatalogEntry.cpp.o -c /build/reproducible-path/rdkit-202503.1/Code/GraphMol/FilterCatalog/FilterCatalogEntry.cpp -[ 37%] Building CXX object Code/GraphMol/ForceFieldHelpers/CMakeFiles/ForceFieldHelpers.dir/UFF/Builder.cpp.o -cd 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-DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202503.1/External -I/build/reproducible-path/rdkit-202503.1/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/Depictor/CMakeFiles/Depictor.dir/DepictUtils.cpp.o -MF CMakeFiles/Depictor.dir/DepictUtils.cpp.o.d -o CMakeFiles/Depictor.dir/DepictUtils.cpp.o -c /build/reproducible-path/rdkit-202503.1/Code/GraphMol/Depictor/DepictUtils.cpp -[ 37%] 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 && 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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 -[ 37%] Building CXX object Code/GraphMol/Fingerprints/CMakeFiles/Fingerprints.dir/MACCS.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 -DFingerprints_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_FINGERPRINTS_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION 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Code/GraphMol/MolChemicalFeatures/Wrap/CMakeFiles/rdMolChemicalFeatures.dir/MolChemicalFeature.cpp.o +cd /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/MolChemicalFeatures/Wrap && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_NUMPY_DYN_LINK -DBOOST_NUMPY_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DrdMolChemicalFeatures_EXPORTS -I/build/reproducible-path/rdkit-202503.1/External -I/build/reproducible-path/rdkit-202503.1/Code -I/usr/lib/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/MolChemicalFeatures/Wrap/CMakeFiles/rdMolChemicalFeatures.dir/MolChemicalFeature.cpp.o -MF CMakeFiles/rdMolChemicalFeatures.dir/MolChemicalFeature.cpp.o.d -o CMakeFiles/rdMolChemicalFeatures.dir/MolChemicalFeature.cpp.o -c /build/reproducible-path/rdkit-202503.1/Code/GraphMol/MolChemicalFeatures/Wrap/MolChemicalFeature.cpp +[ 39%] Building CXX object Code/GraphMol/Fingerprints/CMakeFiles/Fingerprints.dir/MHFP.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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-DRDK_USE_STRICT_ROTOR_DEFINITION -DrdMolChemicalFeatures_EXPORTS -I/build/reproducible-path/rdkit-202503.1/External -I/build/reproducible-path/rdkit-202503.1/Code -I/usr/lib/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/MolChemicalFeatures/Wrap/CMakeFiles/rdMolChemicalFeatures.dir/MolChemicalFeatureFactory.cpp.o -MF CMakeFiles/rdMolChemicalFeatures.dir/MolChemicalFeatureFactory.cpp.o.d -o CMakeFiles/rdMolChemicalFeatures.dir/MolChemicalFeatureFactory.cpp.o -c 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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/Fingerprints/CMakeFiles/Fingerprints.dir/FingerprintGenerator.cpp.o -MF CMakeFiles/Fingerprints.dir/FingerprintGenerator.cpp.o.d -o CMakeFiles/Fingerprints.dir/FingerprintGenerator.cpp.o -c /build/reproducible-path/rdkit-202503.1/Code/GraphMol/Fingerprints/FingerprintGenerator.cpp +[ 39%] 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 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../../../lib/libRDKitSubstructMatch.so.1.2025.03.1 ../../../lib/libRDKitForceField.so.1.2025.03.1 ../../../lib/libRDKitGenericGroups.so.1.2025.03.1 ../../../lib/libRDKitOptimizer.so.1.2025.03.1 ../../../lib/libRDKitTrajectory.so.1.2025.03.1 ../../../lib/libRDKitGraphMol.so.1.2025.03.1 ../../../lib/libRDKitRDGeometryLib.so.1.2025.03.1 ../../../lib/libRDKitDataStructs.so.1.2025.03.1 ../../../lib/libRDKitRDGeneral.so.1.2025.03.1 /usr/lib/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/ForceFieldHelpers && /usr/bin/cmake -E cmake_symlink_library ../../../lib/libRDKitForceFieldHelpers.so.1.2025.03.1 ../../../lib/libRDKitForceFieldHelpers.so.1 ../../../lib/libRDKitForceFieldHelpers.so make[4]: Leaving directory '/build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu' -[ 40%] Built target 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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/MolChemicalFeatures/Wrap/CMakeFiles/rdMolChemicalFeatures.dir/ChemicalFeatureUtils.cpp.o -MF CMakeFiles/rdMolChemicalFeatures.dir/ChemicalFeatureUtils.cpp.o.d -o CMakeFiles/rdMolChemicalFeatures.dir/ChemicalFeatureUtils.cpp.o -c /build/reproducible-path/rdkit-202503.1/Code/GraphMol/MolChemicalFeatures/Wrap/ChemicalFeatureUtils.cpp 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/ForceField /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/ForceField /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/ForceField/CMakeFiles/ForceFieldsCatch.dir/DependInfo.cmake "--color=" -/usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=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/Fingerprints.dir/link.d -Wl,-z,relro -Wl,-z,now -shared -Wl,-soname,libRDKitFingerprints.so.1 -o ../../../lib/libRDKitFingerprints.so.1.2025.03.1 CMakeFiles/Fingerprints.dir/Fingerprints.cpp.o CMakeFiles/Fingerprints.dir/PatternFingerprints.cpp.o CMakeFiles/Fingerprints.dir/MorganFingerprints.cpp.o CMakeFiles/Fingerprints.dir/AtomPairs.cpp.o CMakeFiles/Fingerprints.dir/MACCS.cpp.o CMakeFiles/Fingerprints.dir/MHFP.cpp.o CMakeFiles/Fingerprints.dir/FingerprintGenerator.cpp.o CMakeFiles/Fingerprints.dir/AtomPairGenerator.cpp.o CMakeFiles/Fingerprints.dir/MorganGenerator.cpp.o CMakeFiles/Fingerprints.dir/RDKitFPGenerator.cpp.o CMakeFiles/Fingerprints.dir/FingerprintUtil.cpp.o CMakeFiles/Fingerprints.dir/TopologicalTorsionGenerator.cpp.o ../../../lib/libRDKitSubgraphs.so.1.2025.03.1 ../../../lib/libRDKitSubstructMatch.so.1.2025.03.1 ../../../lib/libRDKitSmilesParse.so.1.2025.03.1 ../../../lib/libRDKitGenericGroups.so.1.2025.03.1 ../../../lib/libRDKitGraphMol.so.1.2025.03.1 ../../../lib/libRDKitRDGeometryLib.so.1.2025.03.1 ../../../lib/libRDKitDataStructs.so.1.2025.03.1 ../../../lib/libRDKitRDGeneral.so.1.2025.03.1 /usr/lib/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/Fingerprints && /usr/bin/cmake -E cmake_symlink_library ../../../lib/libRDKitFingerprints.so.1.2025.03.1 ../../../lib/libRDKitFingerprints.so.1 ../../../lib/libRDKitFingerprints.so make[4]: Leaving directory '/build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu' make -f Code/ForceField/CMakeFiles/ForceFieldsCatch.dir/build.make Code/ForceField/CMakeFiles/ForceFieldsCatch.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' -[ 40%] Building CXX object Code/ForceField/CMakeFiles/ForceFieldsCatch.dir/catch_tests.cpp.o +[ 39%] Building CXX object Code/ForceField/CMakeFiles/ForceFieldsCatch.dir/catch_tests.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 -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_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/ForceField/CMakeFiles/ForceFieldsCatch.dir/catch_tests.cpp.o -MF CMakeFiles/ForceFieldsCatch.dir/catch_tests.cpp.o.d -o CMakeFiles/ForceFieldsCatch.dir/catch_tests.cpp.o -c /build/reproducible-path/rdkit-202503.1/Code/ForceField/catch_tests.cpp -[ 40%] Built target Fingerprints +[ 39%] Building CXX object Code/GraphMol/Fingerprints/CMakeFiles/Fingerprints.dir/AtomPairGenerator.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 -DFingerprints_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_FINGERPRINTS_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT 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Linking CXX shared library ../../../lib/libRDKitDepictor.so +cd /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/Depictor && /usr/bin/cmake -E cmake_link_script CMakeFiles/Depictor.dir/link.txt --verbose=1 +[ 40%] Building CXX object Code/GraphMol/Fingerprints/CMakeFiles/Fingerprints.dir/MorganGenerator.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 -DFingerprints_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_FINGERPRINTS_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202503.1/External -I/build/reproducible-path/rdkit-202503.1/Code -I/build/reproducible-path/rdkit-202503.1/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/Fingerprints/CMakeFiles/Fingerprints.dir/MorganGenerator.cpp.o -MF CMakeFiles/Fingerprints.dir/MorganGenerator.cpp.o.d -o CMakeFiles/Fingerprints.dir/MorganGenerator.cpp.o -c /build/reproducible-path/rdkit-202503.1/Code/GraphMol/Fingerprints/MorganGenerator.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 -Wl,--dependency-file=CMakeFiles/Depictor.dir/link.d -Wl,-z,relro -Wl,-z,now -shared -Wl,-soname,libRDKitDepictor.so.1 -o ../../../lib/libRDKitDepictor.so.1.2025.03.1 CMakeFiles/Depictor.dir/RDDepictor.cpp.o CMakeFiles/Depictor.dir/EmbeddedFrag.cpp.o CMakeFiles/Depictor.dir/DepictUtils.cpp.o CMakeFiles/Depictor.dir/Templates.cpp.o /usr/lib/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 +cd /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/Depictor && /usr/bin/cmake -E cmake_symlink_library ../../../lib/libRDKitDepictor.so.1.2025.03.1 ../../../lib/libRDKitDepictor.so.1 ../../../lib/libRDKitDepictor.so +make[4]: Leaving directory '/build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu' +[ 40%] Built target Depictor make -f Code/DistGeom/CMakeFiles/DistGeometry.dir/build.make Code/DistGeom/CMakeFiles/DistGeometry.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/DistGeom 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-DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202503.1/External -I/build/reproducible-path/rdkit-202503.1/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/DistGeom/CMakeFiles/DistGeometry.dir/DistGeomUtils.cpp.o -MF CMakeFiles/DistGeometry.dir/DistGeomUtils.cpp.o.d -o CMakeFiles/DistGeometry.dir/DistGeomUtils.cpp.o -c /build/reproducible-path/rdkit-202503.1/Code/DistGeom/DistGeomUtils.cpp +[ 40%] Linking CXX shared library ../../../lib/libRDKitFragCatalog.so +cd /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FragCatalog && /usr/bin/cmake -E cmake_link_script CMakeFiles/FragCatalog.dir/link.txt --verbose=1 +/usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=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/FragCatalog.dir/link.d -Wl,-z,relro -Wl,-z,now -shared -Wl,-soname,libRDKitFragCatalog.so.1 -o ../../../lib/libRDKitFragCatalog.so.1.2025.03.1 CMakeFiles/FragCatalog.dir/FragCatalogUtils.cpp.o CMakeFiles/FragCatalog.dir/FragCatGenerator.cpp.o CMakeFiles/FragCatalog.dir/FragCatalogEntry.cpp.o CMakeFiles/FragCatalog.dir/FragCatParams.cpp.o CMakeFiles/FragCatalog.dir/FragFPGenerator.cpp.o ../../../lib/libRDKitSubgraphs.so.1.2025.03.1 ../../../lib/libRDKitSubstructMatch.so.1.2025.03.1 ../../../lib/libRDKitSmilesParse.so.1.2025.03.1 ../../../lib/libRDKitCatalogs.so.1.2025.03.1 ../../../lib/libRDKitGenericGroups.so.1.2025.03.1 ../../../lib/libRDKitGraphMol.so.1.2025.03.1 ../../../lib/libRDKitRDGeometryLib.so.1.2025.03.1 ../../../lib/libRDKitDataStructs.so.1.2025.03.1 ../../../lib/libRDKitRDGeneral.so.1.2025.03.1 /usr/lib/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/FragCatalog && /usr/bin/cmake -E cmake_symlink_library ../../../lib/libRDKitFragCatalog.so.1.2025.03.1 ../../../lib/libRDKitFragCatalog.so.1 ../../../lib/libRDKitFragCatalog.so +make[4]: Leaving directory '/build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu' +[ 40%] Built target FragCatalog make -f Code/ForceField/Wrap/CMakeFiles/rdForceField.dir/build.make Code/ForceField/Wrap/CMakeFiles/rdForceField.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-202503.1/obj-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/ForceField/Wrap /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/ForceField/Wrap /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/ForceField/Wrap/CMakeFiles/rdForceField.dir/DependInfo.cmake "--color=" @@ -4175,24 +4162,23 @@ make[4]: Entering directory '/build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu' [ 40%] Building CXX object Code/ForceField/Wrap/CMakeFiles/rdForceField.dir/ForceField.cpp.o cd /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/ForceField/Wrap && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_NUMPY_DYN_LINK -DBOOST_NUMPY_NO_LIB -DBOOST_PYTHON_DYN_LINK 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Code/ForceField/Wrap/CMakeFiles/rdForceField.dir/ForceField.cpp.o -MF CMakeFiles/rdForceField.dir/ForceField.cpp.o.d -o CMakeFiles/rdForceField.dir/ForceField.cpp.o -c /build/reproducible-path/rdkit-202503.1/Code/ForceField/Wrap/ForceField.cpp -make -f Code/GraphMol/Fingerprints/Wrap/CMakeFiles/rdFingerprintGenerator.dir/build.make Code/GraphMol/Fingerprints/Wrap/CMakeFiles/rdFingerprintGenerator.dir/depend -make[4]: Entering directory '/build/reproducible-path/rdkit-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/Wrap /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/Fingerprints/Wrap /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/Fingerprints/Wrap/CMakeFiles/rdFingerprintGenerator.dir/DependInfo.cmake "--color=" +[ 40%] Building CXX object Code/GraphMol/Fingerprints/CMakeFiles/Fingerprints.dir/RDKitFPGenerator.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 -DFingerprints_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_FINGERPRINTS_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202503.1/External -I/build/reproducible-path/rdkit-202503.1/Code -I/build/reproducible-path/rdkit-202503.1/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/Fingerprints/CMakeFiles/Fingerprints.dir/RDKitFPGenerator.cpp.o -MF CMakeFiles/Fingerprints.dir/RDKitFPGenerator.cpp.o.d -o CMakeFiles/Fingerprints.dir/RDKitFPGenerator.cpp.o -c /build/reproducible-path/rdkit-202503.1/Code/GraphMol/Fingerprints/RDKitFPGenerator.cpp +[ 40%] Building CXX object Code/GraphMol/Fingerprints/CMakeFiles/Fingerprints.dir/FingerprintUtil.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 -DFingerprints_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_FINGERPRINTS_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202503.1/External -I/build/reproducible-path/rdkit-202503.1/Code -I/build/reproducible-path/rdkit-202503.1/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/Fingerprints/CMakeFiles/Fingerprints.dir/FingerprintUtil.cpp.o -MF CMakeFiles/Fingerprints.dir/FingerprintUtil.cpp.o.d -o CMakeFiles/Fingerprints.dir/FingerprintUtil.cpp.o -c /build/reproducible-path/rdkit-202503.1/Code/GraphMol/Fingerprints/FingerprintUtil.cpp +[ 40%] 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 +/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/rdAbbreviations.dir/link.d -Wl,-z,relro -Wl,-z,now -shared -o ../../../../rdkit/Chem/rdAbbreviations.so CMakeFiles/rdAbbreviations.dir/rdAbbreviations.cpp.o ../../../../lib/libRDKitAbbreviations.so.1.2025.03.1 ../../../../lib/libRDKitRDBoost.so.1.2025.03.1 ../../../../lib/libRDKitSmilesParse.so.1.2025.03.1 ../../../../lib/libRDKitSubstructMatch.so.1.2025.03.1 ../../../../lib/libRDKitGenericGroups.so.1.2025.03.1 ../../../../lib/libRDKitGraphMol.so.1.2025.03.1 ../../../../lib/libRDKitRDGeometryLib.so.1.2025.03.1 ../../../../lib/libRDKitDataStructs.so.1.2025.03.1 /usr/lib/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' -make -f Code/GraphMol/Fingerprints/Wrap/CMakeFiles/rdFingerprintGenerator.dir/build.make Code/GraphMol/Fingerprints/Wrap/CMakeFiles/rdFingerprintGenerator.dir/build -make[4]: Entering directory '/build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu' -[ 40%] Building CXX object Code/GraphMol/Fingerprints/Wrap/CMakeFiles/rdFingerprintGenerator.dir/FingerprintGeneratorWrapper.cpp.o -cd /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/Fingerprints/Wrap && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_NUMPY_DYN_LINK -DBOOST_NUMPY_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DrdFingerprintGenerator_EXPORTS -I/build/reproducible-path/rdkit-202503.1/External -I/build/reproducible-path/rdkit-202503.1/Code -I/build/reproducible-path/rdkit-202503.1/External/boost-numeric-bindings -I/usr/lib/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/Fingerprints/Wrap/CMakeFiles/rdFingerprintGenerator.dir/FingerprintGeneratorWrapper.cpp.o -MF CMakeFiles/rdFingerprintGenerator.dir/FingerprintGeneratorWrapper.cpp.o.d -o CMakeFiles/rdFingerprintGenerator.dir/FingerprintGeneratorWrapper.cpp.o -c /build/reproducible-path/rdkit-202503.1/Code/GraphMol/Fingerprints/Wrap/FingerprintGeneratorWrapper.cpp -make -f Code/GraphMol/Fingerprints/Wrap/CMakeFiles/rdMHFPFingerprint.dir/build.make Code/GraphMol/Fingerprints/Wrap/CMakeFiles/rdMHFPFingerprint.dir/depend +[ 40%] Built target rdAbbreviations +make -f Code/GraphMol/Depictor/Wrap/CMakeFiles/rdDepictor.dir/build.make Code/GraphMol/Depictor/Wrap/CMakeFiles/rdDepictor.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-202503.1/obj-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/Wrap /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/Fingerprints/Wrap 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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/Fingerprints/Wrap/CMakeFiles/rdMHFPFingerprint.dir/MHFPWrapper.cpp.o -MF CMakeFiles/rdMHFPFingerprint.dir/MHFPWrapper.cpp.o.d -o CMakeFiles/rdMHFPFingerprint.dir/MHFPWrapper.cpp.o -c /build/reproducible-path/rdkit-202503.1/Code/GraphMol/Fingerprints/Wrap/MHFPWrapper.cpp -[ 40%] Linking CXX shared library ../../../lib/libRDKitFilterCatalog.so -cd 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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/FilterCatalog && /usr/bin/cmake -E cmake_symlink_library ../../../lib/libRDKitFilterCatalog.so.1.2025.03.1 ../../../lib/libRDKitFilterCatalog.so.1 ../../../lib/libRDKitFilterCatalog.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/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 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-I/build/reproducible-path/rdkit-202503.1/External -I/build/reproducible-path/rdkit-202503.1/Code -I/build/reproducible-path/rdkit-202503.1/External/boost-numeric-bindings -I/usr/lib/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/rdfiltercatalog.cpp.o -MF CMakeFiles/rdfiltercatalog.dir/rdfiltercatalog.cpp.o.d -o CMakeFiles/rdfiltercatalog.dir/rdfiltercatalog.cpp.o -c /build/reproducible-path/rdkit-202503.1/Code/GraphMol/FilterCatalog/Wrap/rdfiltercatalog.cpp -[ 41%] Linking CXX executable ForceFieldsCatch -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/DistGeom/CMakeFiles/DistGeometry.dir/TriangleSmooth.cpp.o -MF CMakeFiles/DistGeometry.dir/TriangleSmooth.cpp.o.d -o CMakeFiles/DistGeometry.dir/TriangleSmooth.cpp.o -c /build/reproducible-path/rdkit-202503.1/Code/DistGeom/TriangleSmooth.cpp -[ 42%] 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 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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 -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 +[ 42%] Building CXX object Code/GraphMol/ChemTransforms/CMakeFiles/ChemTransforms.dir/ChemTransforms.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 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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_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_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/DistGeom/CMakeFiles/DistGeometry.dir/DistViolationContribs.cpp.o -MF CMakeFiles/DistGeometry.dir/DistViolationContribs.cpp.o.d -o CMakeFiles/DistGeometry.dir/DistViolationContribs.cpp.o -c /build/reproducible-path/rdkit-202503.1/Code/DistGeom/DistViolationContribs.cpp -make[4]: Leaving directory '/build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu' -[ 42%] Built target MolHash -make -f Code/GraphMol/MolHash/Wrap/CMakeFiles/rdMolHash.dir/build.make Code/GraphMol/MolHash/Wrap/CMakeFiles/rdMolHash.dir/depend -make[4]: Entering directory '/build/reproducible-path/rdkit-202503.1/obj-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/MolHash/Wrap 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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 -[ 42%] 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 -[ 42%] 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 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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/MolHash/CMakeFiles/MolHash.dir/normalize.cpp.o -MF CMakeFiles/MolHash.dir/normalize.cpp.o.d -o CMakeFiles/MolHash.dir/normalize.cpp.o -c /build/reproducible-path/rdkit-202503.1/Code/GraphMol/MolHash/normalize.cpp [ 42%] 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 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&& /usr/bin/c++ -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_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_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/ChemTransforms/CMakeFiles/ChemTransforms.dir/MolFragmenter.cpp.o -MF CMakeFiles/ChemTransforms.dir/MolFragmenter.cpp.o.d -o CMakeFiles/ChemTransforms.dir/MolFragmenter.cpp.o -c /build/reproducible-path/rdkit-202503.1/Code/GraphMol/ChemTransforms/MolFragmenter.cpp +[ 42%] Linking CXX shared library ../../../lib/libRDKitFingerprints.so +cd /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/Fingerprints && /usr/bin/cmake -E cmake_link_script CMakeFiles/Fingerprints.dir/link.txt --verbose=1 +/usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=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/Fingerprints.dir/link.d -Wl,-z,relro -Wl,-z,now -shared -Wl,-soname,libRDKitFingerprints.so.1 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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 +cd /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/Fingerprints && /usr/bin/cmake -E cmake_symlink_library ../../../lib/libRDKitFingerprints.so.1.2025.03.1 ../../../lib/libRDKitFingerprints.so.1 ../../../lib/libRDKitFingerprints.so make[4]: Leaving directory '/build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu' -[ 42%] Built target rdDepictor -[ 42%] Linking CXX shared library ../../../lib/libRDKitChemTransforms.so -cd /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/ChemTransforms && /usr/bin/cmake -E cmake_link_script CMakeFiles/ChemTransforms.dir/link.txt --verbose=1 -/usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection 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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 +[ 42%] Built target Fingerprints +make -f Code/GraphMol/Fingerprints/Wrap/CMakeFiles/rdFingerprintGenerator.dir/build.make Code/GraphMol/Fingerprints/Wrap/CMakeFiles/rdFingerprintGenerator.dir/depend +make[4]: Entering directory '/build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu' +cd /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu && 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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/FileParsers/CMakeFiles/FileParsers.dir/Mol2FileParser.cpp.o -MF CMakeFiles/FileParsers.dir/Mol2FileParser.cpp.o.d -o CMakeFiles/FileParsers.dir/Mol2FileParser.cpp.o -c /build/reproducible-path/rdkit-202503.1/Code/GraphMol/FileParsers/Mol2FileParser.cpp -[ 42%] Building CXX object Code/GraphMol/FileParsers/CMakeFiles/FileParsers.dir/MolFileParser.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 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CXX object Code/GraphMol/Fingerprints/Wrap/CMakeFiles/rdMHFPFingerprint.dir/MHFPWrapper.cpp.o +cd /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/Fingerprints/Wrap && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_NUMPY_DYN_LINK -DBOOST_NUMPY_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DrdMHFPFingerprint_EXPORTS -I/build/reproducible-path/rdkit-202503.1/External -I/build/reproducible-path/rdkit-202503.1/Code -I/build/reproducible-path/rdkit-202503.1/External/boost-numeric-bindings -I/usr/lib/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/Fingerprints/Wrap/CMakeFiles/rdMHFPFingerprint.dir/MHFPWrapper.cpp.o -MF CMakeFiles/rdMHFPFingerprint.dir/MHFPWrapper.cpp.o.d -o CMakeFiles/rdMHFPFingerprint.dir/MHFPWrapper.cpp.o -c /build/reproducible-path/rdkit-202503.1/Code/GraphMol/Fingerprints/Wrap/MHFPWrapper.cpp [ 42%] Linking CXX shared library ../../lib/libRDKitDistGeometry.so cd /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/DistGeom && /usr/bin/cmake -E cmake_link_script CMakeFiles/DistGeometry.dir/link.txt --verbose=1 /usr/bin/c++ -fPIC -g -O2 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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 @@ -4299,102 +4277,160 @@ make[4]: Entering directory '/build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu' [ 42%] Building CXX object Code/GraphMol/DistGeomHelpers/CMakeFiles/DistGeomHelpers.dir/BoundsMatrixBuilder.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_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_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/DistGeomHelpers/CMakeFiles/DistGeomHelpers.dir/BoundsMatrixBuilder.cpp.o -MF CMakeFiles/DistGeomHelpers.dir/BoundsMatrixBuilder.cpp.o.d -o CMakeFiles/DistGeomHelpers.dir/BoundsMatrixBuilder.cpp.o -c /build/reproducible-path/rdkit-202503.1/Code/GraphMol/DistGeomHelpers/BoundsMatrixBuilder.cpp -[ 43%] 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 -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/rdinchi.dir/link.d -Wl,-z,relro -Wl,-z,now -shared -o ../../../rdkit/Chem/rdinchi.so CMakeFiles/rdinchi.dir/pyInchi.cpp.o ../../../lib/libRDKitRDInchiLib.so.1.2025.03.1 ../../../lib/libRDKitRDBoost.so.1.2025.03.1 /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/libRDKitMolTransforms.so.1.2025.03.1 ../../../lib/libRDKitEigenSolvers.so.1.2025.03.1 ../../../lib/libRDKitAlignment.so.1.2025.03.1 ../../../lib/libRDKitSubstructMatch.so.1.2025.03.1 ../../../lib/libRDKitGenericGroups.so.1.2025.03.1 ../../../lib/libRDKitSmilesParse.so.1.2025.03.1 ../../../lib/libRDKitGraphMol.so.1.2025.03.1 ../../../lib/libRDKitRDGeometryLib.so.1.2025.03.1 ../../../lib/libRDKitDataStructs.so.1.2025.03.1 /usr/lib/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 +[ 42%] 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' -[ 43%] Built target rdinchi +[ 42%] Built target MolHash make 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Code/DistGeom/CMakeFiles/testDistGeom.dir/testDistGeom.cpp.o +[ 42%] Building CXX object Code/DistGeom/CMakeFiles/testDistGeom.dir/testDistGeom.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 -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_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/DistGeom/CMakeFiles/testDistGeom.dir/testDistGeom.cpp.o -MF CMakeFiles/testDistGeom.dir/testDistGeom.cpp.o.d -o CMakeFiles/testDistGeom.dir/testDistGeom.cpp.o -c /build/reproducible-path/rdkit-202503.1/Code/DistGeom/testDistGeom.cpp -[ 43%] Linking CXX shared module ../../../../rdkit/Chem/rdMolHash.so -cd /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/MolHash/Wrap && /usr/bin/cmake -E cmake_link_script CMakeFiles/rdMolHash.dir/link.txt --verbose=1 -[ 43%] Linking CXX shared library ../../../lib/libRDKitMolInteractionFields.so +[ 42%] 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 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/build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/MolInteractionFields && /usr/bin/cmake -E cmake_symlink_library ../../../lib/libRDKitMolInteractionFields.so.1.2025.03.1 ../../../lib/libRDKitMolInteractionFields.so.1 ../../../lib/libRDKitMolInteractionFields.so make[4]: Leaving directory '/build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu' -[ 43%] Built target rdMolHash +[ 42%] Built target MolInteractionFields make -f Code/DistGeom/Wrap/CMakeFiles/DistGeom.dir/build.make Code/DistGeom/Wrap/CMakeFiles/DistGeom.dir/depend -/usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=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 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Entering directory '/build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu' -[ 43%] Building CXX object Code/DistGeom/Wrap/CMakeFiles/DistGeom.dir/DistGeom.cpp.o +[ 42%] Building CXX object Code/DistGeom/Wrap/CMakeFiles/DistGeom.dir/DistGeom.cpp.o cd /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/DistGeom/Wrap && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_NUMPY_DYN_LINK -DBOOST_NUMPY_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DDistGeom_EXPORTS -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202503.1/External -I/build/reproducible-path/rdkit-202503.1/Code -I/usr/lib/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/DistGeom/Wrap/CMakeFiles/DistGeom.dir/DistGeom.cpp.o -MF CMakeFiles/DistGeom.dir/DistGeom.cpp.o.d -o CMakeFiles/DistGeom.dir/DistGeom.cpp.o -c /build/reproducible-path/rdkit-202503.1/Code/DistGeom/Wrap/DistGeom.cpp +[ 42%] Linking CXX shared module ../../../rdkit/ForceField/rdForceField.so +cd /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/ForceField/Wrap && /usr/bin/cmake -E cmake_link_script CMakeFiles/rdForceField.dir/link.txt --verbose=1 +/usr/bin/c++ -fPIC -g -O2 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../../../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' +[ 42%] Built target rdForceField +make -f Code/GraphMol/MolHash/Wrap/CMakeFiles/rdMolHash.dir/build.make Code/GraphMol/MolHash/Wrap/CMakeFiles/rdMolHash.dir/depend +make[4]: Entering directory '/build/reproducible-path/rdkit-202503.1/obj-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/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 +[ 42%] 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 +[ 42%] 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 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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/DistGeomHelpers/CMakeFiles/DistGeomHelpers.dir/EmbedderUtils.cpp.o -MF CMakeFiles/DistGeomHelpers.dir/EmbedderUtils.cpp.o.d -o CMakeFiles/DistGeomHelpers.dir/EmbedderUtils.cpp.o -c /build/reproducible-path/rdkit-202503.1/Code/GraphMol/DistGeomHelpers/EmbedderUtils.cpp -[ 43%] Linking CXX executable testDistGeom +[ 42%] Built target RDInchiLib +make -f External/INCHI-API/Wrap/CMakeFiles/rdinchi.dir/build.make External/INCHI-API/Wrap/CMakeFiles/rdinchi.dir/depend +make[4]: Entering directory '/build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu' +cd 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/build/reproducible-path/rdkit-202503.1/Code/GraphMol/FileParsers/MolFileParser.cpp [ 43%] Building CXX object Code/GraphMol/FileParsers/CMakeFiles/FileParsers.dir/MolSGroupParsing.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 -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_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/MolSGroupParsing.cpp.o -MF CMakeFiles/FileParsers.dir/MolSGroupParsing.cpp.o.d -o CMakeFiles/FileParsers.dir/MolSGroupParsing.cpp.o -c /build/reproducible-path/rdkit-202503.1/Code/GraphMol/FileParsers/MolSGroupParsing.cpp -[ 44%] Linking CXX shared module ../../../../rdkit/Chem/rdMHFPFingerprint.so -cd /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/Fingerprints/Wrap && /usr/bin/cmake -E cmake_link_script CMakeFiles/rdMHFPFingerprint.dir/link.txt --verbose=1 -[ 44%] Building CXX object Code/GraphMol/FileParsers/CMakeFiles/FileParsers.dir/MolSGroupWriting.cpp.o +[ 43%] Building CXX object 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-I/build/reproducible-path/rdkit-202503.1/External -I/build/reproducible-path/rdkit-202503.1/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-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/SDMolSupplier.cpp.o -MF CMakeFiles/FileParsers.dir/SDMolSupplier.cpp.o.d -o CMakeFiles/FileParsers.dir/SDMolSupplier.cpp.o -c /build/reproducible-path/rdkit-202503.1/Code/GraphMol/FileParsers/SDMolSupplier.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 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../../../../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' -[ 44%] Built target DistGeom -[ 45%] Building CXX object Code/GraphMol/FileParsers/CMakeFiles/FileParsers.dir/ForwardSDMolSupplier.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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Code/GraphMol/FileParsers/CMakeFiles/FileParsers.dir/SDWriter.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 -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_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 [ 45%] 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 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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' [ 45%] Built target rdFingerprintGenerator -[ 45%] Building CXX object Code/GraphMol/FileParsers/CMakeFiles/FileParsers.dir/SDMolSupplier.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 -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_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/SDMolSupplier.cpp.o -MF CMakeFiles/FileParsers.dir/SDMolSupplier.cpp.o.d -o CMakeFiles/FileParsers.dir/SDMolSupplier.cpp.o -c /build/reproducible-path/rdkit-202503.1/Code/GraphMol/FileParsers/SDMolSupplier.cpp -[ 45%] Building CXX object Code/GraphMol/FileParsers/CMakeFiles/FileParsers.dir/SDWriter.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 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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/FileParsers/CMakeFiles/FileParsers.dir/SmilesMolSupplier.cpp.o -MF CMakeFiles/FileParsers.dir/SmilesMolSupplier.cpp.o.d -o CMakeFiles/FileParsers.dir/SmilesMolSupplier.cpp.o -c /build/reproducible-path/rdkit-202503.1/Code/GraphMol/FileParsers/SmilesMolSupplier.cpp -[ 45%] Linking CXX shared library ../../../lib/libRDKitDistGeomHelpers.so -cd /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/DistGeomHelpers && /usr/bin/cmake -E cmake_link_script CMakeFiles/DistGeomHelpers.dir/link.txt --verbose=1 -/usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong 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Code/GraphMol/FileParsers/CMakeFiles/FileParsers.dir/SmilesWriter.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 -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_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/SmilesWriter.cpp.o -MF CMakeFiles/FileParsers.dir/SmilesWriter.cpp.o.d -o CMakeFiles/FileParsers.dir/SmilesWriter.cpp.o -c /build/reproducible-path/rdkit-202503.1/Code/GraphMol/FileParsers/SmilesWriter.cpp [ 45%] Building CXX object Code/GraphMol/FileParsers/CMakeFiles/FileParsers.dir/TDTMolSupplier.cpp.o @@ -4403,11 +4439,6 @@ 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_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_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/TDTWriter.cpp.o -MF CMakeFiles/FileParsers.dir/TDTWriter.cpp.o.d -o CMakeFiles/FileParsers.dir/TDTWriter.cpp.o -c /build/reproducible-path/rdkit-202503.1/Code/GraphMol/FileParsers/TDTWriter.cpp [ 45%] Building CXX object Code/GraphMol/FileParsers/CMakeFiles/FileParsers.dir/TplFileParser.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 -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_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/TplFileParser.cpp.o -MF CMakeFiles/FileParsers.dir/TplFileParser.cpp.o.d -o CMakeFiles/FileParsers.dir/TplFileParser.cpp.o -c /build/reproducible-path/rdkit-202503.1/Code/GraphMol/FileParsers/TplFileParser.cpp -[ 45%] Linking CXX shared module ../../../../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 ../../../../lib/libRDKitSubstructMatch.so.1.2025.03.1 ../../../../lib/libRDKitSmilesParse.so.1.2025.03.1 ../../../../lib/libRDKitRDBoost.so.1.2025.03.1 ../../../../lib/libRDKitGenericGroups.so.1.2025.03.1 ../../../../lib/libRDKitOptimizer.so.1.2025.03.1 ../../../../lib/libRDKitTrajectory.so.1.2025.03.1 ../../../../lib/libRDKitGraphMol.so.1.2025.03.1 ../../../../lib/libRDKitRDGeometryLib.so.1.2025.03.1 ../../../../lib/libRDKitDataStructs.so.1.2025.03.1 ../../../../lib/libRDKitRDGeneral.so.1.2025.03.1 -ldl /usr/lib/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' -[ 45%] Built target rdMIF [ 45%] Building CXX object Code/GraphMol/FileParsers/CMakeFiles/FileParsers.dir/TplFileWriter.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 -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_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/TplFileWriter.cpp.o -MF CMakeFiles/FileParsers.dir/TplFileWriter.cpp.o.d -o CMakeFiles/FileParsers.dir/TplFileWriter.cpp.o -c /build/reproducible-path/rdkit-202503.1/Code/GraphMol/FileParsers/TplFileWriter.cpp [ 45%] Building CXX object Code/GraphMol/FileParsers/CMakeFiles/FileParsers.dir/PDBParser.cpp.o @@ -4440,11 +4471,6 @@ 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_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_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/MultithreadedSmilesMolSupplier.cpp.o -MF CMakeFiles/FileParsers.dir/MultithreadedSmilesMolSupplier.cpp.o.d -o CMakeFiles/FileParsers.dir/MultithreadedSmilesMolSupplier.cpp.o -c /build/reproducible-path/rdkit-202503.1/Code/GraphMol/FileParsers/MultithreadedSmilesMolSupplier.cpp [ 47%] Building CXX object Code/GraphMol/FileParsers/CMakeFiles/FileParsers.dir/MultithreadedSDMolSupplier.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 -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_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/MultithreadedSDMolSupplier.cpp.o -MF CMakeFiles/FileParsers.dir/MultithreadedSDMolSupplier.cpp.o.d -o CMakeFiles/FileParsers.dir/MultithreadedSDMolSupplier.cpp.o -c /build/reproducible-path/rdkit-202503.1/Code/GraphMol/FileParsers/MultithreadedSDMolSupplier.cpp -[ 47%] Linking CXX shared module ../../../../rdkit/Chem/rdfiltercatalog.so -cd /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FilterCatalog/Wrap && /usr/bin/cmake -E cmake_link_script CMakeFiles/rdfiltercatalog.dir/link.txt --verbose=1 -/usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=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/rdfiltercatalog.dir/link.d -Wl,-z,relro -Wl,-z,now -shared -o ../../../../rdkit/Chem/rdfiltercatalog.so CMakeFiles/rdfiltercatalog.dir/rdfiltercatalog.cpp.o CMakeFiles/rdfiltercatalog.dir/FilterCatalog.cpp.o ../../../../lib/libRDKitFilterCatalog.so.1.2025.03.1 ../../../../lib/libRDKitRDBoost.so.1.2025.03.1 ../../../../lib/libRDKitSubgraphs.so.1.2025.03.1 ../../../../lib/libRDKitSubstructMatch.so.1.2025.03.1 ../../../../lib/libRDKitGenericGroups.so.1.2025.03.1 ../../../../lib/libRDKitSmilesParse.so.1.2025.03.1 ../../../../lib/libRDKitGraphMol.so.1.2025.03.1 ../../../../lib/libRDKitRDGeometryLib.so.1.2025.03.1 ../../../../lib/libRDKitDataStructs.so.1.2025.03.1 ../../../../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' -[ 47%] Built target rdfiltercatalog [ 47%] Linking CXX shared library ../../../lib/libRDKitFileParsers.so cd /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers && /usr/bin/cmake -E cmake_link_script CMakeFiles/FileParsers.dir/link.txt --verbose=1 /usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=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/FileParsers.dir/link.d -Wl,-z,relro -Wl,-z,now -shared -Wl,-soname,libRDKitFileParsers.so.1 -o ../../../lib/libRDKitFileParsers.so.1.2025.03.1 CMakeFiles/FileParsers.dir/CDXMLParser.cpp.o CMakeFiles/FileParsers.dir/Mol2FileParser.cpp.o CMakeFiles/FileParsers.dir/MolFileParser.cpp.o CMakeFiles/FileParsers.dir/MolSGroupParsing.cpp.o CMakeFiles/FileParsers.dir/MolSGroupWriting.cpp.o CMakeFiles/FileParsers.dir/MolFileStereochem.cpp.o CMakeFiles/FileParsers.dir/MolFileWriter.cpp.o CMakeFiles/FileParsers.dir/ForwardSDMolSupplier.cpp.o CMakeFiles/FileParsers.dir/SDMolSupplier.cpp.o CMakeFiles/FileParsers.dir/SDWriter.cpp.o CMakeFiles/FileParsers.dir/SmilesMolSupplier.cpp.o CMakeFiles/FileParsers.dir/SmilesWriter.cpp.o CMakeFiles/FileParsers.dir/TDTMolSupplier.cpp.o CMakeFiles/FileParsers.dir/TDTWriter.cpp.o CMakeFiles/FileParsers.dir/TplFileParser.cpp.o CMakeFiles/FileParsers.dir/TplFileWriter.cpp.o CMakeFiles/FileParsers.dir/PDBParser.cpp.o CMakeFiles/FileParsers.dir/PDBWriter.cpp.o CMakeFiles/FileParsers.dir/CMLWriter.cpp.o CMakeFiles/FileParsers.dir/XYZFileWriter.cpp.o CMakeFiles/FileParsers.dir/XYZFileParser.cpp.o CMakeFiles/FileParsers.dir/MaeMolSupplier.cpp.o CMakeFiles/FileParsers.dir/MaeWriter.cpp.o CMakeFiles/FileParsers.dir/ProximityBonds.cpp.o CMakeFiles/FileParsers.dir/SequenceParsers.cpp.o CMakeFiles/FileParsers.dir/SequenceWriters.cpp.o CMakeFiles/FileParsers.dir/SVGParser.cpp.o CMakeFiles/FileParsers.dir/PNGParser.cpp.o CMakeFiles/FileParsers.dir/MultithreadedMolSupplier.cpp.o CMakeFiles/FileParsers.dir/MultithreadedSmilesMolSupplier.cpp.o CMakeFiles/FileParsers.dir/MultithreadedSDMolSupplier.cpp.o ../../../lib/libRDKitChemTransforms.so.1.2025.03.1 /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/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 @@ -4454,104 +4480,109 @@ make -f External/CoordGen/CMakeFiles/testCoordGen.dir/build.make External/CoordGen/CMakeFiles/testCoordGen.dir/depend make -f Code/ForceField/UFF/CMakeFiles/testUFFForceField.dir/build.make Code/ForceField/UFF/CMakeFiles/testUFFForceField.dir/depend make -f Code/ForceField/MMFF/CMakeFiles/testMMFFForceField.dir/build.make Code/ForceField/MMFF/CMakeFiles/testMMFFForceField.dir/depend -make -f Code/GraphMol/CMakeFiles/graphmolMolOpsTest.dir/build.make Code/GraphMol/CMakeFiles/graphmolMolOpsTest.dir/depend -make -f Code/GraphMol/CMakeFiles/graphmoltestChirality.dir/build.make Code/GraphMol/CMakeFiles/graphmoltestChirality.dir/depend -make -f Code/GraphMol/CMakeFiles/graphmoltestPickler.dir/build.make Code/GraphMol/CMakeFiles/graphmoltestPickler.dir/depend -make -f Code/GraphMol/CMakeFiles/graphmoltestPicklerGlobalSetting.dir/build.make Code/GraphMol/CMakeFiles/graphmoltestPicklerGlobalSetting.dir/depend -make -f Code/GraphMol/CMakeFiles/hanoiTest.dir/build.make Code/GraphMol/CMakeFiles/hanoiTest.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-202503.1/obj-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/CoordGen /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/External/CoordGen /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/External/CoordGen/CMakeFiles/testCoordGen.dir/DependInfo.cmake "--color=" -make -f Code/GraphMol/CMakeFiles/resMolSupplierTest.dir/build.make Code/GraphMol/CMakeFiles/resMolSupplierTest.dir/depend -make -f Code/GraphMol/CMakeFiles/molBundleTest.dir/build.make Code/GraphMol/CMakeFiles/molBundleTest.dir/depend +make -f Code/GraphMol/CMakeFiles/graphmolMolOpsTest.dir/build.make Code/GraphMol/CMakeFiles/graphmolMolOpsTest.dir/depend +make -f Code/GraphMol/CMakeFiles/graphmoltestChirality.dir/build.make Code/GraphMol/CMakeFiles/graphmoltestChirality.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-202503.1/obj-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/ForceField/UFF /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/ForceField/UFF /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/ForceField/UFF/CMakeFiles/testUFFForceField.dir/DependInfo.cmake "--color=" -make -f Code/GraphMol/CMakeFiles/testSGroup.dir/build.make Code/GraphMol/CMakeFiles/testSGroup.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/ForceField/MMFF /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/ForceField/MMFF /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/ForceField/MMFF/CMakeFiles/testMMFFForceField.dir/DependInfo.cmake "--color=" +make -f Code/GraphMol/CMakeFiles/graphmoltestPickler.dir/build.make Code/GraphMol/CMakeFiles/graphmoltestPickler.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/graphmolMolOpsTest.dir/DependInfo.cmake "--color=" -make -f Code/GraphMol/CMakeFiles/test-valgrind.dir/build.make Code/GraphMol/CMakeFiles/test-valgrind.dir/depend +make -f Code/GraphMol/CMakeFiles/graphmoltestPicklerGlobalSetting.dir/build.make Code/GraphMol/CMakeFiles/graphmoltestPicklerGlobalSetting.dir/depend +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' 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 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-DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202503.1/External -I/build/reproducible-path/rdkit-202503.1/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/GraphMol/CMakeFiles/graphmoltestPickler.dir/testPickler.cpp.o -MF CMakeFiles/graphmoltestPickler.dir/testPickler.cpp.o.d -o CMakeFiles/graphmoltestPickler.dir/testPickler.cpp.o -c /build/reproducible-path/rdkit-202503.1/Code/GraphMol/testPickler.cpp +make -f Code/GraphMol/CMakeFiles/molBundleTest.dir/build.make Code/GraphMol/CMakeFiles/molBundleTest.dir/depend +make -f Code/GraphMol/CMakeFiles/testSGroup.dir/build.make Code/GraphMol/CMakeFiles/testSGroup.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/resMolSupplierTest.dir/DependInfo.cmake "--color=" make[4]: Entering directory '/build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu' -make -f Code/GraphMol/CMakeFiles/test-valgrind.dir/build.make Code/GraphMol/CMakeFiles/test-valgrind.dir/build +cd 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-I/build/reproducible-path/rdkit-202503.1/External -I/build/reproducible-path/rdkit-202503.1/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT External/CoordGen/CMakeFiles/testCoordGen.dir/test.cpp.o -MF CMakeFiles/testCoordGen.dir/test.cpp.o.d -o CMakeFiles/testCoordGen.dir/test.cpp.o -c /build/reproducible-path/rdkit-202503.1/External/CoordGen/test.cpp +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 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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/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 -/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 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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 +[ 48%] 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 +[ 48%] 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 +[ 48%] 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=. 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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,-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 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Leaving directory '/build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu' @@ -4612,13 +4643,11 @@ make[4]: Entering directory '/build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu' [ 49%] Building CXX object Code/GraphMol/CMakeFiles/chiralityTestsCatch.dir/catch_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 -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_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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/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' -[ 49%] 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 -[ 49%] Built target testUFFForceField +[ 49%] Built target test-valgrind 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 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/usr/lib/aarch64-linux-gnu/libboost_iostreams.so.1.83.0 /usr/lib/aarch64-linux-gnu/libmaeparser.so +[ 49%] 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 /usr/lib/aarch64-linux-gnu/libcoordgen.so ../../lib/libRDKitMolAlign.so.1.2025.03.1 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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/pickleTestsCatch.dir/DependInfo.cmake "--color=" @@ -4651,11 +4682,11 @@ make[4]: Entering directory '/build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu' [ 50%] 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++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK 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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,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/testMMFFForceField.dir/link.d CMakeFiles/testMMFFForceField.dir/testMMFFForceField.cpp.o -o testMMFFForceField ../../../lib/libRDKitDistGeomHelpers.so.1.2025.03.1 ../../../lib/libRDKitFileParsers.so.1.2025.03.1 ../../../lib/libRDKitDistGeometry.so.1.2025.03.1 ../../../lib/libRDKitForceFieldHelpers.so.1.2025.03.1 ../../../lib/libRDKitForceField.so.1.2025.03.1 ../../../lib/libRDKitOptimizer.so.1.2025.03.1 ../../../lib/libRDKitTrajectory.so.1.2025.03.1 ../../../lib/libRDKitChemTransforms.so.1.2025.03.1 ../../../lib/libRDKitDepictor.so.1.2025.03.1 ../../../lib/libRDKitMolAlign.so.1.2025.03.1 ../../../lib/libRDKitMolTransforms.so.1.2025.03.1 ../../../lib/libRDKitEigenSolvers.so.1.2025.03.1 ../../../lib/libRDKitSmilesParse.so.1.2025.03.1 ../../../lib/libRDKitSubstructMatch.so.1.2025.03.1 ../../../lib/libRDKitGenericGroups.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/libcoordgen.so /usr/lib/aarch64-linux-gnu/libmaeparser.so make[4]: Leaving directory '/build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu' -[ 50%] Built target testSGroup +[ 50%] Built target testMMFFForceField make -f Code/GraphMol/SmilesParse/CMakeFiles/smiTest1.dir/build.make Code/GraphMol/SmilesParse/CMakeFiles/smiTest1.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-202503.1/obj-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/smiTest1.dir/DependInfo.cmake "--color=" @@ -4677,13 +4708,11 @@ make[4]: Entering directory '/build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu' [ 50%] Building CXX object Code/GraphMol/ChemReactions/CMakeFiles/ChemReactions.dir/Reaction.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 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Code/GraphMol/ChemReactions/CMakeFiles/ChemReactions.dir/Reaction.cpp.o -MF CMakeFiles/ChemReactions.dir/Reaction.cpp.o.d -o CMakeFiles/ChemReactions.dir/Reaction.cpp.o -c /build/reproducible-path/rdkit-202503.1/Code/GraphMol/ChemReactions/Reaction.cpp -[ 50%] Linking CXX executable testMMFFForceField -cd /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/ForceField/MMFF && /usr/bin/cmake -E cmake_link_script CMakeFiles/testMMFFForceField.dir/link.txt --verbose=1 -[ 50%] Linking CXX executable pickleTestsCatch -cd /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol && /usr/bin/cmake -E cmake_link_script CMakeFiles/pickleTestsCatch.dir/link.txt --verbose=1 -/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -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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../../../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/libcoordgen.so /usr/lib/aarch64-linux-gnu/libmaeparser.so +[ 50%] 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' -[ 50%] Built target testMMFFForceField +[ 50%] Built target graphmolAdjustQueryCatch make -f Code/GraphMol/SmilesParse/CMakeFiles/smiTestCatch.dir/build.make Code/GraphMol/SmilesParse/CMakeFiles/smiTestCatch.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-202503.1/obj-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/smiTestCatch.dir/DependInfo.cmake "--color=" @@ -4692,9 +4721,11 @@ make[4]: Entering directory '/build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu' [ 50%] Building CXX object Code/GraphMol/SmilesParse/CMakeFiles/smiTestCatch.dir/catch_tests.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 -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_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/SmilesParse/CMakeFiles/smiTestCatch.dir/catch_tests.cpp.o -MF CMakeFiles/smiTestCatch.dir/catch_tests.cpp.o.d -o CMakeFiles/smiTestCatch.dir/catch_tests.cpp.o -c /build/reproducible-path/rdkit-202503.1/Code/GraphMol/SmilesParse/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/pickleTestsCatch.dir/link.d CMakeFiles/pickleTestsCatch.dir/catch_pickles.cpp.o -o pickleTestsCatch ../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 +[ 50%] 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' -[ 50%] Built target pickleTestsCatch +[ 50%] Built target graphmoltestPickler make -f Code/GraphMol/SmilesParse/CMakeFiles/nontetrahedralCatch.dir/build.make Code/GraphMol/SmilesParse/CMakeFiles/nontetrahedralCatch.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-202503.1/obj-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/nontetrahedralCatch.dir/DependInfo.cmake "--color=" @@ -4703,11 +4734,13 @@ make[4]: Entering directory '/build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu' [ 50%] Building CXX object Code/GraphMol/SmilesParse/CMakeFiles/nontetrahedralCatch.dir/nontetrahedral_tests.cpp.o cd 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-std=gnu++17 -MD -MT Code/GraphMol/SmilesParse/CMakeFiles/nontetrahedralCatch.dir/nontetrahedral_tests.cpp.o -MF CMakeFiles/nontetrahedralCatch.dir/nontetrahedral_tests.cpp.o.d -o CMakeFiles/nontetrahedralCatch.dir/nontetrahedral_tests.cpp.o -c /build/reproducible-path/rdkit-202503.1/Code/GraphMol/SmilesParse/nontetrahedral_tests.cpp -[ 50%] 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 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/usr/lib/aarch64-linux-gnu/libmaeparser.so +[ 50%] Linking CXX executable pickleTestsCatch +cd /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol && /usr/bin/cmake -E cmake_link_script CMakeFiles/pickleTestsCatch.dir/link.txt --verbose=1 +[ 50%] Linking CXX executable canonTestsCatch +cd /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol && /usr/bin/cmake -E cmake_link_script CMakeFiles/canonTestsCatch.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/pickleTestsCatch.dir/link.d CMakeFiles/pickleTestsCatch.dir/catch_pickles.cpp.o -o pickleTestsCatch ../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' -[ 50%] Built target graphmolAdjustQueryCatch +[ 50%] Built target pickleTestsCatch make -f Code/GraphMol/Depictor/CMakeFiles/testDepictor.dir/build.make Code/GraphMol/Depictor/CMakeFiles/testDepictor.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-202503.1/obj-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/testDepictor.dir/DependInfo.cmake "--color=" @@ -4716,11 +4749,9 @@ make[4]: Entering directory '/build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu' [ 50%] 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_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_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 -[ 50%] 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 +/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/canonTestsCatch.dir/link.d CMakeFiles/canonTestsCatch.dir/catch_canon.cpp.o -o canonTestsCatch ../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' -[ 50%] Built target graphmoltestPickler +[ 50%] 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=" @@ -4735,8 +4766,6 @@ make[4]: Leaving directory '/build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu' [ 50%] Built target molopsTestsCatch make -f Code/GraphMol/FileParsers/CMakeFiles/fileParsersTest1.dir/build.make Code/GraphMol/FileParsers/CMakeFiles/fileParsersTest1.dir/depend -[ 50%] Linking CXX executable canonTestsCatch -cd /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol && /usr/bin/cmake -E cmake_link_script CMakeFiles/canonTestsCatch.dir/link.txt --verbose=1 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=" make[4]: Leaving directory '/build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu' @@ -4748,33 +4777,35 @@ cd /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol && /usr/bin/cmake -E cmake_link_script CMakeFiles/graphmoltestChirality.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=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/graphmoltestChirality.dir/link.d CMakeFiles/graphmoltestChirality.dir/testChirality.cpp.o -o graphmoltestChirality ../../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 make[4]: Leaving 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/canonTestsCatch.dir/link.d CMakeFiles/canonTestsCatch.dir/catch_canon.cpp.o -o canonTestsCatch ../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' [ 51%] Built target graphmoltestChirality -[ 51%] Built target canonTestsCatch make -f Code/GraphMol/FileParsers/CMakeFiles/testAtropisomers.dir/build.make Code/GraphMol/FileParsers/CMakeFiles/testAtropisomers.dir/depend -make -f Code/GraphMol/FileParsers/CMakeFiles/testSquiggleDoubleBonds.dir/build.make Code/GraphMol/FileParsers/CMakeFiles/testSquiggleDoubleBonds.dir/depend 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=" -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/testSquiggleDoubleBonds.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu' make -f Code/GraphMol/FileParsers/CMakeFiles/testAtropisomers.dir/build.make Code/GraphMol/FileParsers/CMakeFiles/testAtropisomers.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/FileParsers/CMakeFiles/testSquiggleDoubleBonds.dir/build.make Code/GraphMol/FileParsers/CMakeFiles/testSquiggleDoubleBonds.dir/build [ 51%] Building CXX object Code/GraphMol/FileParsers/CMakeFiles/testAtropisomers.dir/testAtropisomers.cpp.o -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/GraphMol/FileParsers && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202503.1/External -I/build/reproducible-path/rdkit-202503.1/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -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/testAtropisomers.dir/testAtropisomers.cpp.o -MF CMakeFiles/testAtropisomers.dir/testAtropisomers.cpp.o.d -o CMakeFiles/testAtropisomers.dir/testAtropisomers.cpp.o -c /build/reproducible-path/rdkit-202503.1/Code/GraphMol/FileParsers/testAtropisomers.cpp -[ 52%] Building CXX object Code/GraphMol/FileParsers/CMakeFiles/testSquiggleDoubleBonds.dir/testSquiggleDoubleBonds.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_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_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/testSquiggleDoubleBonds.dir/testSquiggleDoubleBonds.cpp.o -MF CMakeFiles/testSquiggleDoubleBonds.dir/testSquiggleDoubleBonds.cpp.o.d -o CMakeFiles/testSquiggleDoubleBonds.dir/testSquiggleDoubleBonds.cpp.o -c /build/reproducible-path/rdkit-202503.1/Code/GraphMol/FileParsers/testSquiggleDoubleBonds.cpp -[ 52%] Building CXX object Code/GraphMol/ChemReactions/CMakeFiles/ChemReactions.dir/MDLParser.cpp.o +[ 51%] Building CXX object Code/GraphMol/ChemReactions/CMakeFiles/ChemReactions.dir/MDLParser.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_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_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/MDLParser.cpp.o -MF CMakeFiles/ChemReactions.dir/MDLParser.cpp.o.d -o CMakeFiles/ChemReactions.dir/MDLParser.cpp.o -c /build/reproducible-path/rdkit-202503.1/Code/GraphMol/ChemReactions/MDLParser.cpp -[ 52%] Linking CXX executable nontetrahedralCatch +[ 51%] Linking CXX executable nontetrahedralCatch cd /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/SmilesParse && /usr/bin/cmake -E cmake_link_script CMakeFiles/nontetrahedralCatch.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/nontetrahedralCatch.dir/link.d CMakeFiles/nontetrahedralCatch.dir/nontetrahedral_tests.cpp.o -o nontetrahedralCatch ../../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' -[ 52%] Built target nontetrahedralCatch +[ 51%] Built target nontetrahedralCatch +make -f Code/GraphMol/FileParsers/CMakeFiles/testSquiggleDoubleBonds.dir/build.make Code/GraphMol/FileParsers/CMakeFiles/testSquiggleDoubleBonds.dir/depend +make[4]: Entering directory 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Code/GraphMol/FileParsers/CMakeFiles/testSquiggleDoubleBonds.dir/testSquiggleDoubleBonds.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_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_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 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-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/rdfiltercatalog.dir/link.d -Wl,-z,relro -Wl,-z,now -shared -o ../../../../rdkit/Chem/rdfiltercatalog.so CMakeFiles/rdfiltercatalog.dir/rdfiltercatalog.cpp.o CMakeFiles/rdfiltercatalog.dir/FilterCatalog.cpp.o ../../../../lib/libRDKitFilterCatalog.so.1.2025.03.1 ../../../../lib/libRDKitRDBoost.so.1.2025.03.1 ../../../../lib/libRDKitSubgraphs.so.1.2025.03.1 ../../../../lib/libRDKitSubstructMatch.so.1.2025.03.1 ../../../../lib/libRDKitGenericGroups.so.1.2025.03.1 ../../../../lib/libRDKitSmilesParse.so.1.2025.03.1 ../../../../lib/libRDKitGraphMol.so.1.2025.03.1 ../../../../lib/libRDKitRDGeometryLib.so.1.2025.03.1 ../../../../lib/libRDKitDataStructs.so.1.2025.03.1 ../../../../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' +[ 52%] Built target rdfiltercatalog make -f Code/GraphMol/FileParsers/CMakeFiles/testMolSupplier.dir/build.make Code/GraphMol/FileParsers/CMakeFiles/testMolSupplier.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-202503.1/obj-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/testMolSupplier.dir/DependInfo.cmake "--color=" @@ -4783,11 +4814,11 @@ make[4]: Entering directory '/build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu' [ 52%] 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_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_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 -[ 52%] 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 +[ 52%] 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' -[ 52%] Built target testSquiggleDoubleBonds +[ 52%] Built target testAtropisomers 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=" @@ -4796,11 +4827,13 @@ make[4]: Entering directory '/build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu' [ 52%] 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_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_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 -[ 52%] 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 +[ 52%] 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_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_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 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../../../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 make[4]: Leaving directory '/build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu' -[ 52%] Built target testAtropisomers +[ 52%] Built target testDepictor make -f Code/GraphMol/FileParsers/CMakeFiles/testMultithreadedMolSupplier.dir/build.make 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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 -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_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 -[ 52%] 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_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_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 -[ 52%] 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 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+/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' -[ 52%] Built target testDepictor +[ 52%] Built target testSquiggleDoubleBonds make -f Code/GraphMol/FileParsers/CMakeFiles/testMolWriter.dir/build.make Code/GraphMol/FileParsers/CMakeFiles/testMolWriter.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/testMolWriter.dir/DependInfo.cmake "--color=" @@ -4826,13 +4857,11 @@ 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_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_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 [ 52%] 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_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_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 -[ 52%] 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 -[ 52%] 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 -/usr/bin/c++ -g -O2 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/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 +[ 52%] Linking CXX executable graphmolTestsCatch +cd /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol && /usr/bin/cmake -E cmake_link_script CMakeFiles/graphmolTestsCatch.dir/link.txt --verbose=1 +/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=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/graphmolTestsCatch.dir/link.d CMakeFiles/graphmolTestsCatch.dir/catch_graphmol.cpp.o -o graphmolTestsCatch ../RDGeneral/librdkitCatch.a ../../lib/libRDKitFileParsers.so.1.2025.03.1 /usr/lib/libCatch2.a ../../lib/libRDKitChemTransforms.so.1.2025.03.1 ../../lib/libRDKitDepictor.so.1.2025.03.1 /usr/lib/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 testMultithreadedMolSupplier +[ 52%] Built target graphmolTestsCatch make -f Code/GraphMol/FileParsers/CMakeFiles/testTplParser.dir/build.make Code/GraphMol/FileParsers/CMakeFiles/testTplParser.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-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=" @@ -4841,6 +4870,8 @@ make[4]: Entering directory '/build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu' [ 52%] 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++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202503.1/External -I/build/reproducible-path/rdkit-202503.1/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/GraphMol/FileParsers/CMakeFiles/testTplParser.dir/testTpls.cpp.o -MF CMakeFiles/testTplParser.dir/testTpls.cpp.o.d -o CMakeFiles/testTplParser.dir/testTpls.cpp.o -c /build/reproducible-path/rdkit-202503.1/Code/GraphMol/FileParsers/testTpls.cpp +[ 52%] 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 /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 make[4]: Leaving directory '/build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu' [ 52%] Built target testGeneralFileReader @@ -4852,11 +4883,11 @@ make[4]: Entering directory '/build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu' [ 52%] Building CXX object Code/GraphMol/FileParsers/CMakeFiles/testMol2ToMol.dir/testMol2ToMol.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_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_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/testMol2ToMol.dir/testMol2ToMol.cpp.o -MF CMakeFiles/testMol2ToMol.dir/testMol2ToMol.cpp.o.d -o CMakeFiles/testMol2ToMol.dir/testMol2ToMol.cpp.o -c /build/reproducible-path/rdkit-202503.1/Code/GraphMol/FileParsers/testMol2ToMol.cpp -[ 52%] Linking CXX executable graphmolTestsCatch -cd /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol && /usr/bin/cmake -E cmake_link_script CMakeFiles/graphmolTestsCatch.dir/link.txt --verbose=1 -/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=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/graphmolTestsCatch.dir/link.d CMakeFiles/graphmolTestsCatch.dir/catch_graphmol.cpp.o -o graphmolTestsCatch ../RDGeneral/librdkitCatch.a ../../lib/libRDKitFileParsers.so.1.2025.03.1 /usr/lib/libCatch2.a ../../lib/libRDKitChemTransforms.so.1.2025.03.1 ../../lib/libRDKitDepictor.so.1.2025.03.1 /usr/lib/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 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/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' -[ 52%] Built target graphmolTestsCatch +[ 52%] Built target testMultithreadedMolSupplier make -f Code/GraphMol/FileParsers/CMakeFiles/testSequence.dir/build.make Code/GraphMol/FileParsers/CMakeFiles/testSequence.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-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/testSequence.dir/DependInfo.cmake "--color=" @@ -4865,11 +4896,11 @@ make[4]: Entering directory '/build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu' [ 52%] Building CXX object Code/GraphMol/FileParsers/CMakeFiles/testSequence.dir/testSequence.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_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_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/testSequence.dir/testSequence.cpp.o -MF CMakeFiles/testSequence.dir/testSequence.cpp.o.d -o CMakeFiles/testSequence.dir/testSequence.cpp.o -c /build/reproducible-path/rdkit-202503.1/Code/GraphMol/FileParsers/testSequence.cpp -[ 52%] 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 +[ 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/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' -[ 52%] Built target testMol2ToMol +[ 52%] Built target chiralityTestsCatch make -f Code/GraphMol/FileParsers/CMakeFiles/testExtendedStereoParsing.dir/build.make Code/GraphMol/FileParsers/CMakeFiles/testExtendedStereoParsing.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-202503.1/obj-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/testExtendedStereoParsing.dir/DependInfo.cmake "--color=" @@ -4878,13 +4909,11 @@ make[4]: Entering directory '/build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu' [ 52%] Building CXX object Code/GraphMol/FileParsers/CMakeFiles/testExtendedStereoParsing.dir/testExtendedStereoParsing.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_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_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/testExtendedStereoParsing.dir/testExtendedStereoParsing.cpp.o -MF CMakeFiles/testExtendedStereoParsing.dir/testExtendedStereoParsing.cpp.o.d -o CMakeFiles/testExtendedStereoParsing.dir/testExtendedStereoParsing.cpp.o -c /build/reproducible-path/rdkit-202503.1/Code/GraphMol/FileParsers/testExtendedStereoParsing.cpp -[ 52%] Building CXX object Code/GraphMol/ChemReactions/CMakeFiles/ChemReactions.dir/ReactionWriter.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_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_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/ReactionWriter.cpp.o -MF CMakeFiles/ChemReactions.dir/ReactionWriter.cpp.o.d -o CMakeFiles/ChemReactions.dir/ReactionWriter.cpp.o -c /build/reproducible-path/rdkit-202503.1/Code/GraphMol/ChemReactions/ReactionWriter.cpp -[ 52%] Linking CXX executable testTplParser -cd /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers && /usr/bin/cmake -E cmake_link_script CMakeFiles/testTplParser.dir/link.txt --verbose=1 -/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=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/testTplParser.dir/link.d CMakeFiles/testTplParser.dir/testTpls.cpp.o -o testTplParser ../../../lib/libRDKitFileParsers.so.1.2025.03.1 ../../../lib/libRDKitChemTransforms.so.1.2025.03.1 ../../../lib/libRDKitDepictor.so.1.2025.03.1 /usr/lib/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 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 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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 make[4]: Leaving directory '/build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu' -[ 52%] Built target testTplParser +[ 52%] Built target testSequence make -f Code/GraphMol/FileParsers/CMakeFiles/fileParsersCatchTest.dir/build.make Code/GraphMol/FileParsers/CMakeFiles/fileParsersCatchTest.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-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/fileParsersCatchTest.dir/DependInfo.cmake "--color=" @@ -4893,11 +4922,13 @@ make[4]: Entering directory '/build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu' [ 52%] Building CXX object Code/GraphMol/FileParsers/CMakeFiles/fileParsersCatchTest.dir/file_parsers_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_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_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/fileParsersCatchTest.dir/file_parsers_catch.cpp.o -MF CMakeFiles/fileParsersCatchTest.dir/file_parsers_catch.cpp.o.d -o CMakeFiles/fileParsersCatchTest.dir/file_parsers_catch.cpp.o -c /build/reproducible-path/rdkit-202503.1/Code/GraphMol/FileParsers/file_parsers_catch.cpp -[ 52%] 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 +[ 52%] Linking CXX executable depictorCatch +cd /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/Depictor && /usr/bin/cmake -E cmake_link_script CMakeFiles/depictorCatch.dir/link.txt --verbose=1 +[ 52%] Building CXX object Code/GraphMol/ChemReactions/CMakeFiles/ChemReactions.dir/ReactionWriter.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 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CMakeFiles/ChemReactions.dir/ReactionWriter.cpp.o.d -o CMakeFiles/ChemReactions.dir/ReactionWriter.cpp.o -c /build/reproducible-path/rdkit-202503.1/Code/GraphMol/ChemReactions/ReactionWriter.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/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 ../../../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 testSequence +[ 52%] Built target depictorCatch make -f Code/GraphMol/FileParsers/CMakeFiles/testPropertyLists.dir/build.make Code/GraphMol/FileParsers/CMakeFiles/testPropertyLists.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-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/testPropertyLists.dir/DependInfo.cmake "--color=" @@ -4906,63 +4937,63 @@ make[4]: Entering directory '/build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu' [ 52%] Building CXX object Code/GraphMol/FileParsers/CMakeFiles/testPropertyLists.dir/testPropertyLists.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_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_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/testPropertyLists.dir/testPropertyLists.cpp.o -MF CMakeFiles/testPropertyLists.dir/testPropertyLists.cpp.o.d -o CMakeFiles/testPropertyLists.dir/testPropertyLists.cpp.o -c /build/reproducible-path/rdkit-202503.1/Code/GraphMol/FileParsers/testPropertyLists.cpp -[ 53%] 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 -[ 53%] 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 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=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 +[ 52%] 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' -[ 53%] Built target smiTest1 +[ 52%] 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=" -[ 53%] Linking CXX executable depictorCatch -cd /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/Depictor && /usr/bin/cmake -E cmake_link_script CMakeFiles/depictorCatch.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/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' -[ 53%] Building CXX object Code/GraphMol/FileParsers/CMakeFiles/XYZFileParserCatchTest.dir/XYZFileParserCatchTest.cpp.o +[ 52%] 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_HAS_EIGEN3 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../../../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 testTplParser +cd /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers && /usr/bin/cmake -E cmake_link_script CMakeFiles/testTplParser.dir/link.txt --verbose=1 +/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong 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-Wl,--dependency-file=CMakeFiles/testMolSupplier.dir/link.d CMakeFiles/testMolSupplier.dir/testMolSupplier.cpp.o -o testMolSupplier ../../../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 -make[4]: Leaving 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/smiTestCatch.dir/link.d CMakeFiles/smiTestCatch.dir/catch_tests.cpp.o -o smiTestCatch ../../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' 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=" -[ 53%] Built target testMolSupplier -make -f Code/GraphMol/FileParsers/CMakeFiles/molfileStereoCatchTest.dir/build.make Code/GraphMol/FileParsers/CMakeFiles/molfileStereoCatchTest.dir/depend -[ 53%] Built target smiTestCatch make[4]: Leaving directory '/build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu' make -f Code/GraphMol/FileParsers/CMakeFiles/cdxmlParserCatchTest.dir/build.make Code/GraphMol/FileParsers/CMakeFiles/cdxmlParserCatchTest.dir/build make[4]: Entering directory '/build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu' +[ 52%] 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_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_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 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/build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/CMakeFiles/molfileStereoCatchTest.dir/DependInfo.cmake "--color=" -make -f Code/GraphMol/FileParsers/CMakeFiles/connectTheDotsTest.dir/build.make Code/GraphMol/FileParsers/CMakeFiles/connectTheDotsTest.dir/depend -[ 53%] Building CXX object Code/GraphMol/FileParsers/CMakeFiles/cdxmlParserCatchTest.dir/cdxml_parser_catch.cpp.o -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=" -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_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_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 make[4]: Leaving directory '/build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu' make -f Code/GraphMol/FileParsers/CMakeFiles/molfileStereoCatchTest.dir/build.make Code/GraphMol/FileParsers/CMakeFiles/molfileStereoCatchTest.dir/build make[4]: Entering directory '/build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu' +[ 53%] Building CXX object Code/GraphMol/FileParsers/CMakeFiles/molfileStereoCatchTest.dir/molfile_stereo_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_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_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 +[ 53%] 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 +[ 54%] 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 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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 /usr/lib/aarch64-linux-gnu/libmaeparser.so +make[4]: Leaving directory '/build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu' +[ 54%] Built target smiTestCatch +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' -[ 54%] Building CXX object Code/GraphMol/FileParsers/CMakeFiles/molfileStereoCatchTest.dir/molfile_stereo_catch.cpp.o make -f Code/GraphMol/FileParsers/CMakeFiles/connectTheDotsTest.dir/build.make Code/GraphMol/FileParsers/CMakeFiles/connectTheDotsTest.dir/build -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_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_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 make[4]: Entering directory '/build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu' [ 54%] 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_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_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 -[ 54%] 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 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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 /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/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 make[4]: Leaving directory '/build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu' -[ 54%] Built target testMolWriter +[ 54%] Built target smiTest1 make -f Code/GraphMol/FileParsers/CMakeFiles/v2MolSuppliers.dir/build.make Code/GraphMol/FileParsers/CMakeFiles/v2MolSuppliers.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/v2MolSuppliers.dir/DependInfo.cmake "--color=" @@ -4971,11 +5002,11 @@ make[4]: Entering directory '/build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu' [ 54%] Building CXX object Code/GraphMol/FileParsers/CMakeFiles/v2MolSuppliers.dir/v2_suppliers_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_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_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/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 -[ 54%] 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/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 +[ 54%] 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' -[ 54%] Built target chiralityTestsCatch +[ 54%] Built target testMolWriter make -f Code/GraphMol/FileParsers/CMakeFiles/v2FileParsersCatchTest.dir/build.make Code/GraphMol/FileParsers/CMakeFiles/v2FileParsersCatchTest.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-202503.1/obj-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/v2FileParsersCatchTest.dir/DependInfo.cmake "--color=" @@ -4984,13 +5015,11 @@ make[4]: Entering directory '/build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu' [ 54%] Building CXX object Code/GraphMol/FileParsers/CMakeFiles/v2FileParsersCatchTest.dir/v2_file_parsers_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_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_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/v2FileParsersCatchTest.dir/v2_file_parsers_catch.cpp.o -MF CMakeFiles/v2FileParsersCatchTest.dir/v2_file_parsers_catch.cpp.o.d -o CMakeFiles/v2FileParsersCatchTest.dir/v2_file_parsers_catch.cpp.o -c /build/reproducible-path/rdkit-202503.1/Code/GraphMol/FileParsers/v2_file_parsers_catch.cpp -[ 54%] 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 -[ 54%] Building CXX object Code/GraphMol/ChemReactions/CMakeFiles/ChemReactions.dir/ReactionDepict.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_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_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 -/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 +[ 54%] Linking CXX executable testMolSupplier +cd /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers && /usr/bin/cmake -E cmake_link_script CMakeFiles/testMolSupplier.dir/link.txt --verbose=1 +/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=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/testMolSupplier.dir/link.d CMakeFiles/testMolSupplier.dir/testMolSupplier.cpp.o -o testMolSupplier ../../../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 make[4]: Leaving directory '/build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu' -[ 54%] Built target testExtendedStereoParsing +[ 54%] Built target testMolSupplier 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=" @@ -4999,13 +5028,13 @@ make[4]: Entering directory '/build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu' [ 54%] 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_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_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 -[ 54%] Building CXX object Code/GraphMol/ChemReactions/CMakeFiles/ChemReactions.dir/ReactionFingerprints.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_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_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/ReactionFingerprints.cpp.o -MF CMakeFiles/ChemReactions.dir/ReactionFingerprints.cpp.o.d -o CMakeFiles/ChemReactions.dir/ReactionFingerprints.cpp.o -c /build/reproducible-path/rdkit-202503.1/Code/GraphMol/ChemReactions/ReactionFingerprints.cpp -[ 54%] 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 +[ 54%] Building CXX object Code/GraphMol/ChemReactions/CMakeFiles/ChemReactions.dir/ReactionDepict.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_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_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 +[ 54%] 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' -[ 54%] Built target connectTheDotsTest +[ 54%] Built target XYZFileParserCatchTest 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=" @@ -5014,11 +5043,13 @@ make[4]: Entering directory '/build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu' [ 54%] 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_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_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 -[ 54%] 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 +[ 54%] 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 +[ 54%] Building CXX object Code/GraphMol/ChemReactions/CMakeFiles/ChemReactions.dir/ReactionFingerprints.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_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_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/ReactionFingerprints.cpp.o -MF CMakeFiles/ChemReactions.dir/ReactionFingerprints.cpp.o.d -o CMakeFiles/ChemReactions.dir/ReactionFingerprints.cpp.o -c /build/reproducible-path/rdkit-202503.1/Code/GraphMol/ChemReactions/ReactionFingerprints.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/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' -[ 54%] Built target v2FileParsersCatchTest +[ 54%] Built target connectTheDotsTest 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=" @@ -5027,11 +5058,11 @@ make[4]: Entering directory '/build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu' [ 54%] 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_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_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 -[ 54%] 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 +[ 54%] 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/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' -[ 54%] Built target XYZFileParserCatchTest +[ 54%] Built target cdxmlParserCatchTest 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=" @@ -5040,13 +5071,13 @@ make[4]: Entering directory '/build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu' [ 54%] 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 -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202503.1/External -I/build/reproducible-path/rdkit-202503.1/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/GraphMol/Substruct/CMakeFiles/substructTestCatch.dir/catch_tests.cpp.o -MF CMakeFiles/substructTestCatch.dir/catch_tests.cpp.o.d -o CMakeFiles/substructTestCatch.dir/catch_tests.cpp.o -c /build/reproducible-path/rdkit-202503.1/Code/GraphMol/Substruct/catch_tests.cpp -[ 54%] 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 -[ 54%] 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/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 +[ 54%] 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 +[ 54%] 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/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' -[ 54%] Built target molfileStereoCatchTest +[ 54%] Built target v2FileParsersCatchTest 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=" @@ -5055,9 +5086,9 @@ make[4]: Entering directory '/build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu' [ 54%] 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_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_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/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 +/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' -[ 54%] Built target atropisomersCatch +[ 54%] Built target graphmolMolOpsTest 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=" @@ -5066,11 +5097,15 @@ make[4]: Entering directory '/build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu' [ 54%] 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_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_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 -[ 54%] 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/cdxmlParserCatchTest.dir/link.d CMakeFiles/cdxmlParserCatchTest.dir/cdxml_parser_catch.cpp.o -o cdxmlParserCatchTest ../../RDGeneral/librdkitCatch.a 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+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 +[ 54%] 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 +[ 54%] 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/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' -[ 54%] Built target cdxmlParserCatchTest +[ 54%] Built target testPropertyLists make -f Code/GraphMol/FilterCatalog/CMakeFiles/filterCatalogTest.dir/build.make Code/GraphMol/FilterCatalog/CMakeFiles/filterCatalogTest.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-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/FilterCatalog /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FilterCatalog /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FilterCatalog/CMakeFiles/filterCatalogTest.dir/DependInfo.cmake "--color=" @@ -5079,54 +5114,48 @@ make[4]: Entering directory '/build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu' [ 55%] 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_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_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 -[ 56%] 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_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_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 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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 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-I/build/reproducible-path/rdkit-202503.1/External -I/build/reproducible-path/rdkit-202503.1/Code -I/build/reproducible-path/rdkit-202503.1/External/boost-numeric-bindings -I/usr/lib/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/rdfragcatalog.cpp.o -MF CMakeFiles/rdfragcatalog.dir/rdfragcatalog.cpp.o.d -o CMakeFiles/rdfragcatalog.dir/rdfragcatalog.cpp.o -c /build/reproducible-path/rdkit-202503.1/Code/GraphMol/FragCatalog/Wrap/rdfragcatalog.cpp -[ 56%] Linking CXX executable testPropertyLists -cd 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Code/GraphMol/Descriptors/CMakeFiles/Descriptors.dir/Crippen.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_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_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/Crippen.cpp.o -MF CMakeFiles/Descriptors.dir/Crippen.cpp.o.d -o CMakeFiles/Descriptors.dir/Crippen.cpp.o -c /build/reproducible-path/rdkit-202503.1/Code/GraphMol/Descriptors/Crippen.cpp -[ 56%] 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 -DRDKIT_CHEMREACTIONS_BUILD -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202503.1/External -I/build/reproducible-path/rdkit-202503.1/Code -I/build/reproducible-path/rdkit-202503.1/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-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/MoleculeParser.cpp.o -MF CMakeFiles/ChemReactions.dir/MoleculeParser.cpp.o.d -o CMakeFiles/ChemReactions.dir/MoleculeParser.cpp.o -c /build/reproducible-path/rdkit-202503.1/Code/GraphMol/ChemReactions/MoleculeParser.cpp -[ 56%] 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 +[ 55%] 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 +[ 56%] 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_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_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 +/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' -[ 56%] Built target filterCatalogTest +[ 56%] Built target multithreadedSupplierCatchTest 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=" @@ -5137,10 +5166,14 @@ 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_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_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 [ 56%] 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_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 +[ 56%] 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_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_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 [ 56%] 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 +[ 56%] Linking CXX executable filterCatalogTest /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 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/GraphMol/FilterCatalog && /usr/bin/cmake -E cmake_link_script CMakeFiles/filterCatalogTest.dir/link.txt --verbose=1 [ 56%] Built target testFragCatalog 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' @@ -5150,15 +5183,9 @@ make[4]: Entering directory '/build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu' [ 56%] 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_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_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 -[ 56%] Building CXX object Code/GraphMol/ChemReactions/CMakeFiles/ChemReactions.dir/ReactionRunner.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_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_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/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 -[ 56%] 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 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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/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++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=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/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/MoleculeParser.cpp.o -MF CMakeFiles/ChemReactions.dir/MoleculeParser.cpp.o.d -o CMakeFiles/ChemReactions.dir/MoleculeParser.cpp.o -c /build/reproducible-path/rdkit-202503.1/Code/GraphMol/ChemReactions/MoleculeParser.cpp [ 57%] Linking CXX executable testMHFPFingerprint cd /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/Fingerprints && /usr/bin/cmake -E cmake_link_script CMakeFiles/testMHFPFingerprint.dir/link.txt --verbose=1 -/usr/bin/c++ -g -O2 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../../../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' +[ 57%] Built target chemTransformsTestCatch make -f Code/GraphMol/ForceFieldHelpers/CMakeFiles/forceFieldHelpersCatch.dir/build.make Code/GraphMol/ForceFieldHelpers/CMakeFiles/forceFieldHelpersCatch.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 /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/ForceFieldHelpers /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/ForceFieldHelpers/CMakeFiles/forceFieldHelpersCatch.dir/DependInfo.cmake "--color=" @@ -5236,13 +5271,9 @@ make[4]: Entering directory '/build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu' [ 57%] Building CXX object Code/GraphMol/ForceFieldHelpers/CMakeFiles/forceFieldHelpersCatch.dir/catch_tests.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 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CMakeFiles/forceFieldHelpersCatch.dir/catch_tests.cpp.o -c /build/reproducible-path/rdkit-202503.1/Code/GraphMol/ForceFieldHelpers/catch_tests.cpp -[ 57%] 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_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 -[ 57%] Linking CXX executable testMolTransforms -cd 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-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' -[ 57%] Built target testMolTransforms +[ 57%] Built target testChemTransforms 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 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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/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 -[ 58%] Building CXX object Code/GraphMol/ChemReactions/CMakeFiles/ChemReactions.dir/PreprocessRxn.cpp.o -cd 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-D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/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 -[ 58%] Linking CXX executable molTransformsTestCatch -cd /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/MolTransforms && /usr/bin/cmake -E cmake_link_script CMakeFiles/molTransformsTestCatch.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/molTransformsTestCatch.dir/link.d CMakeFiles/molTransformsTestCatch.dir/catch_tests.cpp.o -o molTransformsTestCatch ../../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 +[ 58%] Building CXX object Code/GraphMol/FragCatalog/Wrap/CMakeFiles/rdfragcatalog.dir/FragCatGenerator.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_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/FragCatGenerator.cpp.o -MF CMakeFiles/rdfragcatalog.dir/FragCatGenerator.cpp.o.d -o CMakeFiles/rdfragcatalog.dir/FragCatGenerator.cpp.o -c /build/reproducible-path/rdkit-202503.1/Code/GraphMol/FragCatalog/Wrap/FragCatGenerator.cpp +[ 58%] Linking CXX executable testMolTransforms +cd /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/MolTransforms && /usr/bin/cmake -E cmake_link_script CMakeFiles/testMolTransforms.dir/link.txt --verbose=1 +/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=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/testMolTransforms.dir/link.d CMakeFiles/testMolTransforms.dir/test1.cpp.o -o testMolTransforms ../../../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/libRDKitSmilesParse.so.1.2025.03.1 ../../../lib/libRDKitAlignment.so.1.2025.03.1 ../../../lib/libRDKitSubstructMatch.so.1.2025.03.1 ../../../lib/libRDKitGenericGroups.so.1.2025.03.1 ../../../lib/libRDKitGraphMol.so.1.2025.03.1 ../../../lib/libRDKitRDGeometryLib.so.1.2025.03.1 ../../../lib/libRDKitDataStructs.so.1.2025.03.1 ../../../lib/libRDKitRDGeneral.so.1.2025.03.1 /usr/lib/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' -[ 58%] Built target molTransformsTestCatch +[ 58%] Built target testMolTransforms make -f Code/GraphMol/ForceFieldHelpers/MMFF/CMakeFiles/testMMFFForceFieldHelpersMultiThread.dir/build.make Code/GraphMol/ForceFieldHelpers/MMFF/CMakeFiles/testMMFFForceFieldHelpersMultiThread.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-202503.1/obj-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=" @@ -5266,11 +5297,11 @@ make[4]: Entering directory '/build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu' [ 58%] 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_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_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 -[ 58%] Linking CXX executable forceFieldHelpersCatch -cd /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/ForceFieldHelpers && /usr/bin/cmake -E cmake_link_script CMakeFiles/forceFieldHelpersCatch.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/forceFieldHelpersCatch.dir/link.d CMakeFiles/forceFieldHelpersCatch.dir/catch_tests.cpp.o -o forceFieldHelpersCatch ../../RDGeneral/librdkitCatch.a ../../../lib/libRDKitForceFieldHelpers.so.1.2025.03.1 ../../../lib/libRDKitFileParsers.so.1.2025.03.1 ../../../lib/libRDKitForceField.so.1.2025.03.1 /usr/lib/libCatch2.a ../../../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/libRDKitMolTransforms.so.1.2025.03.1 ../../../lib/libRDKitEigenSolvers.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/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 +[ 58%] Linking CXX executable molTransformsTestCatch +cd /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/MolTransforms && /usr/bin/cmake -E cmake_link_script CMakeFiles/molTransformsTestCatch.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/molTransformsTestCatch.dir/link.d CMakeFiles/molTransformsTestCatch.dir/catch_tests.cpp.o -o molTransformsTestCatch ../../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' -[ 58%] Built target forceFieldHelpersCatch +[ 58%] Built target molTransformsTestCatch 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 /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/ForceFieldHelpers/UFF /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/ForceFieldHelpers/UFF/CMakeFiles/testUFFForceFieldHelpers.dir/DependInfo.cmake "--color=" @@ -5281,8 +5312,6 @@ cd /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/ForceFieldHelpers/UFF && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202503.1/External -I/build/reproducible-path/rdkit-202503.1/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/GraphMol/ForceFieldHelpers/UFF/CMakeFiles/testUFFForceFieldHelpers.dir/testUFFHelpers.cpp.o -MF CMakeFiles/testUFFForceFieldHelpers.dir/testUFFHelpers.cpp.o.d -o CMakeFiles/testUFFForceFieldHelpers.dir/testUFFHelpers.cpp.o -c /build/reproducible-path/rdkit-202503.1/Code/GraphMol/ForceFieldHelpers/UFF/testUFFHelpers.cpp [ 58%] Linking CXX executable fpGenTestCatch cd /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/Fingerprints && /usr/bin/cmake -E cmake_link_script CMakeFiles/fpGenTestCatch.dir/link.txt --verbose=1 -[ 58%] Building CXX object Code/GraphMol/FragCatalog/Wrap/CMakeFiles/rdfragcatalog.dir/FragCatGenerator.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_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 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-Wl,--dependency-file=CMakeFiles/fpGenTestCatch.dir/link.d CMakeFiles/fpGenTestCatch.dir/fpgen_catch_tests.cpp.o -o fpGenTestCatch ../../RDGeneral/librdkitCatch.a ../../../lib/libRDKitFingerprints.so.1.2025.03.1 ../../../lib/libRDKitFileParsers.so.1.2025.03.1 /usr/lib/libCatch2.a ../../../lib/libRDKitSubgraphs.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 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forceFieldHelpersCatch +cd /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/ForceFieldHelpers && /usr/bin/cmake -E cmake_link_script CMakeFiles/forceFieldHelpersCatch.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/forceFieldHelpersCatch.dir/link.d CMakeFiles/forceFieldHelpersCatch.dir/catch_tests.cpp.o -o forceFieldHelpersCatch ../../RDGeneral/librdkitCatch.a ../../../lib/libRDKitForceFieldHelpers.so.1.2025.03.1 ../../../lib/libRDKitFileParsers.so.1.2025.03.1 ../../../lib/libRDKitForceField.so.1.2025.03.1 /usr/lib/libCatch2.a ../../../lib/libRDKitOptimizer.so.1.2025.03.1 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-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 +[ 59%] Linking CXX executable testFingerprintGenerators +cd /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/Fingerprints && 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target testFingerprintGenerators make -f Code/GraphMol/DistGeomHelpers/Wrap/CMakeFiles/rdDistGeom.dir/build.make Code/GraphMol/DistGeomHelpers/Wrap/CMakeFiles/rdDistGeom.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-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/DistGeomHelpers/Wrap /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/DistGeomHelpers/Wrap /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/DistGeomHelpers/Wrap/CMakeFiles/rdDistGeom.dir/DependInfo.cmake "--color=" @@ -5337,13 +5372,9 @@ make[4]: Entering directory '/build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu' [ 59%] Building CXX object Code/GraphMol/DistGeomHelpers/Wrap/CMakeFiles/rdDistGeom.dir/rdDistGeom.cpp.o cd /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/DistGeomHelpers/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_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_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 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/DistGeomHelpers/Wrap/CMakeFiles/rdDistGeom.dir/rdDistGeom.cpp.o -MF CMakeFiles/rdDistGeom.dir/rdDistGeom.cpp.o.d -o CMakeFiles/rdDistGeom.dir/rdDistGeom.cpp.o -c /build/reproducible-path/rdkit-202503.1/Code/GraphMol/DistGeomHelpers/Wrap/rdDistGeom.cpp -[ 59%] 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_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 -[ 59%] Linking CXX executable testCrystalForceField -cd /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/ForceFieldHelpers/CrystalFF && /usr/bin/cmake -E cmake_link_script CMakeFiles/testCrystalForceField.dir/link.txt --verbose=1 -/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=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/testCrystalForceField.dir/link.d CMakeFiles/testCrystalForceField.dir/testCrystalFF.cpp.o -o testCrystalForceField ../../../../lib/libRDKitDistGeomHelpers.so.1.2025.03.1 ../../../../lib/libRDKitFileParsers.so.1.2025.03.1 ../../../../lib/libRDKitDistGeometry.so.1.2025.03.1 ../../../../lib/libRDKitForceFieldHelpers.so.1.2025.03.1 ../../../../lib/libRDKitForceField.so.1.2025.03.1 ../../../../lib/libRDKitOptimizer.so.1.2025.03.1 ../../../../lib/libRDKitTrajectory.so.1.2025.03.1 ../../../../lib/libRDKitChemTransforms.so.1.2025.03.1 ../../../../lib/libRDKitDepictor.so.1.2025.03.1 ../../../../lib/libRDKitMolAlign.so.1.2025.03.1 ../../../../lib/libRDKitMolTransforms.so.1.2025.03.1 ../../../../lib/libRDKitEigenSolvers.so.1.2025.03.1 ../../../../lib/libRDKitSmilesParse.so.1.2025.03.1 ../../../../lib/libRDKitSubstructMatch.so.1.2025.03.1 ../../../../lib/libRDKitGenericGroups.so.1.2025.03.1 ../../../../lib/libRDKitAlignment.so.1.2025.03.1 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testMMFFForceFieldHelpersMultiThread ../../../../lib/libRDKitDistGeomHelpers.so.1.2025.03.1 ../../../../lib/libRDKitFileParsers.so.1.2025.03.1 ../../../../lib/libRDKitDistGeometry.so.1.2025.03.1 ../../../../lib/libRDKitForceFieldHelpers.so.1.2025.03.1 ../../../../lib/libRDKitForceField.so.1.2025.03.1 ../../../../lib/libRDKitOptimizer.so.1.2025.03.1 ../../../../lib/libRDKitTrajectory.so.1.2025.03.1 ../../../../lib/libRDKitChemTransforms.so.1.2025.03.1 ../../../../lib/libRDKitDepictor.so.1.2025.03.1 ../../../../lib/libRDKitMolAlign.so.1.2025.03.1 ../../../../lib/libRDKitMolTransforms.so.1.2025.03.1 ../../../../lib/libRDKitEigenSolvers.so.1.2025.03.1 ../../../../lib/libRDKitSmilesParse.so.1.2025.03.1 ../../../../lib/libRDKitSubstructMatch.so.1.2025.03.1 ../../../../lib/libRDKitGenericGroups.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/libcoordgen.so /usr/lib/aarch64-linux-gnu/libmaeparser.so make[4]: Leaving directory '/build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu' -[ 59%] Built target testCrystalForceField +[ 59%] Built target testMMFFForceFieldHelpersMultiThread make -f Code/GraphMol/MolAlign/CMakeFiles/testMolAlign.dir/build.make Code/GraphMol/MolAlign/CMakeFiles/testMolAlign.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-202503.1/obj-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/MolAlign /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/MolAlign /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/MolAlign/CMakeFiles/testMolAlign.dir/DependInfo.cmake "--color=" @@ -5352,41 +5383,37 @@ make[4]: Entering directory '/build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu' [ 59%] Building CXX object Code/GraphMol/MolAlign/CMakeFiles/testMolAlign.dir/testMolAlign.cpp.o cd /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/MolAlign && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202503.1/External -I/build/reproducible-path/rdkit-202503.1/Code -isystem /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/testMolAlign.dir/testMolAlign.cpp.o -MF CMakeFiles/testMolAlign.dir/testMolAlign.cpp.o.d -o CMakeFiles/testMolAlign.dir/testMolAlign.cpp.o -c /build/reproducible-path/rdkit-202503.1/Code/GraphMol/MolAlign/testMolAlign.cpp -[ 59%] Building CXX object Code/GraphMol/Descriptors/CMakeFiles/Descriptors.dir/MolSurf.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_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_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/MolSurf.cpp.o -MF CMakeFiles/Descriptors.dir/MolSurf.cpp.o.d -o CMakeFiles/Descriptors.dir/MolSurf.cpp.o -c /build/reproducible-path/rdkit-202503.1/Code/GraphMol/Descriptors/MolSurf.cpp -[ 59%] Linking CXX executable testFingerprintGenerators -cd /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/Fingerprints && /usr/bin/cmake -E cmake_link_script CMakeFiles/testFingerprintGenerators.dir/link.txt --verbose=1 -/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=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/testFingerprintGenerators.dir/link.d CMakeFiles/testFingerprintGenerators.dir/testFingerprintGenerators.cpp.o -o testFingerprintGenerators ../../../lib/libRDKitFingerprints.so.1.2025.03.1 ../../../lib/libRDKitFileParsers.so.1.2025.03.1 ../../../lib/libRDKitSubgraphs.so.1.2025.03.1 ../../../lib/libRDKitChemTransforms.so.1.2025.03.1 ../../../lib/libRDKitDepictor.so.1.2025.03.1 /usr/lib/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' -[ 59%] Built target testFingerprintGenerators -make -f Code/GraphMol/MolAlign/CMakeFiles/molAlignCatchTest.dir/build.make Code/GraphMol/MolAlign/CMakeFiles/molAlignCatchTest.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/MolAlign /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/MolAlign /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/MolAlign/CMakeFiles/molAlignCatchTest.dir/DependInfo.cmake "--color=" -make[4]: Leaving directory '/build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu' -make -f Code/GraphMol/MolAlign/CMakeFiles/molAlignCatchTest.dir/build.make Code/GraphMol/MolAlign/CMakeFiles/molAlignCatchTest.dir/build -make[4]: Entering directory '/build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu' -[ 59%] Building CXX object Code/GraphMol/MolAlign/CMakeFiles/molAlignCatchTest.dir/catch_tests.cpp.o -cd /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/MolAlign && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202503.1/External -I/build/reproducible-path/rdkit-202503.1/Code -isystem /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/molAlignCatchTest.dir/catch_tests.cpp.o -MF CMakeFiles/molAlignCatchTest.dir/catch_tests.cpp.o.d -o CMakeFiles/molAlignCatchTest.dir/catch_tests.cpp.o -c /build/reproducible-path/rdkit-202503.1/Code/GraphMol/MolAlign/catch_tests.cpp [ 59%] Linking CXX executable testFingerprints cd /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/Fingerprints && /usr/bin/cmake -E cmake_link_script CMakeFiles/testFingerprints.dir/link.txt --verbose=1 +[ 59%] Linking CXX executable testMMFFForceFieldHelpers +cd /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/ForceFieldHelpers/MMFF && /usr/bin/cmake -E cmake_link_script CMakeFiles/testMMFFForceFieldHelpers.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=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/testFingerprints.dir/link.d CMakeFiles/testFingerprints.dir/test1.cpp.o -o testFingerprints ../../../lib/libRDKitFingerprints.so.1.2025.03.1 ../../../lib/libRDKitFileParsers.so.1.2025.03.1 ../../../lib/libRDKitSubgraphs.so.1.2025.03.1 ../../../lib/libRDKitChemTransforms.so.1.2025.03.1 ../../../lib/libRDKitDepictor.so.1.2025.03.1 /usr/lib/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' +/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/testMMFFForceFieldHelpers.dir/link.d CMakeFiles/testMMFFForceFieldHelpers.dir/testMMFFHelpers.cpp.o -o testMMFFForceFieldHelpers ../../../../lib/libRDKitDistGeomHelpers.so.1.2025.03.1 ../../../../lib/libRDKitFileParsers.so.1.2025.03.1 ../../../../lib/libRDKitDistGeometry.so.1.2025.03.1 ../../../../lib/libRDKitForceFieldHelpers.so.1.2025.03.1 ../../../../lib/libRDKitForceField.so.1.2025.03.1 ../../../../lib/libRDKitOptimizer.so.1.2025.03.1 ../../../../lib/libRDKitTrajectory.so.1.2025.03.1 ../../../../lib/libRDKitChemTransforms.so.1.2025.03.1 ../../../../lib/libRDKitDepictor.so.1.2025.03.1 ../../../../lib/libRDKitMolAlign.so.1.2025.03.1 ../../../../lib/libRDKitMolTransforms.so.1.2025.03.1 ../../../../lib/libRDKitEigenSolvers.so.1.2025.03.1 ../../../../lib/libRDKitSmilesParse.so.1.2025.03.1 ../../../../lib/libRDKitSubstructMatch.so.1.2025.03.1 ../../../../lib/libRDKitGenericGroups.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/libcoordgen.so /usr/lib/aarch64-linux-gnu/libmaeparser.so +make[4]: Leaving directory '/build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu' [ 59%] Built target testFingerprints +make -f Code/GraphMol/MolAlign/CMakeFiles/molAlignCatchTest.dir/build.make Code/GraphMol/MolAlign/CMakeFiles/molAlignCatchTest.dir/depend +[ 59%] Built target testMMFFForceFieldHelpers make -f Code/GraphMol/MolChemicalFeatures/CMakeFiles/testFeatures.dir/build.make Code/GraphMol/MolChemicalFeatures/CMakeFiles/testFeatures.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-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/MolAlign /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/MolAlign /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/MolAlign/CMakeFiles/molAlignCatchTest.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/MolChemicalFeatures /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/MolChemicalFeatures /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/MolChemicalFeatures/CMakeFiles/testFeatures.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu' +make -f Code/GraphMol/MolAlign/CMakeFiles/molAlignCatchTest.dir/build.make Code/GraphMol/MolAlign/CMakeFiles/molAlignCatchTest.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/MolChemicalFeatures/CMakeFiles/testFeatures.dir/build.make Code/GraphMol/MolChemicalFeatures/CMakeFiles/testFeatures.dir/build +[ 59%] Building CXX object Code/GraphMol/MolAlign/CMakeFiles/molAlignCatchTest.dir/catch_tests.cpp.o 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/GraphMol/MolAlign && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202503.1/External -I/build/reproducible-path/rdkit-202503.1/Code -isystem /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/molAlignCatchTest.dir/catch_tests.cpp.o -MF CMakeFiles/molAlignCatchTest.dir/catch_tests.cpp.o.d -o CMakeFiles/molAlignCatchTest.dir/catch_tests.cpp.o -c /build/reproducible-path/rdkit-202503.1/Code/GraphMol/MolAlign/catch_tests.cpp [ 59%] Building CXX object Code/GraphMol/MolChemicalFeatures/CMakeFiles/testFeatures.dir/testFeatures.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 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CMakeFiles/testFeatures.dir/testFeatures.cpp.o -c /build/reproducible-path/rdkit-202503.1/Code/GraphMol/MolChemicalFeatures/testFeatures.cpp -[ 59%] 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_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_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 -[ 59%] Linking CXX executable testMMFFForceFieldHelpers -cd /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/ForceFieldHelpers/MMFF && /usr/bin/cmake -E cmake_link_script CMakeFiles/testMMFFForceFieldHelpers.dir/link.txt --verbose=1 -/usr/bin/c++ -g -O2 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../../../../lib/libRDKitChemTransforms.so.1.2025.03.1 ../../../../lib/libRDKitDepictor.so.1.2025.03.1 ../../../../lib/libRDKitMolAlign.so.1.2025.03.1 ../../../../lib/libRDKitMolTransforms.so.1.2025.03.1 ../../../../lib/libRDKitEigenSolvers.so.1.2025.03.1 ../../../../lib/libRDKitSmilesParse.so.1.2025.03.1 ../../../../lib/libRDKitSubstructMatch.so.1.2025.03.1 ../../../../lib/libRDKitGenericGroups.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/libcoordgen.so /usr/lib/aarch64-linux-gnu/libmaeparser.so make[4]: Leaving directory '/build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu' -[ 59%] Built target testMMFFForceFieldHelpers +[ 59%] Built target testCrystalForceField make -f Code/GraphMol/ShapeHelpers/CMakeFiles/testShapeHelpers.dir/build.make Code/GraphMol/ShapeHelpers/CMakeFiles/testShapeHelpers.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-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/ShapeHelpers /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/ShapeHelpers /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/ShapeHelpers/CMakeFiles/testShapeHelpers.dir/DependInfo.cmake "--color=" @@ -5395,13 +5422,11 @@ make[4]: Entering directory '/build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu' [ 59%] Building CXX object Code/GraphMol/ShapeHelpers/CMakeFiles/testShapeHelpers.dir/testShapeHelpers.cpp.o cd /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/ShapeHelpers && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_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/ShapeHelpers/CMakeFiles/testShapeHelpers.dir/testShapeHelpers.cpp.o -MF CMakeFiles/testShapeHelpers.dir/testShapeHelpers.cpp.o.d -o CMakeFiles/testShapeHelpers.dir/testShapeHelpers.cpp.o -c /build/reproducible-path/rdkit-202503.1/Code/GraphMol/ShapeHelpers/testShapeHelpers.cpp -[ 59%] Linking CXX executable testUFFForceFieldHelpers -cd /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/ForceFieldHelpers/UFF && /usr/bin/cmake -E cmake_link_script CMakeFiles/testUFFForceFieldHelpers.dir/link.txt --verbose=1 -[ 59%] 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 CMakeFiles/rdfragcatalog.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/testUFFForceFieldHelpers.dir/link.d CMakeFiles/testUFFForceFieldHelpers.dir/testUFFHelpers.cpp.o -o testUFFForceFieldHelpers ../../../../lib/libRDKitDistGeomHelpers.so.1.2025.03.1 ../../../../lib/libRDKitFileParsers.so.1.2025.03.1 ../../../../lib/libRDKitDistGeometry.so.1.2025.03.1 ../../../../lib/libRDKitForceFieldHelpers.so.1.2025.03.1 ../../../../lib/libRDKitForceField.so.1.2025.03.1 ../../../../lib/libRDKitOptimizer.so.1.2025.03.1 ../../../../lib/libRDKitTrajectory.so.1.2025.03.1 ../../../../lib/libRDKitChemTransforms.so.1.2025.03.1 ../../../../lib/libRDKitDepictor.so.1.2025.03.1 ../../../../lib/libRDKitMolAlign.so.1.2025.03.1 ../../../../lib/libRDKitMolTransforms.so.1.2025.03.1 ../../../../lib/libRDKitEigenSolvers.so.1.2025.03.1 ../../../../lib/libRDKitSmilesParse.so.1.2025.03.1 ../../../../lib/libRDKitSubstructMatch.so.1.2025.03.1 ../../../../lib/libRDKitGenericGroups.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/libcoordgen.so /usr/lib/aarch64-linux-gnu/libmaeparser.so +[ 59%] Linking CXX executable fileParsersCatchTest +cd /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers && /usr/bin/cmake -E cmake_link_script CMakeFiles/fileParsersCatchTest.dir/link.txt --verbose=1 +/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=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/fileParsersCatchTest.dir/link.d CMakeFiles/fileParsersCatchTest.dir/file_parsers_catch.cpp.o -o fileParsersCatchTest ../../RDGeneral/librdkitCatch.a ../../../lib/libRDKitFileParsers.so.1.2025.03.1 /usr/lib/libCatch2.a ../../../lib/libRDKitChemTransforms.so.1.2025.03.1 ../../../lib/libRDKitDepictor.so.1.2025.03.1 /usr/lib/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 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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/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/testMolCatalog.dir/DependInfo.cmake "--color=" @@ -5410,6 +5435,10 @@ make[4]: Entering directory '/build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu' [ 59%] Building CXX object Code/GraphMol/MolCatalog/CMakeFiles/testMolCatalog.dir/test1.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 -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202503.1/External -I/build/reproducible-path/rdkit-202503.1/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/GraphMol/MolCatalog/CMakeFiles/testMolCatalog.dir/test1.cpp.o -MF CMakeFiles/testMolCatalog.dir/test1.cpp.o.d -o CMakeFiles/testMolCatalog.dir/test1.cpp.o -c /build/reproducible-path/rdkit-202503.1/Code/GraphMol/MolCatalog/test1.cpp +[ 59%] Building CXX object Code/GraphMol/ChemReactions/CMakeFiles/ChemReactions.dir/SanitizeRxn.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_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_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/SanitizeRxn.cpp.o -MF CMakeFiles/ChemReactions.dir/SanitizeRxn.cpp.o.d -o CMakeFiles/ChemReactions.dir/SanitizeRxn.cpp.o -c /build/reproducible-path/rdkit-202503.1/Code/GraphMol/ChemReactions/SanitizeRxn.cpp +[ 59%] 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 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 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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/libRDKitSubstructMatch.so.1.2025.03.1 ../../../../lib/libRDKitGenericGroups.so.1.2025.03.1 ../../../../lib/libRDKitSmilesParse.so.1.2025.03.1 ../../../../lib/libRDKitMolTransforms.so.1.2025.03.1 ../../../../lib/libRDKitGraphMol.so.1.2025.03.1 ../../../../lib/libRDKitEigenSolvers.so.1.2025.03.1 ../../../../lib/libRDKitAlignment.so.1.2025.03.1 ../../../../lib/libRDKitRDGeometryLib.so.1.2025.03.1 ../../../../lib/libRDKitDataStructs.so.1.2025.03.1 /usr/lib/aarch64-linux-gnu/libmaeparser.so /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' [ 59%] Built target rdfragcatalog @@ -5419,15 +5448,15 @@ make[4]: Leaving directory '/build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu' make -f Code/GraphMol/FMCS/CMakeFiles/FMCS.dir/build.make Code/GraphMol/FMCS/CMakeFiles/FMCS.dir/build make[4]: Entering directory '/build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu' -[ 59%] Building CXX object Code/GraphMol/FMCS/CMakeFiles/FMCS.dir/FMCS.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 -DFMCS_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_FMCS_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED 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-MD -MT Code/GraphMol/Descriptors/CMakeFiles/Descriptors.dir/Lipinski.cpp.o -MF CMakeFiles/Descriptors.dir/Lipinski.cpp.o.d -o CMakeFiles/Descriptors.dir/Lipinski.cpp.o -c /build/reproducible-path/rdkit-202503.1/Code/GraphMol/Descriptors/Lipinski.cpp -[ 59%] Linking CXX executable molAlignCatchTest -cd /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/MolAlign && /usr/bin/cmake -E cmake_link_script CMakeFiles/molAlignCatchTest.dir/link.txt --verbose=1 -/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=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/molAlignCatchTest.dir/link.d CMakeFiles/molAlignCatchTest.dir/catch_tests.cpp.o -o molAlignCatchTest 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CXX object Code/GraphMol/FMCS/CMakeFiles/FMCS.dir/FMCS.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 -DFMCS_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_FMCS_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202503.1/External -I/build/reproducible-path/rdkit-202503.1/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time 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/usr/lib/aarch64-linux-gnu/libcoordgen.so /usr/lib/aarch64-linux-gnu/libmaeparser.so make[4]: Leaving directory '/build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu' -[ 59%] Built target molAlignCatchTest +[ 59%] Built target testShapeHelpers make -f Code/GraphMol/MolHash/CMakeFiles/molHashCatchTest.dir/build.make Code/GraphMol/MolHash/CMakeFiles/molHashCatchTest.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-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/MolHash /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/MolHash /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/MolHash/CMakeFiles/molHashCatchTest.dir/DependInfo.cmake "--color=" @@ -5436,15 +5465,11 @@ make[4]: Entering directory '/build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu' [ 60%] Building CXX object Code/GraphMol/MolHash/CMakeFiles/molHashCatchTest.dir/catch_tests.cpp.o cd /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/MolHash && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202503.1/External -I/build/reproducible-path/rdkit-202503.1/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/GraphMol/MolHash/CMakeFiles/molHashCatchTest.dir/catch_tests.cpp.o -MF CMakeFiles/molHashCatchTest.dir/catch_tests.cpp.o.d -o CMakeFiles/molHashCatchTest.dir/catch_tests.cpp.o -c /build/reproducible-path/rdkit-202503.1/Code/GraphMol/MolHash/catch_tests.cpp -[ 60%] 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_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_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 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/usr/lib/aarch64-linux-gnu/libcoordgen.so /usr/lib/aarch64-linux-gnu/libmaeparser.so +[ 60%] Linking CXX executable molAlignCatchTest +cd /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/MolAlign && /usr/bin/cmake -E cmake_link_script CMakeFiles/molAlignCatchTest.dir/link.txt --verbose=1 +/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=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/molAlignCatchTest.dir/link.d CMakeFiles/molAlignCatchTest.dir/catch_tests.cpp.o -o molAlignCatchTest ../../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 ../../../lib/libRDKitMolAlign.so.1.2025.03.1 ../../../lib/libRDKitAlignment.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/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/libcoordgen.so /usr/lib/aarch64-linux-gnu/libmaeparser.so make[4]: Leaving directory '/build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu' -[ 60%] Built target testShapeHelpers +[ 60%] Built target molAlignCatchTest make -f Code/GraphMol/MMPA/CMakeFiles/MMPA.dir/build.make Code/GraphMol/MMPA/CMakeFiles/MMPA.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/MMPA /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/MMPA /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/MMPA/CMakeFiles/MMPA.dir/DependInfo.cmake "--color=" @@ -5453,9 +5478,11 @@ make[4]: Entering directory '/build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu' [ 60%] Building CXX object Code/GraphMol/MMPA/CMakeFiles/MMPA.dir/MMPA.cpp.o cd /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/MMPA && /usr/bin/c++ 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-Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/RascalMCES/CMakeFiles/RascalMCES.dir/RascalMCES.cpp.o -MF CMakeFiles/RascalMCES.dir/RascalMCES.cpp.o.d -o CMakeFiles/RascalMCES.dir/RascalMCES.cpp.o -c /build/reproducible-path/rdkit-202503.1/Code/GraphMol/RascalMCES/RascalMCES.cpp -[ 60%] Linking CXX executable distGeomHelpersCatch -cd /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/DistGeomHelpers && /usr/bin/cmake -E cmake_link_script CMakeFiles/distGeomHelpersCatch.dir/link.txt --verbose=1 -/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -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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cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202503.1 /build/reproducible-path/rdkit-202503.1/Code/GraphMol/Trajectory /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/Trajectory /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/Trajectory/CMakeFiles/trajectoryTest.dir/DependInfo.cmake "--color=" -[ 60%] Linking CXX shared module ../../../../rdkit/Chem/rdDistGeom.so -cd /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/DistGeomHelpers/Wrap && /usr/bin/cmake -E cmake_link_script CMakeFiles/rdDistGeom.dir/link.txt --verbose=1 make[4]: Leaving directory '/build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu' make -f Code/GraphMol/Trajectory/CMakeFiles/trajectoryTest.dir/build.make Code/GraphMol/Trajectory/CMakeFiles/trajectoryTest.dir/build make[4]: Entering directory 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../../../../lib/libRDKitOptimizer.so.1.2025.03.1 ../../../../lib/libRDKitTrajectory.so.1.2025.03.1 ../../../../lib/libRDKitChemTransforms.so.1.2025.03.1 ../../../../lib/libRDKitDepictor.so.1.2025.03.1 ../../../../lib/libRDKitMolAlign.so.1.2025.03.1 ../../../../lib/libRDKitMolTransforms.so.1.2025.03.1 ../../../../lib/libRDKitEigenSolvers.so.1.2025.03.1 ../../../../lib/libRDKitSmilesParse.so.1.2025.03.1 ../../../../lib/libRDKitSubstructMatch.so.1.2025.03.1 ../../../../lib/libRDKitGenericGroups.so.1.2025.03.1 ../../../../lib/libRDKitAlignment.so.1.2025.03.1 ../../../../lib/libRDKitGraphMol.so.1.2025.03.1 ../../../../lib/libRDKitRDGeometryLib.so.1.2025.03.1 ../../../../lib/libRDKitDataStructs.so.1.2025.03.1 /usr/lib/aarch64-linux-gnu/libcoordgen.so /usr/lib/aarch64-linux-gnu/libmaeparser.so /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 -[ 60%] Built target testFeatures +[ 60%] Linking CXX executable testMolAlign +cd /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/MolAlign && /usr/bin/cmake -E cmake_link_script CMakeFiles/testMolAlign.dir/link.txt --verbose=1 +/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=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/testMolAlign.dir/link.d CMakeFiles/testMolAlign.dir/testMolAlign.cpp.o -o testMolAlign ../../../lib/libRDKitFileParsers.so.1.2025.03.1 ../../../lib/libRDKitDistGeomHelpers.so.1.2025.03.1 ../../../lib/libRDKitChemTransforms.so.1.2025.03.1 ../../../lib/libRDKitDepictor.so.1.2025.03.1 /usr/lib/aarch64-linux-gnu/libcoordgen.so /usr/lib/aarch64-linux-gnu/libmaeparser.so ../../../lib/libRDKitMolAlign.so.1.2025.03.1 ../../../lib/libRDKitMolTransforms.so.1.2025.03.1 ../../../lib/libRDKitAlignment.so.1.2025.03.1 ../../../lib/libRDKitDistGeometry.so.1.2025.03.1 ../../../lib/libRDKitForceFieldHelpers.so.1.2025.03.1 ../../../lib/libRDKitSmilesParse.so.1.2025.03.1 ../../../lib/libRDKitSubstructMatch.so.1.2025.03.1 ../../../lib/libRDKitGenericGroups.so.1.2025.03.1 ../../../lib/libRDKitEigenSolvers.so.1.2025.03.1 ../../../lib/libRDKitForceField.so.1.2025.03.1 ../../../lib/libRDKitOptimizer.so.1.2025.03.1 ../../../lib/libRDKitTrajectory.so.1.2025.03.1 ../../../lib/libRDKitGraphMol.so.1.2025.03.1 ../../../lib/libRDKitRDGeometryLib.so.1.2025.03.1 ../../../lib/libRDKitDataStructs.so.1.2025.03.1 ../../../lib/libRDKitRDGeneral.so.1.2025.03.1 /usr/lib/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' -[ 60%] 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_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 -[ 60%] Built target rdDistGeom +[ 60%] Built target testMolAlign 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/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/molInterchangeTest1.dir/DependInfo.cmake "--color=" @@ -5497,14 +5517,14 @@ make[4]: Entering directory '/build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu' [ 60%] Building CXX object Code/GraphMol/MolInterchange/CMakeFiles/molInterchangeTest1.dir/test1.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 -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -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 -MD -MT Code/GraphMol/MolInterchange/CMakeFiles/molInterchangeTest1.dir/test1.cpp.o -MF CMakeFiles/molInterchangeTest1.dir/test1.cpp.o.d -o CMakeFiles/molInterchangeTest1.dir/test1.cpp.o -c /build/reproducible-path/rdkit-202503.1/Code/GraphMol/MolInterchange/test1.cpp +[ 60%] 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_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_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 [ 60%] Linking CXX executable testMolCatalog cd /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/MolCatalog && /usr/bin/cmake -E cmake_link_script CMakeFiles/testMolCatalog.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=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/testMolCatalog.dir/link.d CMakeFiles/testMolCatalog.dir/test1.cpp.o -o testMolCatalog ../../../lib/libRDKitMolCatalog.so.1.2025.03.1 ../../../lib/libRDKitFileParsers.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/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' [ 60%] Built target testMolCatalog -[ 60%] Building CXX object Code/GraphMol/Descriptors/CMakeFiles/Descriptors.dir/ConnectivityDescriptors.cpp.o make -f Code/GraphMol/MolInterchange/CMakeFiles/molInterchangeCatchTest.dir/build.make Code/GraphMol/MolInterchange/CMakeFiles/molInterchangeCatchTest.dir/depend -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_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_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/ConnectivityDescriptors.cpp.o -MF CMakeFiles/Descriptors.dir/ConnectivityDescriptors.cpp.o.d -o CMakeFiles/Descriptors.dir/ConnectivityDescriptors.cpp.o -c /build/reproducible-path/rdkit-202503.1/Code/GraphMol/Descriptors/ConnectivityDescriptors.cpp 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/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/molInterchangeCatchTest.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu' @@ -5512,13 +5532,13 @@ make[4]: Entering directory '/build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu' [ 60%] Building CXX object Code/GraphMol/MolInterchange/CMakeFiles/molInterchangeCatchTest.dir/molinterchange_catch.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 -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -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 -MD -MT Code/GraphMol/MolInterchange/CMakeFiles/molInterchangeCatchTest.dir/molinterchange_catch.cpp.o -MF CMakeFiles/molInterchangeCatchTest.dir/molinterchange_catch.cpp.o.d -o CMakeFiles/molInterchangeCatchTest.dir/molinterchange_catch.cpp.o -c /build/reproducible-path/rdkit-202503.1/Code/GraphMol/MolInterchange/molinterchange_catch.cpp -[ 60%] Linking CXX executable testDistGeomHelpers -cd /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/DistGeomHelpers && /usr/bin/cmake -E cmake_link_script CMakeFiles/testDistGeomHelpers.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/testDistGeomHelpers.dir/link.d CMakeFiles/testDistGeomHelpers.dir/testDgeomHelpers.cpp.o -o testDistGeomHelpers ../../../lib/libRDKitDistGeomHelpers.so.1.2025.03.1 ../../../lib/libRDKitFileParsers.so.1.2025.03.1 ../../../lib/libRDKitDistGeometry.so.1.2025.03.1 ../../../lib/libRDKitForceFieldHelpers.so.1.2025.03.1 ../../../lib/libRDKitForceField.so.1.2025.03.1 ../../../lib/libRDKitOptimizer.so.1.2025.03.1 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directory '/build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu' -[ 60%] Building CXX object Code/GraphMol/FMCS/CMakeFiles/FMCS.dir/Seed.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 -DFMCS_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_FMCS_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202503.1/External -I/build/reproducible-path/rdkit-202503.1/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security 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-Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/Descriptors/CMakeFiles/Descriptors.dir/MQN.cpp.o -MF CMakeFiles/Descriptors.dir/MQN.cpp.o.d -o CMakeFiles/Descriptors.dir/MQN.cpp.o -c /build/reproducible-path/rdkit-202503.1/Code/GraphMol/Descriptors/MQN.cpp [ 61%] 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 @@ -5556,16 +5571,17 @@ make[4]: Leaving directory '/build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu' make -f Code/GraphMol/MolInteractionFields/CMakeFiles/testMIF.dir/build.make Code/GraphMol/MolInteractionFields/CMakeFiles/testMIF.dir/build make[4]: Entering directory '/build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu' -[ 61%] 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 [ 61%] 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_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_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 -[ 61%] Building CXX object Code/GraphMol/RascalMCES/CMakeFiles/RascalMCES.dir/RascalButinaCluster.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_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/RascalButinaCluster.cpp.o -MF CMakeFiles/RascalMCES.dir/RascalButinaCluster.cpp.o.d -o CMakeFiles/RascalMCES.dir/RascalButinaCluster.cpp.o -c /build/reproducible-path/rdkit-202503.1/Code/GraphMol/RascalMCES/RascalButinaCluster.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/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 /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/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 +[ 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 +/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/MMPA.dir/link.d -Wl,-z,relro -Wl,-z,now -shared -Wl,-soname,libRDKitMMPA.so.1 -o ../../../lib/libRDKitMMPA.so.1.2025.03.1 CMakeFiles/MMPA.dir/MMPA.cpp.o ../../../lib/libRDKitFileParsers.so.1.2025.03.1 ../../../lib/libRDKitChemTransforms.so.1.2025.03.1 ../../../lib/libRDKitDepictor.so.1.2025.03.1 /usr/lib/aarch64-linux-gnu/libcoordgen.so ../../../lib/libRDKitMolAlign.so.1.2025.03.1 ../../../lib/libRDKitSubstructMatch.so.1.2025.03.1 ../../../lib/libRDKitMolTransforms.so.1.2025.03.1 ../../../lib/libRDKitEigenSolvers.so.1.2025.03.1 ../../../lib/libRDKitAlignment.so.1.2025.03.1 ../../../lib/libRDKitGenericGroups.so.1.2025.03.1 ../../../lib/libRDKitSmilesParse.so.1.2025.03.1 ../../../lib/libRDKitGraphMol.so.1.2025.03.1 ../../../lib/libRDKitRDGeometryLib.so.1.2025.03.1 ../../../lib/libRDKitDataStructs.so.1.2025.03.1 ../../../lib/libRDKitRDGeneral.so.1.2025.03.1 /usr/lib/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/MMPA && /usr/bin/cmake -E cmake_symlink_library ../../../lib/libRDKitMMPA.so.1.2025.03.1 ../../../lib/libRDKitMMPA.so.1 ../../../lib/libRDKitMMPA.so make[4]: Leaving directory '/build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu' -[ 61%] Built target molHashCatchTest +[ 61%] Built target MMPA make -f Code/GraphMol/MMPA/CMakeFiles/testMMPA.dir/build.make Code/GraphMol/MMPA/CMakeFiles/testMMPA.dir/depend +[ 61%] 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_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_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 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/MMPA /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/MMPA /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/MMPA/CMakeFiles/testMMPA.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu' @@ -5573,15 +5589,15 @@ make[4]: Entering directory '/build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu' [ 61%] Building CXX object Code/GraphMol/MMPA/CMakeFiles/testMMPA.dir/MMPA_UnitTest.cpp.o cd /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/MMPA && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202503.1/External -I/build/reproducible-path/rdkit-202503.1/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/GraphMol/MMPA/CMakeFiles/testMMPA.dir/MMPA_UnitTest.cpp.o -MF CMakeFiles/testMMPA.dir/MMPA_UnitTest.cpp.o.d -o CMakeFiles/testMMPA.dir/MMPA_UnitTest.cpp.o -c /build/reproducible-path/rdkit-202503.1/Code/GraphMol/MMPA/MMPA_UnitTest.cpp -[ 61%] Building CXX object Code/GraphMol/Descriptors/CMakeFiles/Descriptors.dir/Property.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_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_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/Property.cpp.o -MF CMakeFiles/Descriptors.dir/Property.cpp.o.d -o CMakeFiles/Descriptors.dir/Property.cpp.o -c /build/reproducible-path/rdkit-202503.1/Code/GraphMol/Descriptors/Property.cpp -[ 61%] Building CXX object Code/GraphMol/FMCS/CMakeFiles/FMCS.dir/MaximumCommonSubgraph.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 -DFMCS_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_FMCS_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202503.1/External -I/build/reproducible-path/rdkit-202503.1/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/FMCS/CMakeFiles/FMCS.dir/MaximumCommonSubgraph.cpp.o -MF CMakeFiles/FMCS.dir/MaximumCommonSubgraph.cpp.o.d -o CMakeFiles/FMCS.dir/MaximumCommonSubgraph.cpp.o -c /build/reproducible-path/rdkit-202503.1/Code/GraphMol/FMCS/MaximumCommonSubgraph.cpp -[ 61%] 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 +[ 61%] Building CXX object Code/GraphMol/Descriptors/CMakeFiles/Descriptors.dir/MQN.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_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_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/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' +[ 61%] Built target molHashCatchTest +[ 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_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 +[ 61%] 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 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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/Descriptors/CMakeFiles/Descriptors.dir/Property.cpp.o -MF CMakeFiles/Descriptors.dir/Property.cpp.o.d -o CMakeFiles/Descriptors.dir/Property.cpp.o -c /build/reproducible-path/rdkit-202503.1/Code/GraphMol/Descriptors/Property.cpp [ 61%] 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 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Code/GraphMol/RascalMCES/CMakeFiles/RascalMCES.dir/lap_a_la_scipy.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_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/lap_a_la_scipy.cpp.o -MF CMakeFiles/RascalMCES.dir/lap_a_la_scipy.cpp.o.d -o CMakeFiles/RascalMCES.dir/lap_a_la_scipy.cpp.o -c /build/reproducible-path/rdkit-202503.1/Code/GraphMol/RascalMCES/lap_a_la_scipy.cpp [ 61%] Linking CXX shared library ../../../lib/libRDKitMolProcessing.so @@ -5615,175 +5645,134 @@ 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 -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS 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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_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 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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 +[ 62%] 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_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_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 +[ 62%] Building CXX object Code/GraphMol/FMCS/CMakeFiles/FMCS.dir/MaximumCommonSubgraph.cpp.o +cd /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FMCS && /usr/bin/c++ -DBOOST_IOSTREAMS_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 -fPIC -MD -MT Code/GraphMol/RascalMCES/CMakeFiles/RascalMCES.dir/RascalResult.cpp.o -MF CMakeFiles/RascalMCES.dir/RascalResult.cpp.o.d -o CMakeFiles/RascalMCES.dir/RascalResult.cpp.o -c /build/reproducible-path/rdkit-202503.1/Code/GraphMol/RascalMCES/RascalResult.cpp +[ 63%] 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 +[ 63%] Building CXX object Code/GraphMol/FMCS/CMakeFiles/FMCS.dir/SubstructMatchCustom.cpp.o +cd 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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/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 make[4]: Leaving directory '/build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu' -[ 62%] Built target testAbbreviations +[ 63%] Built target testMMPA make -f Code/GraphMol/MolProcessing/Wrap/CMakeFiles/rdMolProcessing.dir/build.make 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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/Descriptors/CMakeFiles/Descriptors.dir/WHIM.cpp.o -MF CMakeFiles/Descriptors.dir/WHIM.cpp.o.d -o CMakeFiles/Descriptors.dir/WHIM.cpp.o -c /build/reproducible-path/rdkit-202503.1/Code/GraphMol/Descriptors/WHIM.cpp make[4]: Entering directory '/build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu' -[ 66%] 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_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_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 -[ 66%] Linking CXX shared module ../../../../rdkit/Chem/rdMolProcessing.so -cd /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/MolProcessing/Wrap && /usr/bin/cmake -E cmake_link_script CMakeFiles/rdMolProcessing.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/rdMolProcessing.dir/link.d -Wl,-z,relro -Wl,-z,now -shared -o ../../../../rdkit/Chem/rdMolProcessing.so CMakeFiles/rdMolProcessing.dir/rdMolProcessing.cpp.o ../../../../lib/libRDKitMolProcessing.so.1.2025.03.1 ../../../../lib/libRDKitRDBoost.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/libRDKitFingerprints.so.1.2025.03.1 ../../../../lib/libRDKitSmilesParse.so.1.2025.03.1 ../../../../lib/libRDKitSubgraphs.so.1.2025.03.1 ../../../../lib/libRDKitSubstructMatch.so.1.2025.03.1 ../../../../lib/libRDKitGenericGroups.so.1.2025.03.1 ../../../../lib/libRDKitGraphMol.so.1.2025.03.1 ../../../../lib/libRDKitRDGeometryLib.so.1.2025.03.1 ../../../../lib/libRDKitDataStructs.so.1.2025.03.1 ../../../../lib/libRDKitRDStreams.so.1.2025.03.1 /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 && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202503.1 /build/reproducible-path/rdkit-202503.1/Code/GraphMol/FMCS/Wrap /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FMCS/Wrap /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FMCS/Wrap/CMakeFiles/rdFMCS.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu' -[ 66%] Built target rdMolProcessing -make -f Code/GraphMol/FMCS/Wrap/CMakeFiles/rdFMCS.dir/build.make Code/GraphMol/FMCS/Wrap/CMakeFiles/rdFMCS.dir/depend +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' -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/FMCS/Wrap /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FMCS/Wrap /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FMCS/Wrap/CMakeFiles/rdFMCS.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu' make -f Code/GraphMol/FMCS/Wrap/CMakeFiles/rdFMCS.dir/build.make Code/GraphMol/FMCS/Wrap/CMakeFiles/rdFMCS.dir/build make[4]: Entering directory '/build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu' -[ 67%] Building CXX object Code/GraphMol/FMCS/Wrap/CMakeFiles/rdFMCS.dir/rdFMCS.cpp.o +[ 67%] 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_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_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 +[ 68%] Building CXX object Code/GraphMol/FMCS/Wrap/CMakeFiles/rdFMCS.dir/rdFMCS.cpp.o cd /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FMCS/Wrap && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_NUMPY_DYN_LINK -DBOOST_NUMPY_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DrdFMCS_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/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 -[ 68%] Linking CXX shared library ../../../lib/libRDKitChemReactions.so -cd 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-I/build/reproducible-path/rdkit-202503.1/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-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 /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/ChemReactions.dir/link.d -Wl,-z,relro -Wl,-z,now -shared -Wl,-soname,libRDKitChemReactions.so.1 -o ../../../lib/libRDKitChemReactions.so.1.2025.03.1 CMakeFiles/ChemReactions.dir/Reaction.cpp.o CMakeFiles/ChemReactions.dir/MDLParser.cpp.o CMakeFiles/ChemReactions.dir/DaylightParser.cpp.o CMakeFiles/ChemReactions.dir/ReactionPickler.cpp.o CMakeFiles/ChemReactions.dir/ReactionWriter.cpp.o CMakeFiles/ChemReactions.dir/ReactionDepict.cpp.o CMakeFiles/ChemReactions.dir/ReactionFingerprints.cpp.o CMakeFiles/ChemReactions.dir/ReactionUtils.cpp.o CMakeFiles/ChemReactions.dir/MoleculeParser.cpp.o CMakeFiles/ChemReactions.dir/ReactionRunner.cpp.o CMakeFiles/ChemReactions.dir/PreprocessRxn.cpp.o CMakeFiles/ChemReactions.dir/SanitizeRxn.cpp.o CMakeFiles/ChemReactions.dir/PNGParser.cpp.o CMakeFiles/ChemReactions.dir/CDXMLParser.cpp.o CMakeFiles/ChemReactions.dir/Enumerate/Enumerate.cpp.o CMakeFiles/ChemReactions.dir/Enumerate/EnumerationPickler.cpp.o CMakeFiles/ChemReactions.dir/Enumerate/EvenSamplePairs.cpp.o ../../../lib/libRDKitFilterCatalog.so.1.2025.03.1 ../../../lib/libRDKitFingerprints.so.1.2025.03.1 ../../../lib/libRDKitFileParsers.so.1.2025.03.1 ../../../lib/libRDKitChemTransforms.so.1.2025.03.1 ../../../lib/libRDKitCatalogs.so.1.2025.03.1 ../../../lib/libRDKitSubgraphs.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 /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' [ 68%] Built target ChemReactions make -f Code/GraphMol/FMCS/Test/CMakeFiles/FMCStest.dir/build.make Code/GraphMol/FMCS/Test/CMakeFiles/FMCStest.dir/depend +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/FMCS/Test /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FMCS/Test /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FMCS/Test/CMakeFiles/FMCStest.dir/DependInfo.cmake "--color=" -make[4]: Leaving directory '/build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu' -make -f Code/GraphMol/FMCS/Test/CMakeFiles/FMCStest.dir/build.make Code/GraphMol/FMCS/Test/CMakeFiles/FMCStest.dir/build -make[4]: Entering directory '/build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu' -[ 68%] Building CXX object Code/GraphMol/FMCS/Test/CMakeFiles/FMCStest.dir/testFMCS.cpp.o -cd /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FMCS/Test && 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-I/build/reproducible-path/rdkit-202503.1/External -I/build/reproducible-path/rdkit-202503.1/Code -I/build/reproducible-path/rdkit-202503.1/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/GraphMol/ChemReactions/CMakeFiles/rxnTestCatch.dir/catch_tests.cpp.o -MF CMakeFiles/rxnTestCatch.dir/catch_tests.cpp.o.d -o CMakeFiles/rxnTestCatch.dir/catch_tests.cpp.o -c /build/reproducible-path/rdkit-202503.1/Code/GraphMol/ChemReactions/catch_tests.cpp -[ 72%] Linking CXX executable testReactionFingerprints -cd /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/ChemReactions && /usr/bin/cmake -E cmake_link_script 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-fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/GraphMol/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 -[ 72%] 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 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+[ 71%] Linking CXX shared module ../../../../rdkit/Chem/rdRascalMCES.so cd /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/RascalMCES/Wrap && /usr/bin/cmake -E cmake_link_script CMakeFiles/rdRascalMCES.dir/link.txt --verbose=1 /usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=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/rdRascalMCES.dir/link.d -Wl,-z,relro -Wl,-z,now -shared -o ../../../../rdkit/Chem/rdRascalMCES.so CMakeFiles/rdRascalMCES.dir/rdRascalMCES.cpp.o ../../../../lib/libRDKitRascalMCES.so.1.2025.03.1 ../../../../lib/libRDKitRDBoost.so.1.2025.03.1 ../../../../lib/libRDKitFileParsers.so.1.2025.03.1 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../../../../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 +[ 73%] 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 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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/rdmolfiles.dir/rdmolfiles.cpp.o -MF CMakeFiles/rdmolfiles.dir/rdmolfiles.cpp.o.d -o CMakeFiles/rdmolfiles.dir/rdmolfiles.cpp.o -c /build/reproducible-path/rdkit-202503.1/Code/GraphMol/Wrap/rdmolfiles.cpp +[ 78%] 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 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Code/GraphMol/MolStandardize/CMakeFiles/MolStandardize.dir/FragmentCatalog/FragmentCatalogEntry.cpp.o -MF CMakeFiles/MolStandardize.dir/FragmentCatalog/FragmentCatalogEntry.cpp.o.d -o CMakeFiles/MolStandardize.dir/FragmentCatalog/FragmentCatalogEntry.cpp.o -c /build/reproducible-path/rdkit-202503.1/Code/GraphMol/MolStandardize/FragmentCatalog/FragmentCatalogEntry.cpp In file included from /usr/include/c++/14/vector:62, from /build/reproducible-path/rdkit-202503.1/Code/GraphMol/MolDraw2D/DrawMolMCHLasso.cpp:15: In static member function 'static _Up* std::__copy_move<_IsMove, true, std::random_access_iterator_tag>::__copy_m(_Tp*, _Tp*, _Up*) [with _Tp = int; _Up = int; bool _IsMove = false]', @@ -6314,20 +6291,49 @@ /usr/include/c++/14/bits/new_allocator.h:151:55: note: at offset [-9223372036854775808, -1] into destination object of size [4, 9223372036854775804] allocated by 'operator new' 151 | return static_cast<_Tp*>(_GLIBCXX_OPERATOR_NEW(__n * sizeof(_Tp))); | ^ -[ 79%] Building CXX object Code/GraphMol/MolDraw2D/CMakeFiles/MolDraw2D.dir/DrawShape.cpp.o +[ 78%] Building CXX object Code/GraphMol/MolDraw2D/CMakeFiles/MolDraw2D.dir/DrawShape.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_HAS_EIGEN3 -DRDK_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/DrawShape.cpp.o -MF CMakeFiles/MolDraw2D.dir/DrawShape.cpp.o.d -o CMakeFiles/MolDraw2D.dir/DrawShape.cpp.o -c /build/reproducible-path/rdkit-202503.1/Code/GraphMol/MolDraw2D/DrawShape.cpp -[ 79%] Linking CXX shared library ../../../lib/libRDKitO3AAlign.so +[ 78%] Building CXX object Code/GraphMol/Wrap/CMakeFiles/rdmolops.dir/ChiralityOps.cpp.o +cd /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/Wrap && /usr/bin/c++ 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../../../lib/libRDKitEigenSolvers.so.1.2025.03.1 ../../../lib/libRDKitSubstructMatch.so.1.2025.03.1 ../../../lib/libRDKitGenericGroups.so.1.2025.03.1 ../../../lib/libRDKitSmilesParse.so.1.2025.03.1 ../../../lib/libRDKitForceField.so.1.2025.03.1 ../../../lib/libRDKitOptimizer.so.1.2025.03.1 ../../../lib/libRDKitTrajectory.so.1.2025.03.1 ../../../lib/libRDKitGraphMol.so.1.2025.03.1 ../../../lib/libRDKitRDGeometryLib.so.1.2025.03.1 ../../../lib/libRDKitDataStructs.so.1.2025.03.1 ../../../lib/libRDKitRDGeneral.so.1.2025.03.1 /usr/lib/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/libRDKitO3AAlign.so.1.2025.03.1 ../../../lib/libRDKitO3AAlign.so.1 ../../../lib/libRDKitO3AAlign.so make[4]: Leaving directory 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-I/build/reproducible-path/rdkit-202503.1/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/GraphMol/CIPLabeler/CMakeFiles/testCIPLabeler.dir/CIPLabeler.cpp.o -MF CMakeFiles/testCIPLabeler.dir/CIPLabeler.cpp.o.d -o CMakeFiles/testCIPLabeler.dir/CIPLabeler.cpp.o -c /build/reproducible-path/rdkit-202503.1/Code/GraphMol/CIPLabeler/CIPLabeler.cpp 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, @@ -6339,61 +6345,159 @@ /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) | ^~~~~~~~~ -[ 79%] Building CXX object Code/GraphMol/Wrap/CMakeFiles/rdchem.dir/Table.cpp.o +[ 80%] Building CXX object Code/GraphMol/MolDraw2D/CMakeFiles/MolDraw2D.dir/DrawTextNotFT.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_HAS_EIGEN3 -DRDK_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/DrawTextNotFT.cpp.o -MF CMakeFiles/MolDraw2D.dir/DrawTextNotFT.cpp.o.d -o CMakeFiles/MolDraw2D.dir/DrawTextNotFT.cpp.o -c /build/reproducible-path/rdkit-202503.1/Code/GraphMol/MolDraw2D/DrawTextNotFT.cpp +[ 80%] Linking CXX shared module ../../../rdkit/Chem/rdmolops.so +cd /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/Wrap && /usr/bin/cmake -E cmake_link_script 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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' +[ 80%] Built target rdmolops +make -f Code/GraphMol/SmilesParse/CMakeFiles/cxsmilesTest.dir/build.make Code/GraphMol/SmilesParse/CMakeFiles/cxsmilesTest.dir/depend +make[4]: Entering directory '/build/reproducible-path/rdkit-202503.1/obj-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/cxsmilesTest.dir/DependInfo.cmake "--color=" +make[4]: Leaving directory 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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/SmilesParse/CMakeFiles/cxsmilesTest.dir/cxsmiles_test.cpp.o -MF CMakeFiles/cxsmilesTest.dir/cxsmiles_test.cpp.o.d -o CMakeFiles/cxsmilesTest.dir/cxsmiles_test.cpp.o -c /build/reproducible-path/rdkit-202503.1/Code/GraphMol/SmilesParse/cxsmiles_test.cpp +[ 80%] 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++ 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Code/GraphMol/Wrap/CMakeFiles/rdchem.dir/Table.cpp.o -MF CMakeFiles/rdchem.dir/Table.cpp.o.d -o CMakeFiles/rdchem.dir/Table.cpp.o -c /build/reproducible-path/rdkit-202503.1/Code/GraphMol/Wrap/Table.cpp -[ 79%] Linking CXX executable testMrvToMol -cd /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/MarvinParse && /usr/bin/cmake -E cmake_link_script CMakeFiles/testMrvToMol.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/testMrvToMol.dir/link.d CMakeFiles/testMrvToMol.dir/testMrvToMol.cpp.o -o testMrvToMol ../../../lib/libRDKitMarvinParser.so.1.2025.03.1 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Code/GraphMol/MolStandardize/CMakeFiles/MolStandardize.dir/TransformCatalog/TransformCatalogEntry.cpp.o -MF CMakeFiles/MolStandardize.dir/TransformCatalog/TransformCatalogEntry.cpp.o.d -o CMakeFiles/MolStandardize.dir/TransformCatalog/TransformCatalogEntry.cpp.o -c /build/reproducible-path/rdkit-202503.1/Code/GraphMol/MolStandardize/TransformCatalog/TransformCatalogEntry.cpp +[ 81%] 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 +/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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-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/CIPLabeler/CMakeFiles/testCIPLabeler.dir/Edge.cpp.o -MF CMakeFiles/testCIPLabeler.dir/Edge.cpp.o.d -o CMakeFiles/testCIPLabeler.dir/Edge.cpp.o -c /build/reproducible-path/rdkit-202503.1/Code/GraphMol/CIPLabeler/Edge.cpp -[ 81%] Building CXX object Code/GraphMol/CIPLabeler/CMakeFiles/testCIPLabeler.dir/Sort.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 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/build/reproducible-path/rdkit-202503.1/Code/GraphMol/CIPLabeler/configs/AtropisomerBond.cpp +[ 84%] Linking CXX shared library ../../../lib/libRDKitMolStandardize.so +cd /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/MolStandardize && /usr/bin/cmake -E cmake_link_script CMakeFiles/MolStandardize.dir/link.txt --verbose=1 +[ 84%] Building CXX object Code/GraphMol/Wrap/CMakeFiles/rdmolfiles.dir/SDMolSupplier.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 -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED 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CMakeFiles/testCIPLabeler.dir/rules/Rule1b.cpp.o -c /build/reproducible-path/rdkit-202503.1/Code/GraphMol/CIPLabeler/rules/Rule1b.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, @@ -6487,240 +6572,192 @@ /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]); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -[ 81%] Building CXX object Code/GraphMol/CIPLabeler/CMakeFiles/testCIPLabeler.dir/configs/Sp2Bond.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 -DRDKIT_CIPLABELER_BUILD -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD 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/build/reproducible-path/rdkit-202503.1/Code/GraphMol/CIPLabeler/configs/Sp2Bond.cpp -[ 81%] Building CXX object Code/GraphMol/CIPLabeler/CMakeFiles/testCIPLabeler.dir/configs/Tetrahedral.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 -DRDKIT_CIPLABELER_BUILD -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202503.1/External -I/build/reproducible-path/rdkit-202503.1/Code -I/build/reproducible-path/rdkit-202503.1/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 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/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/libcairo.so -cd /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/MolDraw2D && /usr/bin/cmake -E cmake_symlink_library ../../../lib/libRDKitMolDraw2D.so.1.2025.03.1 ../../../lib/libRDKitMolDraw2D.so.1 ../../../lib/libRDKitMolDraw2D.so -make[4]: Leaving directory '/build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu' -[ 86%] Built target MolDraw2D -[ 86%] 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/Wrap/CMakeFiles/rdchem.dir/ResonanceMolSupplier.cpp.o -MF CMakeFiles/rdchem.dir/ResonanceMolSupplier.cpp.o.d -o CMakeFiles/rdchem.dir/ResonanceMolSupplier.cpp.o -c /build/reproducible-path/rdkit-202503.1/Code/GraphMol/Wrap/ResonanceMolSupplier.cpp -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, - from /build/reproducible-path/rdkit-202503.1/Code/RDGeneral/types.h:21, - from /build/reproducible-path/rdkit-202503.1/Code/RDGeneral/utils.h:15, - from /build/reproducible-path/rdkit-202503.1/Code/GraphMol/MolDraw2D/test1.cpp:12: -/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/MolDraw2D/test1.cpp:1592:46: required from here - 1592 | drawer.getAtomCoords(std::make_pair(ocoords.x, ocoords.y)); - | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~ -/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) - | ^~~~~~~~~ -[ 87%] Building CXX object Code/GraphMol/Wrap/CMakeFiles/rdmolfiles.dir/MultithreadedSmilesMolSupplier.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 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-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 +[ 86%] Building CXX object Code/GraphMol/ChemReactions/Wrap/CMakeFiles/rdChemReactions.dir/rdChemReactions.cpp.o +cd 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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' +[ 86%] Built target rdMolAlign 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 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executable testReaction +cd /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/ChemReactions && /usr/bin/cmake -E cmake_link_script CMakeFiles/testReaction.dir/link.txt --verbose=1 +/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=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/testReaction.dir/link.d CMakeFiles/testReaction.dir/testReaction.cpp.o -o testReaction ../../../lib/libRDKitChemReactions.so.1.2025.03.1 ../../../lib/libRDKitFilterCatalog.so.1.2025.03.1 ../../../lib/libRDKitCatalogs.so.1.2025.03.1 ../../../lib/libRDKitFingerprints.so.1.2025.03.1 ../../../lib/libRDKitSubgraphs.so.1.2025.03.1 ../../../lib/libRDKitFileParsers.so.1.2025.03.1 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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/CIPLabeler/CMakeFiles/testCIPLabeler.dir/rules/Rule3.cpp.o -MF CMakeFiles/testCIPLabeler.dir/rules/Rule3.cpp.o.d -o CMakeFiles/testCIPLabeler.dir/rules/Rule3.cpp.o -c /build/reproducible-path/rdkit-202503.1/Code/GraphMol/CIPLabeler/rules/Rule3.cpp make[4]: Entering directory '/build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu' -[ 87%] Building CXX object Code/GraphMol/MolDraw2D/Wrap/CMakeFiles/rdMolDraw2D.dir/rdMolDraw2D.cpp.o +[ 86%] 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 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-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/TDTMolSupplier.cpp.o -MF CMakeFiles/rdmolfiles.dir/TDTMolSupplier.cpp.o.d -o CMakeFiles/rdmolfiles.dir/TDTMolSupplier.cpp.o -c /build/reproducible-path/rdkit-202503.1/Code/GraphMol/Wrap/TDTMolSupplier.cpp +[ 86%] Building CXX object Code/GraphMol/CIPLabeler/CMakeFiles/testCIPLabeler.dir/rules/Rule4a.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 -DRDKIT_CIPLABELER_BUILD -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202503.1/External -I/build/reproducible-path/rdkit-202503.1/Code -I/build/reproducible-path/rdkit-202503.1/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC 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__strip_reference_wrapper::type>::__type = double; typename decay<_Tp2>::type = double]': +/build/reproducible-path/rdkit-202503.1/Code/GraphMol/MolDraw2D/test1.cpp:1592:46: required from here + 1592 | drawer.getAtomCoords(std::make_pair(ocoords.x, ocoords.y)); + | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~ +/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) + | ^~~~~~~~~ +[ 86%] Building CXX object Code/GraphMol/CIPLabeler/CMakeFiles/testCIPLabeler.dir/rules/Rule4b.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 -DRDKIT_CIPLABELER_BUILD -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D 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86%] Building CXX object Code/GraphMol/Wrap/CMakeFiles/rdchem.dir/EditableMol.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 -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -Drdchem_EXPORTS -I/build/reproducible-path/rdkit-202503.1/External -I/build/reproducible-path/rdkit-202503.1/Code -I/build/reproducible-path/rdkit-202503.1/External/boost-numeric-bindings -I/usr/lib/aarch64-linux-gnu/python3-numpy/numpy/_core/include -isystem /usr/include/python3.13 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'/build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu' -[ 89%] Building CXX object Code/GraphMol/MolStandardize/CMakeFiles/molChargeTest.dir/testCharge.cpp.o +[ 88%] Building CXX object Code/GraphMol/MolStandardize/CMakeFiles/molChargeTest.dir/testCharge.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 -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202503.1/External -I/build/reproducible-path/rdkit-202503.1/Code -I/build/reproducible-path/rdkit-202503.1/External/boost-numeric-bindings -isystem 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/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' +[ 88%] Built target molNormalizeTest make -f Code/GraphMol/MolStandardize/CMakeFiles/molStandardizeSmallTest.dir/build.make Code/GraphMol/MolStandardize/CMakeFiles/molStandardizeSmallTest.dir/depend make[4]: Entering directory '/build/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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-Wl,--dependency-file=CMakeFiles/molStandardizeTest.dir/link.d CMakeFiles/molStandardizeTest.dir/test1.cpp.o -o molStandardizeTest ../../../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 /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 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Building CXX object Code/GraphMol/Wrap/CMakeFiles/rdchem.dir/Chirality.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 -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -Drdchem_EXPORTS -I/build/reproducible-path/rdkit-202503.1/External -I/build/reproducible-path/rdkit-202503.1/Code -I/build/reproducible-path/rdkit-202503.1/External/boost-numeric-bindings -I/usr/lib/aarch64-linux-gnu/python3-numpy/numpy/_core/include -isystem /usr/include/python3.13 -isystem 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Code/GraphMol/MolStandardize/CMakeFiles/molStandardizePipelineTest.dir/testPipeline.cpp.o +[ 89%] Building CXX object Code/GraphMol/MolStandardize/CMakeFiles/molStandardizePipelineTest.dir/testPipeline.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 -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_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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/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' -[ 90%] Built target molStandardizeSmallTest +[ 89%] Built target rdMolDraw2D make -f Code/GraphMol/MolStandardize/Wrap/CMakeFiles/rdMolStandardize.dir/build.make Code/GraphMol/MolStandardize/Wrap/CMakeFiles/rdMolStandardize.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/Wrap /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/MolStandardize/Wrap 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-DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DrdMolStandardize_EXPORTS -I/build/reproducible-path/rdkit-202503.1/External -I/build/reproducible-path/rdkit-202503.1/Code -I/build/reproducible-path/rdkit-202503.1/External/boost-numeric-bindings -I/usr/lib/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/rdMolStandardize.cpp.o -MF CMakeFiles/rdMolStandardize.dir/rdMolStandardize.cpp.o.d -o CMakeFiles/rdMolStandardize.dir/rdMolStandardize.cpp.o -c /build/reproducible-path/rdkit-202503.1/Code/GraphMol/MolStandardize/Wrap/rdMolStandardize.cpp -[ 90%] Linking CXX executable molValidateTest -cd /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/MolStandardize && /usr/bin/cmake -E cmake_link_script CMakeFiles/molValidateTest.dir/link.txt --verbose=1 -/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=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/molValidateTest.dir/link.d CMakeFiles/molValidateTest.dir/testValidate.cpp.o -o molValidateTest ../../../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 /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' -[ 90%] Built target molValidateTest +[ 89%] Linking CXX executable molChargeTest +cd /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/MolStandardize && /usr/bin/cmake -E cmake_link_script CMakeFiles/molChargeTest.dir/link.txt --verbose=1 make -f Code/GraphMol/ScaffoldNetwork/CMakeFiles/ScaffoldNetwork.dir/build.make Code/GraphMol/ScaffoldNetwork/CMakeFiles/ScaffoldNetwork.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu' cd 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Code/GraphMol/ScaffoldNetwork/CMakeFiles/ScaffoldNetwork.dir/ScaffoldNetwork.cpp.o cd /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/ScaffoldNetwork && /usr/bin/c++ -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_SCAFFOLDNETWORK_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DScaffoldNetwork_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/ScaffoldNetwork/CMakeFiles/ScaffoldNetwork.dir/ScaffoldNetwork.cpp.o -MF CMakeFiles/ScaffoldNetwork.dir/ScaffoldNetwork.cpp.o.d -o CMakeFiles/ScaffoldNetwork.dir/ScaffoldNetwork.cpp.o -c /build/reproducible-path/rdkit-202503.1/Code/GraphMol/ScaffoldNetwork/ScaffoldNetwork.cpp -[ 90%] Linking CXX executable moldraw2DTest1 -cd /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/MolDraw2D && /usr/bin/cmake -E cmake_link_script CMakeFiles/moldraw2DTest1.dir/link.txt --verbose=1 -/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=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/moldraw2DTest1.dir/link.d CMakeFiles/moldraw2DTest1.dir/test1.cpp.o -o moldraw2DTest1 ../../../lib/libRDKitMolDraw2D.so.1.2025.03.1 ../../../lib/libRDKitChemReactions.so.1.2025.03.1 ../../../lib/libRDKitFilterCatalog.so.1.2025.03.1 ../../../lib/libRDKitCatalogs.so.1.2025.03.1 ../../../lib/libRDKitFingerprints.so.1.2025.03.1 ../../../lib/libRDKitFileParsers.so.1.2025.03.1 /usr/lib/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 ../../../lib/libRDKitGenericGroups.so.1.2025.03.1 ../../../lib/libRDKitSubgraphs.so.1.2025.03.1 ../../../lib/libRDKitGraphMol.so.1.2025.03.1 ../../../lib/libRDKitRDGeometryLib.so.1.2025.03.1 ../../../lib/libRDKitDataStructs.so.1.2025.03.1 ../../../lib/libRDKitEigenSolvers.so.1.2025.03.1 ../../../lib/libRDKitRDGeneral.so.1.2025.03.1 /usr/lib/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/libcairo.so /usr/lib/aarch64-linux-gnu/libfreetype.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/molChargeTest.dir/link.d CMakeFiles/molChargeTest.dir/testCharge.cpp.o -o molChargeTest ../../../lib/libRDKitMolStandardize.so.1.2025.03.1 ../../../lib/libRDKitChemReactions.so.1.2025.03.1 ../../../lib/libRDKitFilterCatalog.so.1.2025.03.1 ../../../lib/libRDKitCatalogs.so.1.2025.03.1 ../../../lib/libRDKitFingerprints.so.1.2025.03.1 ../../../lib/libRDKitSubgraphs.so.1.2025.03.1 ../../../lib/libRDKitFileParsers.so.1.2025.03.1 /usr/lib/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' -[ 90%] Built target moldraw2DTest1 +[ 89%] Built target molChargeTest make -f Code/GraphMol/TautomerQuery/CMakeFiles/TautomerQuery.dir/build.make Code/GraphMol/TautomerQuery/CMakeFiles/TautomerQuery.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/TautomerQuery 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Code/GraphMol/TautomerQuery/CMakeFiles/TautomerQuery.dir/TautomerQuery.cpp.o -MF CMakeFiles/TautomerQuery.dir/TautomerQuery.cpp.o.d -o CMakeFiles/TautomerQuery.dir/TautomerQuery.cpp.o -c /build/reproducible-path/rdkit-202503.1/Code/GraphMol/TautomerQuery/TautomerQuery.cpp -[ 90%] Linking CXX executable molChargeTest -cd /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/MolStandardize && /usr/bin/cmake -E cmake_link_script CMakeFiles/molChargeTest.dir/link.txt --verbose=1 -/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=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/molChargeTest.dir/link.d CMakeFiles/molChargeTest.dir/testCharge.cpp.o -o molChargeTest 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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' -[ 90%] Built target molChargeTest +[ 90%] Linking CXX shared module ../../../rdkit/Chem/rdmolfiles.so +cd /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/Wrap && /usr/bin/cmake -E cmake_link_script CMakeFiles/rdmolfiles.dir/link.txt --verbose=1 [ 90%] Building CXX object Code/GraphMol/MolStandardize/Wrap/CMakeFiles/rdMolStandardize.dir/Validate.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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-fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/MolStandardize/Wrap/CMakeFiles/rdMolStandardize.dir/Validate.cpp.o -MF CMakeFiles/rdMolStandardize.dir/Validate.cpp.o.d -o CMakeFiles/rdMolStandardize.dir/Validate.cpp.o -c /build/reproducible-path/rdkit-202503.1/Code/GraphMol/MolStandardize/Wrap/Validate.cpp +[ 90%] Linking CXX shared module ../../../../rdkit/Chem/rdChemReactions.so +cd /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/ChemReactions/Wrap && /usr/bin/cmake -E cmake_link_script CMakeFiles/rdChemReactions.dir/link.txt --verbose=1 [ 90%] Linking CXX executable molFragmentTest cd /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/MolStandardize && /usr/bin/cmake -E cmake_link_script CMakeFiles/molFragmentTest.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=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/molFragmentTest.dir/link.d CMakeFiles/molFragmentTest.dir/testFragment.cpp.o -o molFragmentTest ../../../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 /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 @@ -6809,15 +6844,18 @@ [ 90%] Built target molFragmentTest [ 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 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../../../lib/libRDKitRDBoost.so.1.2025.03.1 ../../../lib/libRDKitChemReactions.so.1.2025.03.1 ../../../lib/libRDKitFilterCatalog.so.1.2025.03.1 ../../../lib/libRDKitCatalogs.so.1.2025.03.1 ../../../lib/libRDKitFingerprints.so.1.2025.03.1 ../../../lib/libRDKitSubgraphs.so.1.2025.03.1 ../../../lib/libRDKitFileParsers.so.1.2025.03.1 ../../../lib/libRDKitChemTransforms.so.1.2025.03.1 ../../../lib/libRDKitDepictor.so.1.2025.03.1 /usr/lib/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/libRDKitMolTransforms.so.1.2025.03.1 ../../../lib/libRDKitEigenSolvers.so.1.2025.03.1 ../../../lib/libRDKitAlignment.so.1.2025.03.1 ../../../lib/libRDKitGenericGroups.so.1.2025.03.1 ../../../lib/libRDKitGraphMol.so.1.2025.03.1 ../../../lib/libRDKitRDGeometryLib.so.1.2025.03.1 ../../../lib/libRDKitDataStructs.so.1.2025.03.1 /usr/lib/aarch64-linux-gnu/libmaeparser.so 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/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' @@ -6843,8 +6881,12 @@ make[4]: Entering directory '/build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu' [ 92%] Building CXX object Code/GraphMol/ScaffoldNetwork/Wrap/CMakeFiles/rdScaffoldNetwork.dir/rdScaffoldNetwork.cpp.o cd /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/ScaffoldNetwork/Wrap && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_NUMPY_DYN_LINK -DBOOST_NUMPY_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK 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92%] 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 +[ 92%] Linking CXX shared module ../../../rdkit/Chem/rdchem.so +cd /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/Wrap && /usr/bin/cmake -E cmake_link_script CMakeFiles/rdchem.dir/link.txt --verbose=1 /usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=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/TautomerQuery.dir/link.d -Wl,-z,relro -Wl,-z,now -shared -Wl,-soname,libRDKitTautomerQuery.so.1 -o ../../../lib/libRDKitTautomerQuery.so.1.2025.03.1 CMakeFiles/TautomerQuery.dir/TautomerQuery.cpp.o ../../../lib/libRDKitMolStandardize.so.1.2025.03.1 ../../../lib/libRDKitChemReactions.so.1.2025.03.1 ../../../lib/libRDKitFilterCatalog.so.1.2025.03.1 ../../../lib/libRDKitCatalogs.so.1.2025.03.1 ../../../lib/libRDKitFingerprints.so.1.2025.03.1 ../../../lib/libRDKitSubgraphs.so.1.2025.03.1 ../../../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 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' @@ -6857,15 +6899,10 @@ make[4]: Entering directory '/build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu' [ 92%] Building CXX object Code/GraphMol/TautomerQuery/CMakeFiles/tautomerQueryTestCatch.dir/catch_tests.cpp.o 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/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' -[ 92%] Building CXX object Code/GraphMol/MolStandardize/Wrap/CMakeFiles/rdMolStandardize.dir/Tautomer.cpp.o -cd 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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 /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/GeneralizedSubstruct /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/GeneralizedSubstruct/CMakeFiles/GeneralizedSubstruct.dir/DependInfo.cmake "--color=" @@ -6889,13 +6924,11 @@ make[4]: Entering directory '/build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu' [ 92%] Building CXX object Code/GraphMol/GeneralizedSubstruct/CMakeFiles/GeneralizedSubstruct.dir/XQMol.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 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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 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/usr/lib/aarch64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl +[ 92%] Linking CXX executable molStandardizePipelineTest +cd /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/MolStandardize && /usr/bin/cmake -E cmake_link_script CMakeFiles/molStandardizePipelineTest.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/molStandardizePipelineTest.dir/link.d CMakeFiles/molStandardizePipelineTest.dir/testPipeline.cpp.o -o molStandardizePipelineTest ../../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' -[ 92%] Built target molStandardizeCatchTest +[ 92%] Built target molStandardizePipelineTest make -f Code/GraphMol/RGroupDecomposition/CMakeFiles/RGroupDecomposition.dir/build.make Code/GraphMol/RGroupDecomposition/CMakeFiles/RGroupDecomposition.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-202503.1/obj-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 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-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/RGroupDecomp.cpp.o -MF CMakeFiles/RGroupDecomposition.dir/RGroupDecomp.cpp.o.d -o CMakeFiles/RGroupDecomposition.dir/RGroupDecomp.cpp.o -c /build/reproducible-path/rdkit-202503.1/Code/GraphMol/RGroupDecomposition/RGroupDecomp.cpp +[ 92%] Building CXX object Code/GraphMol/GeneralizedSubstruct/CMakeFiles/GeneralizedSubstruct.dir/TextIO.cpp.o +cd 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../../../lib/libRDKitGenericGroups.so.1.2025.03.1 ../../../lib/libRDKitGraphMol.so.1.2025.03.1 ../../../lib/libRDKitRDGeometryLib.so.1.2025.03.1 ../../../lib/libRDKitDataStructs.so.1.2025.03.1 /usr/lib/aarch64-linux-gnu/libmaeparser.so /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' +[ 92%] Built target rdchem +[ 92%] Building CXX object Code/GraphMol/RGroupDecomposition/CMakeFiles/RGroupDecomposition.dir/RGroupData.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 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Code/GraphMol/RGroupDecomposition/CMakeFiles/RGroupDecomposition.dir/RGroupData.cpp.o -MF CMakeFiles/RGroupDecomposition.dir/RGroupData.cpp.o.d -o CMakeFiles/RGroupDecomposition.dir/RGroupData.cpp.o -c /build/reproducible-path/rdkit-202503.1/Code/GraphMol/RGroupDecomposition/RGroupData.cpp [ 92%] Linking CXX executable tautomerQueryTestCatch cd /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/TautomerQuery && /usr/bin/cmake -E cmake_link_script CMakeFiles/tautomerQueryTestCatch.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=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/tautomerQueryTestCatch.dir/link.d 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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/RGroupDecomposition/CMakeFiles/RGroupDecomposition.dir/RGroupDecompParams.cpp.o -MF CMakeFiles/RGroupDecomposition.dir/RGroupDecompParams.cpp.o.d -o CMakeFiles/RGroupDecomposition.dir/RGroupDecompParams.cpp.o -c /build/reproducible-path/rdkit-202503.1/Code/GraphMol/RGroupDecomposition/RGroupDecompParams.cpp [ 93%] Linking CXX shared module ../../../../rdkit/Chem/Scaffolds/rdScaffoldNetwork.so cd 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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/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%] Linking CXX shared library ../../../lib/libRDKitGeneralizedSubstruct.so +cd 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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 +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' +[ 94%] Built target GeneralizedSubstruct +make -f Code/GraphMol/SynthonSpaceSearch/CMakeFiles/SynthonSpaceSearch.dir/build.make Code/GraphMol/SynthonSpaceSearch/CMakeFiles/SynthonSpaceSearch.dir/depend +make -f Code/GraphMol/SubstructLibrary/CMakeFiles/SubstructLibrary.dir/build.make Code/GraphMol/SubstructLibrary/CMakeFiles/SubstructLibrary.dir/depend +make -f Code/GraphMol/GeneralizedSubstruct/CMakeFiles/generalizedSubstructCatch.dir/build.make Code/GraphMol/GeneralizedSubstruct/CMakeFiles/generalizedSubstructCatch.dir/depend +make[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/SubstructLibrary.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 /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=" +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/GeneralizedSubstruct /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/GeneralizedSubstruct 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-I/build/reproducible-path/rdkit-202503.1/External -I/build/reproducible-path/rdkit-202503.1/Code -I/build/reproducible-path/rdkit-202503.1/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/SubstructLibrary/CMakeFiles/SubstructLibrary.dir/SubstructLibrary.cpp.o -MF CMakeFiles/SubstructLibrary.dir/SubstructLibrary.cpp.o.d -o CMakeFiles/SubstructLibrary.dir/SubstructLibrary.cpp.o -c /build/reproducible-path/rdkit-202503.1/Code/GraphMol/SubstructLibrary/SubstructLibrary.cpp +[ 95%] Building CXX object Code/GraphMol/SynthonSpaceSearch/CMakeFiles/SynthonSpaceSearch.dir/SynthonSpaceSearch_details.cpp.o +cd 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/build/reproducible-path/rdkit-202503.1/Code/GraphMol/GeneralizedSubstruct/catch_tests.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, @@ -6973,45 +7044,23 @@ /usr/include/boost/python/suite/indexing/detail/indexing_suite_detail.hpp:603:29: note: '' declared here 603 | long from = extract( slice->start); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ -[ 94%] 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 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/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' -[ 94%] Built target GeneralizedSubstruct -make -f Code/GraphMol/SynthonSpaceSearch/CMakeFiles/SynthonSpaceSearch.dir/build.make Code/GraphMol/SynthonSpaceSearch/CMakeFiles/SynthonSpaceSearch.dir/depend -make -f Code/GraphMol/SubstructLibrary/CMakeFiles/SubstructLibrary.dir/build.make Code/GraphMol/SubstructLibrary/CMakeFiles/SubstructLibrary.dir/depend -make[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 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/build/reproducible-path/rdkit-202503.1/Code/GraphMol/SubstructLibrary/SubstructLibrary.cpp -[ 95%] 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_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 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'/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 -DBOOST_NUMPY_DYN_LINK -DBOOST_NUMPY_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DrdGeneralizedSubstruct_EXPORTS -I/build/reproducible-path/rdkit-202503.1/External -I/build/reproducible-path/rdkit-202503.1/Code 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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_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=. 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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=" @@ -7028,17 +7085,23 @@ 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_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/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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95%] Linking CXX executable moldraw2DTestCatch -cd /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/MolDraw2D && /usr/bin/cmake -E cmake_link_script CMakeFiles/moldraw2DTestCatch.dir/link.txt --verbose=1 -/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=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/moldraw2DTestCatch.dir/link.d CMakeFiles/moldraw2DTestCatch.dir/catch_tests.cpp.o -o moldraw2DTestCatch ../../RDGeneral/librdkitCatch.a ../../../lib/libRDKitMolDraw2D.so.1.2025.03.1 ../../../lib/libRDKitCIPLabeler.so.1.2025.03.1 /usr/lib/libCatch2.a ../../../lib/libRDKitChemReactions.so.1.2025.03.1 ../../../lib/libRDKitFilterCatalog.so.1.2025.03.1 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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 +[ 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_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_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 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 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-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 C object Code/PgSQL/rdkit/CMakeFiles/rdkit.dir/low_gist.c.o -cd 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/usr/include/eigen3 -isystem /usr/include/cairo -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -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%] 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 -[ 95%] Building C object Code/PgSQL/rdkit/CMakeFiles/rdkit.dir/mol_op.c.o -cd 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../../../lib/libRDKitMolEnumerator.so.1.2025.03.1 ../../../lib/libRDKitTautomerQuery.so.1.2025.03.1 ../../../lib/libRDKitMolStandardize.so.1.2025.03.1 ../../../lib/libRDKitChemReactions.so.1.2025.03.1 ../../../lib/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 -make[4]: Leaving directory '/build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu' -[ 96%] Built target generalizedSubstructCatch make -f Code/GraphMol/RGroupDecomposition/CMakeFiles/gaExample.dir/build.make Code/GraphMol/RGroupDecomposition/CMakeFiles/gaExample.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/gaExample.dir/DependInfo.cmake "--color=" @@ -7116,13 +7138,6 @@ make[4]: Entering directory '/build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu' [ 96%] Building CXX object Code/GraphMol/RGroupDecomposition/CMakeFiles/gaExample.dir/GaExample.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_PROGRAM_OPTIONS_DYN_LINK -DBOOST_PROGRAM_OPTIONS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT 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../../../../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 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-I/build/reproducible-path/rdkit-202503.1/External/boost-numeric-bindings -I/usr/include/freetype2 -isystem /usr/include/eigen3 -isystem /usr/include/cairo -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -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 +[ 96%] 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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Code/GraphMol/SubstructLibrary/CMakeFiles/SubstructLibrary.dir/PatternFactory.cpp.o -MF CMakeFiles/SubstructLibrary.dir/PatternFactory.cpp.o.d -o CMakeFiles/SubstructLibrary.dir/PatternFactory.cpp.o -c /build/reproducible-path/rdkit-202503.1/Code/GraphMol/SubstructLibrary/PatternFactory.cpp +[ 96%] 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_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 +[ 96%] Building C object Code/PgSQL/rdkit/CMakeFiles/rdkit.dir/mol_op.c.o +[ 96%] 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_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 +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_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 +[ 96%] 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_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_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 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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 -fPIC -fPIC -MD -MT Code/PgSQL/rdkit/CMakeFiles/rdkit.dir/bfp_gin.c.o -MF CMakeFiles/rdkit.dir/bfp_gin.c.o.d -o CMakeFiles/rdkit.dir/bfp_gin.c.o -c /build/reproducible-path/rdkit-202503.1/Code/PgSQL/rdkit/bfp_gin.c +[ 97%] Building C object Code/PgSQL/rdkit/CMakeFiles/rdkit.dir/bitstring.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_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/bitstring.c.o -MF CMakeFiles/rdkit.dir/bitstring.c.o.d -o CMakeFiles/rdkit.dir/bitstring.c.o -c /build/reproducible-path/rdkit-202503.1/Code/PgSQL/rdkit/bitstring.c +[ 97%] Building C object Code/PgSQL/rdkit/CMakeFiles/rdkit.dir/rdkit_io.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_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_io.c.o -MF CMakeFiles/rdkit.dir/rdkit_io.c.o.d -o CMakeFiles/rdkit.dir/rdkit_io.c.o -c /build/reproducible-path/rdkit-202503.1/Code/PgSQL/rdkit/rdkit_io.c +[ 97%] Building C object Code/PgSQL/rdkit/CMakeFiles/rdkit.dir/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_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 +[ 97%] 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 -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_FREETYPE_SUPPORT -DRDK_BUILD_INCHI_SUPPORT -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_MOLINTERCHANGE_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_TOOLKIT_VERSION=\"2025.03.1\" -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -Drdkit_EXPORTS -I/build/reproducible-path/rdkit-202503.1/External -I/build/reproducible-path/rdkit-202503.1/Code -I/usr/include/postgresql -I/usr/include/postgresql/17/server -I/build/reproducible-path/rdkit-202503.1/External/boost-numeric-bindings -I/usr/include/freetype2 -isystem /usr/include/eigen3 -isystem /usr/include/cairo -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time 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/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 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 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 +/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 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/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 -DBOOST_PYTHON_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DrdSynthonSpaceSearch_EXPORTS -I/build/reproducible-path/rdkit-202503.1/External -I/build/reproducible-path/rdkit-202503.1/Code -I/build/reproducible-path/rdkit-202503.1/External/boost-numeric-bindings -I/usr/lib/aarch64-linux-gnu/python3-numpy/numpy/_core/include -isystem /usr/include/python3.13 -isystem /usr/include/eigen3 -g -O2 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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/SynthonSpaceSearch/CMakeFiles/SynthonSpaceSearch.dir/SynthonSpaceSubstructureSearcher.cpp.o -MF CMakeFiles/SynthonSpaceSearch.dir/SynthonSpaceSubstructureSearcher.cpp.o.d -o CMakeFiles/SynthonSpaceSearch.dir/SynthonSpaceSubstructureSearcher.cpp.o -c /build/reproducible-path/rdkit-202503.1/Code/GraphMol/SynthonSpaceSearch/SynthonSpaceSubstructureSearcher.cpp -[ 96%] 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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../../../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 gaExample +[ 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 +[ 97%] Linking CXX shared library ../../../lib/libRDKitSubstructLibrary.so cd /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/SubstructLibrary && /usr/bin/cmake -E cmake_link_script CMakeFiles/SubstructLibrary.dir/link.txt --verbose=1 /usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=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/SubstructLibrary.dir/link.d -Wl,-z,relro -Wl,-z,now -shared -Wl,-soname,libRDKitSubstructLibrary.so.1 -o ../../../lib/libRDKitSubstructLibrary.so.1.2025.03.1 CMakeFiles/SubstructLibrary.dir/SubstructLibrary.cpp.o CMakeFiles/SubstructLibrary.dir/PatternFactory.cpp.o ../../../lib/libRDKitGeneralizedSubstruct.so.1.2025.03.1 ../../../lib/libRDKitTautomerQuery.so.1.2025.03.1 ../../../lib/libRDKitMolStandardize.so.1.2025.03.1 ../../../lib/libRDKitMolEnumerator.so.1.2025.03.1 ../../../lib/libRDKitChemReactions.so.1.2025.03.1 ../../../lib/libRDKitFingerprints.so.1.2025.03.1 ../../../lib/libRDKitFilterCatalog.so.1.2025.03.1 ../../../lib/libRDKitCatalogs.so.1.2025.03.1 ../../../lib/libRDKitSubgraphs.so.1.2025.03.1 ../../../lib/libRDKitFileParsers.so.1.2025.03.1 ../../../lib/libRDKitChemTransforms.so.1.2025.03.1 ../../../lib/libRDKitDepictor.so.1.2025.03.1 /usr/lib/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 cd /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/SubstructLibrary && /usr/bin/cmake -E cmake_symlink_library ../../../lib/libRDKitSubstructLibrary.so.1.2025.03.1 ../../../lib/libRDKitSubstructLibrary.so.1 ../../../lib/libRDKitSubstructLibrary.so make[4]: Leaving directory '/build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu' -[ 96%] Built target SubstructLibrary +[ 97%] Built target SubstructLibrary +make -f Code/GraphMol/SynthonSpaceSearch/CMakeFiles/testSynthonSpaceSubstructureSearch.dir/build.make Code/GraphMol/SynthonSpaceSearch/CMakeFiles/testSynthonSpaceSubstructureSearch.dir/depend +make -f Code/GraphMol/SynthonSpaceSearch/CMakeFiles/testSynthonSpaceRascalSearch.dir/build.make Code/GraphMol/SynthonSpaceSearch/CMakeFiles/testSynthonSpaceRascalSearch.dir/depend make -f Code/GraphMol/SubstructLibrary/CMakeFiles/substructLibraryTest.dir/build.make Code/GraphMol/SubstructLibrary/CMakeFiles/substructLibraryTest.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-202503.1/obj-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' -make -f Code/GraphMol/SubstructLibrary/CMakeFiles/substructLibraryTest.dir/build.make Code/GraphMol/SubstructLibrary/CMakeFiles/substructLibraryTest.dir/build -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_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_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%] 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' -[ 96%] Built target testRGroupDecompInternals +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/SubstructLibrary/CMakeFiles/substructLibraryCatchTest.dir/build.make Code/GraphMol/SubstructLibrary/CMakeFiles/substructLibraryCatchTest.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 -f Code/GraphMol/SubstructLibrary/Wrap/CMakeFiles/rdSubstructLibrary.dir/build.make Code/GraphMol/SubstructLibrary/Wrap/CMakeFiles/rdSubstructLibrary.dir/depend +make[4]: Entering directory '/build/reproducible-path/rdkit-202503.1/obj-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]: 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/substructLibraryCatchTest.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu' -make -f Code/GraphMol/SubstructLibrary/CMakeFiles/substructLibraryCatchTest.dir/build.make Code/GraphMol/SubstructLibrary/CMakeFiles/substructLibraryCatchTest.dir/build +make[4]: Leaving directory '/build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu' +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' -[ 96%] Building CXX object Code/GraphMol/SubstructLibrary/CMakeFiles/substructLibraryCatchTest.dir/catch_tests.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_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_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/substructLibraryCatchTest.dir/catch_tests.cpp.o -MF CMakeFiles/substructLibraryCatchTest.dir/catch_tests.cpp.o.d -o CMakeFiles/substructLibraryCatchTest.dir/catch_tests.cpp.o -c /build/reproducible-path/rdkit-202503.1/Code/GraphMol/SubstructLibrary/catch_tests.cpp -[ 96%] 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 ../../../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 -f Code/GraphMol/SynthonSpaceSearch/CMakeFiles/testSynthonSpaceRascalSearch.dir/build.make Code/GraphMol/SynthonSpaceSearch/CMakeFiles/testSynthonSpaceRascalSearch.dir/build make[4]: Leaving directory '/build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu' -[ 96%] Built target gaExample -make -f Code/GraphMol/SubstructLibrary/Wrap/CMakeFiles/rdSubstructLibrary.dir/build.make Code/GraphMol/SubstructLibrary/Wrap/CMakeFiles/rdSubstructLibrary.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-202503.1/obj-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/Wrap /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/SubstructLibrary/Wrap 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../../../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' -[ 96%] Built target rgroupCatchTests -[ 97%] Building CXX object Code/GraphMol/SynthonSpaceSearch/CMakeFiles/SynthonSpaceSearch.dir/MemoryMappedFileReader.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_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/MemoryMappedFileReader.cpp.o -MF 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 -[ 97%] Linking CXX shared module ../../../../rdkit/Chem/rdRGroupDecomposition.so +[ 98%] 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 make[4]: Leaving directory '/build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu' -[ 97%] Built target rdRGroupDecomposition -[ 98%] 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 +[ 98%] Built target rdRGroupDecomposition +[ 98%] Linking CXX executable rgroupCatchTests +cd /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/RGroupDecomposition && /usr/bin/cmake -E cmake_link_script CMakeFiles/rgroupCatchTests.dir/link.txt --verbose=1 +/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=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/rgroupCatchTests.dir/link.d CMakeFiles/rgroupCatchTests.dir/catch_rgd.cpp.o -o rgroupCatchTests ../../RDGeneral/librdkitCatch.a ../../../lib/libRDKitRGroupDecomposition.so.1.2025.03.1 /usr/lib/libCatch2.a ../../../lib/libRDKitFMCS.so.1.2025.03.1 ../../../lib/libRDKitga.so.1.2025.03.1 ../../../lib/libRDKitMolEnumerator.so.1.2025.03.1 ../../../lib/libRDKitTautomerQuery.so.1.2025.03.1 ../../../lib/libRDKitMolStandardize.so.1.2025.03.1 ../../../lib/libRDKitChemReactions.so.1.2025.03.1 ../../../lib/libRDKitFingerprints.so.1.2025.03.1 ../../../lib/libRDKitFileParsers.so.1.2025.03.1 ../../../lib/libRDKitChemTransforms.so.1.2025.03.1 ../../../lib/libRDKitDepictor.so.1.2025.03.1 /usr/lib/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' -[ 98%] Built target substructLibraryTest -[ 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 +[ 98%] Built target rgroupCatchTests +[ 98%] Linking CXX shared module ../../../../rdkit/Chem/rdSynthonSpaceSearch.so +cd /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/SynthonSpaceSearch/Wrap && /usr/bin/cmake -E cmake_link_script CMakeFiles/rdSynthonSpaceSearch.dir/link.txt --verbose=1 +/usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=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' +[ 98%] Built target rdSynthonSpaceSearch [ 98%] Linking CXX executable substructLibraryCatchTest cd /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/SubstructLibrary && /usr/bin/cmake -E cmake_link_script CMakeFiles/substructLibraryCatchTest.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=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' [ 98%] Built target substructLibraryCatchTest -/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 -cd /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/SynthonSpaceSearch && /usr/bin/cmake -E cmake_symlink_library ../../../lib/libRDKitSynthonSpaceSearch.so.1.2025.03.1 ../../../lib/libRDKitSynthonSpaceSearch.so.1 ../../../lib/libRDKitSynthonSpaceSearch.so -make[4]: Leaving directory '/build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu' -[ 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[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]: 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[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]: 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/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' +[ 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%] Building CXX object Code/GraphMol/SynthonSpaceSearch/CMakeFiles/testSynthonSpaceSubstructureSearch.dir/substructure_search_catch_tests.cpp.o -make -f Code/GraphMol/SynthonSpaceSearch/Wrap/CMakeFiles/rdSynthonSpaceSearch.dir/build.make Code/GraphMol/SynthonSpaceSearch/Wrap/CMakeFiles/rdSynthonSpaceSearch.dir/build -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_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_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/testSynthonSpaceSubstructureSearch.dir/substructure_search_catch_tests.cpp.o -MF CMakeFiles/testSynthonSpaceSubstructureSearch.dir/substructure_search_catch_tests.cpp.o.d -o CMakeFiles/testSynthonSpaceSubstructureSearch.dir/substructure_search_catch_tests.cpp.o -c /build/reproducible-path/rdkit-202503.1/Code/GraphMol/SynthonSpaceSearch/substructure_search_catch_tests.cpp -make[4]: Entering directory '/build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu' -[ 99%] 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_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_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 -[ 99%] 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 -DBOOST_PYTHON_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DrdSynthonSpaceSearch_EXPORTS -I/build/reproducible-path/rdkit-202503.1/External -I/build/reproducible-path/rdkit-202503.1/Code -I/build/reproducible-path/rdkit-202503.1/External/boost-numeric-bindings -I/usr/lib/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/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 -[ 99%] Linking CXX executable testReaction -cd /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/ChemReactions && /usr/bin/cmake -E cmake_link_script CMakeFiles/testReaction.dir/link.txt --verbose=1 -/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=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/testReaction.dir/link.d CMakeFiles/testReaction.dir/testReaction.cpp.o -o testReaction ../../../lib/libRDKitChemReactions.so.1.2025.03.1 ../../../lib/libRDKitFilterCatalog.so.1.2025.03.1 ../../../lib/libRDKitCatalogs.so.1.2025.03.1 ../../../lib/libRDKitFingerprints.so.1.2025.03.1 ../../../lib/libRDKitSubgraphs.so.1.2025.03.1 ../../../lib/libRDKitFileParsers.so.1.2025.03.1 /usr/lib/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/libRDKitSubstructMatch.so.1.2025.03.1 ../../../lib/libRDKitGenericGroups.so.1.2025.03.1 ../../../lib/libRDKitSmilesParse.so.1.2025.03.1 ../../../lib/libRDKitGraphMol.so.1.2025.03.1 ../../../lib/libRDKitRDGeometryLib.so.1.2025.03.1 ../../../lib/libRDKitDataStructs.so.1.2025.03.1 ../../../lib/libRDKitRDGeneral.so.1.2025.03.1 /usr/lib/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 +[ 99%] Built target substructLibraryTest +[ 99%] Linking CXX executable testSynthonSpaceRascalSearch +cd /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/SynthonSpaceSearch && /usr/bin/cmake -E cmake_link_script CMakeFiles/testSynthonSpaceRascalSearch.dir/link.txt --verbose=1 +/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=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/testSynthonSpaceRascalSearch.dir/link.d CMakeFiles/testSynthonSpaceRascalSearch.dir/rascal_search_catch_tests.cpp.o -o testSynthonSpaceRascalSearch ../../RDGeneral/librdkitCatch.a ../../../lib/libRDKitSubstructLibrary.so.1.2025.03.1 ../../../lib/libRDKitSynthonSpaceSearch.so.1.2025.03.1 /usr/lib/libCatch2.a ../../../lib/libRDKitGeneralizedSubstruct.so.1.2025.03.1 ../../../lib/libRDKitTautomerQuery.so.1.2025.03.1 ../../../lib/libRDKitMolStandardize.so.1.2025.03.1 ../../../lib/libRDKitMolEnumerator.so.1.2025.03.1 ../../../lib/libRDKitChemReactions.so.1.2025.03.1 ../../../lib/libRDKitFilterCatalog.so.1.2025.03.1 ../../../lib/libRDKitCatalogs.so.1.2025.03.1 ../../../lib/libRDKitFingerprints.so.1.2025.03.1 ../../../lib/libRDKitSubgraphs.so.1.2025.03.1 ../../../lib/libRDKitRascalMCES.so.1.2025.03.1 ../../../lib/libRDKitFileParsers.so.1.2025.03.1 /usr/lib/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' -[ 99%] Built target testReaction +[ 99%] Built target testSynthonSpaceRascalSearch [ 99%] 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' [ 99%] Built target testRGroupDecomp -[ 99%] Linking CXX executable testSynthonSpaceRascalSearch -cd /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/SynthonSpaceSearch && /usr/bin/cmake -E cmake_link_script CMakeFiles/testSynthonSpaceRascalSearch.dir/link.txt --verbose=1 -/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=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/testSynthonSpaceRascalSearch.dir/link.d CMakeFiles/testSynthonSpaceRascalSearch.dir/rascal_search_catch_tests.cpp.o -o testSynthonSpaceRascalSearch ../../RDGeneral/librdkitCatch.a ../../../lib/libRDKitSubstructLibrary.so.1.2025.03.1 ../../../lib/libRDKitSynthonSpaceSearch.so.1.2025.03.1 /usr/lib/libCatch2.a ../../../lib/libRDKitGeneralizedSubstruct.so.1.2025.03.1 ../../../lib/libRDKitTautomerQuery.so.1.2025.03.1 ../../../lib/libRDKitMolStandardize.so.1.2025.03.1 ../../../lib/libRDKitMolEnumerator.so.1.2025.03.1 ../../../lib/libRDKitChemReactions.so.1.2025.03.1 ../../../lib/libRDKitFilterCatalog.so.1.2025.03.1 ../../../lib/libRDKitCatalogs.so.1.2025.03.1 ../../../lib/libRDKitFingerprints.so.1.2025.03.1 ../../../lib/libRDKitSubgraphs.so.1.2025.03.1 ../../../lib/libRDKitRascalMCES.so.1.2025.03.1 ../../../lib/libRDKitFileParsers.so.1.2025.03.1 /usr/lib/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' -[ 99%] Built target testSynthonSpaceRascalSearch -[ 99%] Linking CXX shared module ../../../../rdkit/Chem/rdSynthonSpaceSearch.so -cd /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/SynthonSpaceSearch/Wrap && /usr/bin/cmake -E cmake_link_script CMakeFiles/rdSynthonSpaceSearch.dir/link.txt --verbose=1 [ 99%] 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 -/usr/bin/ld: /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' -[ 99%] Built target rdSynthonSpaceSearch -CMakeFiles/testSynthonSpaceSubstructureSearch.dir/substructure_search_catch_tests.cpp.o: in function `CATCH2_INTERNAL_TEST_20()': +/usr/bin/ld: CMakeFiles/testSynthonSpaceSubstructureSearch.dir/substructure_search_catch_tests.cpp.o: in function `CATCH2_INTERNAL_TEST_20()': ./obj-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/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' @@ -12936,7 +12967,7 @@ 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 @@ -15153,47 +15184,24 @@ 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: [16:02:32] Testing Github940: property dictionaries leaking memory -3: [16:02:32] done +3: [12:23:51] Testing Github940: property dictionaries leaking memory +3: [12:23:51] done 3: Testing RDValue 3: Testing RDAny 3: dict set int vect 3: dict get int vect -3: static boost any:0.000246 s -3: dynamic boost any:0.001014 s -3: static RDAny:0.000124 s -3: dynamic RDAny:0.000994 s -3: static RDValue:0 s +3: static boost any:0.000293 s +3: dynamic boost any:0.00104 s +3: static RDAny:0.000126 s +3: dynamic RDAny:0.000993 s +3: static RDValue:1e-06 s 3: dynamic RDValue:0.000155 s 3: deleted! -3: [16:02:32] ------------------------------------- -3: [16:02:32] Testing String Pickle Roundtrips. -3: [16:02:32] done -3: [16:02:32] ------------------------------------- -3: [16:02:32] Testing conversion of vect to string. -3: [16:02:32] done -3: [16:02:32] ------------------------------------- -3: [16:02:32] Testing returning const references. -3: [16:02:32] any cast -3: [16:02:32] done: 0.000808 300000 -3: [16:02:32] copy -3: [16:02:32] done: 0.000834 300000 -3: [16:02:32] ref -3: [16:02:32] done: 0.000812 300000 -3: [16:02:32] dict -3: [16:02:32] done: 0.001963 300000 -3: [16:02:32] ref with hasVal -3: [16:02:32] done: 0.001301 300000 -3: [16:02:32] done -3: [16:02:32] ------------------------------------- -3: [16:02:32] Testing dict update. -3: [16:02:32] done -3: deleted! -3: deleted! -3: deleted! -3: deleted! -3: deleted! -3: deleted! +3: [12:23:51] ------------------------------------- +3: [12:23:51] Testing String Pickle Roundtrips. +3: [12:23:51] done +3: [12:23:51] ------------------------------------- +3: [12:23:51] Testing conversion of vect to string. 4: -- running tests -- 4: min: -2147483648 -2147483648 4: min: 0 0 @@ -15206,65 +15214,88 @@ 4: == unsigned int 4: == bool 4: == std::string -5: [16:02:32] +5: [12:23:51] 5: ----------------------------------------- -5: [16:02:32] Finished: testPushAndPop() -5: [16:02:32] +5: [12:23:51] Finished: testPushAndPop() +5: [12:23:51] 5: ----------------------------------------- -5: [16:02:32] +5: [12:23:51] 5: ----------------------------------------- - 1/236 Test #3: testDict ............................... Passed 0.15 sec - 2/236 Test #4: testRDValue ............................ Passed 0.15 sec -8: [16:02:32] pass +8: [12:23:51] pass +8: [12:23:51] v3 4 +8: [12:23:51] v4 5 +8: [12:23:51] SPARSE ----------------------------------- + 1/236 Test #4: testRDValue ............................ Passed 0.20 sec +3: [12:23:51] done +3: [12:23:51] ------------------------------------- +3: [12:23:51] Testing returning const references. +3: [12:23:51] any cast +3: [12:23:51] done: 0.000819 300000 +3: [12:23:51] copy +3: [12:23:51] done: 0.000836 300000 +3: [12:23:51] ref +3: [12:23:51] done: 0.000801 300000 +3: [12:23:51] dict +3: [12:23:51] done: 0.001975 300000 +3: [12:23:51] ref with hasVal +3: [12:23:51] done: 0.001345 300000 +3: [12:23:51] done +3: [12:23:51] ------------------------------------- +3: [12:23:51] Testing dict update. +3: [12:23:51] done +3: deleted! +3: deleted! +3: deleted! +3: deleted! +3: deleted! +3: deleted! +8: [12:23:51] Set 10: 0 +8: [12:23:51] Set 11: 0 +8: [12:23:51] Set 14: 0 +8: [12:23:51] Set 10: 1 +8: [12:23:51] Get 14: 1 +8: [12:23:51] Num: 20 +8: [12:23:51] NumOn: 3 +8: [12:23:51] NumOff: 17 +8: 10, 11, 14, +8: [12:23:51] t2[19]: 0 +8: [12:23:51] t2[14]: 1 +8: [12:23:51] t2[19]: 0 +8: [12:23:51] t2[14]: 0 +8: t1: 10, 11, 14, +8: t2: 10, 11, 15, 17, +8: t1|t2: 10, 11, 14, 15, 17, +8: t1&t2: 10, 11, +8: t1^t2: 14, 15, 17, +8: ~t1: 0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 12, 13, 15, 16, 17, 18, 19, +8: except 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 + 2/236 Test #3: testDict ............................... Passed 0.26 sec 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: [16:02:32] v3 4 -8: [16:02:32] v4 5 -8: [16:02:32] SPARSE ----------------------------------- -8: [16:02:32] Set 10: 0 -8: [16:02:32] Set 11: 0 -8: [16:02:32] Set 14: 0 -8: [16:02:32] Set 10: 1 -8: [16:02:32] Get 14: 1 -8: [16:02:32] Num: 20 -8: [16:02:32] NumOn: 3 -8: [16:02:32] NumOff: 17 -8: 10, 11, 14, -8: [16:02:32] t2[19]: 0 -8: [16:02:32] t2[14]: 1 -8: [16:02:32] t2[19]: 0 -8: [16:02:32] t2[14]: 0 -8: t1: 10, 11, 14, -8: t2: 10, 11, 15, 17, -8: t1|t2: 10, 11, 14, 15, 17, -8: t1&t2: 10, 11, -8: t1^t2: 14, 15, 17, -8: ~t1: 0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 12, 13, 15, 16, 17, 18, 19, -8: except -8: [16:02:32] Explicit ---------------------------------- -8: [16:02:32] Set 10: 0 -8: [16:02:32] Set 11: 0 -8: [16:02:32] Set 14: 0 -8: [16:02:32] Set 10: 1 -8: [16:02:32] Get 14: 1 -8: [16:02:32] Num: 20 -8: [16:02:32] NumOn: 3 -8: [16:02:32] NumOff: 17 +8: [12:23:51] Explicit ---------------------------------- +8: [12:23:51] Set 10: 0 +8: [12:23:51] Set 11: 0 +8: [12:23:51] Set 14: 0 +8: [12:23:51] Set 10: 1 +8: [12:23:51] Get 14: 1 +8: [12:23:51] Num: 20 +8: [12:23:51] NumOn: 3 +8: [12:23:51] NumOff: 17 8: 10, 11, 14, -8: [16:02:32] t2[19]: 0 -8: [16:02:32] t2[14]: 1 -8: [16:02:32] t2[19]: 0 -8: [16:02:32] t2[14]: 0 +8: [12:23:51] t2[19]: 0 +8: [12:23:51] t2[14]: 1 +8: [12:23:51] t2[19]: 0 +8: [12:23:51] t2[14]: 0 8: t1: 10, 11, 14, 8: t2: 10, 11, 15, 17, 8: t1|t2: 10, 11, 14, 15, 17, @@ -15273,73 +15304,77 @@ 8: ~t1: 0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 12, 13, 15, 16, 17, 18, 19, 8: except 3/236 Test #9: testFPB ................................ Passed 0.16 sec +8: [12:23:51] Done +8: [12:23:51] Test DiscreteValue Vectors 1 ---------------------------- test 15 Start 15: pySparseIntVect 15: Test command: /usr/bin/python3 "/build/reproducible-path/rdkit-202503.1/Code/DataStructs/Wrap/testSparseIntVect.py" 15: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/DataStructs/Wrap 15: Test timeout computed to be: 1500 -8: [16:02:32] Done -8: [16:02:32] Test DiscreteValue Vectors 1 ---------------------------- -8: [16:02:32] Expected failure: Value out of range -8: [16:02:32] Expected failure: Value out of range -8: [16:02:32] Expected failure: Value out of range -8: [16:02:32] Expected failure: Value out of range -8: [16:02:32] Expected failure: Value out of range -8: [16:02:32] Test DiscreteValue Vectors 2 ------------------------------ -8: [16:02:32] Test DiscreteValue Vectors 3 --------------------------- -8: [16:02:32] Test DiscreteValue Operations ----------------------------- -8: [16:02:32] Test DiscreteValue Operations 2 -------------------------- -8: [16:02:32] Test SparseIntVect ------------------------------------ -8: [16:02:32] Test SparseIntVect Serialization -------------------------- -8: [16:02:32] Test BitVect Serialization ------------------------------- -8: [16:02:32] Test BitVect to FPS ------------------------------- -8: [16:02:32] Test BitVect to binary string ------------------------------- -8: [16:02:32] Test Similarity Measures BitVect ------------------------------- -8: [16:02:32] Test Similarity Measures SparseBitVect ------------------------------- -8: [16:02:32] Test BitVect with all ones ------------------------------- -8: [16:02:32] Test Explicit BitVects: Concatenation Operation ------------------------------- -8: [16:02:32] Test bitmap operations ------------------------------- -8: [16:02:32] Test bitmaps as properties ------------------------------- -8: [16:02:32] Test #3944: SparseIntVect copy constructor and assignment operators not clearing existing data------------------------------- -8: [16:02:32] Test RealValue Vectors 1: Constructors and Accessing Values ------------------------------- -8: [16:02:32] Test RealValue Vectors 2: L1Norm ------------------------------- -8: [16:02:32] Test RealValue Vectors 3: Pickles ------------------------------- -8: [16:02:32] Test RealValue Vectors 4: Vector Operations ------------------------------- - 4/236 Test #8: testDataStructs ........................ Passed 0.34 sec +8: [12:23:51] Expected failure: Value out of range +8: [12:23:51] Expected failure: Value out of range +8: [12:23:51] Expected failure: Value out of range +8: [12:23:51] Expected failure: Value out of range +8: [12:23:51] Expected failure: Value out of range +8: [12:23:51] Test DiscreteValue Vectors 2 ------------------------------ +8: [12:23:51] Test DiscreteValue Vectors 3 --------------------------- +8: [12:23:51] Test DiscreteValue Operations ----------------------------- +8: [12:23:51] Test DiscreteValue Operations 2 -------------------------- +8: [12:23:51] Test SparseIntVect ------------------------------------ +8: [12:23:51] Test SparseIntVect Serialization -------------------------- +8: [12:23:51] Test BitVect Serialization ------------------------------- +8: [12:23:51] Test BitVect to FPS ------------------------------- +7: [12:23:51] should not be silent +7: [12:23:51] should not be silent +7: Randomness seeded to: 2105611863 +7: [12:23:51] should not be silent +8: [12:23:51] Test BitVect to binary string ------------------------------- +8: [12:23:51] Test Similarity Measures BitVect ------------------------------- +8: [12:23:51] Test Similarity Measures SparseBitVect ------------------------------- +7: [12:23:51] should not be silent +7: [12:23:51] should not be silent +7: [12:23:51] should not be silent +7: [12:23:51] should not be silent +7: [12:23:51] should not be silent +7: [12:23:51] should not be silent +7: [12:23:51] should not be silent +8: [12:23:51] Test BitVect with all ones ------------------------------- +8: [12:23:51] Test Explicit BitVects: Concatenation Operation ------------------------------- +8: [12:23:51] Test bitmap operations ------------------------------- +8: [12:23:51] Test bitmaps as properties ------------------------------- +7: =============================================================================== +7: All tests passed (26 assertions in 3 test cases) +7: +8: [12:23:51] Test #3944: SparseIntVect copy constructor and assignment operators not clearing existing data------------------------------- + 4/236 Test #7: logTestsCatch .......................... Passed 0.32 sec +8: [12:23:51] Test RealValue Vectors 1: Constructors and Accessing Values ------------------------------- test 16 Start 16: pyFPB 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: [16:02:32] should not be silent -7: [16:02:32] should not be silent -7: Randomness seeded to: 850800645 -7: [16:02:32] should not be silent -7: [16:02:32] should not be silent -7: [16:02:32] should not be silent -7: [16:02:32] should not be silent -7: [16:02:32] should not be silent -7: [16:02:32] should not be silent -7: [16:02:32] should not be silent -7: [16:02:32] should not be silent -7: =============================================================================== -7: All tests passed (26 assertions in 3 test cases) -7: -6: Randomness seeded to: 3395542473 -6: =============================================================================== -6: All tests passed (32 assertions in 2 test cases) -6: - 5/236 Test #10: testMultiFPB ........................... Passed 0.37 sec +8: [12:23:51] Test RealValue Vectors 2: L1Norm ------------------------------- +8: [12:23:51] Test RealValue Vectors 3: Pickles ------------------------------- +8: [12:23:51] Test RealValue Vectors 4: Vector Operations ------------------------------- + 5/236 Test #8: testDataStructs ........................ Passed 0.32 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 - 6/236 Test #6: dictTestsCatch ......................... Passed 0.45 sec - 7/236 Test #7: logTestsCatch .......................... Passed 0.44 sec +11: Randomness seeded to: 1197406482 +11: =============================================================================== +11: All tests passed (3 assertions in 1 test case) +11: +6: Randomness seeded to: 2011750923 +6: =============================================================================== +6: All tests passed (32 assertions in 2 test cases) +6: + 6/236 Test #6: dictTestsCatch ......................... Passed 0.39 sec + 7/236 Test #11: catchDataStructs ....................... Passed 0.29 sec test 18 Start 18: testGrid @@ -15352,17 +15387,37 @@ 19: Test command: /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/Geometry/testRealValueGrid 19: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/Geometry 19: Test timeout computed to be: 1500 -11: Randomness seeded to: 1263034308 -11: =============================================================================== -11: All tests passed (3 assertions in 1 test case) -11: - 8/236 Test #11: catchDataStructs ....................... Passed 0.42 sec + 8/236 Test #10: testMultiFPB ........................... Passed 0.36 sec test 20 Start 20: geometryTestsCatch 20: Test command: /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/Geometry/geometryTestsCatch 20: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/Geometry 20: 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: + 9/236 Test #18: testGrid ............................... Passed 0.07 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 17: **************************************** 17: testPointND 17: **************************************** @@ -15371,8 +15426,8 @@ 17: testPointOps2D 17: **************************************** 17: test12D -17: ref1: 2.96334 2.9921 ref2: 1.42016 2.33877 -17: pt1: 0.724842 0.336592 pt2: 3.43991 3.07492 +17: ref1: 3.20326 2.55467 ref2: 1.77511 4.14202 +17: pt1: 2.99345 4.55239 pt2: 1.84132 0.68104 17: **************************************** 17: test23D 17: **************************************** @@ -15387,13 +15442,13 @@ 17: **************************************** 17: testFromQuaternion 17: **************************************** - 9/236 Test #17: testTransforms ......................... Passed 0.09 sec -test 21 - Start 21: testPyGeometry + 10/236 Test #17: testTransforms ......................... Passed 0.12 sec +test 22 + Start 22: testMatrices -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 +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: --------------------------------- @@ -15408,48 +15463,24 @@ 19: --------------------------------- 19: test4UniformRealValueGrid3DOps 19: - 10/236 Test #19: testRealValueGrid ...................... Passed 0.08 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 -18: *********************************************************** -18: Testing Grid -18: --------------------------------- -18: testUniformGrid1 -18: -18: --------------------------------- -18: testUniformGrid2 -18: -18: --------------------------------- -18: testUniformGridPickling -18: -18: --------------------------------- -18: testGridOps -18: -18: --------------------------------- -18: testUniformGridIndexing -18: - 11/236 Test #18: testGrid ............................... Passed 0.12 sec + 11/236 Test #19: testRealValueGrid ...................... Passed 0.11 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: [16:02:32] ----------------------------------------- -22: [16:02:32] Testing RDNumerics: vectors and matrices Code -22: [16:02:32] --------------------------------------- -22: [16:02:32] test1Vector -22: [16:02:32] --------------------------------------- -22: [16:02:32] test2Matrix -22: [16:02:32] --------------------------------------- -22: [16:02:32] test3SquareMatrix -22: [16:02:32] --------------------------------------- -22: [16:02:32] test4SymmMatrix - 12/236 Test #22: testMatrices ........................... Passed 0.08 sec +22: [12:23:51] ----------------------------------------- +22: [12:23:51] Testing RDNumerics: vectors and matrices Code +22: [12:23:51] --------------------------------------- +22: [12:23:51] test1Vector +22: [12:23:51] --------------------------------------- +22: [12:23:51] test2Matrix +22: [12:23:51] --------------------------------------- +22: [12:23:51] test3SquareMatrix +22: [12:23:51] --------------------------------------- +22: [12:23:51] test4SymmMatrix + 12/236 Test #22: testMatrices ........................... Passed 0.07 sec test 24 Start 24: testAlignment @@ -15474,11 +15505,11 @@ 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 -20: Randomness seeded to: 2315261015 +20: Randomness seeded to: 4053155164 20: =============================================================================== 20: All tests passed (50 assertions in 5 test cases) 20: - 14/236 Test #20: geometryTestsCatch ..................... Passed 0.49 sec + 14/236 Test #20: geometryTestsCatch ..................... Passed 0.36 sec test 26 Start 26: testOptimizer @@ -15490,10 +15521,6 @@ 26: done 26: ------------------------------------- 26: Testing BFGS optimization. -23: Randomness seeded to: 102734542 -23: =============================================================================== -23: All tests passed (76 assertions in 3 test cases) -23: 26: done 15/236 Test #26: testOptimizer .......................... Passed 0.04 sec test 27 @@ -15502,7 +15529,11 @@ 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 - 16/236 Test #23: testConrec ............................. Passed 0.47 sec +23: Randomness seeded to: 928156571 +23: =============================================================================== +23: All tests passed (76 assertions in 3 test cases) +23: + 16/236 Test #23: testConrec ............................. Passed 0.41 sec test 28 Start 28: testUFFForceField @@ -15555,10 +15586,23 @@ 28: done 28: ------------------------------------- 28: Unit tests for all UFF constraint terms. -27: Randomness seeded to: 799579329 +27: Randomness seeded to: 1285998375 27: =============================================================================== 27: All tests passed (20 assertions in 2 test cases) 27: + 17/236 Test #27: ForceFieldsCatch ....................... Passed 0.69 sec +test 29 + Start 29: testMMFFForceField + +29: Test command: /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/ForceField/MMFF/testMMFFForceField +29: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/ForceField/MMFF +29: Test timeout computed to be: 1500 +28: done +28: ------------------------------------- +28: Unit tests for copying UFF ForceFields. +28: done +28: ------------------------------------- +28: Unit test for UFF butane scan. 1: core 1: RDKit 2D 1: @@ -15573,13 +15617,6 @@ 1: 4 1 1 0 1: M END 1: - 17/236 Test #27: ForceFieldsCatch ....................... Passed 0.83 sec -test 29 - Start 29: testMMFFForceField - -29: Test command: /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/ForceField/MMFF/testMMFFForceField -29: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/ForceField/MMFF -29: Test timeout computed to be: 1500 1: core+sidechain 1: RDKit 2D 1: @@ -15808,6 +15845,8 @@ 1: 16 1 1 0 1: M END 1: +29: ------------------------------------- +29: Official MMFF validation suite. 1: core 1: RDKit 2D 1: @@ -15940,9 +15979,6 @@ 1: 4 5 1 0 1: M END 1: -28: done -28: ------------------------------------- -28: Unit tests for copying UFF ForceFields. 1: core+sidechain 1: RDKit 2D 1: @@ -15981,9 +16017,6 @@ 1: 5 7 1 0 1: M END 1: -28: done -28: ------------------------------------- -28: Unit test for UFF butane scan. 1: test1 1: RDKit 2D 1: @@ -16029,10 +16062,13 @@ 1: 2 5 1 0 1: M END 1: -29: ------------------------------------- -29: Official MMFF validation suite. 28: done - 18/236 Test #28: testUFFForceField ...................... Passed 1.05 sec +14: ...... +14: ---------------------------------------------------------------------- +14: Ran 6 tests in 0.077s +14: +14: OK + 18/236 Test #28: testUFFForceField ...................... Passed 1.10 sec test 30 Start 30: pyForceFieldConstraints @@ -16214,6 +16250,16 @@ 1: 6 85 1 0 1: 46 3 1 0 1: M END +15: ......... +15: ---------------------------------------------------------------------- +15: Ran 9 tests in 0.107s +15: +15: OK +16: ......... +16: ---------------------------------------------------------------------- +16: Ran 9 tests in 0.139s +16: +16: OK 1: 1: single-double 1: RDKit 2D @@ -16254,6 +16300,11 @@ 1: 16 17 1 0 1: M END 1: +13: ...... +13: ---------------------------------------------------------------------- +13: Ran 6 tests in 0.123s +13: +13: OK 1: cis-trans 1: RDKit 2D 1: @@ -16279,6 +16330,12 @@ 1: 9 10 1 0 1: M END 1: +25: ..... +25: ---------------------------------------------------------------------- +25: Ran 5 tests in 0.027s +25: +25: OK +25: Testing Alignment Wrapper code: 1: admntn 1: RDKit 2D 1: @@ -16307,6 +16364,13 @@ 1: 10 2 1 0 1: M END 1: + 19/236 Test #14: pyRealValueVect ........................ Passed 2.01 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 1: github 4845 - nan coordinates but no crash 1: RDKit 2D 1: @@ -16399,123 +16463,96 @@ 1: 30 11 1 0 1: M END 1: - 19/236 Test #1: testCoordGen ........................... Passed 2.33 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 -31: *********************************************************** -31: test1 -31: *********************************************************** -31: testIssue216 -31: Rows: 4 Columns: 4 -31: 0 1 1 1 -31: 1 0 1 1 -31: 1 1 0 1 -31: 1 1 1 0 -31: *********************************************************** -31: - 20/236 Test #31: testDistGeom ........................... Passed 0.10 sec + 20/236 Test #16: pyFPB .................................. Passed 1.91 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 -32: ...... -32: ---------------------------------------------------------------------- -32: Ran 6 tests in 0.090s -32: -32: OK -14: ...... -14: ---------------------------------------------------------------------- -14: Ran 6 tests in 0.034s -14: -14: OK - 21/236 Test #32: pyDistGeom ............................. Passed 0.43 sec +21: .................... +21: ---------------------------------------------------------------------- +21: Ran 20 tests in 0.168s +21: +21: OK +21: Testing Geometry wrapper + 21/236 Test #1: testCoordGen ........................... Passed 2.46 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 -16: ......... -16: ---------------------------------------------------------------------- -16: Ran 9 tests in 0.092s -16: -16: OK -15: ......... -15: ---------------------------------------------------------------------- -15: Ran 9 tests in 0.117s -15: -15: OK -13: ...... -13: ---------------------------------------------------------------------- -13: Ran 6 tests in 0.132s -13: -13: OK - 22/236 Test #14: pyRealValueVect ........................ Passed 2.74 sec +31: *********************************************************** +31: test1 +31: *********************************************************** +31: testIssue216 +31: Rows: 4 Columns: 4 +31: 0 1 1 1 +31: 1 0 1 1 +31: 1 1 0 1 +31: 1 1 1 0 +31: *********************************************************** +31: + 22/236 Test #15: pySparseIntVect ........................ Passed 2.12 sec + 23/236 Test #31: testDistGeom ........................... Passed 0.13 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 - 23/236 Test #15: pySparseIntVect ........................ Passed 2.68 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 -33: -33: -33: -33: COPY - 24/236 Test #33: graphmolcpTest ......................... Passed 0.10 sec + 24/236 Test #13: pyDiscreteValueVect .................... Passed 2.21 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 - 25/236 Test #16: pyFPB .................................. Passed 2.56 sec + 25/236 Test #25: pyAlignment ............................ Passed 1.77 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 - 26/236 Test #13: pyDiscreteValueVect .................... Passed 2.83 sec +33: +33: +33: +33: COPY +34: [12:23:53] ---------------------- Test1 + 26/236 Test #33: graphmolcpTest ......................... Passed 0.12 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 -34: [16:02:35] ---------------------- Test1 -34: [16:02:35] Done! -34: [16:02:35] ---------------------- Test2 -34: [16:02:35] Done! -34: [16:02:35] ---------------------- Test3 -37: [16:02:35] ------------------------------------- -37: [16:02:35] Testing String Pickle Roundtrips. -34: [16:02:35] Done! -34: [16:02:35] ---------------------- Test4 -34: [16:02:35] Done! -34: [16:02:35] ---------------------- Test5 -34: [16:02:35] Done! -34: [16:02:35] +34: [12:23:53] Done! +34: [12:23:53] ---------------------- Test2 +34: [12:23:53] Done! +34: [12:23:53] ---------------------- Test3 +34: [12:23:53] Done! +34: [12:23:53] ---------------------- Test4 +34: [12:23:53] Done! +34: [12:23:53] ---------------------- Test5 +34: [12:23:53] Done! +34: [12:23:53] 34: 34: **** -25: ..... -25: ---------------------------------------------------------------------- -25: Ran 5 tests in 0.030s -25: -25: OK -25: Testing Alignment Wrapper code: + 27/236 Test #21: testPyGeometry ......................... Passed 2.03 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 34: Pre-condition Violation 34: Can't expand empty query 34: Violation occurred on line 30 in file ./Code/GraphMol/QueryAtom.cpp @@ -16525,76 +16562,64 @@ 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# 0x0000AAAAAE133610 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/graphmolqueryTest -34: 4# 0x0000AAAAAE130A88 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/graphmolqueryTest -34: 5# 0x0000FFFF8E91229C in /lib/aarch64-linux-gnu/libc.so.6 +34: 3# 0x0000AAAAD9D33610 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/graphmolqueryTest +34: 4# 0x0000AAAAD9D30A88 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/graphmolqueryTest +34: 5# 0x0000FFFFA9FB229C in /lib/aarch64-linux-gnu/libc.so.6 34: 6# __libc_start_main in /lib/aarch64-linux-gnu/libc.so.6 -34: 7# 0x0000AAAAAE130B70 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/graphmolqueryTest +34: 7# 0x0000AAAAD9D30B70 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/graphmolqueryTest 34: ---------- 34: **** 34: -34: [16:02:35] Done! - 27/236 Test #25: pyAlignment ............................ Passed 2.44 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 -34: [16:02:35] ---------------------- Test issue 2892580 -34: [16:02:35] Done! -34: [16:02:35] ---------------------- Test github issue 53: query molecules not matching [R] -34: [16:02:35] Done! -34: [16:02:35] ---------------------- Test queries using qualifiers instead of == -34: [16:02:35] Done! -34: [16:02:35] ---------------------- Test Github issue 165: radicals not used in atom-atom matching -34: [16:02:35] Done! -38: [16:02:35] done - 28/236 Test #38: graphmoltestPicklerGlobalSetting ....... Passed 0.22 sec +34: [12:23:53] Done! +34: [12:23:53] ---------------------- Test issue 2892580 +34: [12:23:53] Done! +34: [12:23:53] ---------------------- Test github issue 53: query molecules not matching [R] +34: [12:23:53] Done! +34: [12:23:53] ---------------------- Test queries using qualifiers instead of == +34: [12:23:53] Done! +29: +29: Computing MMFF94 energies for /build/reproducible-path/rdkit-202503.1/Code/ForceField/MMFF/test_data/MMFF94_dative.sdf... +34: [12:23:53] ---------------------- Test Github issue 165: radicals not used in atom-atom matching +34: [12:23:53] Done! +37: [12:23:53] ------------------------------------- +37: [12:23:53] Testing String Pickle Roundtrips. +34: [12:23:53] ---------------------- Test extra atom queries +34: [12:23:53] Done! +34: [12:23:53] ---------------------- Test extra bond queries +34: [12:23:53] Done! +34: [12:23:53] ---------------------- Test num heteroatom neighbor queries +34: [12:23:53] Done! +34: [12:23:53] ---------------------- Test atom type queries +34: [12:23:53] Done! +34: [12:23:53] ---------------------- Test Github #2471: dummy atom queries are flagged as complex +34: [12:23:53] Done! +34: [12:23:53] ---------------------- Testing hasBondTypeQuery() and hasComplexBondTypeQuery() +34: [12:23:53] Done! + 28/236 Test #34: graphmolqueryTest ...................... Passed 0.23 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 -34: [16:02:35] ---------------------- Test extra atom queries -34: [16:02:35] Done! -34: [16:02:35] ---------------------- Test extra bond queries -34: [16:02:35] Done! -34: [16:02:35] ---------------------- Test num heteroatom neighbor queries -34: [16:02:35] Done! -34: [16:02:35] ---------------------- Test atom type queries -34: [16:02:35] Done! -34: [16:02:35] ---------------------- Test Github #2471: dummy atom queries are flagged as complex -34: [16:02:35] Done! -34: [16:02:35] ---------------------- Testing hasBondTypeQuery() and hasComplexBondTypeQuery() -34: [16:02:35] Done! - 29/236 Test #34: graphmolqueryTest ...................... Passed 0.34 sec + 29/236 Test #39: graphmolIterTest ....................... Passed 0.10 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 -40: [16:02:35] Testing the hanoi sort -40: [16:02:35] populating vectors -21: .................... -21: ---------------------------------------------------------------------- -21: Ran 20 tests in 0.154s -21: -21: OK -21: Testing Geometry wrapper -36: -------------------------- -36: -------------------------- -36: C/C=C/C(C)Cl - 30/236 Test #39: graphmolIterTest ....................... Passed 0.10 sec - 31/236 Test #41: graphmolMemTest1 ....................... Passed 0.05 sec +38: [12:23:53] done + 30/236 Test #38: graphmoltestPicklerGlobalSetting ....... Passed 0.19 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 +40: [12:23:53] Testing the hanoi sort +40: [12:23:53] populating vectors + 31/236 Test #41: graphmolMemTest1 ....................... Passed 0.05 sec test 43 Start 43: molBundleTest @@ -16604,20 +16629,26 @@ 35: 1 1 2 35: 1 1 1 35: 2 1 0.75 -37: [16:02:35] done -37: [16:02:35] ------------------------------------- -37: [16:02:35] Testing reading existing pickle file (v2). +36: -------------------------- +36: -------------------------- +36: C/C=C/C(C)Cl +37: [12:23:53] done +37: [12:23:53] ------------------------------------- +37: [12:23:53] Testing reading existing pickle file (v2). 35: path: 2 - 32/236 Test #21: testPyGeometry ......................... Passed 2.83 sec + 32/236 Test #43: molBundleTest .......................... Passed 0.11 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 -37: [16:02:35] done -37: [16:02:35] ------------------------------------- -37: [16:02:35] Testing combining molecules using pickles. +35: [12:23:53] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 10 ignored +35: [12:23:53] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 10 ignored +35: [12:23:53] Explicit valence for atom # 0 B, 5, is greater than permitted +37: [12:23:53] done +37: [12:23:53] ------------------------------------- +37: [12:23:53] 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 @@ -16634,65 +16665,59 @@ 37: 4 4->5 order: 1 37: 5 5->6 order: 1 37: 6 6->3 order: 1 -37: [16:02:35] done -37: [16:02:35] ------------------------------------- -37: [16:02:35] Testing Issue164: Roundtrip Pickle Failure. -35: [16:02:35] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 10 ignored -35: [16:02:35] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 10 ignored -37: [16:02:35] done -37: [16:02:35] ------------------------------------- -37: [16:02:35] Testing Issue219: Pickle Failure with Conformations. - 33/236 Test #43: molBundleTest .......................... Passed 0.12 sec +37: [12:23:53] done +37: [12:23:53] ------------------------------------- +37: [12:23:53] Testing Issue164: Roundtrip Pickle Failure. +36: [12:23:53] Conflicting single bond directions around double bond at index 2. +36: [12:23:53] BondStereo set to STEREONONE and single bond directions set to NONE. +36: [12:23:53] Conflicting single bond directions around double bond at index 4. +36: [12:23:53] BondStereo set to STEREONONE and single bond directions set to NONE. +36: [12:23:53] Conflicting single bond directions around double bond at index 15. +36: [12:23:53] BondStereo set to STEREONONE and single bond directions set to NONE. +36: [12:23:53] Conflicting single bond directions around double bond at index 2. +36: [12:23:53] BondStereo set to STEREONONE and single bond directions set to NONE. +36: [12:23:53] Conflicting single bond directions around double bond at index 1. +36: [12:23:53] BondStereo set to STEREONONE and single bond directions set to NONE. +37: [12:23:53] done +37: [12:23:53] ------------------------------------- +37: [12:23:53] Testing Issue219: Pickle Failure with Conformations. +37: [12:23:53] done +37: [12:23:53] ------------------------------------- +37: [12:23:53] Testing Issue220: Pickle problems with bond stereochemistry. +37: [12:23:53] done +35: [12:23:53] Explicit valence for atom # 1 C, 5, is greater than permitted +37: [12:23:53] ------------------------------------- +37: [12:23:53] Testing query serialization. +37: [12:23:53] C=[$(C=O)] +37: [12:23:53] S(=O)(=O)-[C&H2][F,Br,I,Cl] S(=O)(=O)-[C&H2][F,Br,I,Cl] +37: [12:23:53] done +37: [12:23:53] ------------------------------------- +37: [12:23:53] Testing radical handling in pickles. +37: [12:23:53] done +35: [12:23:53] Explicit valence for atom # 1 C, 5, is greater than permitted +35: [12:23:53] Explicit valence for atom # 1 C, 5, is greater than permitted +35: [12:23:53] Explicit valence for atom # 1 Si, 7, is greater than permitted +37: [12:23:53] done +37: [12:23:53] ------------------------------------- +37: [12:23:53] Testing sf.net issue 2788233. +37: [12:23:53] done +37: [12:23:53] ------------------------------------- +37: [12:23:53] Testing sf.net issue 3202580. +37: mass! 13.0034 +37: [12:23:53] done +37: [12:23:53] ------------------------------------- +37: [12:23:53] Testing sf.net issue 3316407. +36: -------------------------------------------------- + 33/236 Test #36: graphmoltestChirality .................. Passed 0.50 sec test 45 Start 45: test-valgrind 45: Test command: /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/test-valgrind 45: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol 45: Test timeout computed to be: 1500 -37: [16:02:35] done -37: [16:02:35] ------------------------------------- -37: [16:02:35] Testing Issue220: Pickle problems with bond stereochemistry. -37: [16:02:35] done -37: [16:02:35] ------------------------------------- -37: [16:02:35] Testing query serialization. -40: [16:02:35] sorting (hanoi sort) vectors -35: [16:02:35] Explicit valence for atom # 0 B, 5, is greater than permitted -37: [16:02:35] C=[$(C=O)] -37: [16:02:35] S(=O)(=O)-[C&H2][F,Br,I,Cl] S(=O)(=O)-[C&H2][F,Br,I,Cl] -37: [16:02:35] done -37: [16:02:35] ------------------------------------- -37: [16:02:35] Testing radical handling in pickles. -37: [16:02:35] done - 34/236 Test #45: test-valgrind .......................... Passed 0.04 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: [16:02:35] done -37: [16:02:35] ------------------------------------- -37: [16:02:35] Testing sf.net issue 2788233. -37: [16:02:35] done -37: [16:02:35] ------------------------------------- -37: [16:02:35] Testing sf.net issue 3202580. -37: mass! 13.0034 -37: [16:02:35] done -37: [16:02:35] ------------------------------------- -37: [16:02:35] Testing sf.net issue 3316407. -36: [16:02:35] Conflicting single bond directions around double bond at index 2. -36: [16:02:35] BondStereo set to STEREONONE and single bond directions set to NONE. -36: [16:02:35] Conflicting single bond directions around double bond at index 4. -36: [16:02:35] BondStereo set to STEREONONE and single bond directions set to NONE. -36: [16:02:35] Conflicting single bond directions around double bond at index 15. -36: [16:02:35] BondStereo set to STEREONONE and single bond directions set to NONE. -36: [16:02:35] Conflicting single bond directions around double bond at index 2. -36: [16:02:35] BondStereo set to STEREONONE and single bond directions set to NONE. -36: [16:02:35] Conflicting single bond directions around double bond at index 1. -36: [16:02:35] BondStereo set to STEREONONE and single bond directions set to NONE. -37: [16:02:35] done -37: [16:02:35] ------------------------------------- -37: [16:02:35] Testing sf.net issue 3496759. +37: [12:23:53] done +37: [12:23:53] ------------------------------------- +37: [12:23:53] Testing sf.net issue 3496759. 37: smi match: *C *C 37: smi match: **=* **=* 37: smi match: [N-]=[N+]=NC=O [N-]=[N+]=NC=O @@ -16753,7 +16778,6 @@ 37: smi match: *=N~C *=N~C 37: smi match: CO*(=O)=O CO*(=O)=O 37: smi match: * * -35: [16:02:35] Explicit valence for atom # 1 C, 5, is greater than permitted 37: smi match: * * 37: smi match: *C=C *C=C 37: smi match: N#CS N#CS @@ -16993,9 +17017,6 @@ 37: smi match: SS SS 37: smi match: [SH] [SH] 37: smi match: *C* *C* -35: [16:02:35] Explicit valence for atom # 1 C, 5, is greater than permitted -35: [16:02:35] Explicit valence for atom # 1 C, 5, is greater than permitted -35: [16:02:35] Explicit valence for atom # 1 Si, 7, is greater than permitted 37: smi match: * * 37: smi match: C[nH3+] C[nH3+] 37: smi match: cC(=N)[NH2] cC(=N)[NH2] @@ -17021,6 +17042,13 @@ 37: smi match: *=* *=* 37: smi match: *C *C 37: smi match: C#C C#C + 34/236 Test #45: test-valgrind .......................... Passed 0.07 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: smi match: *[CH]C=C *[CH]C=C 37: smi match: cCC(=O)[OH] cCC(=O)[OH] 37: smi match: *C(*)(*)C(=O)[OH] *C(*)(*)C(=O)[OH] @@ -17046,19 +17074,16 @@ 37: smi match: *c *c 37: smi match: **:*cF **:*cF 37: smi match: cB([OH])[OH] cB([OH])[OH] -36: -------------------------------------------------- - 35/236 Test #36: graphmoltestChirality .................. Passed 0.63 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: smi match: N~N~N N~N~N 37: smi match: *N=N* *N=N* 37: smi match: *CC[OH] *CC[OH] 37: smi match: *CC[OH] *CC[OH] 37: smi match: *=CCC(=O)[OH] *=CCC(=O)[OH] +32: ...... +32: ---------------------------------------------------------------------- +32: Ran 6 tests in 0.045s +32: +32: OK 37: smi match: O=C([OH])CC[OH] O=C([OH])CC[OH] 37: smi match: *CCC(=O)[OH] *CCC(=O)[OH] 37: smi match: CC(=O)CC(=O)[OH] CC(=O)CC(=O)[OH] @@ -17131,78 +17156,72 @@ 37: smi match: * * 37: smi match: ***** ***** 37: smi match: NC(N)=O NC(N)=O -37: [16:02:35] done -37: [16:02:35] ------------------------------------- -37: [16:02:35] Testing sf.net issue 280. -37: [16:02:35] done -37: [16:02:35] ------------------------------------- -37: [16:02:35] Testing sf.net issue 285. -37: [16:02:35] done -37: [16:02:35] done -37: [16:02:35] done -37: [16:02:35] done -37: [16:02:35] done -37: [16:02:35] done -37: [16:02:35] done +37: [12:23:54] done +37: [12:23:54] ------------------------------------- +37: [12:23:54] Testing sf.net issue 280. +37: [12:23:54] done +37: [12:23:54] ------------------------------------- +37: [12:23:54] Testing sf.net issue 285. +37: [12:23:54] done +37: [12:23:54] done +37: [12:23:54] done +37: [12:23:54] done +37: [12:23:54] done +37: [12:23:54] done +37: [12:23:54] done 35: smi: Cc1ccc(S(=O)(=O)/N=C2\CC(=N\C(C)(C)C)/C2=N\C(C)(C)C)cc1 -37: [16:02:35] ------------------------------------- -37: [16:02:35] Testing Github2441: Add RDProps interface to Conformers. -37: [16:02:35] done -37: [16:02:35] ------------------------------------- -37: [16:02:35] Testing Issue2510: Pickle Confs as double. -37: [16:02:35] done -37: [16:02:35] ------------------------------------- -37: [16:02:35] Testing Github #2465: Negative atom-map numbers cause depickling to fail. -37: [16:02:35] done -37: [16:02:35] ------------------------------------- -37: [16:02:35] Testing loading pickled mols with conformers -37: [16:02:36] done -37: [16:02:36] ------------------------------------- -37: [16:02:36] Testing conformer reading/writing options -37: [16:02:36] done -37: [16:02:36] ------------------------------------- -37: [16:02:36] Testing property reading options -37: [16:02:36] done -37: [16:02:36] ------------------------------------- -37: [16:02:36] Testing property reading options -37: [16:02:36] done -37: [16:02:36] ------------------------------------- -37: [16:02:36] Testing boost::serialization integration -37: [16:02:36] done -37: [16:02:36] ------------------------------------- -37: [16:02:36] Testing github issue 6036 - 36/236 Test #37: graphmoltestPickler .................... Passed 0.74 sec +37: [12:23:54] ------------------------------------- +37: [12:23:54] Testing Github2441: Add RDProps interface to Conformers. +37: [12:23:54] done +37: [12:23:54] ------------------------------------- +37: [12:23:54] Testing Issue2510: Pickle Confs as double. +37: [12:23:54] done +37: [12:23:54] ------------------------------------- +37: [12:23:54] Testing Github #2465: Negative atom-map numbers cause depickling to fail. +37: [12:23:54] done +37: [12:23:54] ------------------------------------- +37: [12:23:54] Testing loading pickled mols with conformers +37: [12:23:54] done +37: [12:23:54] ------------------------------------- +37: [12:23:54] Testing conformer reading/writing options +37: [12:23:54] done +37: [12:23:54] ------------------------------------- +37: [12:23:54] Testing property reading options +37: [12:23:54] done +37: [12:23:54] ------------------------------------- +37: [12:23:54] Testing property reading options +37: [12:23:54] done +37: [12:23:54] ------------------------------------- +37: [12:23:54] Testing boost::serialization integration +37: [12:23:54] done +37: [12:23:54] ------------------------------------- +37: [12:23:54] Testing github issue 6036 + 35/236 Test #37: graphmoltestPickler .................... Passed 0.67 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 + 36/236 Test #44: testSGroup ............................. Passed 0.33 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 -2: .... -2: ---------------------------------------------------------------------- -2: Ran 4 tests in 0.040s -2: -2: OK -29: -29: Computing MMFF94 energies for /build/reproducible-path/rdkit-202503.1/Code/ForceField/MMFF/test_data/MMFF94_dative.sdf... - 37/236 Test #44: testSGroup ............................. Passed 0.38 sec + 37/236 Test #32: pyDistGeom ............................. Passed 0.86 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 -35: [16:02:36] non-ring atom 0 marked aromatic -35: [16:02:36] non-ring atom 0 marked aromatic - 38/236 Test #2: pyCoordGen ............................. Passed 3.85 sec -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 -35: [16:02:36] Conflicting single bond directions around double bond at index 17. -35: [16:02:36] BondStereo set to STEREONONE and single bond directions set to NONE. +35: [12:23:54] non-ring atom 0 marked aromatic +40: [12:23:54] sorting (hanoi sort) vectors +35: [12:23:54] non-ring atom 0 marked aromatic +35: [12:23:54] Conflicting single bond directions around double bond at index 17. +35: [12:23:54] BondStereo set to STEREONONE and single bond directions set to NONE. 35: starting ring finding 35: done 35: starting ring finding @@ -17219,88 +17238,100 @@ 35: starting ring finding 35: done 35: smiles: CC[C@]1(C(=O)c([nH])n)CC[C@](C)(O)CC1 -35: [16:02:36] WARNING: not removing hydrogen atom with dummy atom neighbors -47: Randomness seeded to: 515698074 +35: [12:23:54] WARNING: not removing hydrogen atom with dummy atom neighbors +35: ------------------------------- +35: [12:23:54] Explicit valence for atom # 0 N, 4, is greater than permitted +35: [12:23:54] Can't kekulize mol. Unkekulized atoms: 0 1 2 3 4 +35: [12:23:54] Can't kekulize mol. Unkekulized atoms: 6 7 8 9 10 +35: [12:23:54] Can't kekulize mol. Unkekulized atoms: 0 1 2 3 4 +35: [12:23:54] WARNING: merging explicit H queries involved in ORs is not supported. This query will not be merged +35: [12:23:54] WARNING: merging explicit H queries involved in ORs is not supported. This query will not be merged +35: [12:23:54] WARNING: merging explicit H queries involved in ORs is not supported. This query will not be merged +35: [12:23:54] WARNING: merging explicit H queries involved in ORs is not supported. This query will not be merged +35: [12:23:54] WARNING: merging explicit H queries involved in ORs is not supported. This query will not be merged +35: +35: [12:23:54] WARNING: not removing hydrogen atom with dummy atom neighbors +46: Randomness seeded to: 1838158494 +46: [12:23:54] WARNING: not removing hydrogen atom without neighbors +46: [12:23:54] WARNING: could not find number of expected rings. Switching to an approximate ring finding algorithm. +46: [12:23:54] WARNING: could not find number of expected rings. Switching to an approximate ring finding algorithm. +46: [12:23:54] WARNING: could not find number of expected rings. Switching to an approximate ring finding algorithm. +46: [12:23:54] WARNING: could not find number of expected rings. Switching to an approximate ring finding algorithm. +46: [12:23:54] WARNING: could not find number of expected rings. Switching to an approximate ring finding algorithm. +48: Randomness seeded to: 420538809 +48: =============================================================================== +48: All tests passed (136 assertions in 8 test cases) +48: +46: [12:23:54] Explicit valence for atom # 1 N, 5, is greater than permitted + 38/236 Test #48: graphmolSGroupCatch .................... Passed 0.49 sec +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 +2: .... +2: ---------------------------------------------------------------------- +2: Ran 4 tests in 0.075s +2: +2: OK +47: Randomness seeded to: 703246656 47: =============================================================================== 47: All tests passed (62 assertions in 6 test cases) 47: - 39/236 Test #47: graphmolOrganometallicsCatch ........... Passed 0.48 sec + 39/236 Test #47: graphmolOrganometallicsCatch ........... Passed 0.54 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: Randomness seeded to: 2769674227 -46: [16:02:36] WARNING: not removing hydrogen atom without neighbors -46: [16:02:36] WARNING: could not find number of expected rings. Switching to an approximate ring finding algorithm. -46: [16:02:36] WARNING: could not find number of expected rings. Switching to an approximate ring finding algorithm. -46: [16:02:36] WARNING: could not find number of expected rings. Switching to an approximate ring finding algorithm. -35: ------------------------------- -46: [16:02:36] WARNING: could not find number of expected rings. Switching to an approximate ring finding algorithm. -46: [16:02:36] WARNING: could not find number of expected rings. Switching to an approximate ring finding algorithm. -35: [16:02:36] Explicit valence for atom # 0 N, 4, is greater than permitted -46: [16:02:36] Explicit valence for atom # 1 N, 5, is greater than permitted -46: [16:02:36] Explicit valence for atom # 1 N, 6, is greater than permitted -46: [16:02:36] Explicit valence for atom # 1 N, 5, is greater than permitted -46: [16:02:36] Explicit valence for atom # 1 N, 5, is greater than permitted -46: [16:02:36] Explicit valence for atom # 2 O, 3, is greater than permitted -46: [16:02:36] Explicit valence for atom # 2 O, 3, is greater than permitted -46: [16:02:36] non-ring atom 2 marked aromatic -46: [16:02:36] non-ring atom 2 marked aromatic -46: [16:02:36] Can't kekulize mol. Unkekulized atoms: 0 1 2 3 4 -46: [16:02:36] Can't kekulize mol. Unkekulized atoms: 0 1 2 3 4 -46: [16:02:36] Can't kekulize mol. Unkekulized atoms: 1 2 3 -46: [16:02:36] Can't kekulize mol. Unkekulized atoms: 1 2 3 -46: [16:02:36] Can't kekulize mol. Unkekulized atoms: 0 1 2 -46: [16:02:36] Can't kekulize mol. Unkekulized atoms: 0 1 2 -46: [16:02:36] Explicit valence for atom # 1 O, 3, is greater than permitted -46: [16:02:36] Explicit valence for atom # 4 F, 2, is greater than permitted -46: [16:02:36] Can't kekulize mol. Unkekulized atoms: 6 7 8 -46: [16:02:36] Explicit valence for atom # 1 C, 5, is greater than permitted -35: [16:02:36] Can't kekulize mol. Unkekulized atoms: 0 1 2 3 4 -35: [16:02:36] Can't kekulize mol. Unkekulized atoms: 6 7 8 9 10 -46: [16:02:36] WARNING: not removing hydrogen atom with dummy atom neighbors -46: [16:02:36] WARNING: not removing hydrogen atom with dummy atom neighbors -46: [16:02:36] WARNING: not removing hydrogen atom with wedged bond -46: [16:02:36] WARNING: not removing hydrogen atom without neighbors -46: [16:02:36] WARNING: not removing hydrogen atom without neighbors -35: [16:02:36] Can't kekulize mol. Unkekulized atoms: 0 1 2 3 4 -35: [16:02:36] WARNING: merging explicit H queries involved in ORs is not supported. This query will not be merged -35: [16:02:36] WARNING: merging explicit H queries involved in ORs is not supported. This query will not be merged -35: [16:02:36] WARNING: merging explicit H queries involved in ORs is not supported. This query will not be merged -35: [16:02:36] WARNING: merging explicit H queries involved in ORs is not supported. This query will not be merged -35: [16:02:36] WARNING: merging explicit H queries involved in ORs is not supported. This query will not be merged -35: -46: [16:02:36] WARNING: not removing hydrogen atom without neighbors -46: [16:02:36] WARNING: not removing hydrogen atom without neighbors -46: [16:02:36] Unreasonable formal charge on atom # 0. -48: Randomness seeded to: 1159814206 -48: =============================================================================== -48: All tests passed (136 assertions in 8 test cases) -48: - 40/236 Test #48: graphmolSGroupCatch .................... Passed 0.55 sec +46: [12:23:54] Explicit valence for atom # 1 N, 6, is greater than permitted +46: [12:23:54] Explicit valence for atom # 1 N, 5, is greater than permitted +46: [12:23:54] Explicit valence for atom # 1 N, 5, is greater than permitted +46: [12:23:54] Explicit valence for atom # 2 O, 3, is greater than permitted +46: [12:23:54] Explicit valence for atom # 2 O, 3, is greater than permitted +46: [12:23:54] non-ring atom 2 marked aromatic +46: [12:23:54] non-ring atom 2 marked aromatic +46: [12:23:54] Can't kekulize mol. Unkekulized atoms: 0 1 2 3 4 +46: [12:23:54] Can't kekulize mol. Unkekulized atoms: 0 1 2 3 4 +46: [12:23:54] Can't kekulize mol. Unkekulized atoms: 1 2 3 +46: [12:23:54] Can't kekulize mol. Unkekulized atoms: 1 2 3 +46: [12:23:54] Can't kekulize mol. Unkekulized atoms: 0 1 2 +46: [12:23:54] Can't kekulize mol. Unkekulized atoms: 0 1 2 +46: [12:23:54] Explicit valence for atom # 1 O, 3, is greater than permitted +46: [12:23:54] Explicit valence for atom # 4 F, 2, is greater than permitted +46: [12:23:54] Can't kekulize mol. Unkekulized atoms: 6 7 8 +46: [12:23:54] Explicit valence for atom # 1 C, 5, is greater than permitted +46: [12:23:54] WARNING: not removing hydrogen atom with dummy atom neighbors +46: [12:23:54] WARNING: not removing hydrogen atom with dummy atom neighbors +46: [12:23:54] WARNING: not removing hydrogen atom with wedged bond +46: [12:23:54] WARNING: not removing hydrogen atom without neighbors +46: [12:23:54] WARNING: not removing hydrogen atom without neighbors +46: [12:23:54] WARNING: not removing hydrogen atom without neighbors +46: [12:23:54] WARNING: not removing hydrogen atom without neighbors +46: [12:23:54] Unreasonable formal charge on atom # 0. +49: Randomness seeded to: 1632398051 +49: =============================================================================== +49: All tests passed (292 assertions in 12 test cases) +49: + 40/236 Test #2: pyCoordGen ............................. Passed 3.96 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 -35: [16:02:36] WARNING: not removing hydrogen atom with dummy atom neighbors -49: Randomness seeded to: 1043707378 -49: =============================================================================== -49: All tests passed (292 assertions in 12 test cases) -49: -46: [16:02:36] -46: -46: **** - 41/236 Test #49: graphmolAdjustQueryCatch ............... Passed 0.61 sec + 41/236 Test #49: graphmolAdjustQueryCatch ............... Passed 0.77 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 +46: [12:23:54] +46: +46: **** 46: Pre-condition Violation 46: no atom 46: Violation occurred on line 181 in file ./Code/GraphMol/ROMol.cpp @@ -17310,20 +17341,20 @@ 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# 0x0000AAAABEB7C1A4 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch -46: 4# 0x0000AAAABEBC83CC in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch -46: 5# 0x0000AAAABEBC8D80 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch -46: 6# 0x0000AAAABEBC91B4 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch -46: 7# 0x0000AAAABEB9C598 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch -46: 8# 0x0000AAAABEB9CAE4 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch -46: 9# 0x0000AAAABEB1E090 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch -46: 10# 0x0000FFFF8BB0229C in /lib/aarch64-linux-gnu/libc.so.6 +46: 3# 0x0000AAAAEAB2C1A4 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch +46: 4# 0x0000AAAAEAB783CC in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch +46: 5# 0x0000AAAAEAB78D80 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch +46: 6# 0x0000AAAAEAB791B4 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch +46: 7# 0x0000AAAAEAB4C598 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch +46: 8# 0x0000AAAAEAB4CAE4 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch +46: 9# 0x0000AAAAEAACE090 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch +46: 10# 0x0000FFFF96B0229C in /lib/aarch64-linux-gnu/libc.so.6 46: 11# __libc_start_main in /lib/aarch64-linux-gnu/libc.so.6 -46: 12# 0x0000AAAABEB1E170 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch +46: 12# 0x0000AAAAEAACE170 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch 46: ---------- 46: **** 46: -46: [16:02:36] +46: [12:23:54] 46: 46: **** 46: Pre-condition Violation @@ -17335,20 +17366,20 @@ 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# 0x0000AAAABEB7C218 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch -46: 4# 0x0000AAAABEBC83CC in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch -46: 5# 0x0000AAAABEBC8D80 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch -46: 6# 0x0000AAAABEBC91B4 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch -46: 7# 0x0000AAAABEB9C598 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch -46: 8# 0x0000AAAABEB9CAE4 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch -46: 9# 0x0000AAAABEB1E090 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch -46: 10# 0x0000FFFF8BB0229C in /lib/aarch64-linux-gnu/libc.so.6 +46: 3# 0x0000AAAAEAB2C218 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch +46: 4# 0x0000AAAAEAB783CC in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch +46: 5# 0x0000AAAAEAB78D80 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch +46: 6# 0x0000AAAAEAB791B4 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch +46: 7# 0x0000AAAAEAB4C598 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch +46: 8# 0x0000AAAAEAB4CAE4 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch +46: 9# 0x0000AAAAEAACE090 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch +46: 10# 0x0000FFFF96B0229C in /lib/aarch64-linux-gnu/libc.so.6 46: 11# __libc_start_main in /lib/aarch64-linux-gnu/libc.so.6 -46: 12# 0x0000AAAABEB1E170 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch +46: 12# 0x0000AAAAEAACE170 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch 46: ---------- 46: **** 46: -46: [16:02:36] +46: [12:23:54] 46: 46: **** 46: Pre-condition Violation @@ -17360,20 +17391,20 @@ 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# 0x0000AAAABEB7C298 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch -46: 4# 0x0000AAAABEBC83CC in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch -46: 5# 0x0000AAAABEBC8D80 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch -46: 6# 0x0000AAAABEBC91B4 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch -46: 7# 0x0000AAAABEB9C598 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch -46: 8# 0x0000AAAABEB9CAE4 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch -46: 9# 0x0000AAAABEB1E090 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch -46: 10# 0x0000FFFF8BB0229C in /lib/aarch64-linux-gnu/libc.so.6 +46: 3# 0x0000AAAAEAB2C298 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch +46: 4# 0x0000AAAAEAB783CC in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch +46: 5# 0x0000AAAAEAB78D80 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch +46: 6# 0x0000AAAAEAB791B4 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch +46: 7# 0x0000AAAAEAB4C598 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch +46: 8# 0x0000AAAAEAB4CAE4 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch +46: 9# 0x0000AAAAEAACE090 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch +46: 10# 0x0000FFFF96B0229C in /lib/aarch64-linux-gnu/libc.so.6 46: 11# __libc_start_main in /lib/aarch64-linux-gnu/libc.so.6 -46: 12# 0x0000AAAABEB1E170 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch +46: 12# 0x0000AAAAEAACE170 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch 46: ---------- 46: **** 46: -46: [16:02:36] +46: [12:23:54] 46: 46: **** 46: Pre-condition Violation @@ -17385,20 +17416,20 @@ 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# 0x0000AAAABEB7C360 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch -46: 4# 0x0000AAAABEBC83CC in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch -46: 5# 0x0000AAAABEBC8D80 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch -46: 6# 0x0000AAAABEBC91B4 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch -46: 7# 0x0000AAAABEB9C598 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch -46: 8# 0x0000AAAABEB9CAE4 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch -46: 9# 0x0000AAAABEB1E090 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch -46: 10# 0x0000FFFF8BB0229C in /lib/aarch64-linux-gnu/libc.so.6 +46: 3# 0x0000AAAAEAB2C360 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch +46: 4# 0x0000AAAAEAB783CC in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch +46: 5# 0x0000AAAAEAB78D80 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch +46: 6# 0x0000AAAAEAB791B4 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch +46: 7# 0x0000AAAAEAB4C598 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch +46: 8# 0x0000AAAAEAB4CAE4 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch +46: 9# 0x0000AAAAEAACE090 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch +46: 10# 0x0000FFFF96B0229C in /lib/aarch64-linux-gnu/libc.so.6 46: 11# __libc_start_main in /lib/aarch64-linux-gnu/libc.so.6 -46: 12# 0x0000AAAABEB1E170 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch +46: 12# 0x0000AAAAEAACE170 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch 46: ---------- 46: **** 46: -46: [16:02:36] +46: [12:23:54] 46: 46: **** 46: Pre-condition Violation @@ -17410,20 +17441,20 @@ 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# 0x0000AAAABEB7C3D8 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch -46: 4# 0x0000AAAABEBC83CC in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch -46: 5# 0x0000AAAABEBC8D80 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch -46: 6# 0x0000AAAABEBC91B4 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch -46: 7# 0x0000AAAABEB9C598 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch -46: 8# 0x0000AAAABEB9CAE4 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch -46: 9# 0x0000AAAABEB1E090 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch -46: 10# 0x0000FFFF8BB0229C in /lib/aarch64-linux-gnu/libc.so.6 +46: 3# 0x0000AAAAEAB2C3D8 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch +46: 4# 0x0000AAAAEAB783CC in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch +46: 5# 0x0000AAAAEAB78D80 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch +46: 6# 0x0000AAAAEAB791B4 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch +46: 7# 0x0000AAAAEAB4C598 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch +46: 8# 0x0000AAAAEAB4CAE4 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch +46: 9# 0x0000AAAAEAACE090 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch +46: 10# 0x0000FFFF96B0229C in /lib/aarch64-linux-gnu/libc.so.6 46: 11# __libc_start_main in /lib/aarch64-linux-gnu/libc.so.6 -46: 12# 0x0000AAAABEB1E170 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch +46: 12# 0x0000AAAAEAACE170 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch 46: ---------- 46: **** 46: -46: [16:02:36] +46: [12:23:54] 46: 46: **** 46: Pre-condition Violation @@ -17435,20 +17466,20 @@ 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# 0x0000AAAABEB7C45C in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch -46: 4# 0x0000AAAABEBC83CC in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch -46: 5# 0x0000AAAABEBC8D80 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch -46: 6# 0x0000AAAABEBC91B4 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch -46: 7# 0x0000AAAABEB9C598 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch -46: 8# 0x0000AAAABEB9CAE4 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch -46: 9# 0x0000AAAABEB1E090 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch -46: 10# 0x0000FFFF8BB0229C in /lib/aarch64-linux-gnu/libc.so.6 +46: 3# 0x0000AAAAEAB2C45C in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch +46: 4# 0x0000AAAAEAB783CC in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch +46: 5# 0x0000AAAAEAB78D80 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch +46: 6# 0x0000AAAAEAB791B4 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch +46: 7# 0x0000AAAAEAB4C598 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch +46: 8# 0x0000AAAAEAB4CAE4 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch +46: 9# 0x0000AAAAEAACE090 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch +46: 10# 0x0000FFFF96B0229C in /lib/aarch64-linux-gnu/libc.so.6 46: 11# __libc_start_main in /lib/aarch64-linux-gnu/libc.so.6 -46: 12# 0x0000AAAABEB1E170 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch +46: 12# 0x0000AAAAEAACE170 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch 46: ---------- 46: **** 46: -46: [16:02:36] +46: [12:23:54] 46: 46: **** 46: Pre-condition Violation @@ -17460,20 +17491,20 @@ 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# 0x0000AAAABEB7CB70 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch -46: 4# 0x0000AAAABEBC83CC in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch -46: 5# 0x0000AAAABEBC8D80 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch -46: 6# 0x0000AAAABEBC91B4 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch -46: 7# 0x0000AAAABEB9C598 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch -46: 8# 0x0000AAAABEB9CAE4 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch -46: 9# 0x0000AAAABEB1E090 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch -46: 10# 0x0000FFFF8BB0229C in /lib/aarch64-linux-gnu/libc.so.6 +46: 3# 0x0000AAAAEAB2CB70 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch +46: 4# 0x0000AAAAEAB783CC in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch +46: 5# 0x0000AAAAEAB78D80 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch +46: 6# 0x0000AAAAEAB791B4 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch +46: 7# 0x0000AAAAEAB4C598 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch +46: 8# 0x0000AAAAEAB4CAE4 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch +46: 9# 0x0000AAAAEAACE090 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch +46: 10# 0x0000FFFF96B0229C in /lib/aarch64-linux-gnu/libc.so.6 46: 11# __libc_start_main in /lib/aarch64-linux-gnu/libc.so.6 -46: 12# 0x0000AAAABEB1E170 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch +46: 12# 0x0000AAAAEAACE170 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch 46: ---------- 46: **** 46: -46: [16:02:36] +46: [12:23:54] 46: 46: **** 46: Pre-condition Violation @@ -17485,20 +17516,20 @@ 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# 0x0000AAAABEB7C58C in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch -46: 4# 0x0000AAAABEBC83CC in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch -46: 5# 0x0000AAAABEBC8D80 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch -46: 6# 0x0000AAAABEBC91B4 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch -46: 7# 0x0000AAAABEB9C598 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch -46: 8# 0x0000AAAABEB9CAE4 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch -46: 9# 0x0000AAAABEB1E090 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch -46: 10# 0x0000FFFF8BB0229C in /lib/aarch64-linux-gnu/libc.so.6 +46: 3# 0x0000AAAAEAB2C58C in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch +46: 4# 0x0000AAAAEAB783CC in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch +46: 5# 0x0000AAAAEAB78D80 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch +46: 6# 0x0000AAAAEAB791B4 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch +46: 7# 0x0000AAAAEAB4C598 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch +46: 8# 0x0000AAAAEAB4CAE4 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch +46: 9# 0x0000AAAAEAACE090 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch +46: 10# 0x0000FFFF96B0229C in /lib/aarch64-linux-gnu/libc.so.6 46: 11# __libc_start_main in /lib/aarch64-linux-gnu/libc.so.6 -46: 12# 0x0000AAAABEB1E170 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch +46: 12# 0x0000AAAAEAACE170 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch 46: ---------- 46: **** 46: -46: [16:02:36] +46: [12:23:54] 46: 46: **** 46: Pre-condition Violation @@ -17510,20 +17541,20 @@ 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# 0x0000AAAABEB7C610 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch -46: 4# 0x0000AAAABEBC83CC in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch -46: 5# 0x0000AAAABEBC8D80 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch -46: 6# 0x0000AAAABEBC91B4 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch -46: 7# 0x0000AAAABEB9C598 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch -46: 8# 0x0000AAAABEB9CAE4 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch -46: 9# 0x0000AAAABEB1E090 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch -46: 10# 0x0000FFFF8BB0229C in /lib/aarch64-linux-gnu/libc.so.6 +46: 3# 0x0000AAAAEAB2C610 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch +46: 4# 0x0000AAAAEAB783CC in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch +46: 5# 0x0000AAAAEAB78D80 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch +46: 6# 0x0000AAAAEAB791B4 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch +46: 7# 0x0000AAAAEAB4C598 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch +46: 8# 0x0000AAAAEAB4CAE4 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch +46: 9# 0x0000AAAAEAACE090 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch +46: 10# 0x0000FFFF96B0229C in /lib/aarch64-linux-gnu/libc.so.6 46: 11# __libc_start_main in /lib/aarch64-linux-gnu/libc.so.6 -46: 12# 0x0000AAAABEB1E170 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch +46: 12# 0x0000AAAAEAACE170 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch 46: ---------- 46: **** 46: -46: [16:02:36] +46: [12:23:54] 46: 46: **** 46: Pre-condition Violation @@ -17535,20 +17566,20 @@ 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# 0x0000AAAABEB7CB54 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch -46: 4# 0x0000AAAABEBC83CC in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch -46: 5# 0x0000AAAABEBC8D80 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch -46: 6# 0x0000AAAABEBC91B4 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch -46: 7# 0x0000AAAABEB9C598 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch -46: 8# 0x0000AAAABEB9CAE4 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch -46: 9# 0x0000AAAABEB1E090 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch -46: 10# 0x0000FFFF8BB0229C in /lib/aarch64-linux-gnu/libc.so.6 +46: 3# 0x0000AAAAEAB2CB54 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch +46: 4# 0x0000AAAAEAB783CC in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch +46: 5# 0x0000AAAAEAB78D80 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch +46: 6# 0x0000AAAAEAB791B4 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch +46: 7# 0x0000AAAAEAB4C598 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch +46: 8# 0x0000AAAAEAB4CAE4 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch +46: 9# 0x0000AAAAEAACE090 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch +46: 10# 0x0000FFFF96B0229C in /lib/aarch64-linux-gnu/libc.so.6 46: 11# __libc_start_main in /lib/aarch64-linux-gnu/libc.so.6 -46: 12# 0x0000AAAABEB1E170 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch +46: 12# 0x0000AAAAEAACE170 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch 46: ---------- 46: **** 46: -46: [16:02:36] +46: [12:23:54] 46: 46: **** 46: Pre-condition Violation @@ -17560,20 +17591,20 @@ 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# 0x0000AAAABEB7C800 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch -46: 4# 0x0000AAAABEBC83CC in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch -46: 5# 0x0000AAAABEBC8D80 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch -46: 6# 0x0000AAAABEBC91B4 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch -46: 7# 0x0000AAAABEB9C598 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch -46: 8# 0x0000AAAABEB9CAE4 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch -46: 9# 0x0000AAAABEB1E090 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch -46: 10# 0x0000FFFF8BB0229C in /lib/aarch64-linux-gnu/libc.so.6 +46: 3# 0x0000AAAAEAB2C800 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch +46: 4# 0x0000AAAAEAB783CC in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch +46: 5# 0x0000AAAAEAB78D80 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch +46: 6# 0x0000AAAAEAB791B4 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch +46: 7# 0x0000AAAAEAB4C598 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch +46: 8# 0x0000AAAAEAB4CAE4 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch +46: 9# 0x0000AAAAEAACE090 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch +46: 10# 0x0000FFFF96B0229C in /lib/aarch64-linux-gnu/libc.so.6 46: 11# __libc_start_main in /lib/aarch64-linux-gnu/libc.so.6 -46: 12# 0x0000AAAABEB1E170 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch +46: 12# 0x0000AAAAEAACE170 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch 46: ---------- 46: **** 46: -46: [16:02:36] +46: [12:23:54] 46: 46: **** 46: Pre-condition Violation @@ -17585,24 +17616,24 @@ 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# 0x0000AAAABEB7CB34 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch -46: 4# 0x0000AAAABEBC83CC in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch -46: 5# 0x0000AAAABEBC8D80 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch -46: 6# 0x0000AAAABEBC91B4 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch -46: 7# 0x0000AAAABEB9C598 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch -46: 8# 0x0000AAAABEB9CAE4 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch -46: 9# 0x0000AAAABEB1E090 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch -46: 10# 0x0000FFFF8BB0229C in /lib/aarch64-linux-gnu/libc.so.6 +46: 3# 0x0000AAAAEAB2CB34 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch +46: 4# 0x0000AAAAEAB783CC in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch +46: 5# 0x0000AAAAEAB78D80 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch +46: 6# 0x0000AAAAEAB791B4 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch +46: 7# 0x0000AAAAEAB4C598 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch +46: 8# 0x0000AAAAEAB4CAE4 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch +46: 9# 0x0000AAAAEAACE090 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch +46: 10# 0x0000FFFF96B0229C in /lib/aarch64-linux-gnu/libc.so.6 46: 11# __libc_start_main in /lib/aarch64-linux-gnu/libc.so.6 -46: 12# 0x0000AAAABEB1E170 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch +46: 12# 0x0000AAAAEAACE170 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch 46: ---------- 46: **** 46: -46: [16:02:36] WARNING: could not find number of expected rings. Switching to an approximate ring finding algorithm. -46: [16:02:36] WARNING: could not find number of expected rings. Switching to an approximate ring finding algorithm. -46: [16:02:36] WARNING: not removing hydrogen atom without neighbors -46: [16:02:36] Explicit valence for atom # 1 F greater than permitted -46: [16:02:36] +46: [12:23:54] WARNING: could not find number of expected rings. Switching to an approximate ring finding algorithm. +46: [12:23:54] WARNING: could not find number of expected rings. Switching to an approximate ring finding algorithm. +46: [12:23:54] WARNING: not removing hydrogen atom without neighbors +46: [12:23:54] Explicit valence for atom # 1 F greater than permitted +46: [12:23:54] 46: 46: **** 46: Pre-condition Violation @@ -17614,20 +17645,20 @@ 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# 0x0000AAAABEB2AB6C in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch -46: 4# 0x0000AAAABEBC83CC in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch -46: 5# 0x0000AAAABEBC8D80 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch -46: 6# 0x0000AAAABEBC91B4 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch -46: 7# 0x0000AAAABEB9C598 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch -46: 8# 0x0000AAAABEB9CAE4 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch -46: 9# 0x0000AAAABEB1E090 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch -46: 10# 0x0000FFFF8BB0229C in /lib/aarch64-linux-gnu/libc.so.6 +46: 3# 0x0000AAAAEAADAB6C in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch +46: 4# 0x0000AAAAEAB783CC in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch +46: 5# 0x0000AAAAEAB78D80 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch +46: 6# 0x0000AAAAEAB791B4 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch +46: 7# 0x0000AAAAEAB4C598 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch +46: 8# 0x0000AAAAEAB4CAE4 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch +46: 9# 0x0000AAAAEAACE090 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch +46: 10# 0x0000FFFF96B0229C in /lib/aarch64-linux-gnu/libc.so.6 46: 11# __libc_start_main in /lib/aarch64-linux-gnu/libc.so.6 -46: 12# 0x0000AAAABEB1E170 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch +46: 12# 0x0000AAAAEAACE170 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch 46: ---------- 46: **** 46: -46: [16:02:36] +46: [12:23:54] 46: 46: **** 46: Pre-condition Violation @@ -17639,20 +17670,20 @@ 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# 0x0000AAAABEB2ABF8 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch -46: 4# 0x0000AAAABEBC83CC in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch -46: 5# 0x0000AAAABEBC8D80 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch -46: 6# 0x0000AAAABEBC91B4 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch -46: 7# 0x0000AAAABEB9C598 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch -46: 8# 0x0000AAAABEB9CAE4 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch -46: 9# 0x0000AAAABEB1E090 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch -46: 10# 0x0000FFFF8BB0229C in /lib/aarch64-linux-gnu/libc.so.6 +46: 3# 0x0000AAAAEAADABF8 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch +46: 4# 0x0000AAAAEAB783CC in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch +46: 5# 0x0000AAAAEAB78D80 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch +46: 6# 0x0000AAAAEAB791B4 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch +46: 7# 0x0000AAAAEAB4C598 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch +46: 8# 0x0000AAAAEAB4CAE4 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch +46: 9# 0x0000AAAAEAACE090 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch +46: 10# 0x0000FFFF96B0229C in /lib/aarch64-linux-gnu/libc.so.6 46: 11# __libc_start_main in /lib/aarch64-linux-gnu/libc.so.6 -46: 12# 0x0000AAAABEB1E170 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch +46: 12# 0x0000AAAAEAACE170 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch 46: ---------- 46: **** 46: -46: [16:02:36] +46: [12:23:54] 46: 46: **** 46: Pre-condition Violation @@ -17664,20 +17695,20 @@ 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# 0x0000AAAABEB2A7BC in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch -46: 4# 0x0000AAAABEBC83CC in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch -46: 5# 0x0000AAAABEBC8D80 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch -46: 6# 0x0000AAAABEBC91B4 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch -46: 7# 0x0000AAAABEB9C598 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch -46: 8# 0x0000AAAABEB9CAE4 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch -46: 9# 0x0000AAAABEB1E090 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch -46: 10# 0x0000FFFF8BB0229C in /lib/aarch64-linux-gnu/libc.so.6 +46: 3# 0x0000AAAAEAADA7BC in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch +46: 4# 0x0000AAAAEAB783CC in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch +46: 5# 0x0000AAAAEAB78D80 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch +46: 6# 0x0000AAAAEAB791B4 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch +46: 7# 0x0000AAAAEAB4C598 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch +46: 8# 0x0000AAAAEAB4CAE4 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch +46: 9# 0x0000AAAAEAACE090 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch +46: 10# 0x0000FFFF96B0229C in /lib/aarch64-linux-gnu/libc.so.6 46: 11# __libc_start_main in /lib/aarch64-linux-gnu/libc.so.6 -46: 12# 0x0000AAAABEB1E170 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch +46: 12# 0x0000AAAAEAACE170 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch 46: ---------- 46: **** 46: -46: [16:02:36] +46: [12:23:54] 46: 46: **** 46: Pre-condition Violation @@ -17689,190 +17720,185 @@ 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# 0x0000AAAABEB2A848 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch -46: 4# 0x0000AAAABEBC83CC in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch -46: 5# 0x0000AAAABEBC8D80 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch -46: 6# 0x0000AAAABEBC91B4 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch -46: 7# 0x0000AAAABEB9C598 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch -46: 8# 0x0000AAAABEB9CAE4 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch -46: 9# 0x0000AAAABEB1E090 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch -46: 10# 0x0000FFFF8BB0229C in /lib/aarch64-linux-gnu/libc.so.6 +46: 3# 0x0000AAAAEAADA848 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch +46: 4# 0x0000AAAAEAB783CC in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch +46: 5# 0x0000AAAAEAB78D80 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch +46: 6# 0x0000AAAAEAB791B4 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch +46: 7# 0x0000AAAAEAB4C598 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch +46: 8# 0x0000AAAAEAB4CAE4 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch +46: 9# 0x0000AAAAEAACE090 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch +46: 10# 0x0000FFFF96B0229C in /lib/aarch64-linux-gnu/libc.so.6 46: 11# __libc_start_main in /lib/aarch64-linux-gnu/libc.so.6 -46: 12# 0x0000AAAABEB1E170 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch +46: 12# 0x0000AAAAEAACE170 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch 46: ---------- 46: **** 46: -46: [16:02:36] Can't kekulize mol. Unkekulized atoms: 0 1 2 3 4 -46: [16:02:36] Can't kekulize mol. Unkekulized atoms: 0 1 2 3 4 -46: [16:02:36] Can't kekulize mol. Unkekulized atoms: 6 7 8 9 10 -46: [16:02:36] Can't kekulize mol. Unkekulized atoms: 6 7 8 9 10 -46: [16:02:36] Can't kekulize mol. Unkekulized atoms: 0 1 2 3 4 -46: [16:02:36] Unusual charge on atom 0 number of radical electrons set to zero -46: [16:02:36] Unusual charge on atom 0 number of radical electrons set to zero -46: [16:02:36] Unusual charge on atom 0 number of radical electrons set to zero -46: [16:02:36] non-ring atom 0 marked aromatic -46: [16:02:36] non-ring atom 0 marked aromatic -46: [16:02:36] Explicit valence for atom # 1 C, 5, is greater than permitted -46: [16:02:36] Explicit valence for atom # 9 C, 5, is greater than permitted -46: [16:02:36] Explicit valence for atom # 3 N, 4, is greater than permitted -46: [16:02:36] Explicit valence for atom # 15 C, 5, is greater than permitted -46: [16:02:36] Explicit valence for atom # 11 C, 5, is greater than permitted -46: [16:02:36] Explicit valence for atom # 9 C, 5, is greater than permitted -46: [16:02:36] Explicit valence for atom # 9 C, 5, is greater than permitted -46: [16:02:36] Explicit valence for atom # 9 C, 6, is greater than permitted -46: [16:02:36] Can't kekulize mol. Unkekulized atoms: 0 1 2 3 4 -46: [16:02:36] Can't kekulize mol. Unkekulized atoms: 7 -46: [16:02:36] Can't kekulize mol. Unkekulized atoms: 3 -46: [16:02:36] Can't kekulize mol. Unkekulized atoms: 3 7 -46: [16:02:36] Can't kekulize mol. Unkekulized atoms: 3 7 -46: [16:02:36] WARNING: could not find number of expected rings. Switching to an approximate ring finding algorithm. -46: [16:02:36] WARNING: could not find number of expected rings. Switching to an approximate ring finding algorithm. -50: Randomness seeded to: 3889561830 -50: [16:02:36] unable to set wavy bonds for double bonds: 3 -46: [16:02:36] Explicit valence for atom # 1 O, 3, is greater than permitted -46: [16:02:36] WARNING: merging explicit H queries involved in ORs is not supported. This query will not be merged -46: [16:02:36] WARNING: merging explicit H queries involved in ORs is not supported. This query will not be merged -46: [16:02:36] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -46: [16:02:36] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -46: [16:02:36] Invalid value for molAttachPoint: 4 on atom 1. Not expanding this atttachment point. -46: [16:02:36] Invalid value for _fromAttachPoint: -1 on atom 0. Not collapsing this atom -46: [16:02:36] Invalid value for _fromAttachPoint: 4 on atom 0. Not collapsing this atom -52: Randomness seeded to: 1047469692 -52: =============================================================================== -52: All tests passed (14 assertions in 4 test cases) -52: -46: [16:02:36] non-ring atom 0 marked aromatic - 42/236 Test #52: moliteratorTestsCatch .................. Passed 0.34 sec +46: [12:23:54] Can't kekulize mol. Unkekulized atoms: 0 1 2 3 4 +46: [12:23:54] Can't kekulize mol. Unkekulized atoms: 0 1 2 3 4 +46: [12:23:54] Can't kekulize mol. Unkekulized atoms: 6 7 8 9 10 +46: [12:23:54] Can't kekulize mol. Unkekulized atoms: 6 7 8 9 10 +46: [12:23:55] Can't kekulize mol. Unkekulized atoms: 0 1 2 3 4 +46: [12:23:55] Unusual charge on atom 0 number of radical electrons set to zero +46: [12:23:55] Unusual charge on atom 0 number of radical electrons set to zero +46: [12:23:55] Unusual charge on atom 0 number of radical electrons set to zero +46: [12:23:55] non-ring atom 0 marked aromatic +46: [12:23:55] non-ring atom 0 marked aromatic +46: [12:23:55] Explicit valence for atom # 1 C, 5, is greater than permitted +46: [12:23:55] Explicit valence for atom # 9 C, 5, is greater than permitted +46: [12:23:55] Explicit valence for atom # 3 N, 4, is greater than permitted +46: [12:23:55] Explicit valence for atom # 15 C, 5, is greater than permitted +46: [12:23:55] Explicit valence for atom # 11 C, 5, is greater than permitted +46: [12:23:55] Explicit valence for atom # 9 C, 5, is greater than permitted +46: [12:23:55] Explicit valence for atom # 9 C, 5, is greater than permitted +46: [12:23:55] Explicit valence for atom # 9 C, 6, is greater than permitted +46: [12:23:55] Can't kekulize mol. Unkekulized atoms: 0 1 2 3 4 +46: [12:23:55] Can't kekulize mol. Unkekulized atoms: 7 +46: [12:23:55] Can't kekulize mol. Unkekulized atoms: 3 +46: [12:23:55] Can't kekulize mol. Unkekulized atoms: 3 7 +46: [12:23:55] Can't kekulize mol. Unkekulized atoms: 3 7 +46: [12:23:55] WARNING: could not find number of expected rings. Switching to an approximate ring finding algorithm. +30: ...[12:23:55] Molecule does not have explicit Hs. Consider calling AddHs() +46: [12:23:55] WARNING: could not find number of expected rings. Switching to an approximate ring finding algorithm. +53: Randomness seeded to: 1674683312 +53: =============================================================================== +53: All tests passed (10 assertions in 1 test case) +53: +46: [12:23:55] Explicit valence for atom # 1 O, 3, is greater than permitted + 42/236 Test #53: queryTestsCatch ........................ Passed 0.28 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 -46: [16:02:36] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored -46: [16:02:36] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored -35: [16:02:36] Maximum BFS search size exceeded. -35: This is likely due to a highly symmetric fused ring system. -30: ...[16:02:36] Molecule does not have explicit Hs. Consider calling AddHs() -46: [16:02:36] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -50: [16:02:36] WARNING: not removing hydrogen atom with neighbor that has non-tetrahedral stereochemistry -50: [16:02:36] WARNING: not removing hydrogen atom with neighbor that has non-tetrahedral stereochemistry -46: [16:02:36] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -46: [16:02:36] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -46: [16:02:36] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 2 ignored -46: [16:02:36] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 2 ignored -46: [16:02:37] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -46: [16:02:37] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored -46: [16:02:37] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored -46: [16:02:37] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored -46: [16:02:37] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored -46: [16:02:37] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -50: [16:02:37] Warning: ambiguous stereochemistry - zero-length (or near zero-length) bond - at atom 1 ignored. -50: [16:02:37] Warning: ambiguous stereochemistry - zero-length (or near zero-length) bond - at atom 1 ignored. -50: [16:02:37] Warning: ambiguous stereochemistry - overlapping neighbors - at atom 2 ignored -46: [16:02:37] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -46: [16:02:37] Explicit valence for atom # 0 Al, 6, is greater than permitted -46: [16:02:37] Explicit valence for atom # 0 Al, 6, is greater than permitted -46: [16:02:37] Explicit valence for atom # 1 Si, 6, is greater than permitted -46: [16:02:37] Explicit valence for atom # 1 Si, 6, is greater than permitted -46: [16:02:37] Explicit valence for atom # 0 P, 6, is greater than permitted -46: [16:02:37] Explicit valence for atom # 0 P, 6, is greater than permitted -46: [16:02:37] Explicit valence for atom # 0 P, 7, is greater than permitted -46: [16:02:37] Explicit valence for atom # 0 P, 7, is greater than permitted -46: [16:02:37] Explicit valence for atom # 1 As, 6, is greater than permitted -46: [16:02:37] Explicit valence for atom # 1 As, 6, is greater than permitted -46: [16:02:37] Explicit valence for atom # 1 As, 7, is greater than permitted -46: [16:02:37] Explicit valence for atom # 1 As, 7, is greater than permitted -46: [16:02:37] Explicit valence for atom # 0 Sb, 6, is greater than permitted -46: [16:02:37] Explicit valence for atom # 0 Sb, 6, is greater than permitted -46: [16:02:37] Explicit valence for atom # 0 Sb, 7, is greater than permitted -46: [16:02:37] Explicit valence for atom # 0 Sb, 7, is greater than permitted -46: [16:02:37] Explicit valence for atom # 1 Bi, 6, is greater than permitted -46: [16:02:37] Explicit valence for atom # 1 Bi, 6, is greater than permitted -46: [16:02:37] Explicit valence for atom # 1 Bi, 8, is greater than permitted -46: [16:02:37] Explicit valence for atom # 1 Bi, 8, is greater than permitted -46: =============================================================================== -46: All tests passed (4479 assertions in 107 test cases) -46: - 43/236 Test #46: graphmolTestsCatch ..................... Passed 1.38 sec +46: [12:23:55] WARNING: merging explicit H queries involved in ORs is not supported. This query will not be merged +46: [12:23:55] WARNING: merging explicit H queries involved in ORs is not supported. This query will not be merged +46: [12:23:55] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +46: [12:23:55] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +46: [12:23:55] Invalid value for molAttachPoint: 4 on atom 1. Not expanding this atttachment point. +52: Randomness seeded to: 1405391651 +52: =============================================================================== +52: All tests passed (14 assertions in 4 test cases) +52: +46: [12:23:55] Invalid value for _fromAttachPoint: -1 on atom 0. Not collapsing this atom +46: [12:23:55] Invalid value for _fromAttachPoint: 4 on atom 0. Not collapsing this atom + 43/236 Test #52: moliteratorTestsCatch .................. Passed 0.34 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 -50: =============================================================================== -50: All tests passed (2295 assertions in 80 test cases) -50: - 44/236 Test #50: chiralityTestsCatch .................... Passed 1.03 sec +35: [12:23:55] Maximum BFS search size exceeded. +35: This is likely due to a highly symmetric fused ring system. +50: Randomness seeded to: 3574738332 +50: [12:23:55] unable to set wavy bonds for double bonds: 3 +46: [12:23:55] non-ring atom 0 marked aromatic +46: [12:23:55] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored +46: [12:23:55] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored +46: [12:23:55] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +46: [12:23:55] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +50: [12:23:55] WARNING: not removing hydrogen atom with neighbor that has non-tetrahedral stereochemistry +50: [12:23:55] WARNING: not removing hydrogen atom with neighbor that has non-tetrahedral stereochemistry +46: [12:23:55] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +46: [12:23:55] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 2 ignored +46: [12:23:55] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 2 ignored +30: ......[12:23:55] Molecule does not have explicit Hs. Consider calling AddHs() +46: [12:23:55] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +46: [12:23:55] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored +46: [12:23:55] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored +46: [12:23:55] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored +46: [12:23:55] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored +46: [12:23:55] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +50: [12:23:55] Warning: ambiguous stereochemistry - zero-length (or near zero-length) bond - at atom 1 ignored. +50: [12:23:55] Warning: ambiguous stereochemistry - zero-length (or near zero-length) bond - at atom 1 ignored. +50: [12:23:55] Warning: ambiguous stereochemistry - overlapping neighbors - at atom 2 ignored +46: [12:23:55] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +30: ... +30: ---------------------------------------------------------------------- +30: Ran 12 tests in 0.872s +30: +30: OK +54: Randomness seeded to: 1534442013 +54: =============================================================================== +54: All tests passed (6 assertions in 1 test case) +54: +46: [12:23:55] Explicit valence for atom # 0 Al, 6, is greater than permitted +46: [12:23:55] Explicit valence for atom # 0 Al, 6, is greater than permitted +46: [12:23:55] Explicit valence for atom # 1 Si, 6, is greater than permitted +46: [12:23:55] Explicit valence for atom # 1 Si, 6, is greater than permitted +46: [12:23:55] Explicit valence for atom # 0 P, 6, is greater than permitted +46: [12:23:55] Explicit valence for atom # 0 P, 6, is greater than permitted +46: [12:23:55] Explicit valence for atom # 0 P, 7, is greater than permitted +46: [12:23:55] Explicit valence for atom # 0 P, 7, is greater than permitted +46: [12:23:55] Explicit valence for atom # 1 As, 6, is greater than permitted +46: [12:23:55] Explicit valence for atom # 1 As, 6, is greater than permitted +46: [12:23:55] Explicit valence for atom # 1 As, 7, is greater than permitted +46: [12:23:55] Explicit valence for atom # 1 As, 7, is greater than permitted +46: [12:23:55] Explicit valence for atom # 0 Sb, 6, is greater than permitted +46: [12:23:55] Explicit valence for atom # 0 Sb, 6, is greater than permitted +46: [12:23:55] Explicit valence for atom # 0 Sb, 7, is greater than permitted +46: [12:23:55] Explicit valence for atom # 0 Sb, 7, is greater than permitted +46: [12:23:55] Explicit valence for atom # 1 Bi, 6, is greater than permitted +46: [12:23:55] Explicit valence for atom # 1 Bi, 6, is greater than permitted +46: [12:23:55] Explicit valence for atom # 1 Bi, 8, is greater than permitted +46: [12:23:55] Explicit valence for atom # 1 Bi, 8, is greater than permitted + 44/236 Test #54: molbundleTestsCatch .................... Passed 0.42 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 -30: ......[16:02:37] Molecule does not have explicit Hs. Consider calling AddHs() -53: Randomness seeded to: 769761076 -53: =============================================================================== -53: All tests passed (10 assertions in 1 test case) -53: - 45/236 Test #53: queryTestsCatch ........................ Passed 0.50 sec +46: =============================================================================== +46: All tests passed (4479 assertions in 107 test cases) +46: +50: =============================================================================== +50: All tests passed (2295 assertions in 80 test cases) +50: + 45/236 Test #46: graphmolTestsCatch ..................... Passed 1.68 sec + 46/236 Test #50: chiralityTestsCatch .................... Passed 1.03 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 -35: [16:02:37] Maximum BFS search size exceeded. -35: This is likely due to a highly symmetric fused ring system. -35: F/C=C/Cl -35: [H]/C(F)=C(/[H])Cl -35: F/C=C/Cl -35: F/C=C/Cl -35: C/C(F)=C(/C)Cl -35: [16:02:37] ----------------------- -35: Testing isRingFused - 46/236 Test #35: graphmolMolOpsTest ..................... Passed 2.08 sec test 58 Start 58: smiTest1 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 -54: Randomness seeded to: 2361517923 -54: =============================================================================== -54: All tests passed (6 assertions in 1 test case) -54: - 47/236 Test #54: molbundleTestsCatch .................... Passed 0.43 sec +55: Randomness seeded to: 439100017 +55: =============================================================================== +55: All tests passed (45 assertions in 4 test cases) +55: + 47/236 Test #55: pickleTestsCatch ....................... Passed 0.49 sec test 59 Start 59: smiTest2 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: [16:02:37] SMILES Parse Error: Failed parsing SMILES 'CO' for input: 'CO' -59: [16:02:37] SMILES Parse Error: Failed parsing SMILES 'C-O' for input: 'C-O' -59: [16:02:37] SMILES Parse Error: syntax error while parsing: - -59: [16:02:37] SMILES Parse Error: check for mistakes around position 1: -59: [16:02:37] - -59: [16:02:37] ^ -59: [16:02:37] SMILES Parse Error: Failed parsing SMILES '-' for input: '-' -59: [16:02:37] SMILES Parse Error: Failed parsing SMILES '[Bg]' for input: '[Bg]' -59: [16:02:37] SMILES Parse Error: Failed parsing SMILES 'C' for input: 'C' -59: [16:02:37] SMILES Parse Error: Failed parsing SMILES 'C-O' for input: 'C-O' -59: [16:02:37] SMILES Parse Error: Failed parsing SMILES '*' for input: '*' -59: [16:02:37] SMARTS Parse Error: Failed parsing SMARTS 'CO' for input: 'CO' -59: [16:02:37] SMARTS Parse Error: Failed parsing SMARTS 'C-O' for input: 'C-O' -59: [16:02:37] SMARTS Parse Error: Failed parsing SMARTS '-' for input: '-' -59: [16:02:37] SMARTS Parse Error: Failed parsing SMARTS '[Bg]' for input: '[Bg]' -30: ... -30: ---------------------------------------------------------------------- -30: Ran 12 tests in 0.715s -30: -30: OK -59: [16:02:37] SMARTS Parse Error: Failed parsing SMARTS 'C' for input: 'C' -59: [16:02:37] SMARTS Parse Error: Failed parsing SMARTS '-O' for input: '-O' -59: [16:02:37] SMARTS Parse Error: Failed parsing SMARTS '*' for input: '*' +59: [12:23:55] SMILES Parse Error: Failed parsing SMILES 'CO' for input: 'CO' +59: [12:23:55] SMILES Parse Error: Failed parsing SMILES 'C-O' for input: 'C-O' +59: [12:23:55] SMILES Parse Error: syntax error while parsing: - +59: [12:23:55] SMILES Parse Error: check for mistakes around position 1: +59: [12:23:55] - +59: [12:23:55] ^ +59: [12:23:55] SMILES Parse Error: Failed parsing SMILES '-' for input: '-' +59: [12:23:55] SMILES Parse Error: Failed parsing SMILES '[Bg]' for input: '[Bg]' +59: [12:23:55] SMILES Parse Error: Failed parsing SMILES 'C' for input: 'C' +59: [12:23:55] SMILES Parse Error: Failed parsing SMILES 'C-O' for input: 'C-O' +59: [12:23:55] SMILES Parse Error: Failed parsing SMILES '*' for input: '*' +59: [12:23:55] SMARTS Parse Error: Failed parsing SMARTS 'CO' for input: 'CO' +59: [12:23:55] SMARTS Parse Error: Failed parsing SMARTS 'C-O' for input: 'C-O' +59: [12:23:55] SMARTS Parse Error: Failed parsing SMARTS '-' for input: '-' +59: [12:23:55] SMARTS Parse Error: Failed parsing SMARTS '[Bg]' for input: '[Bg]' +59: [12:23:55] SMARTS Parse Error: Failed parsing SMARTS 'C' for input: 'C' +59: [12:23:55] SMARTS Parse Error: Failed parsing SMARTS '-O' for input: '-O' +59: [12:23:55] SMARTS Parse Error: Failed parsing SMARTS '*' for input: '*' 48/236 Test #59: smiTest2 ............................... Passed 0.04 sec test 60 Start 60: cxsmilesTest @@ -17880,70 +17906,153 @@ 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 -58: [16:02:37] WARNING: not removing hydrogen atom without neighbors -58: [16:02:37] WARNING: not removing hydrogen atom without neighbors -58: [16:02:37] WARNING: not removing hydrogen atom without neighbors -58: [16:02:37] WARNING: not removing hydrogen atom without neighbors -58: [16:02:37] WARNING: not removing hydrogen atom without neighbors -58: [16:02:37] WARNING: not removing hydrogen atom without neighbors -58: [16:02:37] WARNING: not removing hydrogen atom without neighbors -58: [16:02:37] WARNING: not removing hydrogen atom without neighbors -58: [16:02:37] WARNING: not removing hydrogen atom without neighbors -58: [16:02:37] WARNING: not removing hydrogen atom without neighbors -58: [16:02:37] WARNING: not removing hydrogen atom without neighbors -58: [16:02:37] Invalid chiral specification on atom 0 -58: [16:02:37] Invalid chiral specification on atom 0 -58: [16:02:37] Invalid chiral specification on atom 0 -58: [16:02:37] Invalid chiral specification on atom 0 -58: [16:02:37] Invalid chiral specification on atom 0 - 49/236 Test #30: pyForceFieldConstraints ................ Passed 3.02 sec +58: [12:23:55] WARNING: not removing hydrogen atom without neighbors +58: [12:23:55] WARNING: not removing hydrogen atom without neighbors +58: [12:23:55] WARNING: not removing hydrogen atom without neighbors +58: [12:23:55] WARNING: not removing hydrogen atom without neighbors +58: [12:23:55] WARNING: not removing hydrogen atom without neighbors +58: [12:23:55] WARNING: not removing hydrogen atom without neighbors +58: [12:23:55] WARNING: not removing hydrogen atom without neighbors +58: [12:23:55] WARNING: not removing hydrogen atom without neighbors +58: [12:23:55] WARNING: not removing hydrogen atom without neighbors +58: [12:23:55] WARNING: not removing hydrogen atom without neighbors +58: [12:23:55] WARNING: not removing hydrogen atom without neighbors +58: [12:23:55] Invalid chiral specification on atom 0 +58: [12:23:55] Invalid chiral specification on atom 0 +58: [12:23:55] Invalid chiral specification on atom 0 +58: [12:23:55] Invalid chiral specification on atom 0 +58: [12:23:55] Invalid chiral specification on atom 0 + 49/236 Test #30: pyForceFieldConstraints ................ Passed 2.80 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 -56: Randomness seeded to: 2931477692 +58: [12:23:55] SMILES Parse Error: unclosed ring for input: 'C1.C11.C' +58: [12:23:55] SMILES Parse Error: unclosed ring for input: 'C1C.CC11CCC' +56: Randomness seeded to: 4050756941 56: =============================================================================== 56: All tests passed (7 assertions in 2 test cases) 56: - 50/236 Test #56: tableTestsCatch ........................ Passed 0.39 sec + 50/236 Test #56: tableTestsCatch ........................ Passed 0.44 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 -58: [16:02:37] SMILES Parse Error: unclosed ring for input: 'C1.C11.C' -58: [16:02:37] SMILES Parse Error: unclosed ring for input: 'C1C.CC11CCC' -57: Randomness seeded to: 3765843609 +35: [12:23:56] Maximum BFS search size exceeded. +35: This is likely due to a highly symmetric fused ring system. +61: [12:23:56] SMARTS Parse Error: syntax error while parsing: [C:10H3]CC +61: [12:23:56] SMARTS Parse Error: Failed parsing SMARTS '[C:10H3]CC' for input: '[C:10H3]CC' +61: [12:23:56] SMARTS Parse Error: syntax error while parsing: [C:10:3]ON +61: [12:23:56] SMARTS Parse Error: Failed parsing SMARTS '[C:10:3]ON' for input: '[C:10:3]ON' +57: Randomness seeded to: 2368391354 57: =============================================================================== 57: All tests passed (230 assertions in 7 test cases) 57: - 51/236 Test #57: molopsTestsCatch ....................... Passed 0.48 sec + 51/236 Test #57: molopsTestsCatch ....................... Passed 0.56 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 -55: Randomness seeded to: 3944593680 -55: =============================================================================== -55: All tests passed (45 assertions in 4 test cases) -55: +61: [12:23:56] WARNING: merging explicit H queries involved in ORs is not supported. This query will not be merged +61: [12:23:56] WARNING: merging explicit H queries involved in ORs is not supported. This query will not be merged +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 58: --C1CCC2(CC1)CCCCC2CCC1CCCC1 -61: [16:02:37] SMARTS Parse Error: syntax error while parsing: [C:10H3]CC -61: [16:02:37] SMARTS Parse Error: Failed parsing SMARTS '[C:10H3]CC' for input: '[C:10H3]CC' -61: [16:02:37] SMARTS Parse Error: syntax error while parsing: [C:10:3]ON -61: [16:02:37] SMARTS Parse Error: Failed parsing SMARTS '[C:10:3]ON' for input: '[C:10:3]ON' - 52/236 Test #55: pickleTestsCatch ....................... Passed 0.59 sec + 52/236 Test #61: smaTest1 ............................... Passed 0.40 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 -60: Randomness seeded to: 1283581466 +35: [12:23:56] ----------------------- +35: Testing isRingFused + 53/236 Test #35: graphmolMolOpsTest ..................... Passed 2.95 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 +58: smi: ClC1CCCCC1 +58: smi: ClC1CCCCC1 +58: smi: ClC1CCCCC1Br +58: smi: c1ccccc1 +58: smi: c1ccncc1 +58: smi: c1cc[nH]c1 +58: smi: c1cc[nH]c1 +58: smi: c1cc[pH]c1 +58: [12:23:56] WARNING: could not find number of expected rings. Switching to an approximate ring finding algorithm. +58: [12:23:56] WARNING: could not find number of expected rings. Switching to an approximate ring finding algorithm. +58: CbC(aC)aC +58: CaC(bC)aC +58: CbC(bC)aC +58: O.C +58: C=C1CC[C@@H]2O[C@@]2(C)CC[C@@](N)(C(C)C)C=C[C@](C)(O)CC[C@@H]1O C=C1CC[C@@H]2O[C@@]2(C)CC[C@@](N)(C(C)C)C=C[C@](C)(O)CC[C@@H]1O +58: [12:23:56] SMILES Parse Error: syntax error while parsing: c%()ccccc%() +58: [12:23:56] SMILES Parse Error: check for mistakes around position 4: +58: [12:23:56] c%()ccccc%() +58: [12:23:56] ~~~^ +58: [12:23:56] SMILES Parse Error: Failed parsing SMILES 'c%()ccccc%()' for input: 'c%()ccccc%()' +58: [12:23:56] SMILES Parse Error: syntax error while parsing: c%(100000)ccccc%(100000) +58: [12:23:56] SMILES Parse Error: check for mistakes around position 9: +58: [12:23:56] c%(100000)ccccc%(100000) +58: [12:23:56] ~~~~~~~~^ +58: [12:23:56] SMILES Parse Error: Failed parsing SMILES 'c%(100000)ccccc%(100000)' for input: 'c%(100000)ccccc%(100000)' +58: [12:23:56] SMILES Parse Error: duplicated ring closure 1 bonds atom 2 to itself for input: 'C1CC111' +58: [12:23:56] SMILES Parse Error: ring closure 1 duplicates bond between atom 0 and atom 1 for input: 'C1C1' +58: [12:23:56] SMILES Parse Error: syntax error while parsing: COc(c1)cccc1C# +58: [12:23:56] SMILES Parse Error: check for mistakes around position 14: +58: [12:23:56] COc(c1)cccc1C# +58: [12:23:56] ~~~~~~~~~~~~~^ +58: [12:23:56] SMILES Parse Error: Failed parsing SMILES 'COc(c1)cccc1C#' for input: 'COc(c1)cccc1C#' +58: [12:23:56] SMARTS Parse Error: syntax error while parsing: COc(c1)cccc1C# +58: [12:23:56] SMARTS Parse Error: Failed parsing SMARTS 'COc(c1)cccc1C#' for input: 'COc(c1)cccc1C#' +58: [12:23:56] SMILES Parse Error: syntax error while parsing: COc(c1)cccc1C# +58: [12:23:56] SMILES Parse Error: check for mistakes around position 14: +58: [12:23:56] COc(c1)cccc1C# +58: [12:23:56] ~~~~~~~~~~~~~^ +58: [12:23:56] SMILES Parse Error: Failed parsing SMILES 'COc(c1)cccc1C#' for input: 'COc(c1)cccc1C#' +58: [12:23:56] SMARTS Parse Error: syntax error while parsing: COc(c1)cccc1C# +58: [12:23:56] SMARTS Parse Error: Failed parsing SMARTS 'COc(c1)cccc1C#' for input: 'COc(c1)cccc1C#' +58: [12:23:56] SMILES Parse Error: syntax error while parsing: COc(c1)cccc1C# +58: [12:23:56] SMILES Parse Error: check for mistakes around position 14: +58: [12:23:56] COc(c1)cccc1C# +58: [12:23:56] ~~~~~~~~~~~~~^ +58: [12:23:56] SMILES Parse Error: Failed parsing SMILES 'COc(c1)cccc1C#' for input: 'COc(c1)cccc1C#' +58: [12:23:56] SMARTS Parse Error: syntax error while parsing: COc(c1)cccc1C# +58: [12:23:56] SMARTS Parse Error: Failed parsing SMARTS 'COc(c1)cccc1C#' for input: 'COc(c1)cccc1C#' +58: C=c1s/c2n(c1=O)CCCCCCC\N=2 +58: C1=C\C/C=C2C3=C\C/C=C\C=C/C/3C\2\C=C/1 +58: [12:23:56] SMILES Parse Error: extra close parentheses while parsing: C) +58: [12:23:56] SMILES Parse Error: check for mistakes around position 2: +58: [12:23:56] C) +58: [12:23:56] ~^ +58: [12:23:56] SMILES Parse Error: Failed parsing SMILES 'C)' for input: 'C)' +63: Randomness seeded to: 3262307488 +63: [12:23:56] WARNING: not removing hydrogen atom with neighbor that has non-tetrahedral stereochemistry + 54/236 Test #58: smiTest1 ............................... Passed 0.80 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: [12:23:56] WARNING: not removing hydrogen atom with neighbor that has non-tetrahedral stereochemistry +63: [12:23:56] WARNING: not removing hydrogen atom with neighbor that has non-tetrahedral stereochemistry +63: [12:23:56] WARNING: not removing hydrogen atom with neighbor that has non-tetrahedral stereochemistry +63: [12:23:56] WARNING: not removing hydrogen atom with neighbor that has non-tetrahedral stereochemistry +63: [12:23:56] WARNING: not removing hydrogen atom with neighbor that has non-tetrahedral stereochemistry +60: Randomness seeded to: 3173530594 60: Test 60: 60: ShortAtropisomerNoCoords.cxsmi @@ -18004,26 +18113,18 @@ 60: 60: BMS-986142_atrop5.cxsmi 60: -60: [16:02:37] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored -60: [16:02:37] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored -60: [16:02:37] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored -60: [16:02:37] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored -60: [16:02:37] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored -60: [16:02:37] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored -60: [16:02:37] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored -60: [16:02:37] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored -60: [16:02:37] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored -60: [16:02:37] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored -58: smi: ClC1CCCCC1 -58: smi: ClC1CCCCC1 -58: smi: ClC1CCCCC1Br -58: smi: c1ccccc1 -58: smi: c1ccncc1 -58: smi: c1cc[nH]c1 -58: smi: c1cc[nH]c1 -58: smi: c1cc[pH]c1 -58: [16:02:37] WARNING: could not find number of expected rings. Switching to an approximate ring finding algorithm. -58: [16:02:37] WARNING: could not find number of expected rings. Switching to an approximate ring finding algorithm. +60: [12:23:56] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored +60: [12:23:56] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored +60: [12:23:56] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored +60: [12:23:56] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored +60: [12:23:56] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored +60: [12:23:56] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored +60: [12:23:56] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored +60: [12:23:56] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored +60: [12:23:56] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored +60: [12:23:56] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored +63: [12:23:56] WARNING: not removing hydrogen atom with neighbor that has non-tetrahedral stereochemistry +63: [12:23:56] WARNING: not removing hydrogen atom with neighbor that has non-tetrahedral stereochemistry 60: Test 60: 60: BMS-986142_atrop6.cxsmi @@ -18032,90 +18133,46 @@ 60: 60: BMS-986142_atropBad1.cxsmi 60: -60: [16:02:37] The 2 defining bonds for an atropisomer are co-planar - atoms are: 6 7 -58: CbC(aC)aC -58: CaC(bC)aC -58: CbC(bC)aC -58: O.C -60: [16:02:37] The 2 defining bonds for an atropisomer are co-planar - atoms are: 6 7 -60: [16:02:37] The 2 defining bonds for an atropisomer are co-planar - atoms are: 6 7 -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 -60: [16:02:37] The 2 defining bonds for an atropisomer are co-planar - atoms are: 6 7 -60: [16:02:37] The 2 defining bonds for an atropisomer are co-planar - atoms are: 6 7 -61: [16:02:37] WARNING: merging explicit H queries involved in ORs is not supported. This query will not be merged -61: [16:02:37] WARNING: merging explicit H queries involved in ORs is not supported. This query will not be merged -58: [16:02:37] SMILES Parse Error: syntax error while parsing: c%()ccccc%() -58: [16:02:37] SMILES Parse Error: check for mistakes around position 4: -58: [16:02:37] c%()ccccc%() -58: [16:02:37] ~~~^ -58: [16:02:37] SMILES Parse Error: Failed parsing SMILES 'c%()ccccc%()' for input: 'c%()ccccc%()' -58: [16:02:37] SMILES Parse Error: syntax error while parsing: c%(100000)ccccc%(100000) -58: [16:02:37] SMILES Parse Error: check for mistakes around position 9: -58: [16:02:37] c%(100000)ccccc%(100000) -58: [16:02:37] ~~~~~~~~^ -58: [16:02:37] SMILES Parse Error: Failed parsing SMILES 'c%(100000)ccccc%(100000)' for input: 'c%(100000)ccccc%(100000)' -58: [16:02:37] SMILES Parse Error: duplicated ring closure 1 bonds atom 2 to itself for input: 'C1CC111' +60: [12:23:56] The 2 defining bonds for an atropisomer are co-planar - atoms are: 6 7 +60: [12:23:56] The 2 defining bonds for an atropisomer are co-planar - atoms are: 6 7 +60: [12:23:56] The 2 defining bonds for an atropisomer are co-planar - atoms are: 6 7 +60: [12:23:56] The 2 defining bonds for an atropisomer are co-planar - atoms are: 6 7 +60: [12:23:56] The 2 defining bonds for an atropisomer are co-planar - atoms are: 6 7 60: Test 60: 60: BMS-986142_atropBad2.cxsmi 60: -60: [16:02:37] The bonds on one end of an atropisomer are both UP or both DOWN - atoms are: 6 7 -60: [16:02:37] The bonds on one end of an atropisomer are both UP or both DOWN - atoms are: 6 7 -58: [16:02:37] SMILES Parse Error: ring closure 1 duplicates bond between atom 0 and atom 1 for input: 'C1C1' -60: [16:02:37] The bonds on one end of an atropisomer are both UP or both DOWN - atoms are: 6 7 -58: [16:02:37] SMILES Parse Error: syntax error while parsing: COc(c1)cccc1C# -58: [16:02:37] SMILES Parse Error: check for mistakes around position 14: -58: [16:02:37] COc(c1)cccc1C# -58: [16:02:37] ~~~~~~~~~~~~~^ -58: [16:02:37] SMILES Parse Error: Failed parsing SMILES 'COc(c1)cccc1C#' for input: 'COc(c1)cccc1C#' -58: [16:02:37] SMARTS Parse Error: syntax error while parsing: COc(c1)cccc1C# -58: [16:02:37] SMARTS Parse Error: Failed parsing SMARTS 'COc(c1)cccc1C#' for input: 'COc(c1)cccc1C#' -58: [16:02:37] SMILES Parse Error: syntax error while parsing: COc(c1)cccc1C# -58: [16:02:37] SMILES Parse Error: check for mistakes around position 14: -58: [16:02:37] COc(c1)cccc1C# -58: [16:02:37] ~~~~~~~~~~~~~^ -58: [16:02:37] SMILES Parse Error: Failed parsing SMILES 'COc(c1)cccc1C#' for input: 'COc(c1)cccc1C#' -58: [16:02:37] SMARTS Parse Error: syntax error while parsing: COc(c1)cccc1C# -58: [16:02:37] SMARTS Parse Error: Failed parsing SMARTS 'COc(c1)cccc1C#' for input: 'COc(c1)cccc1C#' -58: [16:02:37] SMILES Parse Error: syntax error while parsing: COc(c1)cccc1C# -58: [16:02:37] SMILES Parse Error: check for mistakes around position 14: -58: [16:02:37] COc(c1)cccc1C# -58: [16:02:37] ~~~~~~~~~~~~~^ -58: [16:02:37] SMILES Parse Error: Failed parsing SMILES 'COc(c1)cccc1C#' for input: 'COc(c1)cccc1C#' -58: [16:02:37] SMARTS Parse Error: syntax error while parsing: COc(c1)cccc1C# -58: [16:02:37] SMARTS Parse Error: Failed parsing SMARTS 'COc(c1)cccc1C#' for input: 'COc(c1)cccc1C#' -58: C=c1s/c2n(c1=O)CCCCCCC\N=2 -58: C1=C\C/C=C2C3=C\C/C=C\C=C/C/3C\2\C=C/1 -58: [16:02:37] SMILES Parse Error: extra close parentheses while parsing: C) -58: [16:02:37] SMILES Parse Error: check for mistakes around position 2: -58: [16:02:37] C) -58: [16:02:37] ~^ -58: [16:02:37] SMILES Parse Error: Failed parsing SMILES 'C)' for input: 'C)' - 53/236 Test #58: smiTest1 ............................... Passed 0.52 sec -test 65 - Start 65: testDepictor +60: [12:23:56] The bonds on one end of an atropisomer are both UP or both DOWN - atoms are: 6 7 +60: [12:23:56] The bonds on one end of an atropisomer are both UP or both DOWN - atoms are: 6 7 +60: [12:23:56] The bonds on one end of an atropisomer are both UP or both DOWN - atoms are: 6 7 +60: [12:23:56] The bonds on one end of an atropisomer are both UP or both DOWN - atoms are: 6 7 +60: [12:23:56] The bonds on one end of an atropisomer are both UP or both DOWN - atoms are: 6 7 +62: Randomness seeded to: 3605327567 +62: [12:23:56] SMILES Parse Error: unclosed ring for input: 'c1ccccc' +62: [12:23:56] Can't kekulize mol. Unkekulized atoms: 0 1 2 3 4 +62: [12:23:56] SMARTS Parse Error: unclosed ring for input: 'c1ccccc' +63: [12:23:56] ignoring non-tetrahedral stereo specification since setAllowNontetrahedralChirality() is false. +63: =============================================================================== +63: All tests passed (308 assertions in 9 test cases) +63: +64: Randomness seeded to: 913560217 +64: =============================================================================== +64: All tests passed (14 assertions in 2 test cases) +64: + 55/236 Test #64: v2smiTestCatch ......................... Passed 0.33 sec +test 67 + Start 67: pyDepictor -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 -60: [16:02:37] The bonds on one end of an atropisomer are both UP or both DOWN - atoms are: 6 7 -60: [16:02:37] The bonds on one end of an atropisomer are both UP or both DOWN - atoms are: 6 7 - 54/236 Test #61: smaTest1 ............................... Passed 0.43 sec -test 66 - Start 66: depictorCatch +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 + 56/236 Test #63: nontetrahedralCatch .................... Passed 0.42 sec +test 68 + Start 68: testMrvToMol -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: Randomness seeded to: 1872058171 -63: [16:02:38] WARNING: not removing hydrogen atom with neighbor that has non-tetrahedral stereochemistry -63: [16:02:38] WARNING: not removing hydrogen atom with neighbor that has non-tetrahedral stereochemistry -63: [16:02:38] WARNING: not removing hydrogen atom with neighbor that has non-tetrahedral stereochemistry -63: [16:02:38] WARNING: not removing hydrogen atom with neighbor that has non-tetrahedral stereochemistry -63: [16:02:38] WARNING: not removing hydrogen atom with neighbor that has non-tetrahedral stereochemistry -63: [16:02:38] WARNING: not removing hydrogen atom with neighbor that has non-tetrahedral stereochemistry -63: [16:02:38] WARNING: not removing hydrogen atom with neighbor that has non-tetrahedral stereochemistry -63: [16:02:38] WARNING: not removing hydrogen atom with neighbor that has non-tetrahedral stereochemistry +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: Test 60: 60: JDQ443_3d.cxsmi @@ -18140,38 +18197,13 @@ 60: 60: JDQ443_atropBad1.cxsmi 60: -60: [16:02:38] The 2 defining bonds for an atropisomer are co-planar - atoms are: 2 3 -60: [16:02:38] The 2 defining bonds for an atropisomer are co-planar - atoms are: 2 3 -60: [16:02:38] The 2 defining bonds for an atropisomer are co-planar - atoms are: 2 3 -60: [16:02:38] The 2 defining bonds for an atropisomer are co-planar - atoms are: 2 3 -60: [16:02:38] The 2 defining bonds for an atropisomer are co-planar - atoms are: 2 3 -63: [16:02:38] ignoring non-tetrahedral stereo specification since setAllowNontetrahedralChirality() is false. -63: =============================================================================== -63: All tests passed (308 assertions in 9 test cases) -63: -62: Randomness seeded to: 744529925 -62: [16:02:38] SMILES Parse Error: unclosed ring for input: 'c1ccccc' -62: [16:02:38] Can't kekulize mol. Unkekulized atoms: 0 1 2 3 4 - 55/236 Test #63: nontetrahedralCatch .................... Passed 0.41 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 -64: Randomness seeded to: 425236401 -64: =============================================================================== -64: All tests passed (14 assertions in 2 test cases) -64: -29: Checking against /build/reproducible-path/rdkit-202503.1/Code/ForceField/MMFF/test_data/MMFF94_reference.log... - 56/236 Test #64: v2smiTestCatch ......................... Passed 0.35 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 -62: [16:02:38] SMARTS Parse Error: unclosed ring for input: 'c1ccccc' +60: [12:23:56] The 2 defining bonds for an atropisomer are co-planar - atoms are: 2 3 +60: [12:23:56] The 2 defining bonds for an atropisomer are co-planar - atoms are: 2 3 +60: [12:23:56] The 2 defining bonds for an atropisomer are co-planar - atoms are: 2 3 +60: [12:23:56] The 2 defining bonds for an atropisomer are co-planar - atoms are: 2 3 +60: [12:23:56] The 2 defining bonds for an atropisomer are co-planar - atoms are: 2 3 +62: [12:23:56] SMARTS Parse Error: unclosed ring for input: 'C1C' +62: [12:23:56] Can't kekulize mol. Unkekulized atoms: 0 1 2 3 4 60: Test 60: 60: RP-6306_atrop1.cxsmi @@ -18192,17 +18224,20 @@ 60: 60: RP-6306_atrop5.cxsmi 60: -60: [16:02:38] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored -60: [16:02:38] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored -60: [16:02:38] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored -60: [16:02:38] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored -60: [16:02:38] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored -60: [16:02:38] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored -60: [16:02:38] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored -60: [16:02:38] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored -60: [16:02:38] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored -60: [16:02:38] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored -62: [16:02:38] SMARTS Parse Error: unclosed ring for input: 'C1C' +60: [12:23:56] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored +60: [12:23:56] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored +60: [12:23:56] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored +60: [12:23:56] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored +62: [12:23:56] SMARTS Parse Error: syntax error while parsing: C)foo +62: [12:23:56] SMARTS Parse Error: Failed parsing SMARTS 'C)foo' for input: 'C)foo' +60: [12:23:56] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored +60: [12:23:56] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored +60: [12:23:56] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored +60: [12:23:56] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored +60: [12:23:56] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored +60: [12:23:56] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored +62: [12:23:56] SMARTS Parse Error: syntax error while parsing: CCC |$foo;;bar$| +62: [12:23:56] SMARTS Parse Error: Failed parsing SMARTS 'CCC |$foo;;bar$|' for input: 'CCC |$foo;;bar$|' 60: Test 60: 60: RP-6306_atrop6.cxsmi @@ -18211,53 +18246,21 @@ 60: 60: RP-6306_atropBad1.cxsmi 60: -60: [16:02:38] The 2 defining bonds for an atropisomer are co-planar - atoms are: 4 5 -60: [16:02:38] The 2 defining bonds for an atropisomer are co-planar - atoms are: 4 5 -62: [16:02:38] Can't kekulize mol. Unkekulized atoms: 0 1 2 3 4 -60: [16:02:38] The 2 defining bonds for an atropisomer are co-planar - atoms are: 4 5 -60: [16:02:38] The 2 defining bonds for an atropisomer are co-planar - atoms are: 4 5 -60: [16:02:38] The 2 defining bonds for an atropisomer are co-planar - atoms are: 4 5 +60: [12:23:56] The 2 defining bonds for an atropisomer are co-planar - atoms are: 4 5 +60: [12:23:56] The 2 defining bonds for an atropisomer are co-planar - atoms are: 4 5 +60: [12:23:56] The 2 defining bonds for an atropisomer are co-planar - atoms are: 4 5 +60: [12:23:56] The 2 defining bonds for an atropisomer are co-planar - atoms are: 4 5 +60: [12:23:56] The 2 defining bonds for an atropisomer are co-planar - atoms are: 4 5 60: Test 60: 60: RP-6306_atropBad2.cxsmi 60: -60: [16:02:38] The bonds on one end of an atropisomer are both UP or both DOWN - atoms are: 4 5 -40: [16:02:38] done: 500000 -40: [16:02:38] Done -62: [16:02:38] SMARTS Parse Error: syntax error while parsing: C)foo -62: [16:02:38] SMARTS Parse Error: Failed parsing SMARTS 'C)foo' for input: 'C)foo' -12: .................. -12: ---------------------------------------------------------------------- -12: Ran 18 tests in 3.088s -12: -12: OK -60: [16:02:38] The bonds on one end of an atropisomer are both UP or both DOWN - atoms are: 4 5 -60: [16:02:38] The bonds on one end of an atropisomer are both UP or both DOWN - atoms are: 4 5 -60: [16:02:38] The bonds on one end of an atropisomer are both UP or both DOWN - atoms are: 4 5 -60: [16:02:38] The bonds on one end of an atropisomer are both UP or both DOWN - atoms are: 4 5 -62: [16:02:38] SMARTS Parse Error: syntax error while parsing: CCC |$foo;;bar$| -62: [16:02:38] SMARTS Parse Error: Failed parsing SMARTS 'CCC |$foo;;bar$|' for input: 'CCC |$foo;;bar$|' -62: [16:02:38] unrecognized CXSMILES CONNECT value: 'EU'. Assuming 'eu' -40: [16:02:38] Testing hanoi with a functor. -40: [16:02:38] Done -40: [16:02:38] Testing basic partition refinement. -40: [16:02:38] Done -40: [16:02:38] Testing partition refinement with neighbors. - 57/236 Test #12: pyBV ................................... Passed 5.81 sec -test 69 - Start 69: fileParsersTest1 - -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 -40: [16:02:38] Done -40: [16:02:38] testing canonicalization via tie breaking. -40: [16:02:38] Done -40: [16:02:38] testing canonicalization using the wrapper. -40: [16:02:38] Done -40: [16:02:38] testing some specific ordering problems -40: [16:02:38] Finished -40: [16:02:38] testing chiral invariants. +60: [12:23:56] The bonds on one end of an atropisomer are both UP or both DOWN - atoms are: 4 5 +60: [12:23:56] The bonds on one end of an atropisomer are both UP or both DOWN - atoms are: 4 5 +60: [12:23:56] The bonds on one end of an atropisomer are both UP or both DOWN - atoms are: 4 5 +60: [12:23:56] The bonds on one end of an atropisomer are both UP or both DOWN - atoms are: 4 5 +60: [12:23:56] The bonds on one end of an atropisomer are both UP or both DOWN - atoms are: 4 5 +62: [12:23:56] unrecognized CXSMILES CONNECT value: 'EU'. Assuming 'eu' 60: Test 60: 60: RP-6306_3d.cxsmi @@ -18282,55 +18285,96 @@ 60: 60: Sotorasib_atrop5.cxsmi 60: -60: [16:02:38] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 13 ignored -60: [16:02:38] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 13 ignored -60: [16:02:38] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 13 ignored -60: [16:02:38] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 13 ignored -60: [16:02:38] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 13 ignored -60: [16:02:38] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 13 ignored -60: [16:02:38] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 13 ignored -60: [16:02:38] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 13 ignored -60: [16:02:38] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 13 ignored -60: [16:02:38] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 13 ignored +60: [12:23:56] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 13 ignored +60: [12:23:56] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 13 ignored +60: [12:23:56] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 13 ignored +60: [12:23:56] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 13 ignored +60: [12:23:56] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 13 ignored +60: [12:23:56] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 13 ignored +60: [12:23:56] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 13 ignored +60: [12:23:56] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 13 ignored +60: [12:23:56] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 13 ignored +60: [12:23:56] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 13 ignored 60: Test 60: 60: Sotorasib_atropBad1.cxsmi 60: -60: [16:02:38] The 2 defining bonds for an atropisomer are co-planar - atoms are: 13 14 -40: [16:02:38] Finished -40: [16:02:38] testing unique ranks in w.r.t. renumbering. -60: [16:02:38] The 2 defining bonds for an atropisomer are co-planar - atoms are: 13 14 -60: [16:02:38] The 2 defining bonds for an atropisomer are co-planar - atoms are: 13 14 -60: [16:02:38] The 2 defining bonds for an atropisomer are co-planar - atoms are: 13 14 -60: [16:02:38] The 2 defining bonds for an atropisomer are co-planar - atoms are: 13 14 +60: [12:23:56] The 2 defining bonds for an atropisomer are co-planar - atoms are: 13 14 +60: [12:23:56] The 2 defining bonds for an atropisomer are co-planar - atoms are: 13 14 +60: [12:23:56] The 2 defining bonds for an atropisomer are co-planar - atoms are: 13 14 +60: [12:23:56] The 2 defining bonds for an atropisomer are co-planar - atoms are: 13 14 +60: [12:23:56] The 2 defining bonds for an atropisomer are co-planar - atoms are: 13 14 60: Test 60: 60: Sotorasib_atropBad2.cxsmi 60: -60: [16:02:38] The bonds on one end of an atropisomer are both UP or both DOWN - atoms are: 13 14 -60: [16:02:38] The bonds on one end of an atropisomer are both UP or both DOWN - atoms are: 13 14 -60: [16:02:38] The bonds on one end of an atropisomer are both UP or both DOWN - atoms are: 13 14 -60: [16:02:38] The bonds on one end of an atropisomer are both UP or both DOWN - atoms are: 13 14 -40: [16:02:38] Finished -40: [16:02:38] testing mol fragments. -60: [16:02:38] The bonds on one end of an atropisomer are both UP or both DOWN - atoms are: 13 14 -40: [16:02:38] Finished -40: [16:02:38] testing protein round-tripping. -62: [16:02:38] w block attempts to set wedging on bond 0 more than once. -62: [16:02:38] improperly formatted w block -65: [16:02:38] Warning: stereochemistry around double bond may be incorrect in depiction. -62: [16:02:38] atom 3 is not associated with bond 1(1-2) in w block -68: Using new chirality perception -68: Test -68: -68: rxnStereoMarkedCrossed.mrv -68: -68: Test -68: -68: 145323811.mol -68: -68: [16:02:38] unsupported number of radical electrons 5 -62: [16:02:38] +60: [12:23:56] The bonds on one end of an atropisomer are both UP or both DOWN - atoms are: 13 14 +60: [12:23:56] The bonds on one end of an atropisomer are both UP or both DOWN - atoms are: 13 14 +60: [12:23:56] The bonds on one end of an atropisomer are both UP or both DOWN - atoms are: 13 14 +60: [12:23:56] The bonds on one end of an atropisomer are both UP or both DOWN - atoms are: 13 14 +60: [12:23:56] The bonds on one end of an atropisomer are both UP or both DOWN - atoms are: 13 14 +60: Test +60: +60: Sotorasib_3d.cxsmi +60: +60: Test +60: +60: ZM374979_atrop1.cxsmi +60: +60: Test +60: +60: ZM374979_atrop2.cxsmi +60: +60: Test +60: +60: ZM374979_atrop3.cxsmi +60: +60: Test +60: +60: ZM374979_atrop4.cxsmi +60: +60: Test +60: +60: ZM374979_atropBad1.cxsmi +60: +60: [12:23:56] The 2 defining bonds for an atropisomer are co-planar - atoms are: 0 31 +60: [12:23:56] The 2 defining bonds for an atropisomer are co-planar - atoms are: 0 31 +60: [12:23:56] The 2 defining bonds for an atropisomer are co-planar - atoms are: 0 31 +60: [12:23:56] The 2 defining bonds for an atropisomer are co-planar - atoms are: 0 31 +60: [12:23:56] The 2 defining bonds for an atropisomer are co-planar - atoms are: 0 31 +62: [12:23:56] w block attempts to set wedging on bond 0 more than once. +62: [12:23:56] improperly formatted w block +62: [12:23:56] atom 3 is not associated with bond 1(1-2) in w block +60: Test +60: +60: Mrtx1719_3d.cxsmi +60: +60: Test +60: +60: Mrtx1719_atrop1.cxsmi +60: +60: Test +60: +60: Mrtx1719_atrop2.cxsmi +60: +60: Test +60: +60: Mrtx1719_atrop3.cxsmi +60: +60: Test +60: +60: Mrtx1719_atrop4.cxsmi +60: +60: Test +60: +60: Mrtx1719_atropBad1.cxsmi +60: +60: [12:23:56] The 2 defining bonds for an atropisomer are co-planar - atoms are: 11 12 +60: [12:23:56] The 2 defining bonds for an atropisomer are co-planar - atoms are: 11 12 +60: [12:23:56] The 2 defining bonds for an atropisomer are co-planar - atoms are: 11 12 +60: [12:23:56] The 2 defining bonds for an atropisomer are co-planar - atoms are: 11 12 +60: [12:23:56] The 2 defining bonds for an atropisomer are co-planar - atoms are: 11 12 +62: [12:23:56] 62: 62: **** 62: Range Error @@ -18346,20 +18390,20 @@ 62: 4# RDKit::SmilesWrite::FragmentSmilesConstruct(RDKit::ROMol&, int, std::vector >&, std::vector > const&, RDKit::SmilesWriteParams const&, std::vector >&, std::vector >&, boost::dynamic_bitset > const*, boost::dynamic_bitset > const*, std::vector, std::allocator >, std::allocator, std::allocator > > > const*, std::vector, std::allocator >, std::allocator, std::allocator > > > const*) in /build/reproducible-path/rdkit-202503.1/obj-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# 0x0000AAAAB73C9F8C in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/SmilesParse/smiTestCatch -62: 8# 0x0000AAAAB741A9EC in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/SmilesParse/smiTestCatch -62: 9# 0x0000AAAAB741B3A0 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/SmilesParse/smiTestCatch -62: 10# 0x0000AAAAB741B7D4 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/SmilesParse/smiTestCatch -62: 11# 0x0000AAAAB73EFB98 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/SmilesParse/smiTestCatch -62: 12# 0x0000AAAAB73F00E4 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/SmilesParse/smiTestCatch -62: 13# 0x0000AAAAB73857D0 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/SmilesParse/smiTestCatch -62: 14# 0x0000FFFFBBF1229C in /lib/aarch64-linux-gnu/libc.so.6 +62: 7# 0x0000AAAAD92D9F8C in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/SmilesParse/smiTestCatch +62: 8# 0x0000AAAAD932A9EC in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/SmilesParse/smiTestCatch +62: 9# 0x0000AAAAD932B3A0 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/SmilesParse/smiTestCatch +62: 10# 0x0000AAAAD932B7D4 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/SmilesParse/smiTestCatch +62: 11# 0x0000AAAAD92FFB98 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/SmilesParse/smiTestCatch +62: 12# 0x0000AAAAD93000E4 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/SmilesParse/smiTestCatch +62: 13# 0x0000AAAAD92957D0 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/SmilesParse/smiTestCatch +62: 14# 0x0000FFFFBA80229C in /lib/aarch64-linux-gnu/libc.so.6 62: 15# __libc_start_main in /lib/aarch64-linux-gnu/libc.so.6 -62: 16# 0x0000AAAAB73858B0 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/SmilesParse/smiTestCatch +62: 16# 0x0000AAAAD92958B0 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/SmilesParse/smiTestCatch 62: ---------- 62: **** 62: -62: [16:02:38] +62: [12:23:56] 62: 62: **** 62: Range Error @@ -18375,125 +18419,134 @@ 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# 0x0000AAAAB73C9F8C in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/SmilesParse/smiTestCatch -62: 8# 0x0000AAAAB741A9EC in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/SmilesParse/smiTestCatch -62: 9# 0x0000AAAAB741B3A0 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/SmilesParse/smiTestCatch -62: 10# 0x0000AAAAB741B7D4 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/SmilesParse/smiTestCatch -62: 11# 0x0000AAAAB73EFB98 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/SmilesParse/smiTestCatch -62: 12# 0x0000AAAAB73F00E4 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/SmilesParse/smiTestCatch -62: 13# 0x0000AAAAB73857D0 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/SmilesParse/smiTestCatch -62: 14# 0x0000FFFFBBF1229C in /lib/aarch64-linux-gnu/libc.so.6 +62: 7# 0x0000AAAAD92D9F8C in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/SmilesParse/smiTestCatch +62: 8# 0x0000AAAAD932A9EC in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/SmilesParse/smiTestCatch +62: 9# 0x0000AAAAD932B3A0 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/SmilesParse/smiTestCatch +62: 10# 0x0000AAAAD932B7D4 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/SmilesParse/smiTestCatch +62: 11# 0x0000AAAAD92FFB98 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/SmilesParse/smiTestCatch +62: 12# 0x0000AAAAD93000E4 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/SmilesParse/smiTestCatch +62: 13# 0x0000AAAAD92957D0 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/SmilesParse/smiTestCatch +62: 14# 0x0000FFFFBA80229C in /lib/aarch64-linux-gnu/libc.so.6 62: 15# __libc_start_main in /lib/aarch64-linux-gnu/libc.so.6 -62: 16# 0x0000AAAAB73858B0 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/SmilesParse/smiTestCatch +62: 16# 0x0000AAAAD92958B0 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/SmilesParse/smiTestCatch 62: ---------- 62: **** 62: -62: [16:02:38] SMARTS Parse Error: unclosed ring for input: 'C1.C2.C3.C4.C5' -62: [16:02:38] SMILES Parse Error: unclosed ring for input: 'C1.C2.C3.C4.C5' -62: [16:02:38] SMARTS Parse Error: syntax error while parsing: C1C)foo -62: [16:02:38] SMARTS Parse Error: Failed parsing SMARTS 'C1C)foo' for input: 'C1C)foo' -62: [16:02:38] SMILES Parse Error: extra close parentheses while parsing: C1C)foo -62: [16:02:38] SMILES Parse Error: check for mistakes around position 4: -62: [16:02:38] C1C)foo -62: [16:02:38] ~~~^ -62: [16:02:38] SMILES Parse Error: Failed parsing SMILES 'C1C)foo' for input: 'C1C)foo' +62: [12:23:56] SMARTS Parse Error: unclosed ring for input: 'C1.C2.C3.C4.C5' +62: [12:23:56] SMILES Parse Error: unclosed ring for input: 'C1.C2.C3.C4.C5' +62: [12:23:56] SMARTS Parse Error: syntax error while parsing: C1C)foo +62: [12:23:56] SMARTS Parse Error: Failed parsing SMARTS 'C1C)foo' for input: 'C1C)foo' +62: [12:23:56] SMILES Parse Error: extra close parentheses while parsing: C1C)foo +62: [12:23:56] SMILES Parse Error: check for mistakes around position 4: +62: [12:23:56] C1C)foo +62: [12:23:56] ~~~^ +62: [12:23:56] SMILES Parse Error: Failed parsing SMILES 'C1C)foo' for input: 'C1C)foo' 62: =============================================================================== 62: All tests passed (1588 assertions in 69 test cases) 62: - 58/236 Test #62: smiTestCatch ........................... Passed 0.90 sec + 57/236 Test #62: smiTestCatch ........................... Passed 0.97 sec +test 69 + Start 69: fileParsersTest1 + +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 +66: Randomness seeded to: 1976626014 +66: =============================================================================== +66: All tests passed (580 assertions in 18 test cases) +66: + 58/236 Test #66: depictorCatch .......................... Passed 0.63 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 -60: Test -60: -60: Sotorasib_3d.cxsmi -60: -60: Test -60: -60: ZM374979_atrop1.cxsmi -60: -60: Test -60: -60: ZM374979_atrop2.cxsmi -60: -60: Test -60: -60: ZM374979_atrop3.cxsmi -60: -60: Test -60: -60: ZM374979_atrop4.cxsmi -60: -60: Test -60: -60: ZM374979_atropBad1.cxsmi -60: -60: [16:02:38] The 2 defining bonds for an atropisomer are co-planar - atoms are: 0 31 -60: [16:02:38] The 2 defining bonds for an atropisomer are co-planar - atoms are: 0 31 -60: [16:02:38] The 2 defining bonds for an atropisomer are co-planar - atoms are: 0 31 -60: [16:02:38] The 2 defining bonds for an atropisomer are co-planar - atoms are: 0 31 -60: [16:02:38] The 2 defining bonds for an atropisomer are co-planar - atoms are: 0 31 -70: [16:02:38] ---- Running with POSIX locale ----- - 59/236 Test #65: testDepictor ........................... Passed 0.70 sec +70: [12:23:57] ---- Running with POSIX locale ----- +65: [12:23:57] Warning: stereochemistry around double bond may be incorrect in depiction. +70: [12:23:57] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +70: [12:23:57] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +68: Using new chirality perception +68: Test +68: +68: rxnStereoMarkedCrossed.mrv +68: +68: Test +68: +68: 145323811.mol +68: +68: [12:23:57] unsupported number of radical electrons 5 +70: [12:23:57] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +70: [12:23:57] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +70: [12:23:57] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +70: [12:23:57] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +69: *************************************** +69: *************************************** +69: [12:23:57] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +69: [12:23:57] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +70: [12:23:57] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored +70: [12:23:57] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored +70: [12:23:57] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored +70: [12:23:57] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored +70: [12:23:57] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored +70: [12:23:57] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored +70: [12:23:57] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored +70: [12:23:57] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored +70: [12:23:57] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored +70: [12:23:57] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored +70: [12:23:57] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored +70: [12:23:57] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored +70: [12:23:57] The bonds on one end of an atropisomer are both UP or both DOWN - atoms are: 7 29 +70: [12:23:57] The bonds on one end of an atropisomer are both UP or both DOWN - atoms are: 7 29 +70: [12:23:57] The bonds on one end of an atropisomer are both UP or both DOWN - atoms are: 7 29 +70: [12:23:57] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. + 59/236 Test #65: testDepictor ........................... Passed 1.07 sec 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 -69: *************************************** -69: *************************************** -66: Randomness seeded to: 3319491268 -66: =============================================================================== -66: All tests passed (580 assertions in 18 test cases) -66: - 60/236 Test #66: depictorCatch .......................... Passed 0.67 sec -test 72 - Start 72: testMolSupplier - -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 -69: [16:02:38] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -69: [16:02:38] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -70: [16:02:38] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -60: Test -60: -60: Mrtx1719_3d.cxsmi -60: -60: Test -60: -60: Mrtx1719_atrop1.cxsmi -60: -60: Test -60: -60: Mrtx1719_atrop2.cxsmi -60: -60: Test -60: -60: Mrtx1719_atrop3.cxsmi -60: -60: Test -60: -60: Mrtx1719_atrop4.cxsmi -60: -60: Test -60: -60: Mrtx1719_atropBad1.cxsmi -60: -60: [16:02:38] The 2 defining bonds for an atropisomer are co-planar - atoms are: 11 12 -60: [16:02:38] The 2 defining bonds for an atropisomer are co-planar - atoms are: 11 12 -70: [16:02:38] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -70: [16:02:38] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -60: [16:02:38] The 2 defining bonds for an atropisomer are co-planar - atoms are: 11 12 -60: [16:02:38] The 2 defining bonds for an atropisomer are co-planar - atoms are: 11 12 -60: [16:02:38] The 2 defining bonds for an atropisomer are co-planar - atoms are: 11 12 -70: [16:02:38] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -70: [16:02:38] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -70: [16:02:38] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +70: [12:23:57] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +70: [12:23:57] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +70: [12:23:57] The 2 defining bonds for an atropisomer are co-planar - atoms are: 17 21 +70: [12:23:57] The 2 defining bonds for an atropisomer are co-planar - atoms are: 17 21 +70: [12:23:57] The 2 defining bonds for an atropisomer are co-planar - atoms are: 17 21 +70: [12:23:57] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 2 ignored +70: [12:23:57] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 2 ignored +70: [12:23:57] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 2 ignored +70: [12:23:57] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 2 ignored +70: [12:23:57] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 2 ignored +70: [12:23:57] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 2 ignored +70: [12:23:57] The bonds on one end of an atropisomer are both UP or both DOWN - atoms are: 2 8 +70: [12:23:57] The bonds on one end of an atropisomer are both UP or both DOWN - atoms are: 2 8 +70: [12:23:57] The bonds on one end of an atropisomer are both UP or both DOWN - atoms are: 2 8 +70: [12:23:57] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 2 ignored +70: [12:23:57] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 2 ignored +70: [12:23:57] The 2 defining bonds for an atropisomer are co-planar - atoms are: 2 8 +70: [12:23:57] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 2 ignored +70: [12:23:57] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 2 ignored +70: [12:23:57] The 2 defining bonds for an atropisomer are co-planar - atoms are: 2 8 +70: [12:23:57] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 2 ignored +70: [12:23:57] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 2 ignored +70: [12:23:57] The 2 defining bonds for an atropisomer are co-planar - atoms are: 2 8 +70: [12:23:57] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +70: [12:23:57] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +70: [12:23:57] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +70: [12:23:57] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored +70: [12:23:57] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored +70: [12:23:57] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored +70: [12:23:57] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored +70: [12:23:57] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored +70: [12:23:57] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored +70: [12:23:57] The 2 defining bonds for an atropisomer are co-planar - atoms are: 7 20 +70: [12:23:57] The 2 defining bonds for an atropisomer are co-planar - atoms are: 7 20 +70: [12:23:57] The 2 defining bonds for an atropisomer are co-planar - atoms are: 7 20 +70: [12:23:57] The bonds on one end of an atropisomer are both UP or both DOWN - atoms are: 7 20 +70: [12:23:57] The bonds on one end of an atropisomer are both UP or both DOWN - atoms are: 7 20 +70: [12:23:57] The bonds on one end of an atropisomer are both UP or both DOWN - atoms are: 7 20 +70: [12:23:57] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +70: [12:23:57] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 68: Test 68: 68: NewChiralTest.sdf @@ -18526,253 +18579,869 @@ 68: 68: ProblemShort.mol 68: -68: [16:02:38] For a MultipleSgroup expansion, the matching orphaned bond was not found +68: [12:23:57] For a MultipleSgroup expansion, the matching orphaned bond was not found 68: The multiple sgroup will be ignored -70: [16:02:38] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored -70: [16:02:38] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored -70: [16:02:38] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored -70: [16:02:38] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored -70: [16:02:38] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored -70: [16:02:38] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored -70: [16:02:38] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored -70: [16:02:38] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored -70: [16:02:38] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored -70: [16:02:38] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored -70: [16:02:38] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored -70: [16:02:38] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored -70: [16:02:38] The bonds on one end of an atropisomer are both UP or both DOWN - atoms are: 7 29 -70: [16:02:38] The bonds on one end of an atropisomer are both UP or both DOWN - atoms are: 7 29 -70: [16:02:38] The bonds on one end of an atropisomer are both UP or both DOWN - atoms are: 7 29 -70: [16:02:38] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -70: [16:02:38] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -70: [16:02:38] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -72: [16:02:38] -72: ----------------------------------------- -70: [16:02:38] The 2 defining bonds for an atropisomer are co-planar - atoms are: 17 21 -70: [16:02:38] The 2 defining bonds for an atropisomer are co-planar - atoms are: 17 21 -70: [16:02:38] The 2 defining bonds for an atropisomer are co-planar - atoms are: 17 21 -69: [16:02:38] bond with order 0 found on line 7. This is not part of the MDL specification. -70: [16:02:38] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 2 ignored -70: [16:02:38] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 2 ignored -67: ..............[16:02:38] SMILES Parse Error: syntax error while parsing: invalidsmiles -67: [16:02:38] SMILES Parse Error: check for mistakes around position 1: -67: [16:02:38] invalidsmiles -67: [16:02:38] ^ -67: [16:02:38] SMILES Parse Error: Failed parsing SMILES 'invalidsmiles' for input: 'invalidsmiles' -70: [16:02:38] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 2 ignored -70: [16:02:38] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 2 ignored -70: [16:02:38] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 2 ignored -70: [16:02:38] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 2 ignored -70: [16:02:38] The bonds on one end of an atropisomer are both UP or both DOWN - atoms are: 2 8 -70: [16:02:38] The bonds on one end of an atropisomer are both UP or both DOWN - atoms are: 2 8 -70: [16:02:38] The bonds on one end of an atropisomer are both UP or both DOWN - atoms are: 2 8 -70: [16:02:38] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 2 ignored -70: [16:02:38] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 2 ignored -70: [16:02:38] The 2 defining bonds for an atropisomer are co-planar - atoms are: 2 8 -70: [16:02:38] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 2 ignored -70: [16:02:38] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 2 ignored -70: [16:02:38] The 2 defining bonds for an atropisomer are co-planar - atoms are: 2 8 -70: [16:02:38] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 2 ignored -70: [16:02:38] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 2 ignored -70: [16:02:38] The 2 defining bonds for an atropisomer are co-planar - atoms are: 2 8 -70: [16:02:38] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -70: [16:02:38] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -70: [16:02:38] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -70: [16:02:38] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored -70: [16:02:38] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored -70: [16:02:38] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored -70: [16:02:38] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored -70: [16:02:38] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored -70: [16:02:38] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored -70: [16:02:38] The 2 defining bonds for an atropisomer are co-planar - atoms are: 7 20 -70: [16:02:38] The 2 defining bonds for an atropisomer are co-planar - atoms are: 7 20 -70: [16:02:38] The 2 defining bonds for an atropisomer are co-planar - atoms are: 7 20 -70: [16:02:38] The bonds on one end of an atropisomer are both UP or both DOWN - atoms are: 7 20 -70: [16:02:38] The bonds on one end of an atropisomer are both UP or both DOWN - atoms are: 7 20 -70: [16:02:38] The bonds on one end of an atropisomer are both UP or both DOWN - atoms are: 7 20 -70: [16:02:38] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -70: [16:02:38] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -70: [16:02:38] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -69: [16:02:38] Skipping unrecognized collection type at line 26: MDLV30/HILITE BONDS=(1 7) -69: [16:02:38] Skipping unrecognized collection type at line 27: MDLV30/HILITE ATOMS=(1 7) -69: [16:02:38] Warning: molecule is tagged as 3D, but all Z coords are zero and 2D stereo markers have been found, marking the mol as 2D. -70: [16:02:38] The 2 defining bonds for an atropisomer are co-planar - atoms are: 0 31 -70: [16:02:38] The 2 defining bonds for an atropisomer are co-planar - atoms are: 0 31 -70: [16:02:38] The 2 defining bonds for an atropisomer are co-planar - atoms are: 0 31 -70: [16:02:38] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -71: Randomness seeded to: 3091189465 +70: [12:23:57] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +69: [12:23:57] bond with order 0 found on line 7. This is not part of the MDL specification. +70: [12:23:57] The 2 defining bonds for an atropisomer are co-planar - atoms are: 0 31 +70: [12:23:57] The 2 defining bonds for an atropisomer are co-planar - atoms are: 0 31 +70: [12:23:57] The 2 defining bonds for an atropisomer are co-planar - atoms are: 0 31 +70: [12:23:57] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +70: [12:23:57] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +70: [12:23:57] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +70: [12:23:57] The 2 defining bonds for an atropisomer are co-planar - atoms are: 15 16 +70: [12:23:57] The 2 defining bonds for an atropisomer are co-planar - atoms are: 15 16 +70: [12:23:57] The 2 defining bonds for an atropisomer are co-planar - atoms are: 15 16 +69: [12:23:57] Skipping unrecognized collection type at line 26: MDLV30/HILITE BONDS=(1 7) +69: [12:23:57] Skipping unrecognized collection type at line 27: MDLV30/HILITE ATOMS=(1 7) +69: [12:23:57] Warning: molecule is tagged as 3D, but all Z coords are zero and 2D stereo markers have been found, marking the mol as 2D. +69: 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 +71: Randomness seeded to: 3035063568 71: =============================================================================== 71: All tests passed (15 assertions in 3 test cases) 71: -70: [16:02:38] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -70: [16:02:38] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. - 61/236 Test #71: testSquiggleDoubleBonds ................ Passed 0.36 sec + 60/236 Test #71: testSquiggleDoubleBonds ................ Passed 0.39 sec +test 72 + Start 72: testMolSupplier + +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: [12:23:57] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +70: [12:23:57] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +72: [12:23:57] +72: ----------------------------------------- +70: Atropisomers- 1 hits 3 misses +70: Final results: +70: Found atropisomers in TestMultInSDF.sdf - 1 hits 4 misses + 61/236 Test #70: testAtropisomers ....................... Passed 0.81 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 -70: [16:02:38] The 2 defining bonds for an atropisomer are co-planar - atoms are: 15 16 -70: [16:02:38] The 2 defining bonds for an atropisomer are co-planar - atoms are: 15 16 -70: [16:02:38] The 2 defining bonds for an atropisomer are co-planar - atoms are: 15 16 -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 +29: Checking against /build/reproducible-path/rdkit-202503.1/Code/ForceField/MMFF/test_data/MMFF94_reference.log... +73: [12:23:58] +73: ----------------------------------------- +73: [12:23:58] Finished: testDetermineFormat() +73: [12:23:58] ----------------------------------------- +73: +73: [12:23:58] +73: ----------------------------------------- +67: ..............[12:23:58] SMILES Parse Error: syntax error while parsing: invalidsmiles +67: [12:23:58] SMILES Parse Error: check for mistakes around position 1: +67: [12:23:58] invalidsmiles +67: [12:23:58] ^ +67: [12:23:58] SMILES Parse Error: Failed parsing SMILES 'invalidsmiles' for input: 'invalidsmiles' +72: [12:23:58] Ignoring invalid chirality label: '2_bad_chirality' +73: [12:23:58] Finished: testSdf() +73: [12:23:58] ----------------------------------------- +73: +73: [12:23:58] +73: ----------------------------------------- +73: [12:23:58] Finished: testSmi() +73: [12:23:58] ----------------------------------------- +73: +73: [12:23:58] +73: ----------------------------------------- +72: [12:23:58] Finished: testMolSup() +72: [12:23:58] ----------------------------------------- +72: +72: [12:23:58] ----------------------------------------- 67: ..... 67: ---------------------------------------------------------------------- -67: Ran 19 tests in 0.421s +67: Ran 19 tests in 0.877s 67: 67: OK -72: [16:02:38] Ignoring invalid chirality label: '2_bad_chirality' -73: [16:02:38] -73: ----------------------------------------- -73: [16:02:38] Finished: testDetermineFormat() -73: [16:02:38] ----------------------------------------- +72: [12:23:58] Finished: testRandMolSup() +72: [12:23:58] ----------------------------------------- +72: +72: [12:23:58] ----------------------------------------- +73: [12:23:58] Finished: testMae() +73: [12:23:58] ----------------------------------------- 73: -73: [16:02:38] +73: [12:23:58] 73: ----------------------------------------- - 62/236 Test #67: pyDepictor ............................. Passed 0.89 sec +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: + 62/236 Test #60: cxsmilesTest ........................... Passed 2.60 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 -40: [16:02:38] Finished -40: [16:02:39] testing stability w.r.t. renumbering. -40: [16:02:39] Finished -40: [16:02:39] testing smiles round-tripping. -74: [16:02:39] -74: ----------------------------------------- - 63/236 Test #42: resMolSupplierTest ..................... Passed 3.42 sec +72: [12:23:58] Finished: testSmilesSup() +72: [12:23:58] ----------------------------------------- +72: +72: [12:23:58] ----------------------------------------- +72: [12:23:58] ------------------------------------------------------ +72: [12:23:58] SMILES Parse Error: syntax error while parsing: fail +72: [12:23:58] SMILES Parse Error: check for mistakes around position 1: +72: [12:23:58] fail +72: [12:23:58] ^ +72: [12:23:58] SMILES Parse Error: Failed parsing SMILES 'fail' for input: 'fail' +72: [12:23:58] ERROR: Smiles parse error on line 3 +72: [12:23:58] ERROR: Cannot create molecule from : 'fail' +72: [12:23:58] ------------------------------------------------------ +72: [12:23:58] ------------------------------------------------------ +72: [12:23:58] >>> This may result in an infinite loop. It should finish almost immediately: +72: [12:23:58] <<< done. +72: [12:23:58] Finished: testSmilesSupFromText() +72: [12:23:58] ----------------------------------------- +72: +72: [12:23:58] ----------------------------------------- +73: [12:23:58] Finished: testTdt() +73: [12:23:58] ----------------------------------------- +73: + 63/236 Test #73: testGeneralFileReader .................. Passed 0.48 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 -73: [16:02:39] Finished: testSdf() -73: [16:02:39] ----------------------------------------- -73: -73: [16:02:39] -73: ----------------------------------------- -73: [16:02:39] Finished: testSmi() -73: [16:02:39] ----------------------------------------- -73: -73: [16:02:39] -73: ----------------------------------------- -72: [16:02:39] Finished: testMolSup() -72: [16:02:39] ----------------------------------------- +72: [12:23:58] Finished: testSmilesWriter() +72: [12:23:58] ----------------------------------------- 72: -72: [16:02:39] ----------------------------------------- -70: [16:02:39] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -70: [16:02:39] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -72: [16:02:39] Finished: testRandMolSup() -72: [16:02:39] ----------------------------------------- +72: [12:23:58] ----------------------------------------- +72: [12:23:58] Finished: testSDWriter() +72: [12:23:58] ----------------------------------------- 72: -72: [16:02:39] ----------------------------------------- -70: Atropisomers- 1 hits 3 misses -70: Final results: -70: Found atropisomers in TestMultInSDF.sdf - 1 hits 4 misses - 64/236 Test #70: testAtropisomers ....................... Passed 0.68 sec +72: [12:23:58] ----------------------------------------- +72: [12:23:58] Finished: testSDSupplierEnding() +72: [12:23:58] ----------------------------------------- +72: +72: [12:23:58] ----------------------------------------- +72: [12:23:58] Finished: testSuppliersEmptyFile() +72: [12:23:58] ----------------------------------------- +72: +72: [12:23:58] ----------------------------------------- +72: [12:23:58] Finished: testCisTrans() +72: [12:23:58] ----------------------------------------- +72: +72: [12:23:58] ----------------------------------------- +72: [12:23:58] Finished: testStereoRound() +72: [12:23:58] ----------------------------------------- +72: +72: [12:23:58] ----------------------------------------- +74: [12:23:58] +74: ----------------------------------------- +72: [12:23:58] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +72: [12:23:58] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +72: [12:23:58] Finished: testIssue226() +72: [12:23:58] ----------------------------------------- +72: +72: [12:23:58] ----------------------------------------- +72: [12:23:58] Finished: testTDTSupplier1() +72: [12:23:58] ----------------------------------------- +72: +72: [12:23:58] ----------------------------------------- +72: [12:23:58] Finished: testTDTSupplier2() +72: [12:23:58] ----------------------------------------- +72: +72: [12:23:58] ----------------------------------------- +72: [12:23:58] Finished: testTDTSupplier3() +72: [12:23:58] ----------------------------------------- +72: +72: [12:23:58] ----------------------------------------- +72: [12:23:58] Finished: testSDSupplierFromText() +72: [12:23:58] ----------------------------------------- +72: +72: [12:23:58] ----------------------------------------- + 64/236 Test #67: pyDepictor ............................. Passed 1.89 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 -40: [16:02:39] Finished -40: [16:02:39] testing github #1567: Non-canonical result from MolFragmentToSmiles() -40: [16:02:39] Finished - 65/236 Test #40: hanoiTest .............................. Passed 3.65 sec +72: [12:23:58] ERROR: Problems encountered parsing data fields +72: [12:23:58] ERROR: moving to the beginning of the next molecule +72: [12:23:58] ERROR: Problems encountered parsing data fields +72: [12:23:58] ERROR: moving to the beginning of the next molecule +72: [12:23:58] Spurious data before the first property will be ignored +72: [12:23:58] Property will be truncated after the first blank line +72: [12:23:58] Property will be truncated after the first blank line +72: [12:23:58] Property will be truncated after the first blank line +72: [12:23:58] Finished: testSDSupplierStrLax1() +72: [12:23:58] ----------------------------------------- +72: +72: [12:23:58] ----------------------------------------- +72: [12:23:58] ERROR: Problems encountered parsing data fields +72: [12:23:58] ERROR: moving to the beginning of the next molecule +72: [12:23:58] Property will be truncated after the first blank line +72: [12:23:58] Finished: testSDSupplierStrLax2() +72: [12:23:58] ----------------------------------------- +72: +72: [12:23:58] ----------------------------------------- +72: [12:23:58] ERROR: Problems encountered parsing data fields +72: [12:23:58] ERROR: moving to the beginning of the next molecule +72: [12:23:58] ERROR: Problems encountered parsing data fields +72: [12:23:58] ERROR: moving to the beginning of the next molecule +72: [12:23:58] Spurious data before the first property will be ignored +72: [12:23:58] Property will be truncated after the first blank line +72: [12:23:58] Property will be truncated after the first blank line +72: [12:23:58] Property will be truncated after the first blank line +72: [12:23:58] Finished: testSDSupplierFromTextStrLax1() +72: [12:23:58] ----------------------------------------- +72: +72: [12:23:58] ----------------------------------------- +72: [12:23:58] ERROR: Problems encountered parsing data fields +72: [12:23:58] ERROR: moving to the beginning of the next molecule +72: [12:23:58] Property will be truncated after the first blank line +72: [12:23:58] Finished: testSDSupplierFromTextStrLax2() +72: [12:23:58] ----------------------------------------- +72: +72: [12:23:58] ----------------------------------------- +72: [12:23:58] Finished: testIssue265() +72: [12:23:58] ----------------------------------------- +72: +72: [12:23:58] ----------------------------------------- +72: [12:23:58] ERROR: End of data field name not found +72: [12:23:58] ERROR: moving to the beginning of the next molecule +72: [12:23:58] Explicit valence for atom # 0 F, 2, is greater than permitted +72: [12:23:58] ERROR: Could not sanitize molecule ending on line 16 +72: [12:23:58] ERROR: Explicit valence for atom # 0 F, 2, is greater than permitted +72: [12:23:58] ERROR: Atom line too short: ' 1 2 1 0 0 0 0' on line 12 +72: [12:23:58] ERROR: moving to the beginning of the next molecule +72: [12:23:58] ERROR: Bond line too short: 'M END' on line 18 +72: [12:23:58] ERROR: moving to the beginning of the next molecule +72: [12:23:58] Finished: testSDErrorHandling() +72: [12:23:58] ----------------------------------------- +72: +72: [12:23:58] ----------------------------------------- +72: [12:23:58] Finished: testIssue381() +72: [12:23:58] ----------------------------------------- +72: +72: [12:23:58] ----------------------------------------- +72: [12:23:58] Finished: testSetStreamIndices() +72: [12:23:58] ----------------------------------------- +72: +72: [12:23:58] ----------------------------------------- +72: [12:23:58] Finished: testMixIterAndRandom() +72: [12:23:58] ----------------------------------------- +72: +72: [12:23:58] ----------------------------------------- +72: build: +72: [12:23:58] Finished: testRemoveHs() +72: [12:23:58] ----------------------------------------- +72: +72: [12:23:58] ----------------------------------------- +72: [12:23:58] Finished: testGetItemText() +72: [12:23:58] ----------------------------------------- +72: +72: [12:23:58] ----------------------------------------- + 65/236 Test #76: testTplParser .......................... Passed 0.10 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 -72: [16:02:39] Finished: testSmilesSup() -72: [16:02:39] ----------------------------------------- +68: Test +68: +68: badWedgeError.sdf +68: +68: Test +68: +68: CrossedDoubleBondWithChiralNbr2.sdf +68: +68: Test +68: +68: CrossedDoubleBondWithChiralNbr.sdf +68: +68: Test +68: +68: SimpleWiggleDoubleBond.sdf +68: +68: Test +68: +68: lostStereoAnd.sdf +68: +68: Test +68: +68: DoubleBondChain.sdf +68: +68: Test +68: +68: UnitsError.sdf +68: +68: Test +68: +68: StarAtom.sdf +68: +68: Test +68: +68: nonProprietary.mol +68: +68: Test +68: +68: ChiralTest.sdf +68: +68: Test +68: +68: TestBond1.mol +68: +68: Test +68: +68: Sgroup_MUL_ParentInMiddle.sdf +68: +68: Test +68: +68: BadRxn.rxn +68: +68: Test +68: +68: FalseChiral.mrv +68: +68: Test +68: +68: FalseChiral.mrv +68: +68: Test +68: +68: Cubane.mrv +68: +68: Test +68: +68: NewChiralTest.mrv +68: +68: Test +68: +68: NewChiralTest.mrv +68: +68: Test +68: +68: NewChiralTestNoChiral.mrv +68: +68: Test +68: +68: NewChiralTestNoChiral.mrv +68: +68: Test +68: +68: NewChiralTestAllChiral.mrv +68: +68: Test +68: +68: NewChiralTestAllChiral.mrv +68: +68: Test +68: +68: DataSgroupMissingUnitsDisplayed.mrv +68: +68: Test +68: +68: lostStereoAnd.mrv +68: +68: Test +68: +68: DoubleBondChain.mrv +68: +68: Test +68: +68: WigglyAndCrossed.mrv +68: +68: Test +68: +68: BondTypes.mrv +68: +68: Test +68: +68: EmbeddedSGroupSUP_MUL.mrv +68: +68: Test +68: +68: EmbeddedSgroupCOP_SUP.mrv +68: +68: Test +68: +68: EmbeddedSgroupDAT_SUP.mrv +68: +68: Test +68: +68: EmbeddedSgroupMULTICENTER_SUP.mrv +68: +68: Test +68: +68: EmbeddedSgroupMUL_MUL.mrv +68: +68: Test +68: +68: EmbeddedSgroupMUL_MUL2.mrv +68: +68: Test +68: +68: EmbeddedSgroupMUL_SUP.mrv +68: +68: Test +68: +68: EmbeddedSgroupSRU_SUP.mrv +68: +68: Test +68: +68: EmbeddedSgroupSUPEXP_SUP.mrv +68: +68: Test +68: +68: EmbeddedSgroupSUPEXP_SUP2.mrv +68: +68: Test +68: +68: EmbeddedSgroupSUP_MULTICENTER.mrv +68: +68: Test +68: +68: EmbeddedSgroupSUP_SUP.mrv +68: +68: Test +68: +68: EmbeddedSgroupSUP_SUP2.mrv +68: +68: Test +68: +68: RgroupBad.mrv +68: +68: Test +68: +68: valenceLessThanDrawn.mrv +68: +68: Test +68: +68: data_sgroup_no_fieldname.mrv +68: +68: Test +68: +68: data_sgroup_empty_field_data.mrv +68: +68: Test +68: +68: radical_value.mrv +68: +68: Test +68: +68: emptyOneLineAtomList.mrv +68: +68: Test +68: +68: mrvValence_value.mrv +68: +68: Test +68: +68: ChiralTest2.mrv +68: +68: Test +68: +68: ChiralTest.mrv +68: +68: Test +68: +68: SnCl2.mrv +68: +68: Test +68: +68: SnH2Cl2.mrv +68: +68: Test +68: +68: marvin01.mrv +68: +68: Test +68: +68: marvin02.mrv +68: +68: Test +68: +68: marvin07.mrv +68: +68: Test +68: +68: marvin10.mrv +68: +68: Test +68: +68: marvin06.mrv +68: +68: Test +68: +68: marvin12.mrv +68: +68: Test +68: +68: EmptyMol.mrv +68: +68: Test +68: +68: Sparse.mrv +68: +68: Test +68: +68: Sparse2.mrv +68: +68: Test +68: +68: Sparse3.mrv +68: +68: Test +68: +68: MarvinNoCoords.mrv +68: +68: Test +68: +68: aspirin.mrv +68: +68: Test +68: +68: MarvinStereoGroupsZeros.mrv +68: +68: Test +68: +68: MarvinStereoGroupsAbs.mrv +68: +68: Test +68: +68: triphenylphosphine.mrv +68: +68: Test +68: +68: MarvinOldSuperGroupTest.mrv +68: +68: Test +68: +68: RadicalTests.mrv +68: +68: Test +68: +68: AnyBond.mrv +68: +68: Test +68: +68: cisBenzene.mrv +68: +68: Test +68: +68: DativeBond.mrv +68: +68: Test +68: +68: MultipleSgroup.mrv +68: +68: Test +68: +68: SgroupExpanded.mrv +68: +68: Test +68: +68: SgroupMultAttach.mrv +68: +68: Test +68: +68: MarvinMissingX2.mrv +68: +68: Test +68: +68: MarvinMissingY2.mrv +68: +68: Test +68: +68: DataSgroup.mrv +68: +68: Test +68: +68: MulticenterSgroup.mrv +68: +68: [12:23:58] Can't kekulize mol. Unkekulized atoms: 6 7 8 9 10 +68: [12:23:58] Can't kekulize mol. Unkekulized atoms: 6 7 8 9 10 +72: [12:23:58] Finished: testForwardSDSupplier() +72: [12:23:58] ----------------------------------------- 72: -72: [16:02:39] ----------------------------------------- -72: [16:02:39] ------------------------------------------------------ -72: [16:02:39] SMILES Parse Error: syntax error while parsing: fail -72: [16:02:39] SMILES Parse Error: check for mistakes around position 1: -72: [16:02:39] fail -72: [16:02:39] ^ -72: [16:02:39] SMILES Parse Error: Failed parsing SMILES 'fail' for input: 'fail' -72: [16:02:39] ERROR: Smiles parse error on line 3 -72: [16:02:39] ERROR: Cannot create molecule from : 'fail' -72: [16:02:39] ------------------------------------------------------ -73: [16:02:39] Finished: testMae() -73: [16:02:39] ----------------------------------------- -73: -73: [16:02:39] -73: ----------------------------------------- -72: [16:02:39] ------------------------------------------------------ -72: [16:02:39] >>> This may result in an infinite loop. It should finish almost immediately: -72: [16:02:39] <<< done. -72: [16:02:39] Finished: testSmilesSupFromText() -72: [16:02:39] ----------------------------------------- +72: [12:23:58] ----------------------------------------- +72: [12:23:58] Finished: testMissingCRSDSupplier() +72: [12:23:58] ----------------------------------------- 72: -72: [16:02:39] ----------------------------------------- -73: [16:02:39] Finished: testTdt() -73: [16:02:39] ----------------------------------------- -73: -72: [16:02:39] Finished: testSmilesWriter() -72: [16:02:39] ----------------------------------------- +72: [12:23:58] ----------------------------------------- +72: [12:23:58] Finished: testIssue3482695() +72: [12:23:58] ----------------------------------------- 72: -72: [16:02:39] ----------------------------------------- - 66/236 Test #73: testGeneralFileReader .................. Passed 0.33 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 -72: [16:02:39] Finished: testSDWriter() -72: [16:02:39] ----------------------------------------- +72: [12:23:58] ----------------------------------------- +72: [12:23:58] ERROR: Cannot convert 'foo' to unsigned int on line 557 +72: [12:23:58] ERROR: moving to the beginning of the next molecule +72: [12:23:58] Finished: testIssue3525673() +72: [12:23:58] ----------------------------------------- 72: -72: [16:02:39] ----------------------------------------- -72: [16:02:39] Finished: testSDSupplierEnding() -72: [16:02:39] ----------------------------------------- +72: [12:23:58] ----------------------------------------- +72: [12:23:58] Finished: testBlankLinesInProps() +72: [12:23:58] ----------------------------------------- 72: -72: [16:02:39] ----------------------------------------- -72: [16:02:39] Finished: testSuppliersEmptyFile() -72: [16:02:39] ----------------------------------------- +72: [12:23:58] ----------------------------------------- +72: [12:23:58] Finished: testSkipLines() +72: [12:23:58] ----------------------------------------- 72: -72: [16:02:39] ----------------------------------------- -72: [16:02:39] Finished: testCisTrans() -72: [16:02:39] ----------------------------------------- +72: [12:23:58] ----------------------------------------- +72: [12:23:58] Finished: testGitHub23() +72: [12:23:58] ----------------------------------------- 72: -72: [16:02:39] ----------------------------------------- - 67/236 Test #76: testTplParser .......................... Passed 0.11 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 -72: [16:02:39] Finished: testStereoRound() -72: [16:02:39] ----------------------------------------- +72: [12:23:58] ----------------------------------------- +72: [12:23:58] Finished: testGitHub88() +72: [12:23:58] ----------------------------------------- 72: -72: [16:02:39] ----------------------------------------- -72: [16:02:39] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -72: [16:02:39] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -72: [16:02:39] Finished: testIssue226() -72: [16:02:39] ----------------------------------------- +72: [12:23:58] ----------------------------------------- +68: Test +68: +68: GenericSgroup.mrv +68: +68: Test +68: +68: MonomerSgroup.mrv +68: +68: Test +68: +68: modification_sgroup.mrv +68: +68: Test +68: +68: copolymer_sgroup.mrv +68: +68: Test +68: +68: MultipleSgroupParentInMiddleOfAtomBlock.mrv +68: +68: Test +68: +68: EmbeddedSgroups.mrv +68: +68: Test +68: +68: marvin03.mrv +68: +68: Test +68: +68: MarvinBadMissingMolID.mrv +68: +68: [12:23:58] +68: +68: **** +68: Test Assert +68: Expression Failed: +68: Violation occurred on line 329 in file ./Code/GraphMol/MarvinParse/testMrvToMol.cpp +68: Failed Expression: GetExpectedValue(expectedMrvName) == outMolStr +68: ---------- +68: Stacktrace: +68: 0# Invar::Invariant::toString[abi:cxx11]() const in /build/reproducible-path/rdkit-202503.1/obj-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# 0x0000AAAAE829AC5C in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/MarvinParse/testMrvToMol +68: 3# 0x0000AAAAE82A5D5C in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/MarvinParse/testMrvToMol +68: 4# 0x0000AAAAE8294918 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/MarvinParse/testMrvToMol +68: 5# 0x0000FFFFB1B6229C in /lib/aarch64-linux-gnu/libc.so.6 +68: 6# __libc_start_main in /lib/aarch64-linux-gnu/libc.so.6 +68: 7# 0x0000AAAAE8294B70 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/MarvinParse/testMrvToMol +68: ---------- +68: **** +68: +72: [12:23:58] Finished: testGitHub2285() +72: [12:23:58] ----------------------------------------- 72: -72: [16:02:39] ----------------------------------------- -72: [16:02:39] Finished: testTDTSupplier1() -72: [16:02:39] ----------------------------------------- +72: [12:23:58] ----------------------------------------- +72: [12:23:58] SMILES Parse Error: unclosed ring for input: 'c1ccccc' +72: [12:23:58] ERROR: Smiles parse error on line 1 +72: [12:23:58] ERROR: Cannot create molecule from : 'c1ccccc' +72: [12:23:58] SMILES Parse Error: extra open parentheses while parsing: C(C +72: [12:23:58] SMILES Parse Error: check for mistakes around position 2: +72: [12:23:58] C(C +72: [12:23:58] ~^ +72: [12:23:58] SMILES Parse Error: Failed parsing SMILES 'C(C' for input: 'C(C' +72: [12:23:58] ERROR: Smiles parse error on line 3 +72: [12:23:58] ERROR: Cannot create molecule from : 'C(C' +72: [12:23:58] Explicit valence for atom # 1 C, 5, is greater than permitted +68: Test +68: +68: MarvinBadMissingAtomID.mrv +68: +68: Expected id, elementType for an atom definition in MRV file +68: Test +68: +68: MarvinBadX2.mrv +68: +68: The values x2 and y2 must be large floats in MRV file +68: Test +68: +68: MarvinBadY2.mrv +68: +68: The values x2 and y2 must be large floats in MRV file +72: [12:23:58] ERROR: Could not sanitize molecule on line 5 +72: [12:23:58] ERROR: Explicit valence for atom # 1 C, 5, is greater than permitted +72: [12:23:58] Explicit valence for atom # 1 F, 2, is greater than permitted +72: [12:23:58] ERROR: Could not sanitize molecule ending on line 21 +72: [12:23:58] ERROR: Explicit valence for atom # 1 F, 2, is greater than permitted +72: [12:23:58] Explicit valence for atom # 1 F, 2, is greater than permitted +72: [12:23:58] ERROR: Could not sanitize molecule ending on line 21 +72: [12:23:58] ERROR: Explicit valence for atom # 1 F, 2, is greater than permitted +72: [12:23:58] Explicit valence for atom # 1 F, 2, is greater than permitted +72: [12:23:58] ERROR: Could not sanitize molecule ending on line 21 +72: [12:23:58] ERROR: Explicit valence for atom # 1 F, 2, is greater than permitted +72: [12:23:58] ERROR: Atom line too short: ' -9.6' on line 28 +72: [12:23:58] ERROR: moving to the beginning of the next molecule +72: [12:23:58] Explicit valence for atom # 1 F, 2, is greater than permitted +72: [12:23:58] ERROR: Could not sanitize molecule ending on line 21 +72: [12:23:58] ERROR: Explicit valence for atom # 1 F, 2, is greater than permitted +72: [12:23:58] ERROR: Atom line too short: ' -9.6' on line 28 +72: [12:23:58] ERROR: moving to the beginning of the next molecule +72: [12:23:58] Finished: testGitHub2479() +72: [12:23:58] ----------------------------------------- +72: +72: [12:23:58] ----------------------------------------- +72: [12:23:58] Ignoring invalid chirality label: '7_S_8_9_6_10' +72: [12:23:58] Finished: testGitHub2881() +72: [12:23:58] ----------------------------------------- 72: -72: [16:02:39] ----------------------------------------- -72: [16:02:39] Finished: testTDTSupplier2() -72: [16:02:39] ----------------------------------------- +72: [12:23:58] ----------------------------------------- +72: [12:23:58] Finished: testGitHub3517() +72: [12:23:58] ----------------------------------------- 72: -72: [16:02:39] ----------------------------------------- +68: Test +68: +68: MarvinBadStereoGroupsAbs.mrv +68: +68: Unrecognized group definition + 66/236 Test #72: testMolSupplier ........................ Passed 0.89 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: MarvinBadElementType.mrv +68: +68: Test +68: +68: MarvinBadMissingBondID.mrv +68: +68: Test +68: +68: MarvinBadMissingBondAtomRefs +68: +68: Test +68: +68: MarvinBadMissingBondOrder.mrv +68: +68: bond must have one of: order, queryType, or convention in MRV File +68: Test +68: +68: MarvinBadMissingSruMolID.mrv +68: +68: Expected a molID in MRV file +68: Test +68: +68: MarvinBadMissingSruID.mrv +68: +68: Test +68: +68: MarvinBadMissingSruRole.mrv +68: +68: Test +68: +68: MarvinBadMissingSruAtomRef.mrv +68: +68: Test +68: +68: MarvinBadMissingSruTitle.mrv +68: +68: Test +68: +68: MarvinBadSruAtomRef.mrv +68: +68: AtomRef specification for an SRU, Copolymer, or Modification group definition was not found in any parent +68: Test +68: +68: MarvinBadSruID.mrv +68: +68: Test +68: +68: MarvinBadSruRole.mrv +68: +68: Test +68: +68: MarvinBadSruAtomRef.mrv +68: +68: AtomRef specification for an SRU, Copolymer, or Modification group definition was not found in any parent +68: Test +68: +68: MarvinBadSruAtomRef.mrv +68: +68: AtomRef specification for an SRU, Copolymer, or Modification group definition was not found in any parent +68: Test +68: +68: MarvinBadSruConnect.mrv +68: +68: Expected a connect string of "hh, ht, eu" for a SruSgroup definition in MRV file +68: Test +68: +68: MarvinBadSupAttachAtom.mrv +68: +68: Atom specification for an AttachmentPoint definition must be in the parent's atom array in MRV file +68: Test +68: +68: MarvinBadSupAttachBond.mrv +68: +68: Bond specification for an AttachmentPoint definition must be in the bond array in MRV file +68: Test +68: +68: MarvinBadSupAttachOrder.mrv +68: +68: Order for an AttachmentPoint definition must be an integer in MRV file +68: Test +68: +68: MarvinBadSupAttachAtom.mrv +68: +68: Atom specification for an AttachmentPoint definition must be in the parent's atom array in MRV file +68: Test +68: +68: MarvinBadSupAttachAtom.mrv +68: +68: Atom specification for an AttachmentPoint definition must be in the parent's atom array in MRV file +68: Test +68: +68: MarvinBadSupAttachAtom.mrv +68: +68: Atom specification for an AttachmentPoint definition must be in the parent's atom array in MRV file +68: Test +68: +68: MarvinBadSupMissingAttachBond.mrv +68: +68: No attachment point found for bond to the condensed atom in a superatomSgroup +68: Test +68: +68: MarvinBadSupMissingAttachOrder.mrv +68: +68: Expected atom, order and bond, for an AttachmentPoint definition in MRV file 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 @@ -19270,14 +19939,6 @@ 78: CONECT 163 164 164 170 78: CONECT 165 166 78: CONECT 166 167 -72: [16:02:39] Finished: testTDTSupplier3() -72: [16:02:39] ----------------------------------------- -72: -72: [16:02:39] ----------------------------------------- -72: [16:02:39] Finished: testSDSupplierFromText() -72: [16:02:39] ----------------------------------------- -72: -72: [16:02:39] ----------------------------------------- 78: CONECT 167 168 168 169 78: CONECT 170 171 78: CONECT 171 172 174 @@ -19765,311 +20426,30 @@ 78: CONECT 27 28 28 29 78: END 78: -72: [16:02:39] ERROR: Problems encountered parsing data fields -72: [16:02:39] ERROR: moving to the beginning of the next molecule -72: [16:02:39] ERROR: Problems encountered parsing data fields -72: [16:02:39] ERROR: moving to the beginning of the next molecule -72: [16:02:39] Spurious data before the first property will be ignored -72: [16:02:39] Property will be truncated after the first blank line -72: [16:02:39] Property will be truncated after the first blank line -72: [16:02:39] Property will be truncated after the first blank line - 68/236 Test #78: testSequence ........................... Passed 0.08 sec -72: [16:02:39] Finished: testSDSupplierStrLax1() -72: [16:02:39] ----------------------------------------- -72: -72: [16:02:39] ----------------------------------------- + 67/236 Test #77: testMol2ToMol .......................... Passed 0.24 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 + 68/236 Test #78: testSequence ........................... Passed 0.18 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 -72: [16:02:39] ERROR: Problems encountered parsing data fields -72: [16:02:39] ERROR: moving to the beginning of the next molecule -72: [16:02:39] Property will be truncated after the first blank line -72: [16:02:39] Finished: testSDSupplierStrLax2() -72: [16:02:39] ----------------------------------------- -72: -72: [16:02:39] ----------------------------------------- -72: [16:02:39] ERROR: Problems encountered parsing data fields -72: [16:02:39] ERROR: moving to the beginning of the next molecule -72: [16:02:39] ERROR: Problems encountered parsing data fields -72: [16:02:39] ERROR: moving to the beginning of the next molecule -72: [16:02:39] Spurious data before the first property will be ignored -72: [16:02:39] Property will be truncated after the first blank line -72: [16:02:39] Property will be truncated after the first blank line -72: [16:02:39] Property will be truncated after the first blank line -72: [16:02:39] Finished: testSDSupplierFromTextStrLax1() -72: [16:02:39] ----------------------------------------- -72: -72: [16:02:39] ----------------------------------------- -72: [16:02:39] ERROR: Problems encountered parsing data fields -72: [16:02:39] ERROR: moving to the beginning of the next molecule -72: [16:02:39] Property will be truncated after the first blank line -72: [16:02:39] Finished: testSDSupplierFromTextStrLax2() -72: [16:02:39] ----------------------------------------- -72: -72: [16:02:39] ----------------------------------------- - 69/236 Test #79: testExtendedStereoParsing .............. Passed 0.07 sec + 69/236 Test #79: testExtendedStereoParsing .............. Passed 0.08 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 -72: [16:02:39] Finished: testIssue265() -72: [16:02:39] ----------------------------------------- -72: -72: [16:02:39] ----------------------------------------- -72: [16:02:39] ERROR: End of data field name not found -72: [16:02:39] ERROR: moving to the beginning of the next molecule -72: [16:02:39] Explicit valence for atom # 0 F, 2, is greater than permitted -72: [16:02:39] ERROR: Could not sanitize molecule ending on line 16 -72: [16:02:39] ERROR: Explicit valence for atom # 0 F, 2, is greater than permitted - 70/236 Test #77: testMol2ToMol .......................... Passed 0.18 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 -72: [16:02:39] ERROR: Atom line too short: ' 1 2 1 0 0 0 0' on line 12 -72: [16:02:39] ERROR: moving to the beginning of the next molecule -72: [16:02:39] ERROR: Bond line too short: 'M END' on line 18 -72: [16:02:39] ERROR: moving to the beginning of the next molecule -72: [16:02:39] Finished: testSDErrorHandling() -72: [16:02:39] ----------------------------------------- -72: -72: [16:02:39] ----------------------------------------- -72: [16:02:39] Finished: testIssue381() -72: [16:02:39] ----------------------------------------- -72: -72: [16:02:39] ----------------------------------------- -72: [16:02:39] Finished: testSetStreamIndices() -72: [16:02:39] ----------------------------------------- -72: -72: [16:02:39] ----------------------------------------- -72: [16:02:39] Finished: testMixIterAndRandom() -72: [16:02:39] ----------------------------------------- -72: -72: [16:02:39] ----------------------------------------- -72: build: -72: [16:02:39] Finished: testRemoveHs() -72: [16:02:39] ----------------------------------------- -72: -72: [16:02:39] ----------------------------------------- -72: [16:02:39] Finished: testGetItemText() -72: [16:02:39] ----------------------------------------- -72: -72: [16:02:39] ----------------------------------------- -72: [16:02:39] Finished: testForwardSDSupplier() -72: [16:02:39] ----------------------------------------- -72: -72: [16:02:39] ----------------------------------------- -72: [16:02:39] Finished: testMissingCRSDSupplier() -72: [16:02:39] ----------------------------------------- -72: -72: [16:02:39] ----------------------------------------- -72: [16:02:39] Finished: testIssue3482695() -72: [16:02:39] ----------------------------------------- -72: -72: [16:02:39] ----------------------------------------- -72: [16:02:39] ERROR: Cannot convert 'foo' to unsigned int on line 557 -72: [16:02:39] ERROR: moving to the beginning of the next molecule -72: [16:02:39] Finished: testIssue3525673() -72: [16:02:39] ----------------------------------------- -72: -72: [16:02:39] ----------------------------------------- -72: [16:02:39] Finished: testBlankLinesInProps() -72: [16:02:39] ----------------------------------------- -72: -72: [16:02:39] ----------------------------------------- -72: [16:02:39] Finished: testSkipLines() -72: [16:02:39] ----------------------------------------- -72: -72: [16:02:39] ----------------------------------------- -69: [16:02:39] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 1 ignored -69: [16:02:39] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 1 ignored -69: [16:02:39] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 1 ignored -69: [16:02:39] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 1 ignored -72: [16:02:39] Finished: testGitHub23() -72: [16:02:39] ----------------------------------------- -72: -72: [16:02:39] ----------------------------------------- -72: [16:02:39] Finished: testGitHub88() -72: [16:02:39] ----------------------------------------- -72: -72: [16:02:39] ----------------------------------------- -69: [16:02:39] 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*] -72: [16:02:39] Finished: testGitHub2285() -72: [16:02:39] ----------------------------------------- -72: -72: [16:02:39] ----------------------------------------- -72: [16:02:39] SMILES Parse Error: unclosed ring for input: 'c1ccccc' -72: [16:02:39] ERROR: Smiles parse error on line 1 -72: [16:02:39] ERROR: Cannot create molecule from : 'c1ccccc' -72: [16:02:39] SMILES Parse Error: extra open parentheses while parsing: C(C -72: [16:02:39] SMILES Parse Error: check for mistakes around position 2: -72: [16:02:39] C(C -72: [16:02:39] ~^ -72: [16:02:39] SMILES Parse Error: Failed parsing SMILES 'C(C' for input: 'C(C' -72: [16:02:39] ERROR: Smiles parse error on line 3 -72: [16:02:39] ERROR: Cannot create molecule from : 'C(C' -72: [16:02:39] Explicit valence for atom # 1 C, 5, is greater than permitted -72: [16:02:39] ERROR: Could not sanitize molecule on line 5 -72: [16:02:39] ERROR: Explicit valence for atom # 1 C, 5, is greater than permitted -69: [16:02:39] -69: -69: **** -72: [16:02:39] Explicit valence for atom # 1 F, 2, is greater than permitted -72: [16:02:39] ERROR: Could not sanitize molecule ending on line 21 -72: [16:02:39] ERROR: Explicit valence for atom # 1 F, 2, is greater than permitted -72: [16:02:39] Explicit valence for atom # 1 F, 2, is greater than permitted -72: [16:02:39] ERROR: Could not sanitize molecule ending on line 21 -72: [16:02:39] ERROR: Explicit valence for atom # 1 F, 2, is greater than permitted -72: [16:02:39] Explicit valence for atom # 1 F, 2, is greater than permitted -72: [16:02:39] ERROR: Could not sanitize molecule ending on line 21 -72: [16:02:39] ERROR: Explicit valence for atom # 1 F, 2, is greater than permitted -72: [16:02:39] ERROR: Atom line too short: ' -9.6' on line 28 -72: [16:02:39] ERROR: moving to the beginning of the next molecule -72: [16:02:39] Explicit valence for atom # 1 F, 2, is greater than permitted -72: [16:02:39] ERROR: Could not sanitize molecule ending on line 21 -72: [16:02:39] ERROR: Explicit valence for atom # 1 F, 2, is greater than permitted -72: [16:02:39] ERROR: Atom line too short: ' -9.6' on line 28 -72: [16:02:39] ERROR: moving to the beginning of the next molecule -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# 0x0000FFFF8B847F24 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu//lib/libRDKitFileParsers.so.1 -69: 4# 0x0000FFFF8B855B20 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu//lib/libRDKitFileParsers.so.1 -69: 5# 0x0000FFFF8B856A4C 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# 0x0000AAAABE96F77C in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersTest1 -69: 10# 0x0000AAAABE9E4944 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersTest1 -69: 11# 0x0000AAAABE955BF8 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersTest1 -69: 12# 0x0000FFFF8AF1229C in /lib/aarch64-linux-gnu/libc.so.6 -69: 13# __libc_start_main in /lib/aarch64-linux-gnu/libc.so.6 -69: 14# 0x0000AAAABE955E30 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersTest1 -69: ---------- -69: **** -69: -72: [16:02:39] Finished: testGitHub2479() -72: [16:02:39] ----------------------------------------- -72: -72: [16:02:39] ----------------------------------------- -72: [16:02:39] Ignoring invalid chirality label: '7_S_8_9_6_10' -72: [16:02:39] Finished: testGitHub2881() -72: [16:02:39] ----------------------------------------- -72: -72: [16:02:39] ----------------------------------------- -72: [16:02:39] Finished: testGitHub3517() -72: [16:02:39] ----------------------------------------- -72: - 71/236 Test #72: testMolSupplier ........................ Passed 0.95 sec -test 83 - Start 83: cdxmlParserCatchTest - -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 -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: - 72/236 Test #60: cxsmilesTest ........................... Passed 2.21 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 -68: Test -68: -68: badWedgeError.sdf -68: -68: Test -68: -68: CrossedDoubleBondWithChiralNbr2.sdf -68: -68: Test -68: -68: CrossedDoubleBondWithChiralNbr.sdf -68: -68: Test -68: -68: SimpleWiggleDoubleBond.sdf -68: -68: Test -68: -68: lostStereoAnd.sdf -68: -68: Test -68: -68: DoubleBondChain.sdf -68: -68: Test -68: -68: UnitsError.sdf -68: -68: Test -68: -68: StarAtom.sdf -68: -68: Test -68: -68: nonProprietary.mol -68: -68: Test -68: -68: ChiralTest.sdf -68: -68: Test -68: -68: TestBond1.mol -68: -68: Test -68: -68: Sgroup_MUL_ParentInMiddle.sdf -68: -68: Test -68: -68: BadRxn.rxn -68: -68: Test -68: -68: FalseChiral.mrv -68: 68: Test 68: -68: FalseChiral.mrv +68: marvin03.mrv 68: 68: Test 68: @@ -20077,509 +20457,238 @@ 68: 68: Test 68: -68: NewChiralTest.mrv -68: -68: Test -68: -68: NewChiralTest.mrv -68: -68: Test -68: -68: NewChiralTestNoChiral.mrv -68: -68: Test -68: -68: NewChiralTestNoChiral.mrv -68: -68: Test -68: -68: NewChiralTestAllChiral.mrv -68: -68: Test -68: -68: NewChiralTestAllChiral.mrv -68: -68: Test -68: -68: DataSgroupMissingUnitsDisplayed.mrv -68: -68: Test -68: -68: lostStereoAnd.mrv -68: -68: Test -68: -68: DoubleBondChain.mrv -68: -68: Test -68: -68: WigglyAndCrossed.mrv -68: -68: Test -68: -68: BondTypes.mrv -68: -68: Test -68: -68: EmbeddedSGroupSUP_MUL.mrv -68: -68: Test -68: -68: EmbeddedSgroupCOP_SUP.mrv -68: -68: Test -68: -68: EmbeddedSgroupDAT_SUP.mrv -68: -68: Test -68: -68: EmbeddedSgroupMULTICENTER_SUP.mrv -68: -68: Test -68: -68: EmbeddedSgroupMUL_MUL.mrv -68: -68: Test -68: -68: EmbeddedSgroupMUL_MUL2.mrv -68: -68: Test -68: -68: EmbeddedSgroupMUL_SUP.mrv -68: -68: Test -68: -68: EmbeddedSgroupSRU_SUP.mrv -68: -68: Test -68: -68: EmbeddedSgroupSUPEXP_SUP.mrv -68: -68: Test -68: -68: EmbeddedSgroupSUPEXP_SUP2.mrv -68: -68: Test -68: -68: EmbeddedSgroupSUP_MULTICENTER.mrv -68: -68: Test -68: -68: EmbeddedSgroupSUP_SUP.mrv -68: -68: Test -68: -68: EmbeddedSgroupSUP_SUP2.mrv -68: -68: Test -68: -68: RgroupBad.mrv -68: -68: Test -68: -68: valenceLessThanDrawn.mrv -68: -68: Test -68: -68: data_sgroup_no_fieldname.mrv -68: -68: Test -68: -68: data_sgroup_empty_field_data.mrv -68: -68: Test -68: -68: radical_value.mrv -68: -68: Test -68: -68: emptyOneLineAtomList.mrv -68: -68: Test -68: -68: mrvValence_value.mrv -68: -68: Test -68: -68: ChiralTest2.mrv -68: -68: Test -68: -68: ChiralTest.mrv -68: -68: Test -68: -68: SnCl2.mrv -68: -68: Test -68: -68: SnH2Cl2.mrv -68: -68: Test -68: -68: marvin01.mrv -68: -68: Test -68: -68: marvin02.mrv -68: -68: Test -68: -68: marvin07.mrv -68: -68: Test -68: -68: marvin10.mrv -68: -68: Test -68: -68: marvin06.mrv -68: -68: Test -68: -68: marvin12.mrv -68: -68: Test -68: -68: EmptyMol.mrv -68: -68: Test -68: -68: Sparse.mrv -68: -68: Test -68: -68: Sparse2.mrv -68: -68: Test -68: -68: Sparse3.mrv -68: -68: Test -68: -68: MarvinNoCoords.mrv -68: -68: Test -68: -68: aspirin.mrv -68: -68: Test -68: -68: MarvinStereoGroupsZeros.mrv -68: -68: Test -68: -68: MarvinStereoGroupsAbs.mrv -68: -68: Test -68: -68: triphenylphosphine.mrv -68: -68: Test -68: -68: MarvinOldSuperGroupTest.mrv -68: -68: Test -68: -68: RadicalTests.mrv -68: -68: Test -68: -68: AnyBond.mrv -68: -68: Test -68: -68: cisBenzene.mrv -68: -68: Test -68: -68: DativeBond.mrv -68: -68: Test -68: -68: MultipleSgroup.mrv -68: -68: Test -68: -68: SgroupExpanded.mrv -68: -68: Test -68: -68: SgroupMultAttach.mrv -68: -68: Test -68: -68: MarvinMissingX2.mrv -68: -68: Test -68: -68: MarvinMissingY2.mrv +68: FalseAtropisomer.mrv 68: 68: Test 68: -68: DataSgroup.mrv +68: AtropEnhancedStereo.mrv 68: 68: Test 68: -68: MulticenterSgroup.mrv +68: AtropManyChirals.mrv 68: -68: [16:02:39] Can't kekulize mol. Unkekulized atoms: 6 7 8 9 10 -68: [16:02:39] Can't kekulize mol. Unkekulized atoms: 6 7 8 9 10 -69: [16:02:39] 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: [16:02:39] 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: GenericSgroup.mrv +68: AtropManyChiralsEnhanced.mrv 68: 68: Test 68: -68: MonomerSgroup.mrv +68: AtropManyChiralsEnhanced2.mrv 68: 68: Test 68: -68: modification_sgroup.mrv +68: AtropManyChiralsEnhanced3.mrv 68: 68: Test 68: -68: copolymer_sgroup.mrv +68: AtropManyChiralsEnhanced4.mrv 68: 68: Test 68: -68: MultipleSgroupParentInMiddleOfAtomBlock.mrv +68: BMS-986142_3d_chiral.mrv 68: 68: Test 68: -68: EmbeddedSgroups.mrv +68: BMS-986142_3d.mrv 68: 68: Test 68: -68: marvin03.mrv +68: BMS-986142_atrop1.mrv 68: 68: Test 68: -68: MarvinBadMissingMolID.mrv -68: -68: [16:02:39] -68: -68: **** -68: Test Assert -68: Expression Failed: -68: Violation occurred on line 329 in file ./Code/GraphMol/MarvinParse/testMrvToMol.cpp -68: Failed Expression: GetExpectedValue(expectedMrvName) == outMolStr -68: ---------- -68: Stacktrace: -68: 0# Invar::Invariant::toString[abi:cxx11]() const in /build/reproducible-path/rdkit-202503.1/obj-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# 0x0000AAAAD385AC5C in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/MarvinParse/testMrvToMol -68: 3# 0x0000AAAAD3865D5C in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/MarvinParse/testMrvToMol -68: 4# 0x0000AAAAD3854918 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/MarvinParse/testMrvToMol -68: 5# 0x0000FFFFA9AD229C in /lib/aarch64-linux-gnu/libc.so.6 -68: 6# __libc_start_main in /lib/aarch64-linux-gnu/libc.so.6 -68: 7# 0x0000AAAAD3854B70 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/MarvinParse/testMrvToMol -68: ---------- -68: **** +68: BMS-986142_atrop2.mrv 68: 68: Test 68: -68: MarvinBadMissingAtomID.mrv +68: BMS-986142_atrop3.mrv 68: -68: Expected id, elementType for an atom definition in MRV file 68: Test 68: -68: MarvinBadX2.mrv +68: BMS-986142_atrop4.mrv 68: -68: The values x2 and y2 must be large floats in MRV file 68: Test 68: -68: MarvinBadY2.mrv +68: BMS-986142_atrop5.mrv 68: -68: The values x2 and y2 must be large floats in MRV file +68: [12:23:58] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored +68: [12:23:58] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored 68: Test 68: -68: MarvinBadStereoGroupsAbs.mrv +68: BMS-986142_atrop6.mrv 68: -68: Unrecognized group definition 68: Test 68: -68: MarvinBadElementType.mrv +68: BMS-986142_atrop7.mrv 68: 68: Test 68: -68: MarvinBadMissingBondID.mrv +68: BMS-986142_atrop8.mrv 68: +68: [12:23:59] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored +68: [12:23:59] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored 68: Test 68: -68: MarvinBadMissingBondAtomRefs +68: BMS-986142_atropBad2.mrv 68: +68: [12:23:59] The bonds on one end of an atropisomer are both UP or both DOWN - atoms are: 7 29 +75: [12:23:59] 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: MarvinBadMissingBondOrder.mrv +68: JDQ443_3d.mrv 68: -68: bond must have one of: order, queryType, or convention in MRV File 68: Test 68: -68: MarvinBadMissingSruMolID.mrv +68: JDQ443_atrop1.mrv 68: -68: Expected a molID in MRV file 68: Test 68: -68: MarvinBadMissingSruID.mrv +68: JDQ443_atrop2.mrv 68: 68: Test 68: -68: MarvinBadMissingSruRole.mrv +68: JDQ443_atrop3.mrv 68: 68: Test 68: -68: MarvinBadMissingSruAtomRef.mrv +68: JDQ443_atropBad1.mrv 68: +68: [12:23:59] The 2 defining bonds for an atropisomer are co-planar - atoms are: 17 21 +75: 0.40201265 0.40201265 +75: -0.13299436 -0.13299436 +75: 1.00000017 1.00000017 +75: 0.8762226 0.8762226 +75: 0.9973909 0.9973909 +75: 1.00000003 1.00000003 +75: 0.36613799 0.36613799 +75: 2.1107185 2.1107185 +75: 0.99999982 0.99999982 +75: 2.48696157 2.48696157 +75: 1.00479935 1.00479935 +75: 0.99999999 0.99999999 +75: 3.03311841 3.03311841 +75: 2.23739955 2.23739955 +75: 1.0000001 1.0000001 +75: 3.00772337 3.00772337 +75: 0.37399294 0.37399294 +75: 2.07713325 2.07713325 +75: 3.0077234 3.0077234 +75: 0.37399312 0.37399312 +75: -0.07713336 -0.07713336 +75: [12:23:59] bond with order 0 found on line 11. This is not part of the MDL specification. +75: [12:23:59] bond with order 0 found on line 16. This is not part of the MDL specification. 68: Test 68: -68: MarvinBadMissingSruTitle.mrv +68: RP-6306_atrop1.mrv 68: 68: Test 68: -68: MarvinBadSruAtomRef.mrv +68: RP-6306_atrop2.mrv 68: -68: AtomRef specification for an SRU, Copolymer, or Modification group definition was not found in any parent 68: Test 68: -68: MarvinBadSruID.mrv +68: RP-6306_atrop3.mrv 68: 68: Test 68: -68: MarvinBadSruRole.mrv +68: RP-6306_atrop4.mrv 68: 68: Test 68: -68: MarvinBadSruAtomRef.mrv +68: RP-6306_atrop5.mrv 68: -68: AtomRef specification for an SRU, Copolymer, or Modification group definition was not found in any parent +68: [12:23:59] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 2 ignored +68: [12:23:59] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 2 ignored 68: Test 68: -68: MarvinBadSruAtomRef.mrv +68: RP-6306_atropBad1.mrv 68: -68: AtomRef specification for an SRU, Copolymer, or Modification group definition was not found in any parent +68: [12:23:59] The bonds on one end of an atropisomer are both UP or both DOWN - atoms are: 2 8 68: Test 68: -68: MarvinBadSruConnect.mrv +68: RP-6306_atropBad2.mrv 68: -68: Expected a connect string of "hh, ht, eu" for a SruSgroup definition in MRV file +68: [12:23:59] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 2 ignored +68: [12:23:59] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 2 ignored +68: [12:23:59] The 2 defining bonds for an atropisomer are co-planar - atoms are: 2 8 + 70/236 Test #75: testMolWriter .......................... Passed 0.83 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 +81: Randomness seeded to: 2139872786 +81: =============================================================================== +81: All tests passed (95 assertions in 4 test cases) +81: + 71/236 Test #81: testPropertyLists ...................... Passed 0.38 sec +test 83 + Start 83: cdxmlParserCatchTest + +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 +40: [12:23:59] done: 500000 +40: [12:23:59] Done 68: Test 68: -68: MarvinBadSupAttachAtom.mrv +68: RP-6306_3d.mrv 68: -68: Atom specification for an AttachmentPoint definition must be in the parent's atom array in MRV file 68: Test 68: -68: MarvinBadSupAttachBond.mrv +68: Sotorasib_atrop1.mrv 68: -68: Bond specification for an AttachmentPoint definition must be in the bond array in MRV file 68: Test 68: -68: MarvinBadSupAttachOrder.mrv +68: Sotorasib_atrop2.mrv 68: -68: Order for an AttachmentPoint definition must be an integer in MRV file 68: Test 68: -68: MarvinBadSupAttachAtom.mrv +68: Sotorasib_atrop3.mrv 68: -68: Atom specification for an AttachmentPoint definition must be in the parent's atom array in MRV file 68: Test 68: -68: MarvinBadSupAttachAtom.mrv +68: Sotorasib_atrop4.mrv 68: -68: Atom specification for an AttachmentPoint definition must be in the parent's atom array in MRV file 68: Test 68: -68: MarvinBadSupAttachAtom.mrv +68: Sotorasib_atrop5.mrv 68: -68: Atom specification for an AttachmentPoint definition must be in the parent's atom array in MRV file +68: [12:23:59] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored +68: [12:23:59] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored 68: Test 68: -68: MarvinBadSupMissingAttachBond.mrv +68: Sotorasib_atropBad1.mrv 68: -68: No attachment point found for bond to the condensed atom in a superatomSgroup +68: [12:23:59] The 2 defining bonds for an atropisomer are co-planar - atoms are: 7 20 68: Test 68: -68: MarvinBadSupMissingAttachOrder.mrv +68: Sotorasib_atropBad2.mrv 68: -68: Expected atom, order and bond, for an AttachmentPoint definition in MRV file -75: [16:02:39] Warning: molecule is tagged as 3D, but all Z coords are zero and 2D stereo markers have been found, marking the mol as 2D. -75: 0.40201265 0.40201265 -75: -0.13299436 -0.13299436 -75: 1.00000017 1.00000017 -75: 0.8762226 0.8762226 -75: 0.9973909 0.9973909 -75: 1.00000003 1.00000003 -75: 0.36613799 0.36613799 -75: 2.1107185 2.1107185 -75: 0.99999982 0.99999982 -75: 2.48696157 2.48696157 -75: 1.00479935 1.00479935 -75: 0.99999999 0.99999999 -75: 3.03311841 3.03311841 -75: 2.23739955 2.23739955 -75: 1.0000001 1.0000001 -75: 3.00772337 3.00772337 -75: 0.37399294 0.37399294 -75: 2.07713325 2.07713325 -75: 3.0077234 3.0077234 -75: 0.37399312 0.37399312 -75: -0.07713336 -0.07713336 -82: Randomness seeded to: 542466018 -82: =============================================================================== -82: All tests passed (100 assertions in 2 test cases) -82: -81: Randomness seeded to: 1977484081 -81: =============================================================================== -81: All tests passed (95 assertions in 4 test cases) -81: - 73/236 Test #82: XYZFileParserCatchTest ................. Passed 0.44 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 -75: [16:02:39] bond with order 0 found on line 11. This is not part of the MDL specification. -75: [16:02:39] bond with order 0 found on line 16. This is not part of the MDL specification. - 74/236 Test #81: testPropertyLists ...................... Passed 0.47 sec -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 -80: Randomness seeded to: 2079550296 -80: [16:02:39] SGroup SAP line too short: 'M SAP 1 1 8' on line 29 -80: [16:02:39] SGroup SAP line too short: 'M SAP 1 1 8' on line 28 -80: [16:02:39] Could not infer missing lvIdx on malformed SAP line for SGroup 1 -80: [16:02:39] SGroup 1 is invalid and will be ignored -80: [16:02:39] SGroup SAP line too short: 'M SAP 1 1 8' on line 28 -80: [16:02:39] Could not infer missing lvIdx on malformed SAP line for SGroup 1 -80: [16:02:39] SGroup 1 is invalid and will be ignored -80: [16:02:39] SGroup SAP line too short: 'M SAP 1 1 8' on line 35 -80: [16:02:39] SGroup SAP line too short: 'M SAP 2 1 12' on line 39 -80: [16:02:39] SGroup SAP line too short: 'M SAP 1 1 8' on line 34 -80: [16:02:39] SGroup SAP line too short: 'M SAP 2 1 12' on line 38 -80: [16:02:39] Could not infer missing lvIdx on malformed SAP line for SGroup 1 -80: [16:02:39] SGroup 1 is invalid and will be ignored -80: [16:02:39] SGroup SAP line too short: 'M SAP 1 1 8' on line 34 -80: [16:02:39] SGroup SAP line too short: 'M SAP 2 1 12' on line 39 -80: [16:02:39] Could not infer missing lvIdx on malformed SAP line for SGroup 1 -80: [16:02:39] SGroup 1 is invalid and will be ignored -80: [16:02:39] SGroup 3 referenced on line 40 not found. -80: [16:02:39] +68: [12:23:59] The bonds on one end of an atropisomer are both UP or both DOWN - atoms are: 7 20 +80: Randomness seeded to: 1507529985 +80: [12:23:59] SGroup SAP line too short: 'M SAP 1 1 8' on line 29 +80: [12:23:59] SGroup SAP line too short: 'M SAP 1 1 8' on line 28 +80: [12:23:59] Could not infer missing lvIdx on malformed SAP line for SGroup 1 +80: [12:23:59] SGroup 1 is invalid and will be ignored +80: [12:23:59] SGroup SAP line too short: 'M SAP 1 1 8' on line 28 +80: [12:23:59] Could not infer missing lvIdx on malformed SAP line for SGroup 1 +80: [12:23:59] SGroup 1 is invalid and will be ignored +80: [12:23:59] SGroup SAP line too short: 'M SAP 1 1 8' on line 35 +80: [12:23:59] SGroup SAP line too short: 'M SAP 2 1 12' on line 39 +80: [12:23:59] SGroup SAP line too short: 'M SAP 1 1 8' on line 34 +80: [12:23:59] SGroup SAP line too short: 'M SAP 2 1 12' on line 38 +80: [12:23:59] Could not infer missing lvIdx on malformed SAP line for SGroup 1 +80: [12:23:59] SGroup 1 is invalid and will be ignored +80: [12:23:59] SGroup SAP line too short: 'M SAP 1 1 8' on line 34 +80: [12:23:59] SGroup SAP line too short: 'M SAP 2 1 12' on line 39 +80: [12:23:59] Could not infer missing lvIdx on malformed SAP line for SGroup 1 +80: [12:23:59] SGroup 1 is invalid and will be ignored +80: [12:23:59] SGroup 3 referenced on line 40 not found. +80: [12:23:59] 80: 80: **** - 75/236 Test #75: testMolWriter .......................... Passed 0.82 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 80: Pre-condition Violation 80: no bonds 80: Violation occurred on line 181 in file ./Code/GraphMol/SubstanceGroup.cpp @@ -20590,24 +20699,24 @@ 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# 0x0000FFFFB602EDE8 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu//lib/libRDKitFileParsers.so.1 +80: 4# 0x0000FFFFAE49EDE8 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# 0x0000AAAAAECC9C7C in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -80: 8# 0x0000AAAAAED3EAAC in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -80: 9# 0x0000AAAAAED3F460 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -80: 10# 0x0000AAAAAED3F894 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -80: 11# 0x0000AAAAAED13D38 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -80: 12# 0x0000AAAAAED14284 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -80: 13# 0x0000AAAAAEC8C1B0 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -80: 14# 0x0000FFFFB56F229C in /lib/aarch64-linux-gnu/libc.so.6 +80: 7# 0x0000AAAAB3C19C7C in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +80: 8# 0x0000AAAAB3C8EAAC in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +80: 9# 0x0000AAAAB3C8F460 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +80: 10# 0x0000AAAAB3C8F894 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +80: 11# 0x0000AAAAB3C63D38 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +80: 12# 0x0000AAAAB3C64284 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +80: 13# 0x0000AAAAB3BDC1B0 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +80: 14# 0x0000FFFFADB6229C in /lib/aarch64-linux-gnu/libc.so.6 80: 15# __libc_start_main in /lib/aarch64-linux-gnu/libc.so.6 -80: 16# 0x0000AAAAAEC8C270 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +80: 16# 0x0000AAAAB3BDC270 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest 80: ---------- 80: **** 80: -80: [16:02:39] SGroup 3 referenced on line 40 not found. -80: [16:02:39] +80: [12:23:59] SGroup 3 referenced on line 40 not found. +80: [12:23:59] 80: 80: **** 80: Pre-condition Violation @@ -20620,29 +20729,29 @@ 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# 0x0000FFFFB602EDE8 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu//lib/libRDKitFileParsers.so.1 +80: 4# 0x0000FFFFAE49EDE8 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# 0x0000AAAAAECC9CFC in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -80: 8# 0x0000AAAAAED3EAAC in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -80: 9# 0x0000AAAAAED3F460 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -80: 10# 0x0000AAAAAED3F894 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -80: 11# 0x0000AAAAAED13D38 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -80: 12# 0x0000AAAAAED14284 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -80: 13# 0x0000AAAAAEC8C1B0 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -80: 14# 0x0000FFFFB56F229C in /lib/aarch64-linux-gnu/libc.so.6 +80: 7# 0x0000AAAAB3C19CFC in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +80: 8# 0x0000AAAAB3C8EAAC in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +80: 9# 0x0000AAAAB3C8F460 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +80: 10# 0x0000AAAAB3C8F894 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +80: 11# 0x0000AAAAB3C63D38 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +80: 12# 0x0000AAAAB3C64284 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +80: 13# 0x0000AAAAB3BDC1B0 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +80: 14# 0x0000FFFFADB6229C in /lib/aarch64-linux-gnu/libc.so.6 80: 15# __libc_start_main in /lib/aarch64-linux-gnu/libc.so.6 -80: 16# 0x0000AAAAAEC8C270 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +80: 16# 0x0000AAAAB3BDC270 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest 80: ---------- 80: **** 80: -80: [16:02:39] no bonds -80: [16:02:39] SGroup 1 is invalid and will be ignored -80: [16:02:39] SGroup line too short: 'M SBV 1 6' on line 42 -80: [16:02:39] SGroup 1 is invalid and will be ignored -80: [16:02:39] SGroup line too short: 'M SBL 2 3 9 10' on line 46 -80: [16:02:39] SGroup 2 is invalid and will be ignored -80: [16:02:39] +80: [12:23:59] no bonds +80: [12:23:59] SGroup 1 is invalid and will be ignored +80: [12:23:59] SGroup line too short: 'M SBV 1 6' on line 42 +80: [12:23:59] SGroup 1 is invalid and will be ignored +80: [12:23:59] SGroup line too short: 'M SBL 2 3 9 10' on line 46 +80: [12:23:59] SGroup 2 is invalid and will be ignored +80: [12:23:59] 80: 80: **** 80: Pre-condition Violation @@ -20656,23 +20765,23 @@ 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# 0x0000FFFFB602ED50 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu//lib/libRDKitFileParsers.so.1 +80: 5# 0x0000FFFFAE49ED50 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# 0x0000AAAAAECCA6A4 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -80: 9# 0x0000AAAAAED3EAAC in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -80: 10# 0x0000AAAAAED3F460 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -80: 11# 0x0000AAAAAED3F894 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -80: 12# 0x0000AAAAAED13D38 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -80: 13# 0x0000AAAAAED14284 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -80: 14# 0x0000AAAAAEC8C1B0 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -80: 15# 0x0000FFFFB56F229C in /lib/aarch64-linux-gnu/libc.so.6 +80: 8# 0x0000AAAAB3C1A6A4 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +80: 9# 0x0000AAAAB3C8EAAC in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +80: 10# 0x0000AAAAB3C8F460 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +80: 11# 0x0000AAAAB3C8F894 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +80: 12# 0x0000AAAAB3C63D38 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +80: 13# 0x0000AAAAB3C64284 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +80: 14# 0x0000AAAAB3BDC1B0 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +80: 15# 0x0000FFFFADB6229C in /lib/aarch64-linux-gnu/libc.so.6 80: 16# __libc_start_main in /lib/aarch64-linux-gnu/libc.so.6 -80: 17# 0x0000AAAAAEC8C270 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +80: 17# 0x0000AAAAB3BDC270 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest 80: ---------- 80: **** 80: -80: [16:02:39] +80: [12:23:59] 80: 80: **** 80: Pre-condition Violation @@ -20686,24 +20795,24 @@ 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# 0x0000FFFFB602ED50 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu//lib/libRDKitFileParsers.so.1 +80: 5# 0x0000FFFFAE49ED50 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# 0x0000AAAAAECCA724 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -80: 9# 0x0000AAAAAED3EAAC in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -80: 10# 0x0000AAAAAED3F460 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -80: 11# 0x0000AAAAAED3F894 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -80: 12# 0x0000AAAAAED13D38 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -80: 13# 0x0000AAAAAED14284 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -80: 14# 0x0000AAAAAEC8C1B0 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -80: 15# 0x0000FFFFB56F229C in /lib/aarch64-linux-gnu/libc.so.6 +80: 8# 0x0000AAAAB3C1A724 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +80: 9# 0x0000AAAAB3C8EAAC in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +80: 10# 0x0000AAAAB3C8F460 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +80: 11# 0x0000AAAAB3C8F894 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +80: 12# 0x0000AAAAB3C63D38 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +80: 13# 0x0000AAAAB3C64284 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +80: 14# 0x0000AAAAB3BDC1B0 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +80: 15# 0x0000FFFFADB6229C in /lib/aarch64-linux-gnu/libc.so.6 80: 16# __libc_start_main in /lib/aarch64-linux-gnu/libc.so.6 -80: 17# 0x0000AAAAAEC8C270 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +80: 17# 0x0000AAAAB3BDC270 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest 80: ---------- 80: **** 80: -80: [16:02:39] bookmark not found -80: [16:02:39] +80: [12:23:59] bookmark not found +80: [12:23:59] 80: 80: **** 80: Pre-condition Violation @@ -20717,25 +20826,25 @@ 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# 0x0000FFFFB602EDE8 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu//lib/libRDKitFileParsers.so.1 +80: 5# 0x0000FFFFAE49EDE8 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# 0x0000AAAAAECCA724 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -80: 9# 0x0000AAAAAED3EAAC in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -80: 10# 0x0000AAAAAED3F460 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -80: 11# 0x0000AAAAAED3F894 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -80: 12# 0x0000AAAAAED13D38 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -80: 13# 0x0000AAAAAED14284 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -80: 14# 0x0000AAAAAEC8C1B0 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -80: 15# 0x0000FFFFB56F229C in /lib/aarch64-linux-gnu/libc.so.6 +80: 8# 0x0000AAAAB3C1A724 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +80: 9# 0x0000AAAAB3C8EAAC in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +80: 10# 0x0000AAAAB3C8F460 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +80: 11# 0x0000AAAAB3C8F894 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +80: 12# 0x0000AAAAB3C63D38 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +80: 13# 0x0000AAAAB3C64284 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +80: 14# 0x0000AAAAB3BDC1B0 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +80: 15# 0x0000FFFFADB6229C in /lib/aarch64-linux-gnu/libc.so.6 80: 16# __libc_start_main in /lib/aarch64-linux-gnu/libc.so.6 -80: 17# 0x0000AAAAAEC8C270 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +80: 17# 0x0000AAAAB3BDC270 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest 80: ---------- 80: **** 80: -80: [16:02:39] bond is not part of the SubstanceGroup -80: [16:02:39] SGroup 2 is invalid and will be ignored -80: [16:02:39] +80: [12:23:59] bond is not part of the SubstanceGroup +80: [12:23:59] SGroup 2 is invalid and will be ignored +80: [12:23:59] 80: 80: **** 80: Pre-condition Violation @@ -20749,23 +20858,23 @@ 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# 0x0000FFFFB602ED50 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu//lib/libRDKitFileParsers.so.1 +80: 5# 0x0000FFFFAE49ED50 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# 0x0000AAAAAECCAA14 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -80: 9# 0x0000AAAAAED3EAAC in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -80: 10# 0x0000AAAAAED3F460 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -80: 11# 0x0000AAAAAED3F894 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -80: 12# 0x0000AAAAAED13D38 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -80: 13# 0x0000AAAAAED14284 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -80: 14# 0x0000AAAAAEC8C1B0 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -80: 15# 0x0000FFFFB56F229C in /lib/aarch64-linux-gnu/libc.so.6 +80: 8# 0x0000AAAAB3C1AA14 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +80: 9# 0x0000AAAAB3C8EAAC in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +80: 10# 0x0000AAAAB3C8F460 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +80: 11# 0x0000AAAAB3C8F894 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +80: 12# 0x0000AAAAB3C63D38 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +80: 13# 0x0000AAAAB3C64284 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +80: 14# 0x0000AAAAB3BDC1B0 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +80: 15# 0x0000FFFFADB6229C in /lib/aarch64-linux-gnu/libc.so.6 80: 16# __libc_start_main in /lib/aarch64-linux-gnu/libc.so.6 -80: 17# 0x0000AAAAAEC8C270 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +80: 17# 0x0000AAAAB3BDC270 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest 80: ---------- 80: **** 80: -80: [16:02:39] +80: [12:23:59] 80: 80: **** 80: Pre-condition Violation @@ -20779,27 +20888,49 @@ 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# 0x0000FFFFB602ED50 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu//lib/libRDKitFileParsers.so.1 +80: 5# 0x0000FFFFAE49ED50 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# 0x0000AAAAAECCAA94 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -80: 9# 0x0000AAAAAED3EAAC in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -80: 10# 0x0000AAAAAED3F460 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -80: 11# 0x0000AAAAAED3F894 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -80: 12# 0x0000AAAAAED13D38 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -80: 13# 0x0000AAAAAED14284 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -80: 14# 0x0000AAAAAEC8C1B0 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -80: 15# 0x0000FFFFB56F229C in /lib/aarch64-linux-gnu/libc.so.6 +80: 8# 0x0000AAAAB3C1AA94 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +80: 9# 0x0000AAAAB3C8EAAC in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +80: 10# 0x0000AAAAB3C8F460 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +80: 11# 0x0000AAAAB3C8F894 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +80: 12# 0x0000AAAAB3C63D38 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +80: 13# 0x0000AAAAB3C64284 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +80: 14# 0x0000AAAAB3BDC1B0 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +80: 15# 0x0000FFFFADB6229C in /lib/aarch64-linux-gnu/libc.so.6 80: 16# __libc_start_main in /lib/aarch64-linux-gnu/libc.so.6 -80: 17# 0x0000AAAAAEC8C270 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +80: 17# 0x0000AAAAB3BDC270 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest 80: ---------- 80: **** 80: -80: [16:02:39] bookmark not found -80: [16:02:39] Neither beginning nor ending atoms of bond 9 is in this SubstanceGroup. -80: [16:02:39] SGroup 2 is invalid and will be ignored -80: [16:02:39] WARNING: final character of V3000 array is not ')' -80: [16:02:39] +80: [12:23:59] bookmark not found +80: [12:23:59] Neither beginning nor ending atoms of bond 9 is in this SubstanceGroup. +80: [12:23:59] SGroup 2 is invalid and will be ignored +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: [12:23:59] The 2 defining bonds for an atropisomer are co-planar - atoms are: 0 31 +40: [12:23:59] Testing hanoi with a functor. +80: [12:23:59] WARNING: final character of V3000 array is not ')' +80: [12:23:59] 80: 80: **** 80: Pre-condition Violation @@ -20817,21 +20948,21 @@ 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# 0x0000AAAAAECC8698 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -80: 10# 0x0000AAAAAED3EAAC in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -80: 11# 0x0000AAAAAED3F460 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -80: 12# 0x0000AAAAAED3F894 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -80: 13# 0x0000AAAAAED13D38 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -80: 14# 0x0000AAAAAED14284 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -80: 15# 0x0000AAAAAEC8C1B0 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -80: 16# 0x0000FFFFB56F229C in /lib/aarch64-linux-gnu/libc.so.6 +80: 9# 0x0000AAAAB3C18698 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +80: 10# 0x0000AAAAB3C8EAAC in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +80: 11# 0x0000AAAAB3C8F460 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +80: 12# 0x0000AAAAB3C8F894 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +80: 13# 0x0000AAAAB3C63D38 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +80: 14# 0x0000AAAAB3C64284 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +80: 15# 0x0000AAAAB3BDC1B0 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +80: 16# 0x0000FFFFADB6229C in /lib/aarch64-linux-gnu/libc.so.6 80: 17# __libc_start_main in /lib/aarch64-linux-gnu/libc.so.6 -80: 18# 0x0000AAAAAEC8C270 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +80: 18# 0x0000AAAAB3BDC270 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest 80: ---------- 80: **** 80: -80: [16:02:39] WARNING: final character of V3000 array is not ')' -80: [16:02:39] +80: [12:23:59] WARNING: final character of V3000 array is not ')' +80: [12:23:59] 80: 80: **** 80: Pre-condition Violation @@ -20849,23 +20980,23 @@ 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# 0x0000AAAAAECC8714 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -80: 10# 0x0000AAAAAED3EAAC in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -80: 11# 0x0000AAAAAED3F460 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -80: 12# 0x0000AAAAAED3F894 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -80: 13# 0x0000AAAAAED13D38 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -80: 14# 0x0000AAAAAED14284 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -80: 15# 0x0000AAAAAEC8C1B0 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -80: 16# 0x0000FFFFB56F229C in /lib/aarch64-linux-gnu/libc.so.6 +80: 9# 0x0000AAAAB3C18714 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +80: 10# 0x0000AAAAB3C8EAAC in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +80: 11# 0x0000AAAAB3C8F460 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +80: 12# 0x0000AAAAB3C8F894 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +80: 13# 0x0000AAAAB3C63D38 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +80: 14# 0x0000AAAAB3C64284 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +80: 15# 0x0000AAAAB3BDC1B0 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +80: 16# 0x0000FFFFADB6229C in /lib/aarch64-linux-gnu/libc.so.6 80: 17# __libc_start_main in /lib/aarch64-linux-gnu/libc.so.6 -80: 18# 0x0000AAAAAEC8C270 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +80: 18# 0x0000AAAAB3BDC270 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest 80: ---------- 80: **** 80: -80: [16:02:39] bookmark not found -80: [16:02:39] SGroup 1 is invalid and will be ignored -80: [16:02:39] WARNING: final character of V3000 array is not ')' -80: [16:02:39] +80: [12:23:59] bookmark not found +80: [12:23:59] SGroup 1 is invalid and will be ignored +80: [12:23:59] WARNING: final character of V3000 array is not ')' +80: [12:23:59] 80: 80: **** 80: Pre-condition Violation @@ -20883,21 +21014,21 @@ 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# 0x0000AAAAAECC89E8 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -80: 10# 0x0000AAAAAED3EAAC in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -80: 11# 0x0000AAAAAED3F460 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -80: 12# 0x0000AAAAAED3F894 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -80: 13# 0x0000AAAAAED13D38 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -80: 14# 0x0000AAAAAED14284 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -80: 15# 0x0000AAAAAEC8C1B0 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -80: 16# 0x0000FFFFB56F229C in /lib/aarch64-linux-gnu/libc.so.6 +80: 9# 0x0000AAAAB3C189E8 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +80: 10# 0x0000AAAAB3C8EAAC in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +80: 11# 0x0000AAAAB3C8F460 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +80: 12# 0x0000AAAAB3C8F894 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +80: 13# 0x0000AAAAB3C63D38 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +80: 14# 0x0000AAAAB3C64284 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +80: 15# 0x0000AAAAB3BDC1B0 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +80: 16# 0x0000FFFFADB6229C in /lib/aarch64-linux-gnu/libc.so.6 80: 17# __libc_start_main in /lib/aarch64-linux-gnu/libc.so.6 -80: 18# 0x0000AAAAAEC8C270 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +80: 18# 0x0000AAAAB3BDC270 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest 80: ---------- 80: **** 80: -80: [16:02:39] WARNING: final character of V3000 array is not ')' -80: [16:02:39] +80: [12:23:59] WARNING: final character of V3000 array is not ')' +80: [12:23:59] 80: 80: **** 80: Pre-condition Violation @@ -20915,22 +21046,22 @@ 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# 0x0000AAAAAECC8A64 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -80: 10# 0x0000AAAAAED3EAAC in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -80: 11# 0x0000AAAAAED3F460 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -80: 12# 0x0000AAAAAED3F894 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -80: 13# 0x0000AAAAAED13D38 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -80: 14# 0x0000AAAAAED14284 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -80: 15# 0x0000AAAAAEC8C1B0 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -80: 16# 0x0000FFFFB56F229C in /lib/aarch64-linux-gnu/libc.so.6 +80: 9# 0x0000AAAAB3C18A64 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +80: 10# 0x0000AAAAB3C8EAAC in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +80: 11# 0x0000AAAAB3C8F460 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +80: 12# 0x0000AAAAB3C8F894 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +80: 13# 0x0000AAAAB3C63D38 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +80: 14# 0x0000AAAAB3C64284 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +80: 15# 0x0000AAAAB3BDC1B0 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +80: 16# 0x0000FFFFADB6229C in /lib/aarch64-linux-gnu/libc.so.6 80: 17# __libc_start_main in /lib/aarch64-linux-gnu/libc.so.6 -80: 18# 0x0000AAAAAEC8C270 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +80: 18# 0x0000AAAAB3BDC270 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest 80: ---------- 80: **** 80: -80: [16:02:39] bookmark not found -80: [16:02:39] SGroup 1 is invalid and will be ignored -80: [16:02:39] +80: [12:23:59] bookmark not found +80: [12:23:59] SGroup 1 is invalid and will be ignored +80: [12:23:59] 80: 80: **** 80: Pre-condition Violation @@ -20948,20 +21079,20 @@ 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# 0x0000AAAAAECC8D38 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -80: 10# 0x0000AAAAAED3EAAC in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -80: 11# 0x0000AAAAAED3F460 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -80: 12# 0x0000AAAAAED3F894 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -80: 13# 0x0000AAAAAED13D38 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -80: 14# 0x0000AAAAAED14284 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -80: 15# 0x0000AAAAAEC8C1B0 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -80: 16# 0x0000FFFFB56F229C in /lib/aarch64-linux-gnu/libc.so.6 +80: 9# 0x0000AAAAB3C18D38 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +80: 10# 0x0000AAAAB3C8EAAC in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +80: 11# 0x0000AAAAB3C8F460 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +80: 12# 0x0000AAAAB3C8F894 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +80: 13# 0x0000AAAAB3C63D38 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +80: 14# 0x0000AAAAB3C64284 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +80: 15# 0x0000AAAAB3BDC1B0 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +80: 16# 0x0000FFFFADB6229C in /lib/aarch64-linux-gnu/libc.so.6 80: 17# __libc_start_main in /lib/aarch64-linux-gnu/libc.so.6 -80: 18# 0x0000AAAAAEC8C270 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +80: 18# 0x0000AAAAB3BDC270 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest 80: ---------- 80: **** 80: -80: [16:02:39] +80: [12:23:59] 80: 80: **** 80: Pre-condition Violation @@ -20979,26 +21110,24 @@ 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# 0x0000AAAAAECC8DB4 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -80: 10# 0x0000AAAAAED3EAAC in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -80: 11# 0x0000AAAAAED3F460 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -80: 12# 0x0000AAAAAED3F894 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -80: 13# 0x0000AAAAAED13D38 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -80: 14# 0x0000AAAAAED14284 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -80: 15# 0x0000AAAAAEC8C1B0 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -80: 16# 0x0000FFFFB56F229C in /lib/aarch64-linux-gnu/libc.so.6 +80: 9# 0x0000AAAAB3C18DB4 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +80: 10# 0x0000AAAAB3C8EAAC in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +80: 11# 0x0000AAAAB3C8F460 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +80: 12# 0x0000AAAAB3C8F894 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +80: 13# 0x0000AAAAB3C63D38 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +80: 14# 0x0000AAAAB3C64284 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +80: 15# 0x0000AAAAB3BDC1B0 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +80: 16# 0x0000FFFFADB6229C in /lib/aarch64-linux-gnu/libc.so.6 80: 17# __libc_start_main in /lib/aarch64-linux-gnu/libc.so.6 -80: 18# 0x0000AAAAAEC8C270 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +80: 18# 0x0000AAAAB3BDC270 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest 80: ---------- 80: **** 80: -80: [16:02:39] bookmark not found -80: [16:02:39] SGroup 2 is invalid and will be ignored -80: [16:02:39] +80: [12:23:59] bookmark not found +80: [12:23:59] SGroup 2 is invalid and will be ignored +80: [12:23:59] 80: 80: **** -69: ---------------------------------- -69: ---------------------------------- 80: Pre-condition Violation 80: bookmark not found 80: Violation occurred on line 245 in file ./Code/GraphMol/ROMol.cpp @@ -21014,20 +21143,31 @@ 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# 0x0000AAAAAECC9088 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -80: 10# 0x0000AAAAAED3EAAC in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -80: 11# 0x0000AAAAAED3F460 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -80: 12# 0x0000AAAAAED3F894 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -80: 13# 0x0000AAAAAED13D38 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -80: 14# 0x0000AAAAAED14284 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -80: 15# 0x0000AAAAAEC8C1B0 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -80: 16# 0x0000FFFFB56F229C in /lib/aarch64-linux-gnu/libc.so.6 +80: 9# 0x0000AAAAB3C19088 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +80: 10# 0x0000AAAAB3C8EAAC in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +80: 11# 0x0000AAAAB3C8F460 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +80: 12# 0x0000AAAAB3C8F894 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +80: 13# 0x0000AAAAB3C63D38 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +80: 14# 0x0000AAAAB3C64284 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +80: 15# 0x0000AAAAB3BDC1B0 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +80: 16# 0x0000FFFFADB6229C in /lib/aarch64-linux-gnu/libc.so.6 80: 17# __libc_start_main in /lib/aarch64-linux-gnu/libc.so.6 -80: 18# 0x0000AAAAAEC8C270 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +80: 18# 0x0000AAAAB3BDC270 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest 80: ---------- 80: **** 80: -80: [16:02:39] +82: Randomness seeded to: 3600861091 +82: =============================================================================== +82: All tests passed (100 assertions in 2 test cases) +82: + 72/236 Test #82: XYZFileParserCatchTest ................. Passed 0.27 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: [12:23:59] 80: 80: **** 80: Pre-condition Violation @@ -21045,58 +21185,97 @@ 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# 0x0000AAAAAECC9104 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -80: 10# 0x0000AAAAAED3EAAC in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -80: 11# 0x0000AAAAAED3F460 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -80: 12# 0x0000AAAAAED3F894 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -80: 13# 0x0000AAAAAED13D38 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -80: 14# 0x0000AAAAAED14284 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -80: 15# 0x0000AAAAAEC8C1B0 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -80: 16# 0x0000FFFFB56F229C in /lib/aarch64-linux-gnu/libc.so.6 +80: 9# 0x0000AAAAB3C19104 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +80: 10# 0x0000AAAAB3C8EAAC in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +80: 11# 0x0000AAAAB3C8F460 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +80: 12# 0x0000AAAAB3C8F894 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +80: 13# 0x0000AAAAB3C63D38 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +80: 14# 0x0000AAAAB3C64284 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +80: 15# 0x0000AAAAB3BDC1B0 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +80: 16# 0x0000FFFFADB6229C in /lib/aarch64-linux-gnu/libc.so.6 80: 17# __libc_start_main in /lib/aarch64-linux-gnu/libc.so.6 -80: 18# 0x0000AAAAAEC8C270 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +80: 18# 0x0000AAAAB3BDC270 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest 80: ---------- 80: **** 80: -80: [16:02:39] bookmark not found -80: [16:02:39] SGroup 2 is invalid and will be ignored -83: Randomness seeded to: 3298499300 -83: [16:02:39] Invalid or missing fragment id from CDXML fragment, assigning new one... -83: [16:02:39] Explicit valence for atom # 3 N, 4, is greater than permitted -83: [16:02:39] CDXMLParser: failed sanitizing skipping fragment 32 -83: [16:02:39] Bad bond in CDXML skipping fragment 58... -83: [16:02:39] Invalid or missing fragment id from CDXML fragment, assigning new one... -83: [16:02:39] Bad bond in CDXML skipping fragment 58... -69: [16:02:39] -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# 0x0000AAAABE97F23C in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersTest1 -69: 4# 0x0000AAAABE9E49A4 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersTest1 -69: 5# 0x0000AAAABE955BF8 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersTest1 -69: 6# 0x0000FFFF8AF1229C in /lib/aarch64-linux-gnu/libc.so.6 -69: 7# __libc_start_main in /lib/aarch64-linux-gnu/libc.so.6 -69: 8# 0x0000AAAABE955E30 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersTest1 -69: ---------- -69: **** -69: -69: [16:02:39] WARNING: could not find number of expected rings. Switching to an approximate ring finding algorithm. +80: [12:23:59] bookmark not found +80: [12:23:59] SGroup 2 is invalid and will be ignored 68: Test 68: -68: marvin03.mrv +68: mrtx1719_3d.mrv 68: 68: Test 68: -68: Cubane.mrv +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: [12:23:59] The 2 defining bonds for an atropisomer are co-planar - atoms are: 15 16 +40: [12:23:59] Done +40: [12:23:59] Testing basic partition refinement. +40: [12:23:59] Done +40: [12:23:59] Testing partition refinement with neighbors. +40: [12:23:59] Done +40: [12:23:59] testing canonicalization via tie breaking. +40: [12:23:59] Done +40: [12:23:59] testing canonicalization using the wrapper. +80: [12:23:59] Explicit valence for atom # 2 O, 3, is greater than permitted +80: [12:23:59] Explicit valence for atom # 1 O, 3, is greater than permitted +80: [12:23:59] Explicit valence for atom # 1 C, 5, is greater than permitted +40: [12:23:59] Done +40: [12:23:59] testing some specific ordering problems +40: [12:23:59] Finished +40: [12:23:59] testing chiral invariants. +40: [12:23:59] Finished +40: [12:23:59] testing unique ranks in w.r.t. renumbering. +83: Randomness seeded to: 4292551228 +83: [12:23:59] Invalid or missing fragment id from CDXML fragment, assigning new one... +83: [12:23:59] Explicit valence for atom # 3 N, 4, is greater than permitted +83: [12:23:59] CDXMLParser: failed sanitizing skipping fragment 32 +83: [12:23:59] Bad bond in CDXML skipping fragment 58... +83: [12:23:59] Invalid or missing fragment id from CDXML fragment, assigning new one... +83: [12:23:59] Bad bond in CDXML skipping fragment 58... +80: [12:23:59] sanitize [12:23:59] UNK: [12:23:59] 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: [12:23:59] 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: [12:23:59] +80: +80: **** +80: Pre-condition Violation +80: no stream +80: Violation occurred on line 133 in file ./Code/GraphMol/FileParsers/SDMolSupplier.cpp +80: Failed Expression: dp_inStream +80: ---------- +80: Stacktrace: +80: 0# Invar::Invariant::toString[abi:cxx11]() const in /build/reproducible-path/rdkit-202503.1/obj-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# 0x0000AAAAB3C4DBC0 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +80: 4# 0x0000AAAAB3C0B084 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +80: 5# 0x0000AAAAB3C8EAAC in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +80: 6# 0x0000AAAAB3C8F460 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +80: 7# 0x0000AAAAB3C8F894 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +80: 8# 0x0000AAAAB3C63D38 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +80: 9# 0x0000AAAAB3C64284 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +80: 10# 0x0000AAAAB3BDC1B0 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +80: 11# 0x0000FFFFADB6229C in /lib/aarch64-linux-gnu/libc.so.6 +80: 12# __libc_start_main in /lib/aarch64-linux-gnu/libc.so.6 +80: 13# 0x0000AAAAB3BDC270 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +80: ---------- +80: **** +80: 68: Test 68: 68: FalseAtropisomer.mrv @@ -21153,135 +21332,9 @@ 68: 68: BMS-986142_atrop5.mrv 68: -68: [16:02:39] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored -68: [16:02:39] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored -80: [16:02:39] Explicit valence for atom # 2 O, 3, is greater than permitted -80: [16:02:39] Explicit valence for atom # 1 O, 3, is greater than permitted -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: [16:02:39] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored -68: [16:02:39] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored -80: [16:02:39] Explicit valence for atom # 1 C, 5, is greater than permitted -68: Test -68: -68: BMS-986142_atropBad2.mrv -68: -68: [16:02:39] The bonds on one end of an atropisomer are both UP or both DOWN - atoms are: 7 29 -84: Randomness seeded to: 3322306969 -84: [16:02:40] Warning: ambiguous stereochemistry - opposing bonds have opposite wedging - at atom 2 ignored. -84: [16:02:40] Warning: ambiguous stereochemistry - opposing bonds have opposite wedging - at atom 2 ignored. -84: [16:02:40] Warning: ambiguous stereochemistry - opposing bonds have opposite wedging - at atom 2 ignored. -84: [16:02:40] Warning: ambiguous stereochemistry - opposing bonds have opposite wedging - at atom 2 ignored. -84: =============================================================================== -84: All tests passed (142 assertions in 6 test cases) -84: - 76/236 Test #84: molfileStereoCatchTest ................. Passed 0.41 sec -test 88 - Start 88: atropisomersCatch - -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 -80: [16:02:39] sanitize [16:02:39] UNK: [16:02:40] 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: 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: [16:02:40] The 2 defining bonds for an atropisomer are co-planar - atoms are: 17 21 -83: [16:02:40] WARNING: not removing hydrogen atom without neighbors -83: [16:02:40] WARNING: not removing hydrogen atom without neighbors -83: [16:02:40] WARNING: not removing hydrogen atom without neighbors -83: [16:02:40] WARNING: not removing hydrogen atom without neighbors -86: Randomness seeded to: 2258758080 -86: [16:02:40] Ignoring invalid chirality label: '12_R_1_3_4_5' -86: [16:02:40] Ignoring invalid chirality label: '12_ANR_1_3_4_15' -86: [16:02:40] Ignoring invalid chirality label: '2_S_1_3_4' -86: [16:02:40] Ignoring invalid chirality label: '2_ANS_1_3_4_5_2' -83: [16:02:40] WARNING: not removing hydrogen atom without neighbors -83: [16:02:40] WARNING: not removing hydrogen atom without neighbors -83: [16:02:40] WARNING: not removing hydrogen atom without neighbors -83: [16:02:40] WARNING: not removing hydrogen atom without neighbors -83: [16:02:40] WARNING: not removing hydrogen atom without neighbors -83: [16:02:40] WARNING: not removing hydrogen atom without neighbors -83: [16:02:40] CDXMLParser: Schema 80180 step 80181 ReactionStepAgents reaction fragment 64603 not found in document. -86: =============================================================================== -86: All tests passed (24 assertions in 6 test cases) -86: -80: [16:02:40] skipping block at line 7: 'BEGIN ATOM' -85: Randomness seeded to: 1679253720 -85: =============================================================================== -85: All tests passed (8 assertions in 1 test case) -85: - 77/236 Test #85: connectTheDotsTest ..................... Passed 0.26 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 -80: ATOM 1 CHLO CHL 0 0.000 0.000 0.000 1.00 0.00 CL -80: END -80: - 78/236 Test #86: v2MolSuppliers ......................... Passed 0.26 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 -80: [16:02:40] -80: -80: **** -80: Pre-condition Violation -80: no stream -80: Violation occurred on line 133 in file ./Code/GraphMol/FileParsers/SDMolSupplier.cpp -80: Failed Expression: dp_inStream -80: ---------- -80: Stacktrace: -80: 0# Invar::Invariant::toString[abi:cxx11]() const in /build/reproducible-path/rdkit-202503.1/obj-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# 0x0000AAAAAECFDBC0 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -80: 4# 0x0000AAAAAECBB084 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -80: 5# 0x0000AAAAAED3EAAC in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -80: 6# 0x0000AAAAAED3F460 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -80: 7# 0x0000AAAAAED3F894 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -80: 8# 0x0000AAAAAED13D38 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -80: 9# 0x0000AAAAAED14284 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -80: 10# 0x0000AAAAAEC8C1B0 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -80: 11# 0x0000FFFFB56F229C in /lib/aarch64-linux-gnu/libc.so.6 -80: 12# __libc_start_main in /lib/aarch64-linux-gnu/libc.so.6 -80: 13# 0x0000AAAAAEC8C270 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -80: ---------- -80: **** -80: -80: [16:02:40] +68: [12:23:59] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored +68: [12:23:59] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored +80: [12:23:59] 80: 80: **** 80: Pre-condition Violation @@ -21293,21 +21346,21 @@ 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# 0x0000AAAAAECFDBC0 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -80: 4# 0x0000AAAAAECBB1F4 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -80: 5# 0x0000AAAAAED3EAAC in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -80: 6# 0x0000AAAAAED3F460 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -80: 7# 0x0000AAAAAED3F894 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -80: 8# 0x0000AAAAAED13D38 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -80: 9# 0x0000AAAAAED14284 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -80: 10# 0x0000AAAAAEC8C1B0 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -80: 11# 0x0000FFFFB56F229C in /lib/aarch64-linux-gnu/libc.so.6 +80: 3# 0x0000AAAAB3C4DBC0 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +80: 4# 0x0000AAAAB3C0B1F4 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +80: 5# 0x0000AAAAB3C8EAAC in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +80: 6# 0x0000AAAAB3C8F460 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +80: 7# 0x0000AAAAB3C8F894 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +80: 8# 0x0000AAAAB3C63D38 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +80: 9# 0x0000AAAAB3C64284 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +80: 10# 0x0000AAAAB3BDC1B0 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +80: 11# 0x0000FFFFADB6229C in /lib/aarch64-linux-gnu/libc.so.6 80: 12# __libc_start_main in /lib/aarch64-linux-gnu/libc.so.6 -80: 13# 0x0000AAAAAEC8C270 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +80: 13# 0x0000AAAAB3BDC270 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest 80: ---------- 80: **** 80: -80: [16:02:40] +80: [12:23:59] 80: 80: **** 80: Pre-condition Violation @@ -21319,21 +21372,21 @@ 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# 0x0000AAAAAECFDBC0 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -80: 4# 0x0000AAAAAECBB528 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -80: 5# 0x0000AAAAAED3EAAC in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -80: 6# 0x0000AAAAAED3F460 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -80: 7# 0x0000AAAAAED3F894 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -80: 8# 0x0000AAAAAED13D38 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -80: 9# 0x0000AAAAAED14284 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -80: 10# 0x0000AAAAAEC8C1B0 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -80: 11# 0x0000FFFFB56F229C in /lib/aarch64-linux-gnu/libc.so.6 +80: 3# 0x0000AAAAB3C4DBC0 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +80: 4# 0x0000AAAAB3C0B528 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +80: 5# 0x0000AAAAB3C8EAAC in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +80: 6# 0x0000AAAAB3C8F460 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +80: 7# 0x0000AAAAB3C8F894 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +80: 8# 0x0000AAAAB3C63D38 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +80: 9# 0x0000AAAAB3C64284 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +80: 10# 0x0000AAAAB3BDC1B0 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +80: 11# 0x0000FFFFADB6229C in /lib/aarch64-linux-gnu/libc.so.6 80: 12# __libc_start_main in /lib/aarch64-linux-gnu/libc.so.6 -80: 13# 0x0000AAAAAEC8C270 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +80: 13# 0x0000AAAAB3BDC270 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest 80: ---------- 80: **** 80: -80: [16:02:40] +80: [12:23:59] 80: 80: **** 80: Pre-condition Violation @@ -21345,21 +21398,21 @@ 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::TDTMolSupplier::next() in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu//lib/libRDKitFileParsers.so.1 -80: 3# 0x0000AAAAAECFDBC0 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -80: 4# 0x0000AAAAAECBB7C4 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -80: 5# 0x0000AAAAAED3EAAC in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -80: 6# 0x0000AAAAAED3F460 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -80: 7# 0x0000AAAAAED3F894 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -80: 8# 0x0000AAAAAED13D38 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -80: 9# 0x0000AAAAAED14284 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -80: 10# 0x0000AAAAAEC8C1B0 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -80: 11# 0x0000FFFFB56F229C in /lib/aarch64-linux-gnu/libc.so.6 +80: 3# 0x0000AAAAB3C4DBC0 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +80: 4# 0x0000AAAAB3C0B7C4 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +80: 5# 0x0000AAAAB3C8EAAC in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +80: 6# 0x0000AAAAB3C8F460 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +80: 7# 0x0000AAAAB3C8F894 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +80: 8# 0x0000AAAAB3C63D38 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +80: 9# 0x0000AAAAB3C64284 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +80: 10# 0x0000AAAAB3BDC1B0 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +80: 11# 0x0000FFFFADB6229C in /lib/aarch64-linux-gnu/libc.so.6 80: 12# __libc_start_main in /lib/aarch64-linux-gnu/libc.so.6 -80: 13# 0x0000AAAAAEC8C270 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +80: 13# 0x0000AAAAB3BDC270 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest 80: ---------- 80: **** 80: -80: [16:02:40] +80: [12:23:59] 80: 80: **** 80: Pre-condition Violation @@ -21371,29 +21424,29 @@ 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# 0x0000AAAAAECFDBC0 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -80: 4# 0x0000AAAAAECBB9BC in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -80: 5# 0x0000AAAAAED3EAAC in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -80: 6# 0x0000AAAAAED3F460 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -80: 7# 0x0000AAAAAED3F894 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -80: 8# 0x0000AAAAAED13D38 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -80: 9# 0x0000AAAAAED14284 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -80: 10# 0x0000AAAAAEC8C1B0 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -80: 11# 0x0000FFFFB56F229C in /lib/aarch64-linux-gnu/libc.so.6 +80: 3# 0x0000AAAAB3C4DBC0 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +80: 4# 0x0000AAAAB3C0B9BC in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +80: 5# 0x0000AAAAB3C8EAAC in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +80: 6# 0x0000AAAAB3C8F460 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +80: 7# 0x0000AAAAB3C8F894 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +80: 8# 0x0000AAAAB3C63D38 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +80: 9# 0x0000AAAAB3C64284 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +80: 10# 0x0000AAAAB3BDC1B0 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +80: 11# 0x0000FFFFADB6229C in /lib/aarch64-linux-gnu/libc.so.6 80: 12# __libc_start_main in /lib/aarch64-linux-gnu/libc.so.6 -80: 13# 0x0000AAAAAEC8C270 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +80: 13# 0x0000AAAAB3BDC270 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest 80: ---------- 80: **** 80: -80: [16:02:40] Found a SCD/SED line with missing/empty SDT specification at line 21 -80: [16:02:40] Found a SCD/SED line with missing/empty SDT specification at line 20 -80: [16:02:40] BEGIN SGROUP line not found on line 14 -80: [16:02:40] Unhandled CTAB feature: 'Unsupported SGroup type '' on line 18'. Molecule skipped. -80: [16:02:40] END SGROUP line not found on line 14 -80: [16:02:40] END SGROUP line not found on line 14 -80: [16:02:40] MRV_COORDINATE_BOND_TYPE SGroup with value 0 does not reference a query bond, ignoring. -80: [16:02:40] MRV_COORDINATE_BOND_TYPE SGroup with value 1 does not reference a query bond, ignoring. -80: [16:02:40] +80: [12:23:59] Found a SCD/SED line with missing/empty SDT specification at line 21 +80: [12:23:59] Found a SCD/SED line with missing/empty SDT specification at line 20 +80: [12:23:59] BEGIN SGROUP line not found on line 14 +80: [12:23:59] Unhandled CTAB feature: 'Unsupported SGroup type '' on line 18'. Molecule skipped. +80: [12:23:59] END SGROUP line not found on line 14 +80: [12:23:59] END SGROUP line not found on line 14 +80: [12:23:59] MRV_COORDINATE_BOND_TYPE SGroup with value 0 does not reference a query bond, ignoring. +80: [12:23:59] MRV_COORDINATE_BOND_TYPE SGroup with value 1 does not reference a query bond, ignoring. +80: [12:23:59] 80: 80: **** 80: Range Error @@ -21408,65 +21461,96 @@ 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# 0x0000AAAAAECFD834 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -80: 7# 0x0000AAAAAECC0A10 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -80: 8# 0x0000AAAAAED3EAAC in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -80: 9# 0x0000AAAAAED3F460 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -80: 10# 0x0000AAAAAED3F894 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -80: 11# 0x0000AAAAAED13D38 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -80: 12# 0x0000AAAAAED14284 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -80: 13# 0x0000AAAAAEC8C1B0 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -80: 14# 0x0000FFFFB56F229C in /lib/aarch64-linux-gnu/libc.so.6 +80: 6# 0x0000AAAAB3C4D834 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +80: 7# 0x0000AAAAB3C10A10 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +80: 8# 0x0000AAAAB3C8EAAC in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +80: 9# 0x0000AAAAB3C8F460 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +80: 10# 0x0000AAAAB3C8F894 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +80: 11# 0x0000AAAAB3C63D38 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +80: 12# 0x0000AAAAB3C64284 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +80: 13# 0x0000AAAAB3BDC1B0 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +80: 14# 0x0000FFFFADB6229C in /lib/aarch64-linux-gnu/libc.so.6 80: 15# __libc_start_main in /lib/aarch64-linux-gnu/libc.so.6 -80: 16# 0x0000AAAAAEC8C270 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +80: 16# 0x0000AAAAB3BDC270 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest 80: ---------- 80: **** 80: -80: [16:02:40] molecule does not contain a bond matching the MRV_COORDINATE_BOND_TYPE SGroup for bond 99, ignoring. -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: +80: [12:23:59] molecule does not contain a bond matching the MRV_COORDINATE_BOND_TYPE SGroup for bond 99, ignoring. +80: [12:23:59] Multiple ATTCHPT values for atom 2 on line 9 +80: [12:23:59] Found a SCD/SED line with missing/empty SDT specification at line 12 +80: [12:23:59] SMARTS Parse Error: syntax error while parsing: [#6;R +80: [12:23:59] SMARTS Parse Error: Failed parsing SMARTS '[#6;R' for input: '[#6;R' +80: [12:23:59] SMARTS for SMARTSQ '[#6;R' could not be parsed or has no atoms. Ignoring it. +80: [12:23:59] Skipping empty SMARTS value for SMARTSQ. +80: [12:23:59] unrecognized QUERYOP '>' for SMARTSQ. Query ignored. +80: [12:23:59] Found a SCD/SED line with missing/empty SDT specification at line 12 +69: [12:23:59] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 1 ignored +69: [12:23:59] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 1 ignored +69: [12:23:59] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 1 ignored +69: [12:23:59] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 1 ignored +80: [12:23:59] Can't kekulize mol. Unkekulized atoms: 0 1 2 3 4 +83: [12:23:59] WARNING: not removing hydrogen atom without neighbors +83: [12:23:59] WARNING: not removing hydrogen atom without neighbors +83: [12:23:59] WARNING: not removing hydrogen atom without neighbors +83: [12:23:59] WARNING: not removing hydrogen atom without neighbors +83: [12:23:59] WARNING: not removing hydrogen atom without neighbors +83: [12:23:59] WARNING: not removing hydrogen atom without neighbors +83: [12:23:59] WARNING: not removing hydrogen atom without neighbors +83: [12:23:59] WARNING: not removing hydrogen atom without neighbors +83: [12:23:59] WARNING: not removing hydrogen atom without neighbors +83: [12:23:59] WARNING: not removing hydrogen atom without neighbors +83: [12:23:59] CDXMLParser: Schema 80180 step 80181 ReactionStepAgents reaction fragment 64603 not found in document. +69: [12:23:59] 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: [12:23:59] +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# 0x0000FFFF9E927F24 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu//lib/libRDKitFileParsers.so.1 +69: 4# 0x0000FFFF9E935B20 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu//lib/libRDKitFileParsers.so.1 +69: 5# 0x0000FFFF9E936A4C 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# 0x0000AAAAE69AF77C in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersTest1 +69: 10# 0x0000AAAAE6A24944 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersTest1 +69: 11# 0x0000AAAAE6995BF8 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersTest1 +69: 12# 0x0000FFFF9DFF229C in /lib/aarch64-linux-gnu/libc.so.6 +69: 13# __libc_start_main in /lib/aarch64-linux-gnu/libc.so.6 +69: 14# 0x0000AAAAE6995E30 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersTest1 +69: ---------- +69: **** +69: 68: Test 68: -68: RP-6306_atrop4.mrv +68: BMS-986142_atrop6.mrv 68: 68: Test 68: -68: RP-6306_atrop5.mrv +68: BMS-986142_atrop7.mrv 68: -68: [16:02:40] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 2 ignored -68: [16:02:40] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 2 ignored -80: [16:02:40] Multiple ATTCHPT values for atom 2 on line 9 -80: [16:02:40] Found a SCD/SED line with missing/empty SDT specification at line 12 -80: [16:02:40] SMARTS Parse Error: syntax error while parsing: [#6;R -80: [16:02:40] SMARTS Parse Error: Failed parsing SMARTS '[#6;R' for input: '[#6;R' -80: [16:02:40] SMARTS for SMARTSQ '[#6;R' could not be parsed or has no atoms. Ignoring it. -80: [16:02:40] Skipping empty SMARTS value for SMARTSQ. -80: [16:02:40] unrecognized QUERYOP '>' for SMARTSQ. Query ignored. -80: [16:02:40] Found a SCD/SED line with missing/empty SDT specification at line 12 68: Test 68: -68: RP-6306_atropBad1.mrv +68: BMS-986142_atrop8.mrv 68: -68: [16:02:40] The bonds on one end of an atropisomer are both UP or both DOWN - atoms are: 2 8 -80: [16:02:40] Can't kekulize mol. Unkekulized atoms: 0 1 2 3 4 -80: [16:02:40] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -80: [16:02:40] WARNING: Skipping property bar because the value includes an illegal blank line -80: [16:02:40] WARNING: Skipping property baz because the value includes an illegal blank line -80: [16:02:40] WARNING: Skipping property bletch +68: [12:23:59] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored +68: [12:23:59] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored +80: [12:23:59] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +80: [12:23:59] WARNING: Skipping property bar because the value includes an illegal blank line +80: [12:23:59] WARNING: Skipping property baz because the value includes an illegal blank line +80: [12:23:59] WARNING: Skipping property bletch 80: nope because the name includes a newline -80: [16:02:40] WARNING: Skipping property bletch +80: [12:23:59] WARNING: Skipping property bletch 80: nope2 because the name includes a newline -80: [16:02:40] +80: [12:23:59] 80: 80: **** 80: Post-condition Violation @@ -21478,26 +21562,26 @@ 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# 0x0000FFFFB6017F24 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu//lib/libRDKitFileParsers.so.1 -80: 4# 0x0000FFFFB6028190 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu//lib/libRDKitFileParsers.so.1 -80: 5# 0x0000FFFFB6028DCC in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu//lib/libRDKitFileParsers.so.1 +80: 3# 0x0000FFFFAE487F24 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu//lib/libRDKitFileParsers.so.1 +80: 4# 0x0000FFFFAE498190 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu//lib/libRDKitFileParsers.so.1 +80: 5# 0x0000FFFFAE498DCC 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# 0x0000AAAAAEC94EF4 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -80: 10# 0x0000AAAAAED3EAAC in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -80: 11# 0x0000AAAAAED3F460 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -80: 12# 0x0000AAAAAED3F894 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -80: 13# 0x0000AAAAAED13D38 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -80: 14# 0x0000AAAAAED14284 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -80: 15# 0x0000AAAAAEC8C1B0 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -80: 16# 0x0000FFFFB56F229C in /lib/aarch64-linux-gnu/libc.so.6 +80: 9# 0x0000AAAAB3BE4EF4 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +80: 10# 0x0000AAAAB3C8EAAC in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +80: 11# 0x0000AAAAB3C8F460 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +80: 12# 0x0000AAAAB3C8F894 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +80: 13# 0x0000AAAAB3C63D38 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +80: 14# 0x0000AAAAB3C64284 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +80: 15# 0x0000AAAAB3BDC1B0 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +80: 16# 0x0000FFFFADB6229C in /lib/aarch64-linux-gnu/libc.so.6 80: 17# __libc_start_main in /lib/aarch64-linux-gnu/libc.so.6 -80: 18# 0x0000AAAAAEC8C270 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +80: 18# 0x0000AAAAB3BDC270 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest 80: ---------- 80: **** 80: -80: [16:02:40] +80: [12:23:59] 80: 80: **** 80: Post-condition Violation @@ -21509,26 +21593,26 @@ 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# 0x0000FFFFB6017F24 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu//lib/libRDKitFileParsers.so.1 -80: 4# 0x0000FFFFB6028190 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu//lib/libRDKitFileParsers.so.1 -80: 5# 0x0000FFFFB6028DCC in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu//lib/libRDKitFileParsers.so.1 +80: 3# 0x0000FFFFAE487F24 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu//lib/libRDKitFileParsers.so.1 +80: 4# 0x0000FFFFAE498190 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu//lib/libRDKitFileParsers.so.1 +80: 5# 0x0000FFFFAE498DCC 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# 0x0000AAAAAEC94818 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -80: 10# 0x0000AAAAAED3EAAC in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -80: 11# 0x0000AAAAAED3F460 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -80: 12# 0x0000AAAAAED3F894 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -80: 13# 0x0000AAAAAED13D38 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -80: 14# 0x0000AAAAAED14284 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -80: 15# 0x0000AAAAAEC8C1B0 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -80: 16# 0x0000FFFFB56F229C in /lib/aarch64-linux-gnu/libc.so.6 +80: 9# 0x0000AAAAB3BE4818 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +80: 10# 0x0000AAAAB3C8EAAC in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +80: 11# 0x0000AAAAB3C8F460 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +80: 12# 0x0000AAAAB3C8F894 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +80: 13# 0x0000AAAAB3C63D38 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +80: 14# 0x0000AAAAB3C64284 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +80: 15# 0x0000AAAAB3BDC1B0 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +80: 16# 0x0000FFFFADB6229C in /lib/aarch64-linux-gnu/libc.so.6 80: 17# __libc_start_main in /lib/aarch64-linux-gnu/libc.so.6 -80: 18# 0x0000AAAAAEC8C270 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +80: 18# 0x0000AAAAB3BDC270 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest 80: ---------- 80: **** 80: -80: [16:02:40] +80: [12:23:59] 80: 80: **** 80: Post-condition Violation @@ -21540,26 +21624,26 @@ 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# 0x0000FFFFB6017F24 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu//lib/libRDKitFileParsers.so.1 -80: 4# 0x0000FFFFB6025B20 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu//lib/libRDKitFileParsers.so.1 -80: 5# 0x0000FFFFB6026A4C in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu//lib/libRDKitFileParsers.so.1 +80: 3# 0x0000FFFFAE487F24 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu//lib/libRDKitFileParsers.so.1 +80: 4# 0x0000FFFFAE495B20 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu//lib/libRDKitFileParsers.so.1 +80: 5# 0x0000FFFFAE496A4C 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# 0x0000AAAAAEC94EB0 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -80: 10# 0x0000AAAAAED3EAAC in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -80: 11# 0x0000AAAAAED3F460 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -80: 12# 0x0000AAAAAED3F894 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -80: 13# 0x0000AAAAAED13D38 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -80: 14# 0x0000AAAAAED14284 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -80: 15# 0x0000AAAAAEC8C1B0 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -80: 16# 0x0000FFFFB56F229C in /lib/aarch64-linux-gnu/libc.so.6 +80: 9# 0x0000AAAAB3BE4EB0 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +80: 10# 0x0000AAAAB3C8EAAC in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +80: 11# 0x0000AAAAB3C8F460 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +80: 12# 0x0000AAAAB3C8F894 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +80: 13# 0x0000AAAAB3C63D38 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +80: 14# 0x0000AAAAB3C64284 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +80: 15# 0x0000AAAAB3BDC1B0 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +80: 16# 0x0000FFFFADB6229C in /lib/aarch64-linux-gnu/libc.so.6 80: 17# __libc_start_main in /lib/aarch64-linux-gnu/libc.so.6 -80: 18# 0x0000AAAAAEC8C270 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +80: 18# 0x0000AAAAB3BDC270 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest 80: ---------- 80: **** 80: -80: [16:02:40] +80: [12:23:59] 80: 80: **** 80: Post-condition Violation @@ -21571,76 +21655,39 @@ 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# 0x0000FFFFB6017F24 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu//lib/libRDKitFileParsers.so.1 -80: 4# 0x0000FFFFB6025B20 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu//lib/libRDKitFileParsers.so.1 -80: 5# 0x0000FFFFB6026A4C in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu//lib/libRDKitFileParsers.so.1 +80: 3# 0x0000FFFFAE487F24 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu//lib/libRDKitFileParsers.so.1 +80: 4# 0x0000FFFFAE495B20 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu//lib/libRDKitFileParsers.so.1 +80: 5# 0x0000FFFFAE496A4C 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# 0x0000AAAAAEC94BE8 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -80: 10# 0x0000AAAAAED3EAAC in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -80: 11# 0x0000AAAAAED3F460 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -80: 12# 0x0000AAAAAED3F894 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -80: 13# 0x0000AAAAAED13D38 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -80: 14# 0x0000AAAAAED14284 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -80: 15# 0x0000AAAAAEC8C1B0 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -80: 16# 0x0000FFFFB56F229C in /lib/aarch64-linux-gnu/libc.so.6 +80: 9# 0x0000AAAAB3BE4BE8 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +80: 10# 0x0000AAAAB3C8EAAC in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +80: 11# 0x0000AAAAB3C8F460 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +80: 12# 0x0000AAAAB3C8F894 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +80: 13# 0x0000AAAAB3C63D38 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +80: 14# 0x0000AAAAB3C64284 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +80: 15# 0x0000AAAAB3BDC1B0 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +80: 16# 0x0000FFFFADB6229C in /lib/aarch64-linux-gnu/libc.so.6 80: 17# __libc_start_main in /lib/aarch64-linux-gnu/libc.so.6 -80: 18# 0x0000AAAAAEC8C270 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +80: 18# 0x0000AAAAB3BDC270 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest 80: ---------- 80: **** 80: +80: [12:23:59] atom 3 has a negative isotope value. line: 15 +83: [12:23:59] Incomplete atom labelling, cannot make bond +83: [12:23:59] Incomplete atom labelling, cannot make bond +40: [12:23:59] Finished +40: [12:23:59] testing mol fragments. 68: Test 68: -68: RP-6306_atropBad2.mrv +68: BMS-986142_atropBad2.mrv 68: -68: [16:02:40] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 2 ignored -68: [16:02:40] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 2 ignored -68: [16:02:40] The 2 defining bonds for an atropisomer are co-planar - atoms are: 2 8 -87: Randomness seeded to: 1302120588 -87: =============================================================================== -87: All tests passed (6 assertions in 1 test case) -87: - 79/236 Test #87: v2FileParsersCatchTest ................. Passed 0.29 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 -83: [16:02:40] Incomplete atom labelling, cannot make bond -83: [16:02:40] Incomplete atom labelling, cannot make bond -90: ----------------- Test 1 -90: Done -90: -90: ----------------- Test 2 -90: Done -90: -90: ----------------- Test 3 -90: Done -90: -90: ----------------- Test 4 -80: [16:02:40] atom 3 has a negative isotope value. line: 15 -90: Done -90: -90: ----------------- Test 5 -90: Done -90: -90: ----------------- Test 5 QueryRoot -90: Done -90: -90: ----------------- Test 6 (Issue71 related) -90: Done -90: -90: ----------------- Testing serial numbers on recursive queries -90: Done -90: -90: [16:02:40] ------------------------------------- -90: [16:02:40] Test multithreading -90: reading molecules -83: [16:02:40] Incomplete atom labelling, cannot make bond -80: [16:02:40] Ignoring invalid chirality label: '2_bad_chirality' -80: [16:02:40] +68: [12:23:59] The bonds on one end of an atropisomer are both UP or both DOWN - atoms are: 7 29 +40: [12:23:59] Finished +40: [12:23:59] testing protein round-tripping. +80: [12:23:59] Ignoring invalid chirality label: '2_bad_chirality' +80: [12:23:59] 80: 80: **** 80: Pre-condition Violation @@ -21653,499 +21700,35 @@ 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# 0x0000AAAAAECD2054 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -80: 5# 0x0000AAAAAED3EAAC in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -80: 6# 0x0000AAAAAED3F460 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -80: 7# 0x0000AAAAAED3F894 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -80: 8# 0x0000AAAAAED13D38 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -80: 9# 0x0000AAAAAED14284 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -80: 10# 0x0000AAAAAEC8C1B0 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -80: 11# 0x0000FFFFB56F229C in /lib/aarch64-linux-gnu/libc.so.6 +80: 4# 0x0000AAAAB3C22054 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +80: 5# 0x0000AAAAB3C8EAAC in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +80: 6# 0x0000AAAAB3C8F460 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +80: 7# 0x0000AAAAB3C8F894 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +80: 8# 0x0000AAAAB3C63D38 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +80: 9# 0x0000AAAAB3C64284 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +80: 10# 0x0000AAAAB3BDC1B0 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +80: 11# 0x0000FFFFADB6229C in /lib/aarch64-linux-gnu/libc.so.6 80: 12# __libc_start_main in /lib/aarch64-linux-gnu/libc.so.6 -80: 13# 0x0000AAAAAEC8C270 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +80: 13# 0x0000AAAAB3BDC270 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest 80: ---------- 80: **** 80: -90: hits: 1111110111111111111111011111100011011011111101010111011110111101111111111111111111111011111011111110 -90: processing -90: launch :0 -90: launch :1 -90: launch :2 -90: launch :3 -83: [16:02:40] Failed to parse XML fragment 5 node: n attribute: id: mydoghasfleas -83: [16:02:40] Failed to parse XML fragment 5 node: n attribute: id: mydoghasfleas -83: [16:02:40] Failed to parse XML fragment 5 node: b attribute: Order: slartibartfast -83: [16:02:40] Failed to parse XML fragment 5 node: b attribute: Order: 5 -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: [16:02:40] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored -68: [16:02:40] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored -83: [16:02:40] Invalid or missing fragment id from CDXML fragment, assigning new one... -68: Test -68: -68: Sotorasib_atropBad1.mrv -68: -68: [16:02:40] The 2 defining bonds for an atropisomer are co-planar - atoms are: 7 20 -68: Test -68: -68: Sotorasib_atropBad2.mrv -68: -68: [16:02:40] The bonds on one end of an atropisomer are both UP or both DOWN - atoms are: 7 20 -90: done -90: hits2: 1111110111111111111111011111100011011011111101010111011110111101111111111111111111111011111011111110 -90: processing2 -90: launch2 :0 -90: launch2 :1 -90: launch2 :2 -90: launch2 :3 -83: =============================================================================== -83: All tests passed (263 assertions in 7 test cases) -83: -90: done -90: preprocessing 3 -90: hits3: 1110100011001000010011100110100011011000010101000100110010101111011100101000001111110000010100100110 -90: processing3 -90: launch3 :0 -90: launch3 :1 -90: launch3 :2 -90: launch3 :3 - 80/236 Test #83: cdxmlParserCatchTest ................... Passed 0.77 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: [16:02:40] SMARTS Parse Error: syntax error while parsing: MyDogHasFleas -69: [16:02:40] SMARTS Parse Error: Failed parsing SMARTS 'MyDogHasFleas' for input: 'MyDogHasFleas' -88: Randomness seeded to: 1487894369 -88: =============================================================================== -88: All tests passed (26 assertions in 2 test cases) -88: - 81/236 Test #88: atropisomersCatch ...................... Passed 0.29 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 -80: [16:02:40] Can't kekulize mol. Unkekulized atoms: 0 1 2 3 4 -80: [16:02:40] 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.[16:02:40] 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: [16:02:40] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -80: [16:02:40] 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: [16:02:40] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -90: done -90: [16:02:40] done -90: [16:02:40] ------------------------------------- -90: [16:02:40] Test GitHub issue 15 -90: [16:02:40] done -93: smi: O=C1CNC(=O)CN1 -93: 1: O=C1CNC(=O)CN1 -93: 2: COOC -93: [16:02:40] SMARTS Parse Error: syntax error while parsing: [Q:1][C:2][C:3](=[O:4])[O:5] -93: [16:02:40] 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]' -90: [16:02:40] ------------------------------------- -90: [16:02:40] Test GitHub issue 409 -90: [16:02:40] done -90: [16:02:40] ------------------------------------- -90: [16:02:40] Test chiral matching -93: O=C1CNC(=O)CN1 -93: [16:02:40] product atom-mapping number 1 found multiple times. -93: [16:02:40] mapped atoms in the reactants were not mapped in the products. -93: unmapped numbers are: 4 -90: [16:02:40] done -90: [16:02:40] ------------------------------------- -90: [16:02:40] Test GitHub issue 688: partially specified chiral substructure queries don't work properly -93: [16:02:40] atom 0 in product 0 has multiple charge specifications. -93: mass: 15.0001 -90: [16:02:40] done -90: [16:02:40] ------------------------------------- -90: [16:02:40] Test dative-bond matching -90: [16:02:40] done -90: [16:02:40] ------------------------------------- -90: [16:02:40] Test cis/trans matching -90: [16:02:40] done -90: [16:02:40] ------------------------------------- -90: [16:02:40] Test cis/trans matching part 2 -93: Oc1ccccn1 -93: Oc1ccc[nH]1 -90: [16:02:40] done -90: [16:02:40] ------------------------------------- -90: [16:02:40] Testing Github #1389: Substructure matching with chirality failure when query is built from SMARTS -90: [16:02:40] done -90: [16:02:40] ------------------------------------- -90: [16:02:40] Testing matching E/Z against Cis/Trans stereo bonds -90: [16:02:40] -90: -90: **** -90: Pre-condition Violation -90: matches must not be empty -90: Violation occurred on line 44 in file ./Code/GraphMol/Substruct/SubstructUtils.cpp -90: Failed Expression: !matches.empty() -90: ---------- -90: Stacktrace: -90: 0# Invar::Invariant::toString[abi:cxx11]() const in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu//lib/libRDKitRDGeneral.so.1 -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# 0x0000AAAAC366AD50 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/Substruct/testSubstructMatch -90: 5# 0x0000AAAAC36599A8 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/Substruct/testSubstructMatch -90: 6# 0x0000FFFF8737229C in /lib/aarch64-linux-gnu/libc.so.6 -90: 7# __libc_start_main in /lib/aarch64-linux-gnu/libc.so.6 -90: 8# 0x0000AAAAC3659BB0 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/Substruct/testSubstructMatch -90: ---------- -90: **** -90: -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: [16:02:40] The 2 defining bonds for an atropisomer are co-planar - atoms are: 0 31 -90: [16:02:40] -90: -90: **** -90: Pre-condition Violation -90: matches must not be empty -90: Violation occurred on line 44 in file ./Code/GraphMol/Substruct/SubstructUtils.cpp -90: Failed Expression: !matches.empty() -90: ---------- -90: Stacktrace: -90: 0# Invar::Invariant::toString[abi:cxx11]() const in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu//lib/libRDKitRDGeneral.so.1 -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# 0x0000AAAAC366B3A0 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/Substruct/testSubstructMatch -90: 5# 0x0000AAAAC36599A8 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/Substruct/testSubstructMatch -90: 6# 0x0000FFFF8737229C in /lib/aarch64-linux-gnu/libc.so.6 -90: 7# __libc_start_main in /lib/aarch64-linux-gnu/libc.so.6 -90: 8# 0x0000AAAAC3659BB0 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/Substruct/testSubstructMatch -90: ---------- -90: **** -90: -90: [16:02:40] ------------------------------------- -90: [16:02:40] Test substructure matching with a pathological case for symmetric SSSR -90: [16:02:40] ------------------------------------- -90: [16:02:40] Test isAtomTerminalRGroupOrQueryHydrogen -93: [16:02:40] SMARTS Parse Error: syntax error while parsing: ([C:1](=O)O.[C:2] -93: [16:02:40] SMARTS Parse Error: Failed parsing SMARTS '([C:1](=O)O.[C:2]' for input: '([C:1](=O)O.[C:2]' -93: [16:02:40] SMARTS Parse Error: syntax error while parsing: ([C:2] -93: [16:02:40] SMARTS Parse Error: Failed parsing SMARTS '([C:2]' for input: '([C:2]' -93: [16:02:40] SMARTS Parse Error: syntax error while parsing: [C:1](=O)O).[C:2] -93: [16:02:40] SMARTS Parse Error: Failed parsing SMARTS '[C:1](=O)O).[C:2]' for input: '[C:1](=O)O).[C:2]' -93: [16:02:40] SMARTS Parse Error: syntax error while parsing: [C:2]) -93: [16:02:40] SMARTS Parse Error: Failed parsing SMARTS '[C:2])' for input: '[C:2])' - 82/236 Test #90: testSubstructMatch ..................... Passed 0.34 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: [16:02:40] SMILES Parse Error: syntax error while parsing: [Q:1][C:2][C:3](=[O:4])[O:5] -93: [16:02:40] SMILES Parse Error: check for mistakes around position 2: -93: [16:02:40] [Q:1][C:2][C:3](=[O:4])[O:5] -93: [16:02:40] ~^ -93: [16:02:40] 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: [16:02:40] reactant 2 has no mapped atoms. -93: [16:02:40] >> Atoms within one molecule have different RXN roles. -93: [16:02:40] >> Fragment 0 not included in the reaction, atoms do not have a correct RXN role. -93: [16:02:40] SMARTS Parse Error: syntax error while parsing: ([C:1][C:2] -93: [16:02:40] SMARTS Parse Error: Failed parsing SMARTS '([C:1][C:2]' for input: '([C:1][C:2]' -93: [16:02:40] SMARTS Parse Error: syntax error while parsing: ([C:2] -93: [16:02:40] SMARTS Parse Error: Failed parsing SMARTS '([C:2]' for input: '([C:2]' -93: [16:02:40] SMARTS Parse Error: syntax error while parsing: [C:1][C:2]) -93: [16:02:40] SMARTS Parse Error: Failed parsing SMARTS '[C:1][C:2])' for input: '[C:1][C:2])' -93: [16:02:40] SMARTS Parse Error: syntax error while parsing: [C:1]).[C:2] -93: [16:02:40] SMARTS Parse Error: Failed parsing SMARTS '[C:1]).[C:2]' for input: '[C:1]).[C:2]' -93: [16:02:40] reactant 0 has no mapped atoms. -93: [16:02:40] reactant 1 has no mapped atoms. -93: [16:02:40] reactant 3 has no mapped atoms. -93: [16:02:40] product atom-mapping number 2 found multiple times. -93: [16:02:40] product atom-mapping number 3 found multiple times. -93: [16:02:40] product atom-mapping number 4 found multiple times. -93: [16:02:40] product atom-mapping number 5 found multiple times. -93: [16:02:40] product atom-mapping number 6 found multiple times. -93: [16:02:40] product atom-mapping number 7 found multiple times. -93: [16:02:40] product atom-mapping number 8 found multiple times. -93: [16:02:40] product atom-mapping number 12 found multiple times. -93: [16:02:40] product atom-mapping number 9 found multiple times. -93: [16:02:40] product atom-mapping number 10 found multiple times. -93: [16:02:40] product atom-mapping number 11 found multiple times. -93: [16:02:40] reactant 0 has no mapped atoms. -93: [16:02:40] reactant 1 has no mapped atoms. -93: [16:02:40] reactant 3 has no mapped atoms. -93: [16:02:40] reactant atom-mapping number 19 found multiple times. -93: [16:02:40] reactant atom-mapping number 25 found multiple times. -93: [16:02:40] reactant atom-mapping number 20 found multiple times. -93: [16:02:40] reactant atom-mapping number 21 found multiple times. -93: [16:02:40] reactant atom-mapping number 22 found multiple times. -93: [16:02:40] reactant atom-mapping number 23 found multiple times. -93: [16:02:40] reactant atom-mapping number 24 found multiple times. -93: [16:02:40] product atom-mapping number 1 found multiple times. -93: [16:02:40] product atom-mapping number 1 found multiple times. -93: [16:02:40] product atom-mapping number 1 found multiple times. -93: [16:02:40] product atom-mapping number 1 found multiple times. -93: [16:02:40] product atom-mapping number 2 found multiple times. -93: [16:02:40] product atom-mapping number 1 found multiple times. -93: [16:02:40] product atom-mapping number 2 found multiple times. -93: [16:02:40] product atom-mapping number 1 found multiple times. -93: [16:02:40] product atom-mapping number 2 found multiple times. -93: [16:02:40] product atom-mapping number 1 found multiple times. -93: [16:02:40] product atom-mapping number 2 found multiple times. -93: [16:02:40] product atom-mapping number 1 found multiple times. -93: F[C@@](Cl)(Br)ONO[C@](F)(Cl)Br -93: [16:02:40] product atom-mapping number 2 found multiple times. -93: [16:02:40] product atom-mapping number 1 found multiple times. -93: [16:02:40] product atom-mapping number 2 found multiple times. -93: [16:02:40] product atom-mapping number 1 found multiple times. -93: F[C@](Cl)(Br)ONO[C@](F)(Cl)Br -93: [16:02:40] product atom-mapping number 5 found multiple times. -93: [16:02:40] product atom-mapping number 2 found multiple times. -93: [16:02:40] product atom-mapping number 3 found multiple times. -93: [16:02:40] product atom-mapping number 1 found multiple times. -93: [16:02:40] product atom-mapping number 4 found multiple times. -93: [16:02:40] product atom-mapping number 5 found multiple times. -93: [16:02:40] product atom-mapping number 2 found multiple times. -93: [16:02:40] product atom-mapping number 3 found multiple times. -93: [16:02:40] product atom-mapping number 1 found multiple times. -93: [16:02:40] product atom-mapping number 4 found multiple times. -93: F[C@@](Cl)(Br)ONO[C@](F)(Cl)Br -93: [16:02:40] product atom-mapping number 5 found multiple times. -93: [16:02:40] product atom-mapping number 2 found multiple times. -93: [16:02:40] product atom-mapping number 3 found multiple times. -93: [16:02:40] product atom-mapping number 1 found multiple times. -93: [16:02:40] product atom-mapping number 4 found multiple times. -93: [16:02:40] product atom-mapping number 5 found multiple times. -93: [16:02:40] product atom-mapping number 2 found multiple times. -93: [16:02:40] product atom-mapping number 3 found multiple times. -93: [16:02:40] product atom-mapping number 1 found multiple times. -93: [16:02:40] product atom-mapping number 4 found multiple times. -93: F[C@](Cl)(Br)ONO[C@](F)(Cl)Br -93: [16:02:40] product atom-mapping number 2 found multiple times. -93: [16:02:40] product atom-mapping number 3 found multiple times. -93: [16:02:40] product atom-mapping number 1 found multiple times. -93: [16:02:40] product atom-mapping number 4 found multiple times. -93: [16:02:40] product atom-mapping number 2 found multiple times. -93: [16:02:40] product atom-mapping number 3 found multiple times. -93: [16:02:40] product atom-mapping number 1 found multiple times. -93: [16:02:40] product atom-mapping number 4 found multiple times. -93: F[C@@](Cl)(Br)O[C@](F)(Cl)Br -93: [16:02:40] product atom-mapping number 2 found multiple times. -93: [16:02:40] product atom-mapping number 3 found multiple times. -93: [16:02:40] product atom-mapping number 1 found multiple times. -93: [16:02:40] product atom-mapping number 4 found multiple times. -93: [16:02:40] product atom-mapping number 2 found multiple times. -93: [16:02:40] product atom-mapping number 3 found multiple times. -93: [16:02:40] product atom-mapping number 1 found multiple times. -93: [16:02:40] product atom-mapping number 4 found multiple times. -93: F[C@](Cl)(Br)O[C@](F)(Cl)Br -93: [16:02:40] product atom-mapping number 4 found multiple times. -93: [16:02:40] product atom-mapping number 3 found multiple times. -93: [16:02:40] product atom-mapping number 2 found multiple times. -93: [16:02:40] product atom-mapping number 1 found multiple times. -93: [16:02:40] product atom-mapping number 4 found multiple times. -93: [16:02:40] product atom-mapping number 3 found multiple times. -93: [16:02:40] product atom-mapping number 2 found multiple times. -93: [16:02:40] product atom-mapping number 1 found multiple times. -93: [16:02:40] product atom-mapping number 4 found multiple times. -93: [16:02:40] product atom-mapping number 3 found multiple times. -93: [16:02:40] product atom-mapping number 2 found multiple times. -93: [16:02:40] product atom-mapping number 1 found multiple times. -93: [16:02:40] product atom-mapping number 4 found multiple times. -93: [16:02:40] product atom-mapping number 3 found multiple times. -93: [16:02:40] product atom-mapping number 2 found multiple times. -93: [16:02:40] product atom-mapping number 1 found multiple times. -93: [16:02:40] product atom-mapping number 3 found multiple times. -93: [16:02:40] product atom-mapping number 2 found multiple times. -93: [16:02:40] product atom-mapping number 1 found multiple times. -93: [16:02:40] mapped atoms in the reactants were not mapped in the products. -93: unmapped numbers are: 4 -93: [16:02:40] product atom-mapping number 3 found multiple times. -93: [16:02:40] product atom-mapping number 2 found multiple times. -93: [16:02:40] product atom-mapping number 1 found multiple times. -93: [16:02:40] mapped atoms in the reactants were not mapped in the products. -93: unmapped numbers are: 4 -94: [16:02:40] ------------------------------------- -94: [16:02:40] Test Reaction StructuralFingerprint -93: [16:02:40] product atom-mapping number 6 not found in reactants. -93: [16:02:40] product atom-mapping number 7 not found in reactants. -93: [16:02:40] product atom-mapping number 8 not found in reactants. -93: [16:02:40] product atom-mapping number 7 not found in reactants. -93: [16:02:40] product atom-mapping number 8 not found in reactants. -93: [16:02:40] product atom-mapping number 9 not found in reactants. -93: [16:02:40] product atom-mapping number 10 not found in reactants. -93: [16:02:40] mapped atoms in the reactants were not mapped in the products. -93: unmapped numbers are: 6 -93: [16:02:40] product atom-mapping number 7 not found in reactants. -93: [16:02:40] product atom-mapping number 8 not found in reactants. -93: [16:02:40] product atom-mapping number 9 not found in reactants. -93: [16:02:40] product atom-mapping number 10 not found in reactants. -93: [16:02:40] mapped atoms in the reactants were not mapped in the products. -93: unmapped numbers are: 6 -93: smi1 [C:1][C:2][C:3]([O:4])([N:5])[Cl:6]>>[C:1][C:3]([C:2])([O:4])[N:5].[ClH:6] -93: smi2 [C:1][C:2][C:3]([O:4])([N:5])[Cl:6]>>[C:1][C:3]([C:2])([O:4])[N:5].[ClH:6] -93: [16:02:40] 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 -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: [16:02:40] The 2 defining bonds for an atropisomer are co-planar - atoms are: 15 16 -93: [16:02:40] product atom-mapping number 17 not found in reactants. -93: [16:02:40] product atom-mapping number 18 not found in reactants. -93: [16:02:40] mapped atoms in the reactants were not mapped in the products. -93: unmapped numbers are: 12 -94: [16:02:40] ------------------------------------- -94: [16:02:40] Test Reaction DifferenceFingerprint - 83/236 Test #94: testReactionFingerprints ............... Passed 0.16 sec -test 95 - Start 95: testEnumeration +83: [12:23:59] Incomplete atom labelling, cannot make bond +84: Randomness seeded to: 1639013654 +84: [12:23:59] Warning: ambiguous stereochemistry - opposing bonds have opposite wedging - at atom 2 ignored. +84: [12:23:59] Warning: ambiguous stereochemistry - opposing bonds have opposite wedging - at atom 2 ignored. +84: [12:23:59] Warning: ambiguous stereochemistry - opposing bonds have opposite wedging - at atom 2 ignored. +84: [12:23:59] Warning: ambiguous stereochemistry - opposing bonds have opposite wedging - at atom 2 ignored. +84: =============================================================================== +84: All tests passed (142 assertions in 6 test cases) +84: + 73/236 Test #84: molfileStereoCatchTest ................. Passed 0.37 sec +test 85 + Start 85: connectTheDotsTest -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 -69: [16:02:40] Empty atom list: 'M ALS 1 0 F' on line 8. -93: [16:02:40] Reaction has explicit hydrogens, reactants will need explicit hydrogens (addHs) -93: [16:02:40] Reaction has explicit hydrogens, reactants will need explicit hydrogens (addHs) -93: -93: [16:02:40] Mismatched potential rlabels: 1 unmapped reactant dummy atom rlabels,0 unmappped product dummy atom rlabels -93: ------------- -93: CCOc1ccccc1 -68: Test -68: -68: FalseAtropisomer.mrv -68: -68: Test -68: -68: AtropEnhancedStereo.mrv -68: -68: Test -68: -68: AtropManyChirals.mrv -68: -68: Test -68: -68: AtropManyChiralsEnhanced.mrv -68: -68: Test -68: -68: AtropManyChiralsEnhanced2.mrv -68: -68: Test -68: -68: AtropManyChiralsEnhanced3.mrv -68: -68: Test -68: -68: AtropManyChiralsEnhanced4.mrv -68: -68: Test -68: -68: BMS-986142_3d_chiral.mrv -68: -68: Test -68: -68: BMS-986142_3d.mrv -68: -68: Test -68: -68: BMS-986142_atrop1.mrv -68: -68: Test -68: -68: BMS-986142_atrop2.mrv -68: -68: Test -68: -68: BMS-986142_atrop3.mrv -68: -68: Test -68: -68: BMS-986142_atrop4.mrv -68: -68: Test -68: -68: BMS-986142_atrop5.mrv -68: -68: [16:02:40] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored -68: [16:02:40] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored -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: [16:02:40] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored -68: [16:02:40] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored -68: Test -68: -68: BMS-986142_atropBad2.mrv -68: -68: [16:02:40] The bonds on one end of an atropisomer are both UP or both DOWN - atoms are: 7 29 -69: de_DE.UTF-8 -69: [16:02:40] ------------------------------------- -69: [16:02:40] Test multithreading Locale Switching -95: 30000000 30000000 +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 68: Test 68: 68: JDQ443_3d.mrv @@ -22166,20 +21749,12 @@ 68: 68: JDQ443_atropBad1.mrv 68: -68: [16:02:40] The 2 defining bonds for an atropisomer are co-planar - atoms are: 17 21 -89: Randomness seeded to: 448257681 -89: [16:02:40] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [16:02:40] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [16:02:40] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [16:02:40] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [16:02:40] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [16:02:40] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [16:02:40] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [16:02:40] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [16:02:40] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [16:02:40] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [16:02:40] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [16:02:40] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +68: [12:23:59] The 2 defining bonds for an atropisomer are co-planar - atoms are: 17 21 +83: [12:23:59] Failed to parse XML fragment 5 node: n attribute: id: mydoghasfleas +83: [12:23:59] Failed to parse XML fragment 5 node: n attribute: id: mydoghasfleas +83: [12:23:59] Failed to parse XML fragment 5 node: b attribute: Order: slartibartfast +83: [12:23:59] Failed to parse XML fragment 5 node: b attribute: Order: 5 +83: [12:23:59] Invalid or missing fragment id from CDXML fragment, assigning new one... 68: Test 68: 68: RP-6306_atrop1.mrv @@ -22200,181 +21775,30 @@ 68: 68: RP-6306_atrop5.mrv 68: -68: [16:02:40] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 2 ignored -68: [16:02:40] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 2 ignored -89: [16:02:40] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [16:02:40] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [16:02:40] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [16:02:40] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [16:02:40] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [16:02:40] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [16:02:40] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [16:02:40] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [16:02:40] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [16:02:40] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [16:02:40] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [16:02:40] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [16:02:40] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [16:02:40] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [16:02:40] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [16:02:40] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [16:02:40] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [16:02:40] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [16:02:40] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [16:02:40] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [16:02:40] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [16:02:40] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [16:02:40] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [16:02:40] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [16:02:40] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [16:02:40] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +68: [12:23:59] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 2 ignored +68: [12:23:59] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 2 ignored 68: Test 68: 68: RP-6306_atropBad1.mrv 68: -68: [16:02:40] The bonds on one end of an atropisomer are both UP or both DOWN - atoms are: 2 8 +68: [12:23:59] 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: [16:02:40] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 2 ignored -68: [16:02:40] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 2 ignored -68: [16:02:40] The 2 defining bonds for an atropisomer are co-planar - atoms are: 2 8 -89: [16:02:40] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [16:02:40] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [16:02:40] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [16:02:40] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [16:02:40] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -91: Randomness seeded to: 1411774696 -91: =============================================================================== -91: All tests passed (242 assertions in 12 test cases) -91: -89: [16:02:40] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [16:02:40] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [16:02:40] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [16:02:40] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [16:02:40] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [16:02:40] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. - 84/236 Test #91: substructTestCatch ..................... Passed 0.64 sec -test 96 - Start 96: rxnTestCatch +68: [12:23:59] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 2 ignored +68: [12:23:59] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 2 ignored +68: [12:23:59] The 2 defining bonds for an atropisomer are co-planar - atoms are: 2 8 +83: =============================================================================== +83: All tests passed (263 assertions in 7 test cases) +83: + 74/236 Test #83: cdxmlParserCatchTest ................... Passed 0.66 sec +test 86 + Start 86: v2MolSuppliers -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: [16:02:40] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [16:02:40] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [16:02:40] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [16:02:40] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [16:02:40] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [16:02:40] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [16:02:40] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [16:02:40] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [16:02:40] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [16:02:40] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [16:02:40] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [16:02:40] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [16:02:40] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [16:02:40] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [16:02:40] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [16:02:40] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [16:02:40] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [16:02:40] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -69: [16:02:40] Test multithreading (Done) -69: [16:02:40] ------------------------------------- -89: [16:02:40] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [16:02:40] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [16:02:40] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [16:02:40] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [16:02:40] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [16:02:40] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [16:02:40] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [16:02:40] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [16:02:40] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [16:02:40] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [16:02:40] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [16:02:40] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [16:02:40] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [16:02:40] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [16:02:40] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -69: *************************************** -69: *************************************** -89: [16:02:40] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [16:02:40] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [16:02:40] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [16:02:40] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [16:02:40] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [16:02:40] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [16:02:40] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [16:02:40] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [16:02:40] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [16:02:40] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [16:02:40] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [16:02:40] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [16:02:40] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [16:02:40] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [16:02:40] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [16:02:40] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [16:02:40] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [16:02:40] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [16:02:40] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [16:02:40] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [16:02:40] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [16:02:40] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [16:02:40] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [16:02:40] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [16:02:40] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -69: [16:02:40] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -69: [16:02:40] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -89: [16:02:40] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [16:02:40] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [16:02:40] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [16:02:40] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [16:02:40] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [16:02:40] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [16:02:40] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [16:02:40] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [16:02:40] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [16:02:40] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [16:02:40] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [16:02:40] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [16:02:40] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [16:02:40] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [16:02:40] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [16:02:40] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [16:02:40] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [16:02:40] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [16:02:40] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [16:02:40] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [16:02:40] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [16:02:40] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -69: [16:02:40] bond with order 0 found on line 7. This is not part of the MDL specification. -89: [16:02:40] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [16:02:40] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [16:02:40] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [16:02:40] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [16:02:40] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [16:02:40] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [16:02:40] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [16:02:40] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [16:02:40] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [16:02:40] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [16:02:40] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [16:02:40] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [16:02:40] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [16:02:40] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [16:02:40] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [16:02:40] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [16:02:40] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [16:02:40] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [16:02:40] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [16:02:40] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [16:02:40] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [16:02:40] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [16:02:40] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [16:02:40] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [16:02:40] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [16:02:40] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +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 68: Test 68: 68: RP-6306_3d.mrv @@ -22399,70 +21823,29 @@ 68: 68: Sotorasib_atrop5.mrv 68: -68: [16:02:40] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored -68: [16:02:40] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored -89: [16:02:40] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [16:02:40] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [16:02:40] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [16:02:40] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [16:02:40] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [16:02:40] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [16:02:40] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [16:02:40] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [16:02:40] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [16:02:40] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +68: [12:24:00] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored +68: [12:24:00] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored 68: Test 68: 68: Sotorasib_atropBad1.mrv 68: -68: [16:02:40] The 2 defining bonds for an atropisomer are co-planar - atoms are: 7 20 +68: [12:24:00] The 2 defining bonds for an atropisomer are co-planar - atoms are: 7 20 68: Test 68: 68: Sotorasib_atropBad2.mrv 68: -68: [16:02:40] The bonds on one end of an atropisomer are both UP or both DOWN - atoms are: 7 20 -89: [16:02:40] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [16:02:40] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [16:02:40] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [16:02:40] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [16:02:40] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [16:02:40] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [16:02:40] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [16:02:40] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [16:02:40] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [16:02:40] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -69: [16:02:40] Skipping unrecognized collection type at line 26: MDLV30/HILITE BONDS=(1 7) -69: [16:02:40] Skipping unrecognized collection type at line 27: MDLV30/HILITE ATOMS=(1 7) -69: [16:02:40] 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: [16:02:40] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [16:02:40] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [16:02:40] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [16:02:40] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [16:02:40] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [16:02:40] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [16:02:40] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [16:02:40] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [16:02:40] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [16:02:40] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -96: Randomness seeded to: 3234806838 -96: [16:02:40] atom 0 in product 0 has multiple charge specifications. -89: [16:02:40] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [16:02:40] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [16:02:40] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [16:02:40] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [16:02:40] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [16:02:40] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [16:02:40] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [16:02:40] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [16:02:40] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [16:02:40] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [16:02:40] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [16:02:40] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [16:02:40] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [16:02:40] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [16:02:40] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [16:02:40] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -69: generating smiles +68: [12:24:00] The bonds on one end of an atropisomer are both UP or both DOWN - atoms are: 7 20 +80: [12:24:00] Can't kekulize mol. Unkekulized atoms: 0 1 2 3 4 +80: [12:24:00] 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.[12:24:00] Warning: molecule is tagged as 3D, but all Z coords are zero and 2D stereo markers have been found, marking the mol as 2D. +80: [12:24:00] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +80: [12:24:00] Warning: molecule is tagged as 3D, but all Z coords are zero and 2D stereo markers have been found, marking the mol as 2D. +80: [12:24:00] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +69: [12:24:00] Warning: molecule is tagged as 3D, but all Z coords are zero and 2D stereo markers have been found, marking the mol as 2D. +69: [12:24:00] Warning: molecule is tagged as 3D, but all Z coords are zero and 2D stereo markers have been found, marking the mol as 2D. +85: Randomness seeded to: 1967752515 +85: =============================================================================== +85: All tests passed (8 assertions in 1 test case) +85: 68: Test 68: 68: Sotorasib_3d.mrv @@ -22483,45 +21866,29 @@ 68: 68: ZM374979_atropBad1.mrv 68: -68: [16:02:40] The 2 defining bonds for an atropisomer are co-planar - atoms are: 0 31 -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: [16:02:40] Found a SCD/SED line with missing/empty SDT specification at line 34 -96: [16:02:40] Found a SCD/SED line with missing/empty SDT specification at line 36 -96: [16:02:40] Found a SCD/SED line with missing/empty SDT specification at line 38 -96: [16:02:40] Found a SCD/SED line with missing/empty SDT specification at line 40 -96: [16:02:40] Found a SCD/SED line with missing/empty SDT specification at line 42 -96: [16:02:40] Found a SCD/SED line with missing/empty SDT specification at line 87 -96: [16:02:40] Found a SCD/SED line with missing/empty SDT specification at line 89 -96: [16:02:40] Found a SCD/SED line with missing/empty SDT specification at line 91 -96: [16:02:40] Found a SCD/SED line with missing/empty SDT specification at line 93 -96: [16:02:40] Found a SCD/SED line with missing/empty SDT specification at line 95 -96: [16:02:40] mapped atoms in the reactants were not mapped in the products. -96: unmapped numbers are: 2 -96: [16:02:40] mapped atoms in the reactants were not mapped in the products. -96: unmapped numbers are: 2 -96: [16:02:40] SMARTS Parse Error: unclosed ring for input: 'CC1' -96: [16:02:40] SMILES Parse Error: unclosed ring for input: 'CC1' -96: [16:02:40] mapped atoms in the reactants were not mapped in the products. -96: unmapped numbers are: 2 -96: [16:02:40] product atom-mapping number 2 not found in reactants. -96: [16:02:40] mapped atoms in the reactants were not mapped in the products. -96: unmapped numbers are: 2 -96: [16:02:40] product atom-mapping number 2 not found in reactants. -96: [16:02:40] CX Extensions: Substance group hierarchy is not always preserved. -96: [16:02:40] CX Extensions: Substance group hierarchy is not always preserved. -69: check isomorphism -93: [16:02:40] reactant 0 has no mapped atoms. -93: [16:02:40] product 0 has no mapped atoms. -93: [16:02:40] WARNING: neither stereo atoms nor CIP codes found for double bond. Stereochemistry info will not be propagated to product. -96: [16:02:40] reactant 0 has no mapped atoms. -96: [16:02:40] product 0 has no mapped atoms. -96: [16:02:40] Can't kekulize mol. Unkekulized atoms: 0 1 2 3 4 -96: [16:02:40] Can't kekulize mol. Unkekulized atoms: 0 1 2 3 4 -96: [16:02:40] Explicit valence for atom # 1 O, 5, is greater than permitted -96: =============================================================================== -96: All tests passed (722 assertions in 30 test cases) -96: +68: [12:24:00] The 2 defining bonds for an atropisomer are co-planar - atoms are: 0 31 + 75/236 Test #85: connectTheDotsTest ..................... Passed 0.29 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 +86: Randomness seeded to: 3856057390 +86: [12:24:00] Ignoring invalid chirality label: '12_R_1_3_4_5' +86: [12:24:00] Ignoring invalid chirality label: '12_ANR_1_3_4_15' +86: [12:24:00] Ignoring invalid chirality label: '2_S_1_3_4' +86: [12:24:00] Ignoring invalid chirality label: '2_ANS_1_3_4_5_2' +86: =============================================================================== +86: All tests passed (24 assertions in 6 test cases) +86: + 76/236 Test #86: v2MolSuppliers ......................... Passed 0.27 sec +test 88 + Start 88: atropisomersCatch + +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 68: Test 68: 68: mrtx1719_3d.mrv @@ -22542,21 +21909,42 @@ 68: 68: mrtx1719_atropBad1.mrv 68: -68: [16:02:40] The 2 defining bonds for an atropisomer are co-planar - atoms are: 15 16 - 85/236 Test #96: rxnTestCatch ........................... Passed 0.18 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 - 86/236 Test #93: testReaction ........................... Passed 0.67 sec -test 98 - Start 98: pyChemReactionEnumerations +68: [12:24:00] The 2 defining bonds for an atropisomer are co-planar - atoms are: 15 16 +87: Randomness seeded to: 1242238851 +87: =============================================================================== +87: All tests passed (6 assertions in 1 test case) +87: + 77/236 Test #87: v2FileParsersCatchTest ................. Passed 0.20 sec +test 89 + Start 89: multithreadedSupplierCatchTest -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 +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: ---------------------------------- +69: ---------------------------------- +69: [12:24:00] +69: +69: **** +69: Pre-condition Violation +69: rlabel out of range for MDL files +69: Violation occurred on line 863 in file ./Code/GraphMol/Atom.cpp +69: Failed Expression: rlabel >= 0 && rlabel < 100 +69: ---------- +69: Stacktrace: +69: 0# Invar::Invariant::toString[abi:cxx11]() const in /build/reproducible-path/rdkit-202503.1/obj-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# 0x0000AAAAE69BF23C in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersTest1 +69: 4# 0x0000AAAAE6A249A4 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersTest1 +69: 5# 0x0000AAAAE6995BF8 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersTest1 +69: 6# 0x0000FFFF9DFF229C in /lib/aarch64-linux-gnu/libc.so.6 +69: 7# __libc_start_main in /lib/aarch64-linux-gnu/libc.so.6 +69: 8# 0x0000AAAAE6995E30 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersTest1 +69: ---------- +69: **** +69: +69: [12:24:00] WARNING: could not find number of expected rings. Switching to an approximate ring finding algorithm. 68: Test 68: 68: AlexRxn.mrv @@ -22597,18 +21985,45 @@ 68: 68: EmptyRxn.mrv 68: -68: [16:02:41] initialization failed -92: Randomness seeded to: 2463818060 -92: =============================================================================== -92: All tests passed (11480 assertions in 38 test cases) -92: - 87/236 Test #92: testGenericGroups ...................... Passed 0.87 sec -test 99 - Start 99: pyChemReactionSanitize +68: [12:24:00] initialization failed +88: Randomness seeded to: 3108766804 +88: =============================================================================== +88: All tests passed (26 assertions in 2 test cases) +88: + 78/236 Test #88: atropisomersCatch ...................... Passed 0.25 sec +test 90 + Start 90: testSubstructMatch -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 +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 +90: ----------------- Test 1 +90: Done +90: +90: ----------------- Test 2 +90: Done +90: +90: ----------------- Test 3 +90: Done +90: +90: ----------------- Test 4 +90: Done +90: +90: ----------------- Test 5 +90: Done +90: +90: ----------------- Test 5 QueryRoot +90: Done +90: +90: ----------------- Test 6 (Issue71 related) +90: Done +90: +90: ----------------- Testing serial numbers on recursive queries +90: Done +90: +90: [12:24:00] ------------------------------------- +90: [12:24:00] Test multithreading +90: reading molecules 68: Test 68: 68: RxnNoCoords.mrv @@ -22697,13 +22112,674 @@ 68: 68: Smiles1 68: - 88/236 Test #68: testMrvToMol ........................... Passed 3.15 sec + 79/236 Test #68: testMrvToMol ........................... Passed 3.96 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 +90: hits: 1111110111111111111111011111100011011011111101010111011110111101111111111111111111111011111011111110 +90: processing +90: launch :0 +90: launch :1 +90: launch :2 +90: launch :3 +12: .................. +12: ---------------------------------------------------------------------- +12: Ran 18 tests in 7.696s +12: +12: OK +90: done +90: hits2: 1111110111111111111111011111100011011011111101010111011110111101111111111111111111111011111011111110 +90: processing2 +90: launch2 :0 +90: launch2 :1 +90: launch2 :2 +90: launch2 :3 + 80/236 Test #12: pyBV ................................... Passed 9.74 sec +90: done +90: preprocessing 3 +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 +90: hits3: 1110100011001000010011100110100011011000010101000100110010101111011100101000001111110000010100100110 +90: processing3 +90: launch3 :0 +90: launch3 :1 +90: launch3 :2 +90: launch3 :3 +29: All 191 tests passed +90: done +90: [12:24:01] done +90: [12:24:01] ------------------------------------- +90: [12:24:01] Test GitHub issue 15 +90: [12:24:01] done +90: [12:24:01] ------------------------------------- +90: [12:24:01] Test GitHub issue 409 +90: [12:24:01] done +89: Randomness seeded to: 2917613370 +89: [12:24:01] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [12:24:01] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [12:24:01] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [12:24:01] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [12:24:01] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [12:24:01] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [12:24:01] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [12:24:01] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [12:24:01] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [12:24:01] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [12:24:01] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [12:24:01] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [12:24:01] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [12:24:01] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +90: [12:24:01] ------------------------------------- +90: [12:24:01] Test chiral matching +90: [12:24:01] done +90: [12:24:01] ------------------------------------- +90: [12:24:01] Test GitHub issue 688: partially specified chiral substructure queries don't work properly +90: [12:24:01] done +90: [12:24:01] ------------------------------------- +90: [12:24:01] Test dative-bond matching +90: [12:24:01] done +90: [12:24:01] ------------------------------------- +90: [12:24:01] Test cis/trans matching +90: [12:24:01] done +90: [12:24:01] ------------------------------------- +90: [12:24:01] Test cis/trans matching part 2 +90: [12:24:01] done +90: [12:24:01] ------------------------------------- +90: [12:24:01] Testing Github #1389: Substructure matching with chirality failure when query is built from SMARTS +89: [12:24:01] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [12:24:01] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [12:24:01] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [12:24:01] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [12:24:01] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [12:24:01] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [12:24:01] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [12:24:01] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [12:24:01] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [12:24:01] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [12:24:01] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [12:24:01] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [12:24:01] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [12:24:01] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [12:24:01] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [12:24:01] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [12:24:01] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [12:24:01] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [12:24:01] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [12:24:01] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [12:24:01] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [12:24:01] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [12:24:01] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [12:24:01] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [12:24:01] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [12:24:01] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [12:24:01] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [12:24:01] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [12:24:01] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [12:24:01] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [12:24:01] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [12:24:01] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [12:24:01] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [12:24:01] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [12:24:01] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [12:24:01] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [12:24:01] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [12:24:01] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [12:24:01] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [12:24:01] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [12:24:01] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +90: [12:24:01] done +89: [12:24:01] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [12:24:01] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [12:24:01] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [12:24:01] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [12:24:01] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +90: [12:24:01] ------------------------------------- +90: [12:24:01] Testing matching E/Z against Cis/Trans stereo bonds +69: [12:24:01] SMARTS Parse Error: syntax error while parsing: MyDogHasFleas +69: [12:24:01] SMARTS Parse Error: Failed parsing SMARTS 'MyDogHasFleas' for input: 'MyDogHasFleas' +89: [12:24:01] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [12:24:01] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [12:24:01] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [12:24:01] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [12:24:01] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [12:24:01] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [12:24:01] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [12:24:01] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [12:24:01] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [12:24:01] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [12:24:01] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [12:24:01] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [12:24:01] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [12:24:01] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [12:24:01] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [12:24:01] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [12:24:01] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [12:24:01] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [12:24:01] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [12:24:01] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [12:24:01] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [12:24:01] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [12:24:01] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [12:24:01] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [12:24:01] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [12:24:01] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [12:24:01] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +90: [12:24:01] +90: +90: **** +89: [12:24:01] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [12:24:01] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [12:24:01] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [12:24:01] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [12:24:01] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [12:24:01] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [12:24:01] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [12:24:01] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [12:24:01] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [12:24:01] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +90: Pre-condition Violation +90: matches must not be empty +90: Violation occurred on line 44 in file ./Code/GraphMol/Substruct/SubstructUtils.cpp +90: Failed Expression: !matches.empty() +90: ---------- +90: Stacktrace: +90: 0# Invar::Invariant::toString[abi:cxx11]() const in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu//lib/libRDKitRDGeneral.so.1 +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# 0x0000AAAAAFC7AD50 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/Substruct/testSubstructMatch +90: 5# 0x0000AAAAAFC699A8 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/Substruct/testSubstructMatch +90: 6# 0x0000FFFF9E28229C in /lib/aarch64-linux-gnu/libc.so.6 +90: 7# __libc_start_main in /lib/aarch64-linux-gnu/libc.so.6 +90: 8# 0x0000AAAAAFC69BB0 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/Substruct/testSubstructMatch +90: ---------- +90: **** +90: +89: [12:24:01] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +90: [12:24:01] +90: +90: **** +90: Pre-condition Violation +90: matches must not be empty +90: Violation occurred on line 44 in file ./Code/GraphMol/Substruct/SubstructUtils.cpp +90: Failed Expression: !matches.empty() +90: ---------- +90: Stacktrace: +90: 0# Invar::Invariant::toString[abi:cxx11]() const in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu//lib/libRDKitRDGeneral.so.1 +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# 0x0000AAAAAFC7B3A0 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/Substruct/testSubstructMatch +90: 5# 0x0000AAAAAFC699A8 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/Substruct/testSubstructMatch +90: 6# 0x0000FFFF9E28229C in /lib/aarch64-linux-gnu/libc.so.6 +90: 7# __libc_start_main in /lib/aarch64-linux-gnu/libc.so.6 +90: 8# 0x0000AAAAAFC69BB0 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/Substruct/testSubstructMatch +90: ---------- +90: **** +90: +90: [12:24:01] ------------------------------------- +90: [12:24:01] Test substructure matching with a pathological case for symmetric SSSR +90: [12:24:01] ------------------------------------- +90: [12:24:01] Test isAtomTerminalRGroupOrQueryHydrogen +89: [12:24:01] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [12:24:01] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [12:24:01] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [12:24:01] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [12:24:01] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [12:24:01] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [12:24:01] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [12:24:01] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [12:24:01] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [12:24:01] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [12:24:01] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [12:24:01] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [12:24:01] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [12:24:01] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [12:24:01] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [12:24:01] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [12:24:01] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [12:24:01] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [12:24:01] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [12:24:01] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [12:24:01] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [12:24:01] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [12:24:01] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [12:24:01] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [12:24:01] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [12:24:01] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. + 81/236 Test #90: testSubstructMatch ..................... Passed 0.67 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 +89: [12:24:01] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [12:24:01] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [12:24:01] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [12:24:01] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [12:24:01] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [12:24:01] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [12:24:01] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [12:24:01] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [12:24:01] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [12:24:01] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [12:24:01] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [12:24:01] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [12:24:01] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [12:24:01] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [12:24:01] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [12:24:01] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [12:24:01] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [12:24:01] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [12:24:01] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [12:24:01] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [12:24:01] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [12:24:01] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [12:24:01] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [12:24:01] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [12:24:01] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [12:24:01] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [12:24:01] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [12:24:01] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [12:24:01] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [12:24:01] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [12:24:01] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [12:24:01] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [12:24:01] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [12:24:01] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [12:24:01] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [12:24:01] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [12:24:01] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [12:24:01] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [12:24:01] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [12:24:01] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [12:24:01] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [12:24:01] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [12:24:01] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [12:24:01] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [12:24:01] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [12:24:01] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [12:24:01] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [12:24:01] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [12:24:01] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [12:24:01] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [12:24:01] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [12:24:01] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [12:24:01] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [12:24:01] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [12:24:01] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [12:24:01] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [12:24:01] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [12:24:01] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [12:24:01] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [12:24:01] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [12:24:01] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [12:24:01] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [12:24:01] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [12:24:01] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [12:24:01] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [12:24:01] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [12:24:01] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [12:24:01] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [12:24:01] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [12:24:01] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [12:24:01] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [12:24:01] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [12:24:01] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [12:24:01] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [12:24:01] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [12:24:01] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [12:24:01] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +93: smi: O=C1CNC(=O)CN1 +93: 1: O=C1CNC(=O)CN1 +93: 2: COOC +69: [12:24:01] Empty atom list: 'M ALS 1 0 F' on line 8. +93: [12:24:01] SMARTS Parse Error: syntax error while parsing: [Q:1][C:2][C:3](=[O:4])[O:5] +93: [12:24:01] 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: [12:24:01] product atom-mapping number 1 found multiple times. +93: [12:24:01] mapped atoms in the reactants were not mapped in the products. +93: unmapped numbers are: 4 +69: de_DE.UTF-8 +69: [12:24:01] ------------------------------------- +69: [12:24:01] Test multithreading Locale Switching +93: [12:24:01] atom 0 in product 0 has multiple charge specifications. +93: mass: 15.0001 +93: Oc1ccccn1 +93: Oc1ccc[nH]1 +91: Randomness seeded to: 980234107 +91: =============================================================================== +91: All tests passed (242 assertions in 12 test cases) +91: + 82/236 Test #91: substructTestCatch ..................... Passed 0.80 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 +29: +29: Computing MMFF94 energies for /build/reproducible-path/rdkit-202503.1/Code/ForceField/MMFF/test_data/MMFF94_hypervalent.sdf... +69: [12:24:01] Test multithreading (Done) +69: [12:24:01] ------------------------------------- +69: *************************************** +69: *************************************** +69: [12:24:01] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +69: [12:24:01] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +93: [12:24:01] SMARTS Parse Error: syntax error while parsing: ([C:1](=O)O.[C:2] +93: [12:24:01] SMARTS Parse Error: Failed parsing SMARTS '([C:1](=O)O.[C:2]' for input: '([C:1](=O)O.[C:2]' +93: [12:24:01] SMARTS Parse Error: syntax error while parsing: ([C:2] +93: [12:24:01] SMARTS Parse Error: Failed parsing SMARTS '([C:2]' for input: '([C:2]' +93: [12:24:01] SMARTS Parse Error: syntax error while parsing: [C:1](=O)O).[C:2] +93: [12:24:01] SMARTS Parse Error: Failed parsing SMARTS '[C:1](=O)O).[C:2]' for input: '[C:1](=O)O).[C:2]' +93: [12:24:01] SMARTS Parse Error: syntax error while parsing: [C:2]) +93: [12:24:01] SMARTS Parse Error: Failed parsing SMARTS '[C:2])' for input: '[C:2])' +69: [12:24:01] bond with order 0 found on line 7. This is not part of the MDL specification. +93: [12:24:01] SMILES Parse Error: syntax error while parsing: [Q:1][C:2][C:3](=[O:4])[O:5] +93: [12:24:01] SMILES Parse Error: check for mistakes around position 2: +93: [12:24:01] [Q:1][C:2][C:3](=[O:4])[O:5] +93: [12:24:01] ~^ +93: [12:24:01] 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: [12:24:01] reactant 2 has no mapped atoms. +93: [12:24:01] >> Atoms within one molecule have different RXN roles. +69: [12:24:01] Skipping unrecognized collection type at line 26: MDLV30/HILITE BONDS=(1 7) +69: [12:24:01] Skipping unrecognized collection type at line 27: MDLV30/HILITE ATOMS=(1 7) +69: [12:24:01] Warning: molecule is tagged as 3D, but all Z coords are zero and 2D stereo markers have been found, marking the mol as 2D. +93: [12:24:01] >> Fragment 0 not included in the reaction, atoms do not have a correct RXN role. +93: [12:24:01] SMARTS Parse Error: syntax error while parsing: ([C:1][C:2] +93: [12:24:01] SMARTS Parse Error: Failed parsing SMARTS '([C:1][C:2]' for input: '([C:1][C:2]' +93: [12:24:01] SMARTS Parse Error: syntax error while parsing: ([C:2] +93: [12:24:01] SMARTS Parse Error: Failed parsing SMARTS '([C:2]' for input: '([C:2]' +93: [12:24:01] SMARTS Parse Error: syntax error while parsing: [C:1][C:2]) +93: [12:24:01] SMARTS Parse Error: Failed parsing SMARTS '[C:1][C:2])' for input: '[C:1][C:2])' +93: [12:24:01] SMARTS Parse Error: syntax error while parsing: [C:1]).[C:2] +93: [12:24:01] SMARTS Parse Error: Failed parsing SMARTS '[C:1]).[C:2]' for input: '[C:1]).[C:2]' +93: [12:24:01] reactant 0 has no mapped atoms. +93: [12:24:01] reactant 1 has no mapped atoms. +93: [12:24:01] reactant 3 has no mapped atoms. +93: [12:24:01] product atom-mapping number 2 found multiple times. +93: [12:24:01] product atom-mapping number 3 found multiple times. +93: [12:24:01] product atom-mapping number 4 found multiple times. +93: [12:24:01] product atom-mapping number 5 found multiple times. +93: [12:24:01] product atom-mapping number 6 found multiple times. +93: [12:24:01] product atom-mapping number 7 found multiple times. +93: [12:24:01] product atom-mapping number 8 found multiple times. +93: [12:24:01] product atom-mapping number 12 found multiple times. +93: [12:24:01] product atom-mapping number 9 found multiple times. +93: [12:24:01] product atom-mapping number 10 found multiple times. +93: [12:24:01] product atom-mapping number 11 found multiple times. +93: [12:24:01] reactant 0 has no mapped atoms. +93: [12:24:01] reactant 1 has no mapped atoms. +93: [12:24:01] reactant 3 has no mapped atoms. +93: [12:24:01] reactant atom-mapping number 19 found multiple times. +93: [12:24:01] reactant atom-mapping number 25 found multiple times. +93: [12:24:01] reactant atom-mapping number 20 found multiple times. +93: [12:24:01] reactant atom-mapping number 21 found multiple times. +93: [12:24:01] reactant atom-mapping number 22 found multiple times. +93: [12:24:01] reactant atom-mapping number 23 found multiple times. +93: [12:24:01] reactant atom-mapping number 24 found multiple times. +93: [12:24:01] product atom-mapping number 1 found multiple times. +93: [12:24:01] product atom-mapping number 1 found multiple times. +93: [12:24:01] product atom-mapping number 1 found multiple times. +93: [12:24:01] product atom-mapping number 1 found multiple times. +93: [12:24:01] product atom-mapping number 2 found multiple times. +93: [12:24:01] product atom-mapping number 1 found multiple times. +93: [12:24:01] product atom-mapping number 2 found multiple times. +93: [12:24:01] product atom-mapping number 1 found multiple times. +93: [12:24:01] product atom-mapping number 2 found multiple times. +93: [12:24:01] product atom-mapping number 1 found multiple times. +93: [12:24:01] product atom-mapping number 2 found multiple times. +93: [12:24:01] product atom-mapping number 1 found multiple times. +93: F[C@@](Cl)(Br)ONO[C@](F)(Cl)Br +93: [12:24:01] product atom-mapping number 2 found multiple times. +93: [12:24:01] product atom-mapping number 1 found multiple times. +93: [12:24:01] product atom-mapping number 2 found multiple times. +93: [12:24:01] product atom-mapping number 1 found multiple times. +93: F[C@](Cl)(Br)ONO[C@](F)(Cl)Br +93: [12:24:01] product atom-mapping number 5 found multiple times. +93: [12:24:01] product atom-mapping number 2 found multiple times. +93: [12:24:01] product atom-mapping number 3 found multiple times. +93: [12:24:01] product atom-mapping number 1 found multiple times. +93: [12:24:01] product atom-mapping number 4 found multiple times. +93: [12:24:01] product atom-mapping number 5 found multiple times. +93: [12:24:01] product atom-mapping number 2 found multiple times. +93: [12:24:01] product atom-mapping number 3 found multiple times. +93: [12:24:01] product atom-mapping number 1 found multiple times. +93: [12:24:01] product atom-mapping number 4 found multiple times. +93: F[C@@](Cl)(Br)ONO[C@](F)(Cl)Br +93: [12:24:01] product atom-mapping number 5 found multiple times. +93: [12:24:01] product atom-mapping number 2 found multiple times. +93: [12:24:01] product atom-mapping number 3 found multiple times. +93: [12:24:01] product atom-mapping number 1 found multiple times. +93: [12:24:01] product atom-mapping number 4 found multiple times. +93: [12:24:01] product atom-mapping number 5 found multiple times. +93: [12:24:01] product atom-mapping number 2 found multiple times. +93: [12:24:01] product atom-mapping number 3 found multiple times. +93: [12:24:01] product atom-mapping number 1 found multiple times. +93: [12:24:01] product atom-mapping number 4 found multiple times. +93: F[C@](Cl)(Br)ONO[C@](F)(Cl)Br +93: [12:24:01] product atom-mapping number 2 found multiple times. +93: [12:24:01] product atom-mapping number 3 found multiple times. +93: [12:24:01] product atom-mapping number 1 found multiple times. +93: [12:24:01] product atom-mapping number 4 found multiple times. +93: [12:24:01] product atom-mapping number 2 found multiple times. +93: [12:24:01] product atom-mapping number 3 found multiple times. +93: [12:24:01] product atom-mapping number 1 found multiple times. +93: [12:24:01] product atom-mapping number 4 found multiple times. +93: F[C@@](Cl)(Br)O[C@](F)(Cl)Br +93: [12:24:01] product atom-mapping number 2 found multiple times. +93: [12:24:01] product atom-mapping number 3 found multiple times. +93: [12:24:01] product atom-mapping number 1 found multiple times. +93: [12:24:01] product atom-mapping number 4 found multiple times. +93: [12:24:01] product atom-mapping number 2 found multiple times. +93: [12:24:01] product atom-mapping number 3 found multiple times. +93: [12:24:01] product atom-mapping number 1 found multiple times. +93: [12:24:01] product atom-mapping number 4 found multiple times. +93: F[C@](Cl)(Br)O[C@](F)(Cl)Br +93: [12:24:01] product atom-mapping number 4 found multiple times. +93: [12:24:01] product atom-mapping number 3 found multiple times. +93: [12:24:01] product atom-mapping number 2 found multiple times. +93: [12:24:01] product atom-mapping number 1 found multiple times. +93: [12:24:01] product atom-mapping number 4 found multiple times. +93: [12:24:01] product atom-mapping number 3 found multiple times. +93: [12:24:01] product atom-mapping number 2 found multiple times. +93: [12:24:01] product atom-mapping number 1 found multiple times. +93: [12:24:01] product atom-mapping number 4 found multiple times. +93: [12:24:01] product atom-mapping number 3 found multiple times. +93: [12:24:01] product atom-mapping number 2 found multiple times. +93: [12:24:01] product atom-mapping number 1 found multiple times. +93: [12:24:01] product atom-mapping number 4 found multiple times. +93: [12:24:01] product atom-mapping number 3 found multiple times. +93: [12:24:01] product atom-mapping number 2 found multiple times. +94: [12:24:01] ------------------------------------- +94: [12:24:01] Test Reaction StructuralFingerprint +69: generating smiles +93: [12:24:01] product atom-mapping number 1 found multiple times. +93: [12:24:01] product atom-mapping number 3 found multiple times. +93: [12:24:01] product atom-mapping number 2 found multiple times. +93: [12:24:01] product atom-mapping number 1 found multiple times. +93: [12:24:01] mapped atoms in the reactants were not mapped in the products. +93: unmapped numbers are: 4 +93: [12:24:01] product atom-mapping number 3 found multiple times. +93: [12:24:01] product atom-mapping number 2 found multiple times. +93: [12:24:01] product atom-mapping number 1 found multiple times. +93: [12:24:01] mapped atoms in the reactants were not mapped in the products. +93: unmapped numbers are: 4 +93: [12:24:01] product atom-mapping number 6 not found in reactants. +93: [12:24:01] product atom-mapping number 7 not found in reactants. +93: [12:24:01] product atom-mapping number 8 not found in reactants. +93: [12:24:01] product atom-mapping number 7 not found in reactants. +93: [12:24:01] product atom-mapping number 8 not found in reactants. +93: [12:24:01] product atom-mapping number 9 not found in reactants. +93: [12:24:01] product atom-mapping number 10 not found in reactants. +93: [12:24:01] mapped atoms in the reactants were not mapped in the products. +93: unmapped numbers are: 6 +93: [12:24:01] product atom-mapping number 7 not found in reactants. +93: [12:24:01] product atom-mapping number 8 not found in reactants. +93: [12:24:01] product atom-mapping number 9 not found in reactants. +93: [12:24:01] product atom-mapping number 10 not found in reactants. +93: [12:24:01] mapped atoms in the reactants were not mapped in the products. +93: unmapped numbers are: 6 +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 +40: [12:24:01] Finished +40: [12:24:01] testing stability w.r.t. renumbering. +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: [12:24:01] Finished +40: [12:24:01] testing smiles round-tripping. +93: [12:24:01] 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 +94: [12:24:01] ------------------------------------- +94: [12:24:01] Test Reaction DifferenceFingerprint + 83/236 Test #94: testReactionFingerprints ............... Passed 0.26 sec +test 95 + Start 95: testEnumeration + +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 +89: [12:24:01] Explicit valence for atom # 9 N, 5, is greater than permitted +93: [12:24:01] product atom-mapping number 17 not found in reactants. +93: [12:24:01] product atom-mapping number 18 not found in reactants. +93: [12:24:01] mapped atoms in the reactants were not mapped in the products. +93: unmapped numbers are: 12 +89: [12:24:01] Explicit valence for atom # 3 Al, 6, is greater than permitted +92: Randomness seeded to: 2130900043 +92: =============================================================================== +92: All tests passed (11480 assertions in 38 test cases) +92: + 84/236 Test #92: testGenericGroups ...................... Passed 0.93 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: [12:24:01] Explicit valence for atom # 4 Al, 6, is greater than permitted +89: [12:24:01] Explicit valence for atom # 10 Si, 6, is greater than permitted +95: 30000000 30000000 +93: [12:24:01] Reaction has explicit hydrogens, reactants will need explicit hydrogens (addHs) +93: [12:24:01] Reaction has explicit hydrogens, reactants will need explicit hydrogens (addHs) +93: +93: [12:24:01] Mismatched potential rlabels: 1 unmapped reactant dummy atom rlabels,0 unmappped product dummy atom rlabels +93: ------------- +93: CCOc1ccccc1 +89: [12:24:02] Explicit valence for atom # 2 O, 4, is greater than permitted +89: [12:24:02] Explicit valence for atom # 3 Al, 6, is greater than permitted +89: [12:24:02] Explicit valence for atom # 3 Be, 4, is greater than permitted +89: [12:24:02] Explicit valence for atom # 27 P, 6, is greater than permitted +40: [12:24:02] Finished +40: [12:24:02] testing github #1567: Non-canonical result from MolFragmentToSmiles() +40: [12:24:02] Finished + 85/236 Test #40: hanoiTest .............................. Passed 8.51 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 +96: Randomness seeded to: 2584533141 +96: [12:24:02] atom 0 in product 0 has multiple charge specifications. +96: [12:24:02] Found a SCD/SED line with missing/empty SDT specification at line 34 +96: [12:24:02] Found a SCD/SED line with missing/empty SDT specification at line 36 +96: [12:24:02] Found a SCD/SED line with missing/empty SDT specification at line 38 +96: [12:24:02] Found a SCD/SED line with missing/empty SDT specification at line 40 +96: [12:24:02] Found a SCD/SED line with missing/empty SDT specification at line 42 +96: [12:24:02] Found a SCD/SED line with missing/empty SDT specification at line 87 +96: [12:24:02] Found a SCD/SED line with missing/empty SDT specification at line 89 +96: [12:24:02] Found a SCD/SED line with missing/empty SDT specification at line 91 +96: [12:24:02] Found a SCD/SED line with missing/empty SDT specification at line 93 +96: [12:24:02] Found a SCD/SED line with missing/empty SDT specification at line 95 +96: [12:24:02] mapped atoms in the reactants were not mapped in the products. +96: unmapped numbers are: 2 +96: [12:24:02] mapped atoms in the reactants were not mapped in the products. +96: unmapped numbers are: 2 +96: [12:24:02] SMARTS Parse Error: unclosed ring for input: 'CC1' +96: [12:24:02] SMILES Parse Error: unclosed ring for input: 'CC1' +96: [12:24:02] mapped atoms in the reactants were not mapped in the products. +96: unmapped numbers are: 2 +96: [12:24:02] product atom-mapping number 2 not found in reactants. +96: [12:24:02] mapped atoms in the reactants were not mapped in the products. +96: unmapped numbers are: 2 +96: [12:24:02] product atom-mapping number 2 not found in reactants. +93: [12:24:02] reactant 0 has no mapped atoms. +93: [12:24:02] product 0 has no mapped atoms. +93: [12:24:02] WARNING: neither stereo atoms nor CIP codes found for double bond. Stereochemistry info will not be propagated to product. + 86/236 Test #93: testReaction ........................... Passed 1.26 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 +96: [12:24:02] CX Extensions: Substance group hierarchy is not always preserved. +96: [12:24:02] CX Extensions: Substance group hierarchy is not always preserved. +96: [12:24:02] reactant 0 has no mapped atoms. +96: [12:24:02] product 0 has no mapped atoms. +96: [12:24:02] Can't kekulize mol. Unkekulized atoms: 0 1 2 3 4 +96: [12:24:02] Can't kekulize mol. Unkekulized atoms: 0 1 2 3 4 +96: [12:24:02] Explicit valence for atom # 1 O, 5, is greater than permitted +96: =============================================================================== +96: All tests passed (722 assertions in 30 test cases) +96: + 87/236 Test #96: rxnTestCatch ........................... Passed 0.67 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 + 88/236 Test #42: resMolSupplierTest ..................... Passed 9.28 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 +69: [12:24:02] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 1 ignored +69: [12:24:02] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 1 ignored +69: [12:24:02] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 1 ignored +69: [12:24:02] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 1 ignored +69: [12:24:02] 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: [12:24:02] +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# 0x0000FFFF9E927F24 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu//lib/libRDKitFileParsers.so.1 +69: 4# 0x0000FFFF9E935B20 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu//lib/libRDKitFileParsers.so.1 +69: 5# 0x0000FFFF9E936A4C 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# 0x0000AAAAE69AF77C in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersTest1 +69: 10# 0x0000AAAAE6A24944 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersTest1 +69: 11# 0x0000AAAAE6995C6C in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersTest1 +69: 12# 0x0000FFFF9DFF229C in /lib/aarch64-linux-gnu/libc.so.6 +69: 13# __libc_start_main in /lib/aarch64-linux-gnu/libc.so.6 +69: 14# 0x0000AAAAE6995E30 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersTest1 +69: ---------- +69: **** +69: +89: [12:24:02] Explicit valence for atom # 9 N, 5, is greater than permitted 100: 1 smi: CC 100: 1 smi: CC 100: 2 smi: CCO[C@H](N)P @@ -22712,23 +22788,63 @@ 100: replaceSub smi1:CCNCC 100: sidechains chiral=true smi1;;; [1*]P([2*])[C@H](N)O 100: sidechains chiral=false smi1;;; [1*]P([2*])[C@H](N)O -100: [16:02:41] SMARTS Parse Error: syntax error while parsing: bar -100: [16:02:41] SMARTS Parse Error: Failed parsing SMARTS 'bar' for input: 'bar' -89: [16:02:41] Explicit valence for atom # 9 N, 5, is greater than permitted - 89/236 Test #100: testChemTransforms ..................... Passed 0.20 sec +89: [12:24:03] Explicit valence for atom # 3 Al, 6, is greater than permitted +100: [12:24:03] SMARTS Parse Error: syntax error while parsing: bar +100: [12:24:03] SMARTS Parse Error: Failed parsing SMARTS 'bar' for input: 'bar' +89: [12:24:03] Explicit valence for atom # 4 Al, 6, is greater than permitted +89: [12:24:03] Explicit valence for atom # 10 Si, 6, is greater than permitted +69: [12:24:03] Warning: molecule is tagged as 3D, but all Z coords are zero and 2D stereo markers have been found, marking the mol as 2D. +69: [12:24:03] Warning: molecule is tagged as 3D, but all Z coords are zero and 2D stereo markers have been found, marking the mol as 2D. + 89/236 Test #100: testChemTransforms ..................... Passed 0.37 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: [16:02:41] Explicit valence for atom # 3 Al, 6, is greater than permitted -101: Randomness seeded to: 2946158187 -101: [16:02:41] Incomplete atom labelling, cannot make bond -101: [16:02:41] +89: [12:24:03] Explicit valence for atom # 2 O, 4, is greater than permitted +89: [12:24:03] Explicit valence for atom # 3 Al, 6, is greater than permitted +89: [12:24:03] Explicit valence for atom # 3 Be, 4, is greater than permitted +89: [12:24:03] Explicit valence for atom # 27 P, 6, is greater than permitted +69: ---------------------------------- +69: ---------------------------------- +69: [12:24:03] +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# 0x0000AAAAE69BF23C in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersTest1 +69: 4# 0x0000AAAAE6A249A4 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersTest1 +69: 5# 0x0000AAAAE6995C6C in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersTest1 +69: 6# 0x0000FFFF9DFF229C in /lib/aarch64-linux-gnu/libc.so.6 +69: 7# __libc_start_main in /lib/aarch64-linux-gnu/libc.so.6 +69: 8# 0x0000AAAAE6995E30 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersTest1 +69: ---------- +69: **** +69: +69: [12:24:03] WARNING: could not find number of expected rings. Switching to an approximate ring finding algorithm. +89: =============================================================================== +89: All tests passed (21562 assertions in 3 test cases) +89: + 90/236 Test #89: multithreadedSupplierCatchTest ......... Passed 3.09 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 +101: Randomness seeded to: 2644471300 +101: [12:24:03] Incomplete atom labelling, cannot make bond +101: [12:24:03] 101: 101: **** -89: [16:02:41] Explicit valence for atom # 4 Al, 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 @@ -22739,22 +22855,21 @@ 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# 0x0000AAAADE1672AC in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/ChemTransforms/chemTransformsTestCatch -101: 5# 0x0000AAAADE1B52CC in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/ChemTransforms/chemTransformsTestCatch -101: 6# 0x0000AAAADE1B5C80 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/ChemTransforms/chemTransformsTestCatch -101: 7# 0x0000AAAADE1B60B4 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/ChemTransforms/chemTransformsTestCatch -101: 8# 0x0000AAAADE18A638 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/ChemTransforms/chemTransformsTestCatch -101: 9# 0x0000AAAADE18AB84 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/ChemTransforms/chemTransformsTestCatch -101: 10# 0x0000AAAADE15C550 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/ChemTransforms/chemTransformsTestCatch -101: 11# 0x0000FFFF88B0229C in /lib/aarch64-linux-gnu/libc.so.6 +101: 4# 0x0000AAAAB2B972AC in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/ChemTransforms/chemTransformsTestCatch +101: 5# 0x0000AAAAB2BE52CC in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/ChemTransforms/chemTransformsTestCatch +101: 6# 0x0000AAAAB2BE5C80 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/ChemTransforms/chemTransformsTestCatch +101: 7# 0x0000AAAAB2BE60B4 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/ChemTransforms/chemTransformsTestCatch +101: 8# 0x0000AAAAB2BBA638 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/ChemTransforms/chemTransformsTestCatch +101: 9# 0x0000AAAAB2BBAB84 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/ChemTransforms/chemTransformsTestCatch +101: 10# 0x0000AAAAB2B8C550 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/ChemTransforms/chemTransformsTestCatch +101: 11# 0x0000FFFF9F48229C in /lib/aarch64-linux-gnu/libc.so.6 101: 12# __libc_start_main in /lib/aarch64-linux-gnu/libc.so.6 -101: 13# 0x0000AAAADE15C630 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/ChemTransforms/chemTransformsTestCatch +101: 13# 0x0000AAAAB2B8C630 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/ChemTransforms/chemTransformsTestCatch 101: ---------- 101: **** 101: -89: [16:02:41] Explicit valence for atom # 10 Si, 6, is greater than permitted -101: [16:02:41] Incomplete atom labelling, cannot make bond -101: [16:02:41] +101: [12:24:03] Incomplete atom labelling, cannot make bond +101: [12:24:03] 101: 101: **** 101: Invariant Violation @@ -22767,21 +22882,21 @@ 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# 0x0000AAAADE1672AC in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/ChemTransforms/chemTransformsTestCatch -101: 5# 0x0000AAAADE1B52CC in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/ChemTransforms/chemTransformsTestCatch -101: 6# 0x0000AAAADE1B5C80 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/ChemTransforms/chemTransformsTestCatch -101: 7# 0x0000AAAADE1B60B4 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/ChemTransforms/chemTransformsTestCatch -101: 8# 0x0000AAAADE18A638 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/ChemTransforms/chemTransformsTestCatch -101: 9# 0x0000AAAADE18AB84 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/ChemTransforms/chemTransformsTestCatch -101: 10# 0x0000AAAADE15C550 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/ChemTransforms/chemTransformsTestCatch -101: 11# 0x0000FFFF88B0229C in /lib/aarch64-linux-gnu/libc.so.6 +101: 4# 0x0000AAAAB2B972AC in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/ChemTransforms/chemTransformsTestCatch +101: 5# 0x0000AAAAB2BE52CC in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/ChemTransforms/chemTransformsTestCatch +101: 6# 0x0000AAAAB2BE5C80 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/ChemTransforms/chemTransformsTestCatch +101: 7# 0x0000AAAAB2BE60B4 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/ChemTransforms/chemTransformsTestCatch +101: 8# 0x0000AAAAB2BBA638 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/ChemTransforms/chemTransformsTestCatch +101: 9# 0x0000AAAAB2BBAB84 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/ChemTransforms/chemTransformsTestCatch +101: 10# 0x0000AAAAB2B8C550 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/ChemTransforms/chemTransformsTestCatch +101: 11# 0x0000FFFF9F48229C in /lib/aarch64-linux-gnu/libc.so.6 101: 12# __libc_start_main in /lib/aarch64-linux-gnu/libc.so.6 -101: 13# 0x0000AAAADE15C630 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/ChemTransforms/chemTransformsTestCatch +101: 13# 0x0000AAAAB2B8C630 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/ChemTransforms/chemTransformsTestCatch 101: ---------- 101: **** 101: -101: [16:02:41] Incomplete atom labelling, cannot make bond -101: [16:02:41] +101: [12:24:03] Incomplete atom labelling, cannot make bond +101: [12:24:03] 101: 101: **** 101: Invariant Violation @@ -22794,23 +22909,23 @@ 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# 0x0000AAAADE1672AC in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/ChemTransforms/chemTransformsTestCatch -101: 5# 0x0000AAAADE1B52CC in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/ChemTransforms/chemTransformsTestCatch -101: 6# 0x0000AAAADE1B5C80 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/ChemTransforms/chemTransformsTestCatch -101: 7# 0x0000AAAADE1B60B4 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/ChemTransforms/chemTransformsTestCatch -101: 8# 0x0000AAAADE18A638 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/ChemTransforms/chemTransformsTestCatch -101: 9# 0x0000AAAADE18AB84 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/ChemTransforms/chemTransformsTestCatch -101: 10# 0x0000AAAADE15C550 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/ChemTransforms/chemTransformsTestCatch -101: 11# 0x0000FFFF88B0229C in /lib/aarch64-linux-gnu/libc.so.6 +101: 4# 0x0000AAAAB2B972AC in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/ChemTransforms/chemTransformsTestCatch +101: 5# 0x0000AAAAB2BE52CC in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/ChemTransforms/chemTransformsTestCatch +101: 6# 0x0000AAAAB2BE5C80 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/ChemTransforms/chemTransformsTestCatch +101: 7# 0x0000AAAAB2BE60B4 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/ChemTransforms/chemTransformsTestCatch +101: 8# 0x0000AAAAB2BBA638 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/ChemTransforms/chemTransformsTestCatch +101: 9# 0x0000AAAAB2BBAB84 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/ChemTransforms/chemTransformsTestCatch +101: 10# 0x0000AAAAB2B8C550 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/ChemTransforms/chemTransformsTestCatch +101: 11# 0x0000FFFF9F48229C in /lib/aarch64-linux-gnu/libc.so.6 101: 12# __libc_start_main in /lib/aarch64-linux-gnu/libc.so.6 -101: 13# 0x0000AAAADE15C630 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/ChemTransforms/chemTransformsTestCatch +101: 13# 0x0000AAAAB2B8C630 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/ChemTransforms/chemTransformsTestCatch 101: ---------- 101: **** 101: -101: [16:02:41] Incomplete atom labelling, cannot make bond -101: [16:02:41] Incomplete atom labelling, cannot make bond -101: [16:02:41] Incomplete atom labelling, cannot make bond -101: [16:02:41] +101: [12:24:03] Incomplete atom labelling, cannot make bond +101: [12:24:03] Incomplete atom labelling, cannot make bond +101: [12:24:03] Incomplete atom labelling, cannot make bond +101: [12:24:03] 101: 101: **** 101: Invariant Violation @@ -22823,21 +22938,21 @@ 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# 0x0000AAAADE1672AC in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/ChemTransforms/chemTransformsTestCatch -101: 5# 0x0000AAAADE1B52CC in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/ChemTransforms/chemTransformsTestCatch -101: 6# 0x0000AAAADE1B5C80 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/ChemTransforms/chemTransformsTestCatch -101: 7# 0x0000AAAADE1B60B4 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/ChemTransforms/chemTransformsTestCatch -101: 8# 0x0000AAAADE18A638 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/ChemTransforms/chemTransformsTestCatch -101: 9# 0x0000AAAADE18AB84 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/ChemTransforms/chemTransformsTestCatch -101: 10# 0x0000AAAADE15C550 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/ChemTransforms/chemTransformsTestCatch -101: 11# 0x0000FFFF88B0229C in /lib/aarch64-linux-gnu/libc.so.6 +101: 4# 0x0000AAAAB2B972AC in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/ChemTransforms/chemTransformsTestCatch +101: 5# 0x0000AAAAB2BE52CC in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/ChemTransforms/chemTransformsTestCatch +101: 6# 0x0000AAAAB2BE5C80 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/ChemTransforms/chemTransformsTestCatch +101: 7# 0x0000AAAAB2BE60B4 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/ChemTransforms/chemTransformsTestCatch +101: 8# 0x0000AAAAB2BBA638 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/ChemTransforms/chemTransformsTestCatch +101: 9# 0x0000AAAAB2BBAB84 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/ChemTransforms/chemTransformsTestCatch +101: 10# 0x0000AAAAB2B8C550 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/ChemTransforms/chemTransformsTestCatch +101: 11# 0x0000FFFF9F48229C in /lib/aarch64-linux-gnu/libc.so.6 101: 12# __libc_start_main in /lib/aarch64-linux-gnu/libc.so.6 -101: 13# 0x0000AAAADE15C630 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/ChemTransforms/chemTransformsTestCatch +101: 13# 0x0000AAAAB2B8C630 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/ChemTransforms/chemTransformsTestCatch 101: ---------- 101: **** 101: -101: [16:02:41] Incomplete atom labelling, cannot make bond -101: [16:02:41] +101: [12:24:03] Incomplete atom labelling, cannot make bond +101: [12:24:03] 101: 101: **** 101: Invariant Violation @@ -22850,20 +22965,20 @@ 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# 0x0000AAAADE1672AC in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/ChemTransforms/chemTransformsTestCatch -101: 5# 0x0000AAAADE1B52CC in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/ChemTransforms/chemTransformsTestCatch -101: 6# 0x0000AAAADE1B5C80 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/ChemTransforms/chemTransformsTestCatch -101: 7# 0x0000AAAADE1B60B4 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/ChemTransforms/chemTransformsTestCatch -101: 8# 0x0000AAAADE18A638 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/ChemTransforms/chemTransformsTestCatch -101: 9# 0x0000AAAADE18AB84 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/ChemTransforms/chemTransformsTestCatch -101: 10# 0x0000AAAADE15C550 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/ChemTransforms/chemTransformsTestCatch -101: 11# 0x0000FFFF88B0229C in /lib/aarch64-linux-gnu/libc.so.6 +101: 4# 0x0000AAAAB2B972AC in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/ChemTransforms/chemTransformsTestCatch +101: 5# 0x0000AAAAB2BE52CC in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/ChemTransforms/chemTransformsTestCatch +101: 6# 0x0000AAAAB2BE5C80 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/ChemTransforms/chemTransformsTestCatch +101: 7# 0x0000AAAAB2BE60B4 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/ChemTransforms/chemTransformsTestCatch +101: 8# 0x0000AAAAB2BBA638 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/ChemTransforms/chemTransformsTestCatch +101: 9# 0x0000AAAAB2BBAB84 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/ChemTransforms/chemTransformsTestCatch +101: 10# 0x0000AAAAB2B8C550 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/ChemTransforms/chemTransformsTestCatch +101: 11# 0x0000FFFF9F48229C in /lib/aarch64-linux-gnu/libc.so.6 101: 12# __libc_start_main in /lib/aarch64-linux-gnu/libc.so.6 -101: 13# 0x0000AAAADE15C630 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/ChemTransforms/chemTransformsTestCatch +101: 13# 0x0000AAAAB2B8C630 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/ChemTransforms/chemTransformsTestCatch 101: ---------- 101: **** 101: -101: [16:02:41] +101: [12:24:03] 101: 101: **** 101: Invariant Violation @@ -22877,114 +22992,40 @@ 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# 0x0000AAAADE15D6DC in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/ChemTransforms/chemTransformsTestCatch -101: 6# 0x0000AAAADE1B52CC in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/ChemTransforms/chemTransformsTestCatch -101: 7# 0x0000AAAADE1B5C80 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/ChemTransforms/chemTransformsTestCatch -101: 8# 0x0000AAAADE1B60B4 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/ChemTransforms/chemTransformsTestCatch -101: 9# 0x0000AAAADE18A638 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/ChemTransforms/chemTransformsTestCatch -101: 10# 0x0000AAAADE18AB84 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/ChemTransforms/chemTransformsTestCatch -101: 11# 0x0000AAAADE15C550 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/ChemTransforms/chemTransformsTestCatch -101: 12# 0x0000FFFF88B0229C in /lib/aarch64-linux-gnu/libc.so.6 +101: 5# 0x0000AAAAB2B8D6DC in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/ChemTransforms/chemTransformsTestCatch +101: 6# 0x0000AAAAB2BE52CC in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/ChemTransforms/chemTransformsTestCatch +101: 7# 0x0000AAAAB2BE5C80 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/ChemTransforms/chemTransformsTestCatch +101: 8# 0x0000AAAAB2BE60B4 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/ChemTransforms/chemTransformsTestCatch +101: 9# 0x0000AAAAB2BBA638 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/ChemTransforms/chemTransformsTestCatch +101: 10# 0x0000AAAAB2BBAB84 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/ChemTransforms/chemTransformsTestCatch +101: 11# 0x0000AAAAB2B8C550 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/ChemTransforms/chemTransformsTestCatch +101: 12# 0x0000FFFF9F48229C in /lib/aarch64-linux-gnu/libc.so.6 101: 13# __libc_start_main in /lib/aarch64-linux-gnu/libc.so.6 -101: 14# 0x0000AAAADE15C630 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/ChemTransforms/chemTransformsTestCatch +101: 14# 0x0000AAAAB2B8C630 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: - 90/236 Test #101: chemTransformsTestCatch ................ Passed 0.22 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 -89: [16:02:41] Explicit valence for atom # 2 O, 4, is greater than permitted -89: [16:02:41] Explicit valence for atom # 3 Al, 6, is greater than permitted -89: [16:02:41] Explicit valence for atom # 3 Be, 4, is greater than permitted -89: [16:02:41] Explicit valence for atom # 27 P, 6, is greater than permitted -69: [16:02:41] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 1 ignored -69: [16:02:41] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 1 ignored -69: [16:02:41] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 1 ignored -69: [16:02:41] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 1 ignored -69: [16:02:41] 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: [16:02:41] -69: -69: **** -69: Post-condition Violation -69: Element 'Mv' not found -69: Violation occurred on line 93 in file ./Code/GraphMol/PeriodicTable.h -69: Failed Expression: anum > -1 -69: ---------- -69: Stacktrace: -69: 0# Invar::Invariant::toString[abi:cxx11]() const in /build/reproducible-path/rdkit-202503.1/obj-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# 0x0000FFFF8B847F24 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu//lib/libRDKitFileParsers.so.1 -69: 4# 0x0000FFFF8B855B20 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu//lib/libRDKitFileParsers.so.1 -69: 5# 0x0000FFFF8B856A4C 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# 0x0000AAAABE96F77C in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersTest1 -69: 10# 0x0000AAAABE9E4944 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersTest1 -69: 11# 0x0000AAAABE955C6C in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersTest1 -69: 12# 0x0000FFFF8AF1229C in /lib/aarch64-linux-gnu/libc.so.6 -69: 13# __libc_start_main in /lib/aarch64-linux-gnu/libc.so.6 -69: 14# 0x0000AAAABE955E30 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersTest1 -69: ---------- -69: **** -69: -69: [16:02:41] 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: [16:02:41] Warning: molecule is tagged as 3D, but all Z coords are zero and 2D stereo markers have been found, marking the mol as 2D. -102: Randomness seeded to: 1411019745 -102: =============================================================================== -102: All tests passed (93 assertions in 13 test cases) -102: - 91/236 Test #102: tautomerQueryTestCatch ................. Passed 0.24 sec + 91/236 Test #101: chemTransformsTestCatch ................ Passed 0.44 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 -69: ---------------------------------- -69: ---------------------------------- -69: [16:02:41] -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# 0x0000AAAABE97F23C in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersTest1 -69: 4# 0x0000AAAABE9E49A4 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersTest1 -69: 5# 0x0000AAAABE955C6C in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersTest1 -69: 6# 0x0000FFFF8AF1229C in /lib/aarch64-linux-gnu/libc.so.6 -69: 7# __libc_start_main in /lib/aarch64-linux-gnu/libc.so.6 -69: 8# 0x0000AAAABE955E30 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersTest1 -69: ---------- -69: **** -69: -69: [16:02:41] WARNING: could not find number of expected rings. Switching to an approximate ring finding algorithm. -69: [16:02:42] SMARTS Parse Error: syntax error while parsing: MyDogHasFleas -69: [16:02:42] SMARTS Parse Error: Failed parsing SMARTS 'MyDogHasFleas' for input: 'MyDogHasFleas' -69: [16:02:42] Empty atom list: 'M ALS 1 0 F' on line 8. - 92/236 Test #69: fileParsersTest1 ....................... Passed 3.94 sec +102: Randomness seeded to: 2531457125 +102: =============================================================================== +102: All tests passed (93 assertions in 13 test cases) +102: + 92/236 Test #102: tautomerQueryTestCatch ................. Passed 0.47 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 -89: [16:02:42] Explicit valence for atom # 9 N, 5, is greater than permitted 104: ----------------------- 104: Subgraph retrieval 104: Finished @@ -22993,219 +23034,71 @@ 104: Finished 104: ----------------------- 104: testSubgraphs2 -89: [16:02:42] Explicit valence for atom # 3 Al, 6, is greater than permitted +69: [12:24:04] SMARTS Parse Error: syntax error while parsing: MyDogHasFleas +69: [12:24:04] SMARTS Parse Error: Failed parsing SMARTS 'MyDogHasFleas' for input: 'MyDogHasFleas' 104: Finished 104: ----------------------- 104: Path retrieval -89: [16:02:42] Explicit valence for atom # 4 Al, 6, is greater than permitted 104: Finished 104: ----------------------- 104: Path retrieval2 104: Finished 104: ----------------------- 104: Unique Subgraph retrieval +98: [12:24:04] == testCartesianProduct 104: Finished 104: ----------------------- 104: testUniqueSubgraphs2 -103: ..... -103: ---------------------------------------------------------------------- -103: Ran 5 tests in 0.061s -103: -103: OK -89: [16:02:42] Explicit valence for atom # 10 Si, 6, is greater than permitted - 93/236 Test #103: pyTautomerQuery ........................ Passed 0.52 sec -test 105 - Start 105: testSubgraphs2 - -105: Test command: /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/Subgraphs/testSubgraphs2 -105: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/Subgraphs -105: Test timeout computed to be: 1500 -105: ----------------------- -105: Test1: pathToSubmol -89: [16:02:42] Explicit valence for atom # 2 O, 4, is greater than permitted -105: Finished -105: ----------------------- -105: Test2: Atom Environments -89: [16:02:42] Explicit valence for atom # 3 Al, 6, is greater than permitted -89: [16:02:42] Explicit valence for atom # 3 Be, 4, is greater than permitted -105: Finished -105: ----------------------- -105: Test 3: Atom Environments (Extension) -105: Finished -105: ----------------------- -105: Testing github Issue103: stereochemistry and pathToSubmol -105: Finished -105: ----------------------- -105: Testing github Issue103: more stereochemistry and pathToSubmol (path needs to be in sorted order) -105: Finished - 94/236 Test #105: testSubgraphs2 ......................... Passed 0.09 sec -test 106 - Start 106: subgraphsCatch - -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 -89: [16:02:42] Explicit valence for atom # 27 P, 6, is greater than permitted -89: =============================================================================== -89: All tests passed (21562 assertions in 3 test cases) -89: - 95/236 Test #89: multithreadedSupplierCatchTest ......... Passed 2.51 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 -104: Finished -104: ----------------------- -104: testRootedSubgraphs -104: Finished -104: ----------------------- -104: testRootedPaths -104: Finished - 96/236 Test #104: testSubgraphs1 ......................... Passed 0.40 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 -107: Warning: molecule failed filter -107: Warning: molecule failed filter: reason hzone_phenol_A(479) -107: v = { -107: 0,23}, -107: 1,22}, -107: 2,20}, -107: 3,19}, -107: 4,25}, -107: 5,24}, -107: 6,18}, -107: 7,17}, -107: 8,16}, -107: 9,21}, -107: } -107: match = { -107: 0,23}, -107: 1,22}, -107: 2,20}, -107: 3,19}, -107: 4,25}, -107: 5,24}, -107: 6,18}, -107: 7,17}, -107: 8,16}, -107: 9,21}, -107: } -107: Warning: molecule failed filter -107: Warning: molecule failed filter: reason cyano_imine_B(17) -107: v = { -107: 0,11}, -107: 1,12}, -107: 2,13}, -107: 3,14}, -107: 4,15}, -107: 5,10}, -107: 6,9}, -107: 7,8}, -107: 8,7}, -107: 9,6}, -107: 10,5}, -107: 11,17}, -107: 12,16}, -107: } -107: match = { -107: 0,11}, -107: 1,12}, -107: 2,13}, -107: 3,14}, -107: 4,15}, -107: 5,10}, -107: 6,9}, -107: 7,8}, -107: 8,7}, -107: 9,6}, -107: 10,5}, -107: 11,17}, -107: 12,16}, -107: } -107: Warning: molecule failed filter -107: Warning: molecule failed filter: reason keto_keto_gamma(5) -107: v = { -107: 0,0}, -107: 1,1}, -107: 2,2}, -107: 3,4}, -107: 4,5}, -107: 5,6}, -107: 6,7}, -107: 7,8}, -107: 8,9}, -107: 9,14}, -107: 10,15}, -107: 11,16}, -107: } -107: match = { -107: 0,0}, -107: 1,1}, -107: 2,2}, -107: 3,4}, -107: 4,5}, -107: 5,6}, -107: 6,7}, -107: 7,8}, -107: 8,9}, -107: 9,14}, -107: 10,15}, -107: 11,16}, -107: } -98: [16:02:42] == testCartesianProduct -99: .[16:02:42] reactant 0 has no mapped atoms. -99: [16:02:42] product 0 has no mapped atoms. -99: [16:02:42] reactant 0 has no mapped atoms. -99: [16:02:42] product 0 has no mapped atoms. -98: .[16:02:42] == testEnumerateLibrary -99: .[16:02:42] reactant 0 has no mapped atoms. -99: [16:02:42] reactant 1 has no mapped atoms. -99: [16:02:42] product 0 has no mapped atoms. -99: [16:02:42] reactant 0 has no mapped atoms. -99: [16:02:42] reactant 1 has no mapped atoms. -99: [16:02:42] product 0 has no mapped atoms. -99: [16:02:42] reactant 0 has no mapped atoms. -99: [16:02:42] reactant 1 has no mapped atoms. -99: [16:02:42] product 0 has no mapped atoms. -99: [16:02:42] reactant 0 has no mapped atoms. -99: [16:02:42] reactant 1 has no mapped atoms. -99: [16:02:42] product 0 has no mapped atoms. -99: [16:02:42] reactant 0 has no mapped atoms. -99: [16:02:42] reactant 1 has no mapped atoms. -99: [16:02:42] product 0 has no mapped atoms. -99: [16:02:42] reactant 0 has no mapped atoms. -99: [16:02:42] reactant 1 has no mapped atoms. -99: [16:02:42] product 0 has no mapped atoms. -99: [16:02:42] reactant 0 has no mapped atoms. -99: [16:02:42] reactant 1 has no mapped atoms. -99: [16:02:42] product 0 has no mapped atoms. -99: [16:02:42] reactant 0 has no mapped atoms. -99: [16:02:42] reactant 1 has no mapped atoms. -99: [16:02:42] product 0 has no mapped atoms. -99: [16:02:42] reactant 0 has no mapped atoms. -99: [16:02:42] reactant 1 has no mapped atoms. -99: [16:02:42] product 0 has no mapped atoms. -99: [16:02:42] reactant 0 has no mapped atoms. -99: [16:02:42] reactant 1 has no mapped atoms. -99: [16:02:42] product 0 has no mapped atoms. -99: [16:02:42] reactant 0 has no mapped atoms. -99: [16:02:42] reactant 1 has no mapped atoms. -99: [16:02:42] product 0 has no mapped atoms. -99: [16:02:42] reactant 0 has no mapped atoms. -99: [16:02:42] reactant 1 has no mapped atoms. -99: [16:02:42] product 0 has no mapped atoms. -99: [16:02:42] reactant 0 has no mapped atoms. -99: [16:02:42] reactant 1 has no mapped atoms. -99: [16:02:42] product 0 has no mapped atoms. -99: [16:02:42] reactant 0 has no mapped atoms. -99: [16:02:42] reactant 1 has no mapped atoms. -99: [16:02:42] product 0 has no mapped atoms. +99: .[12:24:04] reactant 0 has no mapped atoms. +99: [12:24:04] product 0 has no mapped atoms. +99: [12:24:04] reactant 0 has no mapped atoms. +99: [12:24:04] product 0 has no mapped atoms. +98: .[12:24:04] == testEnumerateLibrary +97: ...[12:24:04] +97: +97: **** +99: .[12:24:04] reactant 0 has no mapped atoms. +99: [12:24:04] reactant 1 has no mapped atoms. +99: [12:24:04] product 0 has no mapped atoms. +99: [12:24:04] reactant 0 has no mapped atoms. +99: [12:24:04] reactant 1 has no mapped atoms. +99: [12:24:04] product 0 has no mapped atoms. +99: [12:24:04] reactant 0 has no mapped atoms. +99: [12:24:04] reactant 1 has no mapped atoms. +99: [12:24:04] product 0 has no mapped atoms. +99: [12:24:04] reactant 0 has no mapped atoms. +99: [12:24:04] reactant 1 has no mapped atoms. +99: [12:24:04] product 0 has no mapped atoms. +99: [12:24:04] reactant 0 has no mapped atoms. +99: [12:24:04] reactant 1 has no mapped atoms. +99: [12:24:04] product 0 has no mapped atoms. +99: [12:24:04] reactant 0 has no mapped atoms. +99: [12:24:04] reactant 1 has no mapped atoms. +99: [12:24:04] product 0 has no mapped atoms. +99: [12:24:04] reactant 0 has no mapped atoms. +99: [12:24:04] reactant 1 has no mapped atoms. +99: [12:24:04] product 0 has no mapped atoms. +99: [12:24:04] reactant 0 has no mapped atoms. +99: [12:24:04] reactant 1 has no mapped atoms. +99: [12:24:04] product 0 has no mapped atoms. +99: [12:24:04] reactant 0 has no mapped atoms. +99: [12:24:04] reactant 1 has no mapped atoms. +99: [12:24:04] product 0 has no mapped atoms. +99: [12:24:04] reactant 0 has no mapped atoms. +99: [12:24:04] reactant 1 has no mapped atoms. +99: [12:24:04] product 0 has no mapped atoms. +99: [12:24:04] reactant 0 has no mapped atoms. +99: [12:24:04] reactant 1 has no mapped atoms. +99: [12:24:04] product 0 has no mapped atoms. +99: [12:24:04] reactant 0 has no mapped atoms. +99: [12:24:04] reactant 1 has no mapped atoms. +99: [12:24:04] product 0 has no mapped atoms. +99: [12:24:04] reactant 0 has no mapped atoms. +99: [12:24:04] reactant 1 has no mapped atoms. +99: [12:24:04] product 0 has no mapped atoms. +99: [12:24:04] reactant 0 has no mapped atoms. +99: [12:24:04] reactant 1 has no mapped atoms. +99: [12:24:04] product 0 has no mapped atoms. 99: () 99: ******************************************** 99: $RXN @@ -23569,16 +23462,16 @@ 99: 1 2 1 0 99: M ISO 2 1 1 2 2 99: M END -99: [16:02:42] reactant 0 has no mapped atoms. -99: [16:02:42] reactant 1 has no mapped atoms. -99: [16:02:42] product 0 has no mapped atoms. -99: [16:02:42] Could not find RLabel mapping for atom: 0 in template: 1 -99: [16:02:42] reactant 1 has no mapped atoms. -99: [16:02:42] reactant 1 has no mapped atoms. -99: [16:02:42] reactant 1 has no mapped atoms. +99: [12:24:04] reactant 0 has no mapped atoms. +99: [12:24:04] reactant 1 has no mapped atoms. +99: [12:24:04] product 0 has no mapped atoms. +99: [12:24:04] Could not find RLabel mapping for atom: 0 in template: 1 +99: [12:24:04] reactant 1 has no mapped atoms. +99: [12:24:04] reactant 1 has no mapped atoms. +99: [12:24:04] reactant 1 has no mapped atoms. 99: .. 99: ---------------------------------------------------------------------- -99: Ran 4 tests in 0.044s +99: Ran 4 tests in 0.089s 99: 99: OK 99: @@ -23635,31 +23528,22 @@ 99: M END 99: 99: $RXN Failed -106: Randomness seeded to: 774488649 -106: --------- 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 -106: =============================================================================== -106: All tests passed (11 assertions in 1 test case) -106: -97: ...[16:02:42] -97: -97: **** - 97/236 Test #106: subgraphsCatch ......................... Passed 0.34 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 - 98/236 Test #107: filterCatalogTest ...................... Passed 0.39 sec -test 110 - Start 110: pyFragCatalog +103: ..... +103: ---------------------------------------------------------------------- +103: Ran 5 tests in 0.125s +103: +103: OK +69: [12:24:04] Empty atom list: 'M ALS 1 0 F' on line 8. + 93/236 Test #69: fileParsersTest1 ....................... Passed 7.25 sec +test 105 + Start 105: testSubgraphs2 -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 +105: Test command: /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/Subgraphs/testSubgraphs2 +105: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/Subgraphs +105: Test timeout computed to be: 1500 97: Pre-condition Violation 97: getNumImplicitHs() called without preceding call to calcImplicitValence() 97: Violation occurred on line 301 in file ./Code/GraphMol/Atom.cpp @@ -23691,7 +23575,7 @@ 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# 0x0000FFFFA2312680 in /lib/aarch64-linux-gnu/libboost_python313.so.1.83.0 +97: 25# 0x0000FFFF834A2680 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 @@ -23702,17 +23586,17 @@ 97: 33# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202503.1/obj-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# 0x0000FFFFA091C320 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so -97: 37# 0x0000FFFFA091C2B8 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so -97: 38# 0x0000FFFFA091C248 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so -97: 39# 0x0000FFFFA091C1E0 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so -97: 40# 0x0000FFFFA091C178 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so +97: 36# 0x0000FFFF81AAC320 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so +97: 37# 0x0000FFFF81AAC2B8 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so +97: 38# 0x0000FFFF81AAC248 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so +97: 39# 0x0000FFFF81AAC1E0 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so +97: 40# 0x0000FFFF81AAC178 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# 0x0000FFFFA230F25C in /lib/aarch64-linux-gnu/libboost_python313.so.1.83.0 +97: 46# 0x0000FFFF8349F25C 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# 0x000000000053DD10 in /usr/bin/python3 @@ -23744,13 +23628,13 @@ 97: 75# 0x000000000065F5F0 in /usr/bin/python3 97: 76# Py_RunMain in /usr/bin/python3 97: 77# Py_BytesMain in /usr/bin/python3 -97: 78# 0x0000FFFFA2E4229C in /lib/aarch64-linux-gnu/libc.so.6 +97: 78# 0x0000FFFF83FD229C 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: [16:02:42] +97: [12:24:04] 97: 97: **** 97: Pre-condition Violation @@ -23784,7 +23668,7 @@ 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# 0x0000FFFFA2312680 in /lib/aarch64-linux-gnu/libboost_python313.so.1.83.0 +97: 25# 0x0000FFFF834A2680 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 @@ -23795,17 +23679,17 @@ 97: 33# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202503.1/obj-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# 0x0000FFFFA091C320 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so -97: 37# 0x0000FFFFA091C2B8 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so -97: 38# 0x0000FFFFA091C248 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so -97: 39# 0x0000FFFFA091C1E0 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so -97: 40# 0x0000FFFFA091C178 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so +97: 36# 0x0000FFFF81AAC320 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so +97: 37# 0x0000FFFF81AAC2B8 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so +97: 38# 0x0000FFFF81AAC248 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so +97: 39# 0x0000FFFF81AAC1E0 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so +97: 40# 0x0000FFFF81AAC178 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# 0x0000FFFFA230F25C in /lib/aarch64-linux-gnu/libboost_python313.so.1.83.0 +97: 46# 0x0000FFFF8349F25C 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# 0x000000000053DD10 in /usr/bin/python3 @@ -23837,155 +23721,333 @@ 97: 75# 0x000000000065F5F0 in /usr/bin/python3 97: 76# Py_RunMain in /usr/bin/python3 97: 77# Py_BytesMain in /usr/bin/python3 -97: 78# 0x0000FFFFA2E4229C in /lib/aarch64-linux-gnu/libc.so.6 +97: 78# 0x0000FFFF83FD229C 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: .........[16:02:42] stereo atoms in input cannot be mapped to output (atoms are no longer bonded) -97: [16:02:42] stereo atoms in input cannot be mapped to output (atoms are no longer bonded) -97: [16:02:42] stereo atoms in input cannot be mapped to output (atoms are no longer bonded) -97: [16:02:42] stereo atoms in input cannot be mapped to output (atoms are no longer bonded) -97: .[16:02:42] product atom-mapping number 1 found multiple times. -97: [16:02:42] product atom-mapping number 1 found multiple times. - 99/236 Test #99: pyChemReactionSanitize ................. Passed 1.84 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 -97: ................[16:02:43] mapped atoms in the reactants were not mapped in the products. +97: .........[12:24:04] stereo atoms in input cannot be mapped to output (atoms are no longer bonded) +97: [12:24:04] stereo atoms in input cannot be mapped to output (atoms are no longer bonded) +97: [12:24:04] stereo atoms in input cannot be mapped to output (atoms are no longer bonded) +97: [12:24:04] stereo atoms in input cannot be mapped to output (atoms are no longer bonded) +97: .[12:24:04] product atom-mapping number 1 found multiple times. +97: [12:24:04] product atom-mapping number 1 found multiple times. +105: ----------------------- +105: Test1: pathToSubmol +98: ..[12:24:04] == testRGroupState +97: ................[12:24:04] mapped atoms in the reactants were not mapped in the products. 97: unmapped numbers are: 3 -97: [16:02:43] mapped atoms in the reactants were not mapped in the products. +97: [12:24:04] mapped atoms in the reactants were not mapped in the products. 97: unmapped numbers are: 3 -111: [16:02:43] ------------------------------------- -111: [16:02:43] Test Crippen parameter acquisition. -111: [16:02:43] done -111: [16:02:43] ------------------------------------- -111: [16:02:43] Test Crippen calculation. -111: [16:02:43] done -111: [16:02:43] ------------------------------------- -111: [16:02:43] Test Issue262: problems with Crippen calculation from pickles. -111: [16:02:43] done -111: [16:02:43] ------------------------------------- -111: [16:02:43] Test AMW calculation. -111: [16:02:43] done -111: [16:02:43] ------------------------------------- -111: [16:02:43] Test Exact MW calculation. -111: [16:02:43] done -111: [16:02:43] ------------------------------------- -111: [16:02:43] Test Labute ASA descriptors. -111: [16:02:43] done -111: [16:02:43] ------------------------------------- -111: [16:02:43] Test TPSA descriptors. -98: ..[16:02:43] == testRGroupState -98: .[16:02:43] == testRandomEnumerateAllBBsLibrary +105: Finished +105: ----------------------- +105: Test2: Atom Environments +98: .[12:24:04] == testRandomEnumerateAllBBsLibrary +105: Finished +105: ----------------------- +105: Test 3: Atom Environments (Extension) +105: Finished 98: ** [1, 1] 98: ** [0, 2] 98: ** [1, 0] +105: ----------------------- +105: Testing github Issue103: stereochemistry and pathToSubmol +105: Finished +105: ----------------------- +105: Testing github Issue103: more stereochemistry and pathToSubmol (path needs to be in sorted order) +105: Finished + 94/236 Test #105: testSubgraphs2 ......................... Passed 0.13 sec +test 106 + Start 106: subgraphsCatch + +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 +98: .[12:24:04] == testRandomEnumerateLibrary + 95/236 Test #103: pyTautomerQuery ........................ Passed 0.70 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 +98: .[12:24:04] == testRandomSample +98: .[12:24:04] == testRandomSampleAllBBs +98: .[12:24:04] deprecated -- please use MatchOnlyAtRgroupsAdjustParams instead +98: [12:24:04] deprecated -- please use MatchOnlyAtRgroupsAdjustParams instead +98: .[12:24:04] == testRemoveBadMatches +98: .[12:24:04] == testTimings + 96/236 Test #99: pyChemReactionSanitize ................. Passed 2.01 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 +104: Finished +104: ----------------------- +104: testRootedSubgraphs +104: Finished +104: ----------------------- +104: testRootedPaths +107: Warning: molecule failed filter +104: Finished +107: Warning: molecule failed filter: reason hzone_phenol_A(479) + 97/236 Test #104: testSubgraphs1 ......................... Passed 0.77 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: v = { +107: 0,23}, +107: 1,22}, +107: 2,20}, +107: 3,19}, +107: 4,25}, +107: 5,24}, +107: 6,18}, +107: 7,17}, +107: 8,16}, +107: 9,21}, +107: } +107: match = { +107: 0,23}, +107: 1,22}, +107: 2,20}, +107: 3,19}, +107: 4,25}, +107: 5,24}, +107: 6,18}, +107: 7,17}, +107: 8,16}, +107: 9,21}, +107: } +107: Warning: molecule failed filter +107: Warning: molecule failed filter: reason cyano_imine_B(17) +107: v = { +107: 0,11}, +107: 1,12}, +107: 2,13}, +107: 3,14}, +107: 4,15}, +107: 5,10}, +107: 6,9}, +107: 7,8}, +107: 8,7}, +107: 9,6}, +107: 10,5}, +107: 11,17}, +107: 12,16}, +107: } +107: match = { +107: 0,11}, +107: 1,12}, +107: 2,13}, +107: 3,14}, +107: 4,15}, +107: 5,10}, +107: 6,9}, +107: 7,8}, +107: 8,7}, +107: 9,6}, +107: 10,5}, +107: 11,17}, +107: 12,16}, +107: } +107: Warning: molecule failed filter +107: Warning: molecule failed filter: reason keto_keto_gamma(5) +107: v = { +107: 0,0}, +107: 1,1}, +107: 2,2}, +107: 3,4}, +107: 4,5}, +107: 5,6}, +107: 6,7}, +107: 7,8}, +107: 8,9}, +107: 9,14}, +107: 10,15}, +107: 11,16}, +107: } +107: match = { +107: 0,0}, +107: 1,1}, +107: 2,2}, +107: 3,4}, +107: 4,5}, +107: 5,6}, +107: 6,7}, +107: 7,8}, +107: 8,9}, +107: 9,14}, +107: 10,15}, +107: 11,16}, +107: } +106: Randomness seeded to: 3906066741 +106: --------- +106: =============================================================================== +106: All tests passed (11 assertions in 1 test case) +106: + 98/236 Test #106: subgraphsCatch ......................... Passed 0.35 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 109: 21 -98: .[16:02:43] == testRandomEnumerateLibrary -111: [16:02:43] done -111: [16:02:43] ------------------------------------- -111: [16:02:43] Test Lipinski parameters. -98: .[16:02:43] == testRandomSample -98: .[16:02:43] == testRandomSampleAllBBs -98: .[16:02:43] deprecated -- please use MatchOnlyAtRgroupsAdjustParams instead -98: [16:02:43] deprecated -- please use MatchOnlyAtRgroupsAdjustParams instead -98: .[16:02:43] == testRemoveBadMatches -98: .[16:02:43] == testTimings -108: :488: RuntimeWarning: to-Python converter for boost::shared_ptr already registered; second conversion method ignored. 97: .:488: RuntimeWarning: to-Python converter for boost::shared_ptr already registered; second conversion method ignored. -97: [16:02:43] mapped atoms in the reactants were not mapped in the products. +97: [12:24:04] mapped atoms in the reactants were not mapped in the products. 97: unmapped numbers are: 3 -97: ..[16:02:43] reactant 2 has no mapped atoms. -97: [16:02:43] reactant 2 has no mapped atoms. -97: [16:02:43] product 1 has no mapped atoms. -97: ........[16:02:43] SMARTS Parse Error: syntax error while parsing: [C:1](=[O:2])Q -97: [16:02:43] SMARTS Parse Error: Failed parsing SMARTS '[C:1](=[O:2])Q' for input: '[C:1](=[O:2])Q' -97: [16:02:43] SMARTS Parse Error: syntax error while parsing: [C:1](=[O:2])[N:3]Q -97: [16:02:43] SMARTS Parse Error: Failed parsing SMARTS '[C:1](=[O:2])[N:3]Q' for input: '[C:1](=[O:2])[N:3]Q' -97: .[16:02:43] reactant atom-mapping number 1 found multiple times. -97: [16:02:43] product atom-mapping number 2 not found in reactants. -97: [16:02:43] mapped atoms in the reactants were not mapped in the products. +97: ..[12:24:04] reactant 2 has no mapped atoms. +97: [12:24:04] reactant 2 has no mapped atoms. +97: [12:24:04] product 1 has no mapped atoms. +97: ........[12:24:05] SMARTS Parse Error: syntax error while parsing: [C:1](=[O:2])Q +97: [12:24:05] SMARTS Parse Error: Failed parsing SMARTS '[C:1](=[O:2])Q' for input: '[C:1](=[O:2])Q' +97: [12:24:05] SMARTS Parse Error: syntax error while parsing: [C:1](=[O:2])[N:3]Q +97: [12:24:05] SMARTS Parse Error: Failed parsing SMARTS '[C:1](=[O:2])[N:3]Q' for input: '[C:1](=[O:2])[N:3]Q' +97: .[12:24:05] reactant atom-mapping number 1 found multiple times. +97: [12:24:05] product atom-mapping number 2 not found in reactants. +97: [12:24:05] mapped atoms in the reactants were not mapped in the products. 97: unmapped numbers are: 4 -97: [16:02:43] product atom-mapping number 5 not found in reactants. +97: [12:24:05] product atom-mapping number 5 not found in reactants. +29: Checking against /build/reproducible-path/rdkit-202503.1/Code/ForceField/MMFF/test_data/MMFF94_reference.log... 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: [16:02:43] Found a SCD/SED line with missing/empty SDT specification at line 34 -97: [16:02:43] Found a SCD/SED line with missing/empty SDT specification at line 36 -97: [16:02:43] Found a SCD/SED line with missing/empty SDT specification at line 38 -97: [16:02:43] Found a SCD/SED line with missing/empty SDT specification at line 40 -97: [16:02:43] Found a SCD/SED line with missing/empty SDT specification at line 42 -97: [16:02:43] Found a SCD/SED line with missing/empty SDT specification at line 87 -97: [16:02:43] Found a SCD/SED line with missing/empty SDT specification at line 89 -97: [16:02:43] Found a SCD/SED line with missing/empty SDT specification at line 91 -97: [16:02:43] Found a SCD/SED line with missing/empty SDT specification at line 93 -97: [16:02:43] Found a SCD/SED line with missing/empty SDT specification at line 95 -97: ..[16:02:43] SMARTS Parse Error: syntax error while parsing: boromicacid -97: [16:02:43] SMARTS Parse Error: Failed parsing SMARTS 'boromicacid' for input: 'boromicacid' -97: [16:02:43] SMARTS Parse Error: syntax error while parsing: carboxylicacid,acidchlroide -97: [16:02:43] SMARTS Parse Error: Failed parsing SMARTS 'carboxylicacid,acidchlroide' for input: 'carboxylicacid,acidchlroide' -97: [16:02:43] SMARTS Parse Error: syntax error while parsing: carboxyliccaid,acidchloride -97: [16:02:43] SMARTS Parse Error: Failed parsing SMARTS 'carboxyliccaid,acidchloride' for input: 'carboxyliccaid,acidchloride' -97: [16:02:43] reaction has no reactants -97: [16:02:43] reaction has no products -97: [16:02:43] initialization failed -97: [16:02:43] reaction has no reactants -97: [16:02:43] reaction has no products -97: .[16:02:43] SMARTS Parse Error: syntax error while parsing: boromicacid -97: [16:02:43] SMARTS Parse Error: Failed parsing SMARTS 'boromicacid' for input: 'boromicacid' -97: [16:02:43] SMARTS Parse Error: syntax error while parsing: carboxylicacid,acidchlroide -97: [16:02:43] SMARTS Parse Error: Failed parsing SMARTS 'carboxylicacid,acidchlroide' for input: 'carboxylicacid,acidchlroide' -97: [16:02:43] SMARTS Parse Error: syntax error while parsing: carboxyliccaid,acidchloride -97: [16:02:43] SMARTS Parse Error: Failed parsing SMARTS 'carboxyliccaid,acidchloride' for input: 'carboxyliccaid,acidchloride' -97: [16:02:43] reaction has no reactants -97: [16:02:43] reaction has no products -97: [16:02:43] initialization failed -97: [16:02:43] reaction has no reactants -97: [16:02:43] reaction has no products +97: [12:24:05] Found a SCD/SED line with missing/empty SDT specification at line 34 +97: [12:24:05] Found a SCD/SED line with missing/empty SDT specification at line 36 +97: [12:24:05] Found a SCD/SED line with missing/empty SDT specification at line 38 +97: [12:24:05] Found a SCD/SED line with missing/empty SDT specification at line 40 +97: [12:24:05] Found a SCD/SED line with missing/empty SDT specification at line 42 +97: [12:24:05] Found a SCD/SED line with missing/empty SDT specification at line 87 +97: [12:24:05] Found a SCD/SED line with missing/empty SDT specification at line 89 +97: [12:24:05] Found a SCD/SED line with missing/empty SDT specification at line 91 +97: [12:24:05] Found a SCD/SED line with missing/empty SDT specification at line 93 +97: [12:24:05] Found a SCD/SED line with missing/empty SDT specification at line 95 + 99/236 Test #107: filterCatalogTest ...................... Passed 0.79 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 +97: ..[12:24:05] SMARTS Parse Error: syntax error while parsing: boromicacid +97: [12:24:05] SMARTS Parse Error: Failed parsing SMARTS 'boromicacid' for input: 'boromicacid' +29: All 191 tests passed +108: :488: RuntimeWarning: to-Python converter for boost::shared_ptr already registered; second conversion method ignored. +97: [12:24:05] SMARTS Parse Error: syntax error while parsing: carboxylicacid,acidchlroide +97: [12:24:05] SMARTS Parse Error: Failed parsing SMARTS 'carboxylicacid,acidchlroide' for input: 'carboxylicacid,acidchlroide' +97: [12:24:05] SMARTS Parse Error: syntax error while parsing: carboxyliccaid,acidchloride +97: [12:24:05] SMARTS Parse Error: Failed parsing SMARTS 'carboxyliccaid,acidchloride' for input: 'carboxyliccaid,acidchloride' +97: [12:24:05] reaction has no reactants +97: [12:24:05] reaction has no products +97: [12:24:05] initialization failed +97: [12:24:05] reaction has no reactants +97: [12:24:05] reaction has no products +111: [12:24:05] ------------------------------------- +111: [12:24:05] Test Crippen parameter acquisition. +97: .[12:24:05] SMARTS Parse Error: syntax error while parsing: boromicacid +97: [12:24:05] SMARTS Parse Error: Failed parsing SMARTS 'boromicacid' for input: 'boromicacid' +97: [12:24:05] SMARTS Parse Error: syntax error while parsing: carboxylicacid,acidchlroide +97: [12:24:05] SMARTS Parse Error: Failed parsing SMARTS 'carboxylicacid,acidchlroide' for input: 'carboxylicacid,acidchlroide' +97: [12:24:05] SMARTS Parse Error: syntax error while parsing: carboxyliccaid,acidchloride +97: [12:24:05] SMARTS Parse Error: Failed parsing SMARTS 'carboxyliccaid,acidchloride' for input: 'carboxyliccaid,acidchloride' +111: [12:24:05] done +111: [12:24:05] ------------------------------------- +111: [12:24:05] Test Crippen calculation. +97: [12:24:05] reaction has no reactants +97: [12:24:05] reaction has no products +97: [12:24:05] initialization failed +97: [12:24:05] reaction has no reactants +97: [12:24:05] reaction has no products 97: . 97: ---------------------------------------------------------------------- -97: Ran 54 tests in 0.466s +97: Ran 54 tests in 1.187s 97: 97: OK 97: ******************************************** 97: /build/reproducible-path/rdkit-202503.1/Code/GraphMol/ChemReactions/testData/AmideBond.rxn -97: -111: [16:02:43] done -111: [16:02:43] ------------------------------------- -111: [16:02:43] Test VSA descriptors. -111: [16:02:43] done -111: [16:02:43] ------------------------------------- -111: [16:02:43] Test molecular formula calculation. -111: [16:02:43] done -111: [16:02:43] ------------------------------------- -111: [16:02:43] Test Issue 3415534. -111: [16:02:43] done -111: [16:02:43] ------------------------------------- -111: [16:02:43] Test Issue3433771: Bad definition for Crippen atom type O11. -111: [16:02:43] done -111: [16:02:43] ------------------------------------- -111: [16:02:43] Test multithreading -111: reading molecules -100/236 Test #97: pyChemReactions ........................ Passed 2.41 sec +97: +111: [12:24:05] done +111: [12:24:05] ------------------------------------- +111: [12:24:05] Test Issue262: problems with Crippen calculation from pickles. +111: [12:24:05] done +111: [12:24:05] ------------------------------------- +111: [12:24:05] Test AMW calculation. +111: [12:24:05] done +111: [12:24:05] ------------------------------------- +111: [12:24:05] Test Exact MW calculation. +111: [12:24:05] done +111: [12:24:05] ------------------------------------- +111: [12:24:05] Test Labute ASA descriptors. +111: [12:24:05] done +111: [12:24:05] ------------------------------------- +111: [12:24:05] Test TPSA descriptors. +29: +29: Computing MMFF94 energies for /build/reproducible-path/rdkit-202503.1/Code/ForceField/MMFF/test_data/MMFF94_dative.smi... +111: [12:24:05] done +111: [12:24:05] ------------------------------------- +111: [12:24:05] Test Lipinski parameters. +100/236 Test #97: pyChemReactions ........................ Passed 3.54 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 +112: [12:24:05] ---------------------------- +112: start test autocorr2D +111: [12:24:05] done +111: [12:24:05] ------------------------------------- +111: [12:24:05] Test VSA descriptors. +111: [12:24:05] done +111: [12:24:05] ------------------------------------- +111: [12:24:05] Test molecular formula calculation. +111: [12:24:05] done +111: [12:24:05] ------------------------------------- +111: [12:24:05] Test Issue 3415534. +111: [12:24:05] done +111: [12:24:05] ------------------------------------- +111: [12:24:05] Test Issue3433771: Bad definition for Crippen atom type O11. +111: [12:24:05] done +111: [12:24:05] ------------------------------------- +111: [12:24:05] Test multithreading +111: reading molecules 111: processing 111: launch :0 111: launch :1 111: launch :2 111: launch :3 -112: [16:02:43] ---------------------------- -112: start test autocorr2D -109: [16:02:43] +110: ......... +110: ---------------------------------------------------------------------- +110: Ran 9 tests in 0.143s +110: +110: OK +101/236 Test #110: pyFragCatalog .......................... Passed 1.30 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 +102/236 Test #113: testATF ................................ Passed 0.10 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: [12:24:06] ------------------------------------- +114: [12:24:06] Basic BCUT tests. +114: [12:24:06] done +114: [12:24:06] ------------------------------------- +114: [12:24:06] Larger BCUT tests. +109: [12:24:06] 109: 109: **** 109: Invariant Violation @@ -23996,17 +24058,17 @@ 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# 0x0000FFFF99521948 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu//lib/libRDKitFragCatalog.so.1 +109: 2# 0x0000FFFFB38B1948 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# 0x0000AAAADCC17B08 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FragCatalog/testFragCatalog -109: 5# 0x0000AAAADCC14960 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FragCatalog/testFragCatalog -109: 6# 0x0000FFFF98AF229C in /lib/aarch64-linux-gnu/libc.so.6 +109: 4# 0x0000AAAAEA917B08 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FragCatalog/testFragCatalog +109: 5# 0x0000AAAAEA914960 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FragCatalog/testFragCatalog +109: 6# 0x0000FFFFB2E8229C in /lib/aarch64-linux-gnu/libc.so.6 109: 7# __libc_start_main in /lib/aarch64-linux-gnu/libc.so.6 -109: 8# 0x0000AAAADCC14B30 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FragCatalog/testFragCatalog +109: 8# 0x0000AAAAEA914B30 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FragCatalog/testFragCatalog 109: ---------- 109: **** 109: -109: [16:02:43] +109: [12:24:06] 109: 109: **** 109: Invariant Violation @@ -24017,17 +24079,17 @@ 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# 0x0000FFFF99521948 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu//lib/libRDKitFragCatalog.so.1 +109: 2# 0x0000FFFFB38B1948 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# 0x0000AAAADCC17B08 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FragCatalog/testFragCatalog -109: 5# 0x0000AAAADCC14960 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FragCatalog/testFragCatalog -109: 6# 0x0000FFFF98AF229C in /lib/aarch64-linux-gnu/libc.so.6 +109: 4# 0x0000AAAAEA917B08 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FragCatalog/testFragCatalog +109: 5# 0x0000AAAAEA914960 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FragCatalog/testFragCatalog +109: 6# 0x0000FFFFB2E8229C in /lib/aarch64-linux-gnu/libc.so.6 109: 7# __libc_start_main in /lib/aarch64-linux-gnu/libc.so.6 -109: 8# 0x0000AAAADCC14B30 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FragCatalog/testFragCatalog +109: 8# 0x0000AAAAEA914B30 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FragCatalog/testFragCatalog 109: ---------- 109: **** 109: -109: [16:02:43] +109: [12:24:06] 109: 109: **** 109: Invariant Violation @@ -24038,41 +24100,17 @@ 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# 0x0000FFFF99521948 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu//lib/libRDKitFragCatalog.so.1 +109: 2# 0x0000FFFFB38B1948 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# 0x0000AAAADCC17B08 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FragCatalog/testFragCatalog -109: 5# 0x0000AAAADCC14960 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FragCatalog/testFragCatalog -109: 6# 0x0000FFFF98AF229C in /lib/aarch64-linux-gnu/libc.so.6 +109: 4# 0x0000AAAAEA917B08 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FragCatalog/testFragCatalog +109: 5# 0x0000AAAAEA914960 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FragCatalog/testFragCatalog +109: 6# 0x0000FFFFB2E8229C in /lib/aarch64-linux-gnu/libc.so.6 109: 7# __libc_start_main in /lib/aarch64-linux-gnu/libc.so.6 -109: 8# 0x0000AAAADCC14B30 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FragCatalog/testFragCatalog +109: 8# 0x0000AAAAEA914B30 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FragCatalog/testFragCatalog 109: ---------- 109: **** 109: -101/236 Test #109: testFragCatalog ........................ Passed 0.61 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 -102/236 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: [16:02:43] ------------------------------------- -114: [16:02:43] Basic BCUT tests. -114: [16:02:43] done -114: [16:02:43] ------------------------------------- -114: [16:02:43] Larger BCUT tests. -110: ......... -110: ---------------------------------------------------------------------- -110: Ran 9 tests in 0.108s -110: -110: OK -103/236 Test #110: pyFragCatalog .......................... Passed 0.86 sec +103/236 Test #109: testFragCatalog ........................ Passed 1.63 sec test 115 Start 115: testEEM @@ -24080,607 +24118,767 @@ 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: [16:02:44] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [12:24:06] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 115: 0 -115: [16:02:44] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [16:02:44] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [16:02:44] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [16:02:44] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [16:02:44] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [16:02:44] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [16:02:44] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [16:02:44] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [16:02:44] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [16:02:44] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [16:02:44] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [16:02:44] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [16:02:44] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [16:02:44] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [16:02:44] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [16:02:44] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [16:02:44] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [16:02:44] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [16:02:44] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [16:02:44] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [16:02:44] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [16:02:44] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [16:02:44] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [16:02:44] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [16:02:44] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [16:02:44] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [16:02:44] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [16:02:44] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [16:02:44] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [16:02:44] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [16:02:44] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [16:02:44] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [16:02:44] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [16:02:44] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [16:02:44] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [16:02:44] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [16:02:44] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [16:02:44] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [16:02:44] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [16:02:44] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [16:02:44] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [16:02:44] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [16:02:44] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [16:02:44] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [16:02:44] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [16:02:44] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [16:02:44] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [16:02:44] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [16:02:44] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [16:02:44] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [16:02:44] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [16:02:44] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [16:02:44] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [16:02:44] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [16:02:44] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [16:02:44] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [16:02:44] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [16:02:44] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [16:02:44] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [16:02:44] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [16:02:44] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [16:02:44] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [16:02:44] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [16:02:44] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [16:02:44] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [16:02:44] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [16:02:44] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [16:02:44] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [16:02:44] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [16:02:44] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [16:02:44] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [16:02:44] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [16:02:44] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [16:02:44] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [16:02:44] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [16:02:44] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [16:02:44] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [16:02:44] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [16:02:44] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [16:02:44] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [16:02:44] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [16:02:44] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [16:02:44] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [16:02:44] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [16:02:44] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [16:02:44] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [16:02:44] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [16:02:44] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [16:02:44] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [16:02:44] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [16:02:44] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [16:02:44] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [16:02:44] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [16:02:44] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [16:02:44] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [16:02:44] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [16:02:44] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [16:02:44] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [16:02:44] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [16:02:44] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [12:24:06] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [12:24:06] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [12:24:06] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [12:24:06] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [12:24:06] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [12:24:06] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +98: . +98: ---------------------------------------------------------------------- +98: Ran 11 tests in 2.443s +98: +98: OK +98: True +98: == CartesianProductStrategy CartesianProductStrategy +98: 197 out of 300 +98: 0 6 out of 10 +98: 1 3 out of 5 +98: 2 4 out of 6 +98: 198 out of 300 +98: 0 10 out of 10 +98: 1 5 out of 5 +98: 2 6 out of 6 +98: Skipped 10000000 in 0.16598153114318848 seconds +98: Skipped 10000000 in 1.206385612487793 seconds +98: Skipped 10000000 in 0.4142730236053467 seconds +115: [12:24:06] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [12:24:06] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [12:24:06] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [12:24:06] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [12:24:06] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [12:24:06] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [12:24:06] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [12:24:06] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [12:24:06] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [12:24:06] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [12:24:06] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [12:24:06] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [12:24:06] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [12:24:06] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [12:24:06] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [12:24:06] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [12:24:06] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [12:24:06] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [12:24:06] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [12:24:06] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [12:24:06] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [12:24:06] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [12:24:06] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [12:24:06] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [12:24:06] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [12:24:06] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [12:24:06] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [12:24:06] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [12:24:06] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [12:24:06] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [12:24:06] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [12:24:06] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [12:24:06] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [12:24:06] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [12:24:06] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [12:24:06] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [12:24:06] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [12:24:06] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [12:24:06] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [12:24:06] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [12:24:06] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [12:24:06] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [12:24:06] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [12:24:06] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [12:24:06] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [12:24:06] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [12:24:06] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [12:24:06] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [12:24:06] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [12:24:06] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [12:24:06] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [12:24:06] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [12:24:06] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [12:24:06] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [12:24:06] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [12:24:06] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [12:24:06] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [12:24:06] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [12:24:06] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [12:24:06] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [12:24:06] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [12:24:06] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [12:24:06] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [12:24:06] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [12:24:06] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [12:24:06] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [12:24:06] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [12:24:06] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [12:24:06] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [12:24:06] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [12:24:06] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [12:24:06] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [12:24:06] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [12:24:06] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [12:24:06] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [12:24:06] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [12:24:06] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [12:24:06] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [12:24:06] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [12:24:06] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [12:24:06] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [12:24:06] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [12:24:06] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [12:24:06] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [12:24:06] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [12:24:06] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [12:24:06] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [12:24:06] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [12:24:06] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [12:24:06] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [12:24:06] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [12:24:06] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [12:24:06] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [12:24:06] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 115: 100 -115: [16:02:44] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [16:02:44] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [16:02:44] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [16:02:44] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [16:02:44] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [16:02:44] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [16:02:44] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [16:02:44] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [16:02:44] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [16:02:44] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -112: [16:02:44] done -112: [16:02:44] ------------------------------------- -112: [16:02:44] Test Github #3806: NaNs from AUTOCORR2D descriptor -112: [16:02:44] done -115: [16:02:44] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [16:02:44] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -104/236 Test #112: testAUTOCORR2D ......................... Passed 0.87 sec -115: [16:02:44] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [12:24:06] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [12:24:06] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [12:24:06] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [12:24:06] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [12:24:06] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [12:24:06] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [12:24:06] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [12:24:06] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [12:24:06] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [12:24:06] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +104/236 Test #98: pyChemReactionEnumerations ............. Passed 4.42 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 -115: [16:02:44] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [16:02:44] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [16:02:44] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [16:02:44] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [16:02:44] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [16:02:44] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [16:02:44] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [16:02:44] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [16:02:44] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [16:02:44] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [16:02:44] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [16:02:44] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [16:02:44] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [16:02:44] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -116: [16:02:44] ------------------------------------- -116: [16:02:44] Basic PBF tests. -115: [16:02:44] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [16:02:44] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -114: [16:02:44] ------------------------------------- -114: [16:02:44] Test empty molecule BCUT. -105/236 Test #114: testBCUT ............................... Passed 0.78 sec +115: [12:24:06] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [12:24:06] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [12:24:06] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [12:24:06] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [12:24:06] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [12:24:06] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [12:24:06] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [12:24:06] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [12:24:06] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [12:24:06] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [12:24:06] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [12:24:06] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [12:24:06] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [12:24:06] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [12:24:06] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [12:24:06] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [12:24:06] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [12:24:06] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +112: [12:24:06] done +112: [12:24:06] ------------------------------------- +112: [12:24:06] Test Github #3806: NaNs from AUTOCORR2D descriptor +112: [12:24:06] done +115: [12:24:06] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [12:24:06] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [12:24:06] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [12:24:06] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [12:24:06] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [12:24:06] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [12:24:06] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +105/236 Test #112: testAUTOCORR2D ......................... Passed 1.26 sec 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: [16:02:44] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [16:02:44] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [16:02:44] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [16:02:44] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [16:02:44] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [16:02:44] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [16:02:44] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [16:02:44] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [16:02:44] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [16:02:44] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [16:02:44] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [16:02:44] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [16:02:44] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [16:02:44] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [16:02:44] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [16:02:44] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [16:02:44] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [16:02:44] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [16:02:44] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [16:02:44] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [16:02:44] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [16:02:44] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [16:02:44] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [16:02:44] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [16:02:44] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [16:02:44] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [16:02:44] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [16:02:44] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [16:02:44] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [16:02:44] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [16:02:44] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [16:02:44] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [16:02:44] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [16:02:44] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [16:02:44] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [16:02:44] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [16:02:44] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [16:02:44] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [16:02:44] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [16:02:44] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [16:02:44] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [16:02:44] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [16:02:44] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [16:02:44] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [16:02:44] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [16:02:44] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [16:02:44] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [16:02:44] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [16:02:44] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [16:02:44] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [16:02:44] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [16:02:44] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [16:02:44] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [16:02:44] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [16:02:44] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [16:02:44] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [16:02:44] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [16:02:44] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [16:02:44] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [16:02:44] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [16:02:44] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [16:02:44] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [16:02:44] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [16:02:44] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [16:02:44] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [16:02:44] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [16:02:44] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [16:02:44] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [16:02:44] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [16:02:44] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [16:02:44] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [12:24:06] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [12:24:06] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [12:24:06] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [12:24:06] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [12:24:06] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [12:24:06] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [12:24:06] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [12:24:06] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [12:24:06] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [12:24:06] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [12:24:06] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [12:24:06] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +116: [12:24:06] ------------------------------------- +116: [12:24:06] Basic PBF tests. +115: [12:24:06] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [12:24:06] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [12:24:06] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [12:24:06] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [12:24:06] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [12:24:06] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [12:24:06] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [12:24:06] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [12:24:06] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [12:24:06] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [12:24:06] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [12:24:06] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [12:24:06] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [12:24:06] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [12:24:06] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [12:24:06] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [12:24:06] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [12:24:06] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [12:24:06] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [12:24:06] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [12:24:06] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [12:24:06] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [12:24:06] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [12:24:06] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [12:24:06] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [12:24:06] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [12:24:06] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [12:24:07] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [12:24:07] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [12:24:07] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [12:24:07] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [12:24:07] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [12:24:07] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [12:24:07] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [12:24:07] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [12:24:07] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [12:24:07] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [12:24:07] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [12:24:07] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [12:24:07] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [12:24:07] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [12:24:07] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [12:24:07] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [12:24:07] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [12:24:07] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [12:24:07] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [12:24:07] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [12:24:07] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [12:24:07] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [12:24:07] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [12:24:07] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [12:24:07] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [12:24:07] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 115: 200 -115: [16:02:44] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [16:02:44] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [16:02:44] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [16:02:44] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [16:02:44] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [16:02:44] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [16:02:44] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [16:02:44] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [16:02:44] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [16:02:44] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [16:02:44] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [16:02:44] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [16:02:44] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [16:02:44] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [16:02:44] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [16:02:44] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [16:02:44] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [16:02:44] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [16:02:44] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [16:02:44] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [16:02:44] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [16:02:44] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [16:02:44] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [16:02:44] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [16:02:44] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [16:02:44] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [16:02:44] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [16:02:44] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [16:02:44] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [16:02:44] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [16:02:44] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [16:02:44] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -108: .............[16:02:44] SMILES Parse Error: syntax error while parsing: --- -108: [16:02:44] SMILES Parse Error: check for mistakes around position 1: -108: [16:02:44] --- -108: [16:02:44] ^ -108: [16:02:44] SMILES Parse Error: Failed parsing SMILES '---' for input: '---' -108: [16:02:44] dasfsadf -108: [16:02:44] SMILES Parse Error: syntax error while parsing: --- -108: [16:02:44] SMILES Parse Error: check for mistakes around position 1: -108: [16:02:44] --- -108: [16:02:44] ^ -108: [16:02:44] SMILES Parse Error: Failed parsing SMILES '---' for input: '---' -108: [16:02:44] dasfsadf -108: [16:02:44] SMILES Parse Error: syntax error while parsing: --- -108: [16:02:44] SMILES Parse Error: check for mistakes around position 1: -108: [16:02:44] --- -108: [16:02:44] ^ -108: [16:02:44] SMILES Parse Error: Failed parsing SMILES '---' for input: '---' -108: [16:02:44] dasfsadf -108: [16:02:44] SMILES Parse Error: syntax error while parsing: --- -108: [16:02:44] SMILES Parse Error: check for mistakes around position 1: -108: [16:02:44] --- -108: [16:02:44] ^ -108: [16:02:44] SMILES Parse Error: Failed parsing SMILES '---' for input: '---' -108: [16:02:44] dasfsadf -108: [16:02:44] SMILES Parse Error: syntax error while parsing: --- -108: [16:02:44] SMILES Parse Error: check for mistakes around position 1: -108: [16:02:44] --- -108: [16:02:44] ^ -108: [16:02:44] SMILES Parse Error: Failed parsing SMILES '---' for input: '---' -108: [16:02:44] dasfsadf -108: [16:02:44] SMILES Parse Error: syntax error while parsing: --- -108: [16:02:44] SMILES Parse Error: check for mistakes around position 1: -108: [16:02:44] --- -108: [16:02:44] ^ -108: [16:02:44] SMILES Parse Error: Failed parsing SMILES '---' for input: '---' -108: [16:02:44] dasfsadf -108: [16:02:44] SMILES Parse Error: syntax error while parsing: --- -108: [16:02:44] SMILES Parse Error: check for mistakes around position 1: -108: [16:02:44] --- -108: [16:02:44] ^ -108: [16:02:44] SMILES Parse Error: Failed parsing SMILES '---' for input: '---' -108: [16:02:44] dasfsadf -108: [16:02:44] SMILES Parse Error: syntax error while parsing: --- -108: [16:02:44] SMILES Parse Error: check for mistakes around position 1: -108: [16:02:44] --- -108: [16:02:44] ^ -108: [16:02:44] SMILES Parse Error: Failed parsing SMILES '---' for input: '---' -108: [16:02:44] dasfsadf -108: [16:02:44] SMILES Parse Error: syntax error while parsing: --- -108: [16:02:44] SMILES Parse Error: check for mistakes around position 1: -108: [16:02:44] --- -108: [16:02:44] ^ -108: [16:02:44] SMILES Parse Error: Failed parsing SMILES '---' for input: '---' -108: [16:02:44] dasfsadf -108: [16:02:44] SMILES Parse Error: syntax error while parsing: --- -108: [16:02:44] SMILES Parse Error: check for mistakes around position 1: -108: [16:02:44] --- -108: [16:02:44] ^ -108: [16:02:44] SMILES Parse Error: Failed parsing SMILES '---' for input: '---' -108: [16:02:44] dasfsadf -115: [16:02:44] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [16:02:44] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [16:02:44] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [16:02:44] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [16:02:44] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -108: [16:02:44] SMILES Parse Error: syntax error while parsing: --- -108: [16:02:44] SMILES Parse Error: check for mistakes around position 1: -108: [16:02:44] --- -108: [16:02:44] ^ -108: [16:02:44] SMILES Parse Error: Failed parsing SMILES '---' for input: '---' -108: [16:02:44] dasfsadf -108: [16:02:44] SMILES Parse Error: syntax error while parsing: --- -108: [16:02:44] SMILES Parse Error: check for mistakes around position 1: -108: [16:02:44] --- -108: [16:02:44] ^ -108: [16:02:44] SMILES Parse Error: Failed parsing SMILES '---' for input: '---' -108: [16:02:44] dasfsadf -108: [16:02:44] SMILES Parse Error: syntax error while parsing: --- -108: [16:02:44] SMILES Parse Error: check for mistakes around position 1: -108: [16:02:44] --- -108: [16:02:44] ^ -108: [16:02:44] SMILES Parse Error: Failed parsing SMILES '---' for input: '---' -108: [16:02:44] dasfsadf -108: [16:02:44] SMILES Parse Error: syntax error while parsing: --- -108: [16:02:44] SMILES Parse Error: check for mistakes around position 1: -108: [16:02:44] --- -108: [16:02:44] ^ -108: [16:02:44] SMILES Parse Error: Failed parsing SMILES '---' for input: '---' -108: [16:02:44] dasfsadf -108: [16:02:44] SMILES Parse Error: syntax error while parsing: --- -108: [16:02:44] SMILES Parse Error: check for mistakes around position 1: -108: [16:02:44] --- -108: [16:02:44] ^ -108: [16:02:44] SMILES Parse Error: Failed parsing SMILES '---' for input: '---' -108: [16:02:44] dasfsadf -108: [16:02:44] SMILES Parse Error: syntax error while parsing: --- -108: [16:02:44] SMILES Parse Error: check for mistakes around position 1: -108: [16:02:44] --- -108: [16:02:44] ^ -108: [16:02:44] SMILES Parse Error: Failed parsing SMILES '---' for input: '---' -108: [16:02:44] dasfsadf -108: [16:02:44] SMILES Parse Error: syntax error while parsing: --- -108: [16:02:44] SMILES Parse Error: check for mistakes around position 1: -108: [16:02:44] --- -108: [16:02:44] ^ -108: [16:02:44] SMILES Parse Error: Failed parsing SMILES '---' for input: '---' -108: [16:02:44] dasfsadf -108: [16:02:44] SMILES Parse Error: syntax error while parsing: --- -108: [16:02:44] SMILES Parse Error: check for mistakes around position 1: -108: [16:02:44] --- -108: [16:02:44] ^ -108: [16:02:44] SMILES Parse Error: Failed parsing SMILES '---' for input: '---' -108: [16:02:44] dasfsadf -108: [16:02:44] SMILES Parse Error: syntax error while parsing: --- -108: [16:02:44] SMILES Parse Error: check for mistakes around position 1: -108: [16:02:44] --- -108: [16:02:44] ^ -108: [16:02:44] SMILES Parse Error: Failed parsing SMILES '---' for input: '---' -108: [16:02:44] dasfsadf -108: [16:02:44] SMILES Parse Error: syntax error while parsing: --- -108: [16:02:44] SMILES Parse Error: check for mistakes around position 1: -108: [16:02:44] --- -108: [16:02:44] ^ -108: [16:02:44] SMILES Parse Error: Failed parsing SMILES '---' for input: '---' -108: [16:02:44] dasfsadf -108: [16:02:44] SMILES Parse Error: syntax error while parsing: --- -108: [16:02:44] SMILES Parse Error: check for mistakes around position 1: -108: [16:02:44] --- -108: [16:02:44] ^ -108: [16:02:44] SMILES Parse Error: Failed parsing SMILES '---' for input: '---' -108: [16:02:44] dasfsadf -108: [16:02:44] SMILES Parse Error: syntax error while parsing: --- -108: [16:02:44] SMILES Parse Error: check for mistakes around position 1: -108: [16:02:44] --- -108: [16:02:44] ^ -108: [16:02:44] SMILES Parse Error: Failed parsing SMILES '---' for input: '---' -108: [16:02:44] dasfsadf -115: [16:02:44] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [16:02:44] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [16:02:44] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [16:02:44] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [16:02:44] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [16:02:44] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [16:02:44] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [16:02:44] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -108: [16:02:44] SMILES Parse Error: syntax error while parsing: --- -108: [16:02:44] SMILES Parse Error: check for mistakes around position 1: -108: [16:02:44] --- -108: [16:02:44] ^ -108: [16:02:44] SMILES Parse Error: Failed parsing SMILES '---' for input: '---' -108: [16:02:44] dasfsadf -108: [16:02:44] SMILES Parse Error: syntax error while parsing: --- -108: [16:02:44] SMILES Parse Error: check for mistakes around position 1: -108: [16:02:44] --- -108: [16:02:44] ^ -108: [16:02:44] SMILES Parse Error: Failed parsing SMILES '---' for input: '---' -108: [16:02:44] dasfsadf -108: [16:02:44] SMILES Parse Error: syntax error while parsing: --- -108: [16:02:44] SMILES Parse Error: check for mistakes around position 1: -108: [16:02:44] --- -108: [16:02:44] ^ -108: [16:02:44] SMILES Parse Error: Failed parsing SMILES '---' for input: '---' -108: [16:02:44] dasfsadf -108: [16:02:44] SMILES Parse Error: syntax error while parsing: --- -108: [16:02:44] SMILES Parse Error: check for mistakes around position 1: -108: [16:02:44] --- -108: [16:02:44] ^ -108: [16:02:44] SMILES Parse Error: Failed parsing SMILES '---' for input: '---' -108: [16:02:44] dasfsadf -108: [16:02:44] SMILES Parse Error: syntax error while parsing: --- -108: [16:02:44] SMILES Parse Error: check for mistakes around position 1: -108: [16:02:44] --- -108: [16:02:44] ^ -108: [16:02:44] SMILES Parse Error: Failed parsing SMILES '---' for input: '---' -108: [16:02:44] dasfsadf -108: [16:02:44] SMILES Parse Error: syntax error while parsing: --- -108: [16:02:44] SMILES Parse Error: check for mistakes around position 1: -108: [16:02:44] --- -108: [16:02:44] ^ -108: [16:02:44] SMILES Parse Error: Failed parsing SMILES '---' for input: '---' -108: [16:02:44] dasfsadf -108: [16:02:44] SMILES Parse Error: syntax error while parsing: --- -108: [16:02:44] SMILES Parse Error: check for mistakes around position 1: -108: [16:02:44] --- -108: [16:02:44] ^ -108: [16:02:44] SMILES Parse Error: Failed parsing SMILES '---' for input: '---' -108: [16:02:44] dasfsadf -108: [16:02:44] SMILES Parse Error: syntax error while parsing: --- -108: [16:02:44] SMILES Parse Error: check for mistakes around position 1: -108: [16:02:44] --- -108: [16:02:44] ^ -108: [16:02:44] SMILES Parse Error: Failed parsing SMILES '---' for input: '---' -108: [16:02:44] dasfsadf -115: [16:02:44] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [16:02:44] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -116: [16:02:44] done -116: [16:02:44] ------------------------------------- -116: [16:02:44] PBF edge cases. -115: [16:02:44] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [16:02:44] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [16:02:44] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [16:02:44] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [16:02:44] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [16:02:44] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [16:02:44] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -116: [16:02:44] done -115: [16:02:44] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [16:02:44] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -106/236 Test #116: testPBF ................................ Passed 0.28 sec +115: [12:24:07] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [12:24:07] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [12:24:07] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [12:24:07] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [12:24:07] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [12:24:07] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [12:24:07] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [12:24:07] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [12:24:07] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [12:24:07] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [12:24:07] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [12:24:07] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [12:24:07] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [12:24:07] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [12:24:07] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [12:24:07] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [12:24:07] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [12:24:07] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [12:24:07] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [12:24:07] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [12:24:07] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [12:24:07] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [12:24:07] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [12:24:07] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [12:24:07] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [12:24:07] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [12:24:07] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [12:24:07] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [12:24:07] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [12:24:07] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [12:24:07] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [12:24:07] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [12:24:07] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [12:24:07] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [12:24:07] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [12:24:07] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [12:24:07] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [12:24:07] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [12:24:07] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [12:24:07] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [12:24:07] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [12:24:07] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [12:24:07] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [12:24:07] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [12:24:07] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [12:24:07] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [12:24:07] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [12:24:07] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [12:24:07] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [12:24:07] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [12:24:07] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [12:24:07] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [12:24:07] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [12:24:07] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [12:24:07] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [12:24:07] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [12:24:07] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [12:24:07] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [12:24:07] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [12:24:07] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [12:24:07] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [12:24:07] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [12:24:07] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [12:24:07] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [12:24:07] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [12:24:07] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [12:24:07] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [12:24:07] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [12:24:07] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [12:24:07] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [12:24:07] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [12:24:07] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [12:24:07] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [12:24:07] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [12:24:07] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [12:24:07] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [12:24:07] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [12:24:07] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [12:24:07] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [12:24:07] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [12:24:07] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [12:24:07] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [12:24:07] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [12:24:07] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [12:24:07] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [12:24:07] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [12:24:07] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [12:24:07] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [12:24:07] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [12:24:07] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +108: .............[12:24:07] SMILES Parse Error: syntax error while parsing: --- +108: [12:24:07] SMILES Parse Error: check for mistakes around position 1: +108: [12:24:07] --- +108: [12:24:07] ^ +108: [12:24:07] SMILES Parse Error: Failed parsing SMILES '---' for input: '---' +108: [12:24:07] dasfsadf +108: [12:24:07] SMILES Parse Error: syntax error while parsing: --- +108: [12:24:07] SMILES Parse Error: check for mistakes around position 1: +108: [12:24:07] --- +108: [12:24:07] ^ +108: [12:24:07] SMILES Parse Error: Failed parsing SMILES '---' for input: '---' +108: [12:24:07] dasfsadf +108: [12:24:07] SMILES Parse Error: syntax error while parsing: --- +108: [12:24:07] SMILES Parse Error: check for mistakes around position 1: +108: [12:24:07] --- +108: [12:24:07] ^ +108: [12:24:07] SMILES Parse Error: Failed parsing SMILES '---' for input: '---' +108: [12:24:07] dasfsadf +108: [12:24:07] SMILES Parse Error: syntax error while parsing: --- +108: [12:24:07] SMILES Parse Error: check for mistakes around position 1: +108: [12:24:07] --- +108: [12:24:07] ^ +108: [12:24:07] SMILES Parse Error: Failed parsing SMILES '---' for input: '---' +108: [12:24:07] dasfsadf +115: [12:24:07] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [12:24:07] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [12:24:07] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [12:24:07] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [12:24:07] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +108: [12:24:07] SMILES Parse Error: syntax error while parsing: --- +108: [12:24:07] SMILES Parse Error: check for mistakes around position 1: +108: [12:24:07] --- +108: [12:24:07] ^ +108: [12:24:07] SMILES Parse Error: Failed parsing SMILES '---' for input: '---' +108: [12:24:07] dasfsadf +115: [12:24:07] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +108: [12:24:07] SMILES Parse Error: syntax error while parsing: --- +108: [12:24:07] SMILES Parse Error: check for mistakes around position 1: +108: [12:24:07] --- +108: [12:24:07] ^ +108: [12:24:07] SMILES Parse Error: Failed parsing SMILES '---' for input: '---' +108: [12:24:07] dasfsadf +108: [12:24:07] SMILES Parse Error: syntax error while parsing: --- +108: [12:24:07] SMILES Parse Error: check for mistakes around position 1: +108: [12:24:07] --- +108: [12:24:07] ^ +108: [12:24:07] SMILES Parse Error: Failed parsing SMILES '---' for input: '---' +108: [12:24:07] dasfsadf +108: [12:24:07] SMILES Parse Error: syntax error while parsing: --- +108: [12:24:07] SMILES Parse Error: check for mistakes around position 1: +108: [12:24:07] --- +108: [12:24:07] ^ +108: [12:24:07] SMILES Parse Error: Failed parsing SMILES '---' for input: '---' +108: [12:24:07] dasfsadf +108: [12:24:07] SMILES Parse Error: syntax error while parsing: --- +108: [12:24:07] SMILES Parse Error: check for mistakes around position 1: +108: [12:24:07] --- +108: [12:24:07] ^ +108: [12:24:07] SMILES Parse Error: Failed parsing SMILES '---' for input: '---' +108: [12:24:07] dasfsadf +108: [12:24:07] SMILES Parse Error: syntax error while parsing: --- +108: [12:24:07] SMILES Parse Error: check for mistakes around position 1: +108: [12:24:07] --- +108: [12:24:07] ^ +108: [12:24:07] SMILES Parse Error: Failed parsing SMILES '---' for input: '---' +108: [12:24:07] dasfsadf +108: [12:24:07] SMILES Parse Error: syntax error while parsing: --- +108: [12:24:07] SMILES Parse Error: check for mistakes around position 1: +108: [12:24:07] --- +108: [12:24:07] ^ +108: [12:24:07] SMILES Parse Error: Failed parsing SMILES '---' for input: '---' +108: [12:24:07] dasfsadf +108: [12:24:07] SMILES Parse Error: syntax error while parsing: --- +108: [12:24:07] SMILES Parse Error: check for mistakes around position 1: +108: [12:24:07] --- +108: [12:24:07] ^ +108: [12:24:07] SMILES Parse Error: Failed parsing SMILES '---' for input: '---' +108: [12:24:07] dasfsadf +108: [12:24:07] SMILES Parse Error: syntax error while parsing: --- +108: [12:24:07] SMILES Parse Error: check for mistakes around position 1: +108: [12:24:07] --- +108: [12:24:07] ^ +108: [12:24:07] SMILES Parse Error: Failed parsing SMILES '---' for input: '---' +108: [12:24:07] dasfsadf +108: [12:24:07] SMILES Parse Error: syntax error while parsing: --- +108: [12:24:07] SMILES Parse Error: check for mistakes around position 1: +108: [12:24:07] --- +108: [12:24:07] ^ +108: [12:24:07] SMILES Parse Error: Failed parsing SMILES '---' for input: '---' +108: [12:24:07] dasfsadf +108: [12:24:07] SMILES Parse Error: syntax error while parsing: --- +108: [12:24:07] SMILES Parse Error: check for mistakes around position 1: +108: [12:24:07] --- +108: [12:24:07] ^ +108: [12:24:07] SMILES Parse Error: Failed parsing SMILES '---' for input: '---' +108: [12:24:07] dasfsadf +108: [12:24:07] SMILES Parse Error: syntax error while parsing: --- +108: [12:24:07] SMILES Parse Error: check for mistakes around position 1: +108: [12:24:07] --- +108: [12:24:07] ^ +108: [12:24:07] SMILES Parse Error: Failed parsing SMILES '---' for input: '---' +108: [12:24:07] dasfsadf +108: [12:24:07] SMILES Parse Error: syntax error while parsing: --- +108: [12:24:07] SMILES Parse Error: check for mistakes around position 1: +108: [12:24:07] --- +108: [12:24:07] ^ +108: [12:24:07] SMILES Parse Error: Failed parsing SMILES '---' for input: '---' +108: [12:24:07] dasfsadf +108: [12:24:07] SMILES Parse Error: syntax error while parsing: --- +108: [12:24:07] SMILES Parse Error: check for mistakes around position 1: +108: [12:24:07] --- +108: [12:24:07] ^ +108: [12:24:07] SMILES Parse Error: Failed parsing SMILES '---' for input: '---' +108: [12:24:07] dasfsadf +115: [12:24:07] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +108: [12:24:07] SMILES Parse Error: syntax error while parsing: --- +108: [12:24:07] SMILES Parse Error: check for mistakes around position 1: +108: [12:24:07] --- +108: [12:24:07] ^ +108: [12:24:07] SMILES Parse Error: Failed parsing SMILES '---' for input: '---' +108: [12:24:07] dasfsadf +108: [12:24:07] SMILES Parse Error: syntax error while parsing: --- +108: [12:24:07] SMILES Parse Error: check for mistakes around position 1: +108: [12:24:07] --- +108: [12:24:07] ^ +108: [12:24:07] SMILES Parse Error: Failed parsing SMILES '---' for input: '---' +108: [12:24:07] dasfsadf +108: [12:24:07] SMILES Parse Error: syntax error while parsing: --- +108: [12:24:07] SMILES Parse Error: check for mistakes around position 1: +108: [12:24:07] --- +108: [12:24:07] ^ +108: [12:24:07] SMILES Parse Error: Failed parsing SMILES '---' for input: '---' +108: [12:24:07] dasfsadf +108: [12:24:07] SMILES Parse Error: syntax error while parsing: --- +108: [12:24:07] SMILES Parse Error: check for mistakes around position 1: +108: [12:24:07] --- +108: [12:24:07] ^ +108: [12:24:07] SMILES Parse Error: Failed parsing SMILES '---' for input: '---' +108: [12:24:07] dasfsadf +108: [12:24:07] SMILES Parse Error: syntax error while parsing: --- +108: [12:24:07] SMILES Parse Error: check for mistakes around position 1: +108: [12:24:07] --- +108: [12:24:07] ^ +108: [12:24:07] SMILES Parse Error: Failed parsing SMILES '---' for input: '---' +108: [12:24:07] dasfsadf +108: [12:24:07] SMILES Parse Error: syntax error while parsing: --- +108: [12:24:07] SMILES Parse Error: check for mistakes around position 1: +108: [12:24:07] --- +108: [12:24:07] ^ +108: [12:24:07] SMILES Parse Error: Failed parsing SMILES '---' for input: '---' +108: [12:24:07] dasfsadf +108: [12:24:07] SMILES Parse Error: syntax error while parsing: --- +108: [12:24:07] SMILES Parse Error: check for mistakes around position 1: +108: [12:24:07] --- +108: [12:24:07] ^ +108: [12:24:07] SMILES Parse Error: Failed parsing SMILES '---' for input: '---' +108: [12:24:07] dasfsadf +108: [12:24:07] SMILES Parse Error: syntax error while parsing: --- +108: [12:24:07] SMILES Parse Error: check for mistakes around position 1: +108: [12:24:07] --- +108: [12:24:07] ^ +108: [12:24:07] SMILES Parse Error: Failed parsing SMILES '---' for input: '---' +108: [12:24:07] dasfsadf +108: [12:24:07] SMILES Parse Error: syntax error while parsing: --- +108: [12:24:07] SMILES Parse Error: check for mistakes around position 1: +108: [12:24:07] --- +108: [12:24:07] ^ +108: [12:24:07] SMILES Parse Error: Failed parsing SMILES '---' for input: '---' +108: [12:24:07] dasfsadf +108: [12:24:07] SMILES Parse Error: syntax error while parsing: --- +108: [12:24:07] SMILES Parse Error: check for mistakes around position 1: +108: [12:24:07] --- +108: [12:24:07] ^ +108: [12:24:07] SMILES Parse Error: Failed parsing SMILES '---' for input: '---' +108: [12:24:07] dasfsadf +115: [12:24:07] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [12:24:07] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [12:24:07] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: 300 +115: [12:24:07] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [12:24:07] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +108: [12:24:07] SMILES Parse Error: syntax error while parsing: --- +108: [12:24:07] SMILES Parse Error: check for mistakes around position 1: +108: [12:24:07] --- +108: [12:24:07] ^ +108: [12:24:07] SMILES Parse Error: Failed parsing SMILES '---' for input: '---' +108: [12:24:07] dasfsadf +108: [12:24:07] SMILES Parse Error: syntax error while parsing: --- +108: [12:24:07] SMILES Parse Error: check for mistakes around position 1: +108: [12:24:07] --- +108: [12:24:07] ^ +108: [12:24:07] SMILES Parse Error: Failed parsing SMILES '---' for input: '---' +108: [12:24:07] dasfsadf +115: [12:24:07] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [12:24:07] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [12:24:07] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [12:24:07] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [12:24:07] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [12:24:07] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [12:24:07] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [12:24:07] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [12:24:07] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [12:24:07] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [12:24:07] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [12:24:07] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [12:24:07] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [12:24:07] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [12:24:07] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [12:24:07] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [12:24:07] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [12:24:07] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [12:24:07] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [12:24:07] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [12:24:07] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [12:24:07] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [12:24:07] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [12:24:07] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [12:24:07] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [12:24:07] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [12:24:07] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [12:24:07] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [12:24:07] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [12:24:07] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [12:24:07] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [12:24:07] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [12:24:07] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [12:24:07] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [12:24:07] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [12:24:07] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [12:24:07] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [12:24:07] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [12:24:07] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [12:24:07] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [12:24:07] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [12:24:07] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [12:24:07] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [12:24:07] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [12:24:07] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [12:24:07] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [12:24:07] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [12:24:07] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [12:24:07] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [12:24:07] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [12:24:07] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [12:24:07] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [12:24:07] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [12:24:07] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [12:24:07] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [12:24:07] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [12:24:07] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [12:24:07] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +116: [12:24:07] done +116: [12:24:07] ------------------------------------- +116: [12:24:07] PBF edge cases. +115: [12:24:07] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [12:24:07] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [12:24:07] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [12:24:07] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [12:24:07] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [12:24:07] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [12:24:07] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +116: [12:24:07] done +106/236 Test #116: testPBF ................................ Passed 0.59 sec 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: [16:02:44] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [16:02:44] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [16:02:44] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [16:02:44] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [16:02:44] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [16:02:44] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [16:02:44] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [16:02:44] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [16:02:44] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [16:02:44] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [16:02:44] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [16:02:44] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [16:02:44] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [16:02:44] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [16:02:44] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [16:02:44] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [16:02:44] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [16:02:44] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [16:02:44] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -108: .[16:02:44] SMILES Parse Error: syntax error while parsing: mydoghasfleas -108: [16:02:44] SMILES Parse Error: check for mistakes around position 1: -108: [16:02:44] mydoghasfleas -108: [16:02:44] ^ -108: [16:02:44] SMILES Parse Error: Failed parsing SMILES 'mydoghasfleas' for input: 'mydoghasfleas' -115: [16:02:44] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [16:02:44] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [16:02:44] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [16:02:44] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [16:02:44] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [16:02:44] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [16:02:44] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [16:02:44] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [16:02:44] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [16:02:44] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [16:02:44] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [16:02:44] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [16:02:44] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [16:02:44] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [16:02:44] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [16:02:44] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [16:02:44] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [16:02:44] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [16:02:44] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [16:02:44] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [16:02:44] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [16:02:44] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [16:02:44] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [16:02:44] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [16:02:44] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: 300 -115: [16:02:44] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [16:02:44] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [16:02:44] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [16:02:44] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [16:02:44] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [16:02:44] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [16:02:44] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [16:02:44] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [16:02:44] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [16:02:44] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [16:02:44] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [16:02:44] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [16:02:44] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [16:02:44] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [16:02:44] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [16:02:44] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [16:02:44] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [16:02:44] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [16:02:44] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [16:02:44] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [16:02:44] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -98: . -98: ---------------------------------------------------------------------- -98: Ran 11 tests in 1.879s -98: -98: OK -98: True -98: == CartesianProductStrategy CartesianProductStrategy -98: 197 out of 300 -98: 0 6 out of 10 -98: 1 3 out of 5 -98: 2 4 out of 6 -98: 198 out of 300 -98: 0 10 out of 10 -98: 1 5 out of 5 -98: 2 6 out of 6 -98: Skipped 10000000 in 0.10892391204833984 seconds -98: Skipped 10000000 in 0.8740329742431641 seconds -98: Skipped 10000000 in 0.28384947776794434 seconds -115: [16:02:44] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [16:02:44] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [16:02:44] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [16:02:44] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [16:02:44] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [16:02:44] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [16:02:44] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [16:02:44] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -74: [16:02:44] Finished: testSmiCorrectness() -74: [16:02:44] ----------------------------------------- -74: -74: [16:02:44] -74: ----------------------------------------- -115: [16:02:44] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [16:02:44] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [16:02:44] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [16:02:44] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [16:02:44] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [16:02:44] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [16:02:44] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [16:02:44] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [16:02:44] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [16:02:44] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [16:02:44] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [16:02:44] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [16:02:44] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [16:02:44] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [16:02:44] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [16:02:44] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [16:02:44] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [16:02:44] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [16:02:44] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [16:02:44] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [16:02:44] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [16:02:44] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [16:02:44] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [12:24:07] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [12:24:07] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [12:24:07] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [12:24:07] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [12:24:07] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [12:24:07] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [12:24:07] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [12:24:07] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [12:24:07] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [12:24:07] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [12:24:07] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [12:24:07] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [12:24:07] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [12:24:07] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [12:24:07] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [12:24:07] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +108: .[12:24:07] SMILES Parse Error: syntax error while parsing: mydoghasfleas +108: [12:24:07] SMILES Parse Error: check for mistakes around position 1: +108: [12:24:07] mydoghasfleas +108: [12:24:07] ^ +108: [12:24:07] SMILES Parse Error: Failed parsing SMILES 'mydoghasfleas' for input: 'mydoghasfleas' +115: [12:24:07] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [12:24:07] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [12:24:07] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [12:24:07] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [12:24:07] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [12:24:07] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [12:24:07] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [12:24:07] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [12:24:07] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [12:24:07] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [12:24:07] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [12:24:07] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [12:24:07] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [12:24:07] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [12:24:07] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [12:24:07] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [12:24:07] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: 400 +115: [12:24:07] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [12:24:07] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [12:24:07] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [12:24:07] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [12:24:07] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [12:24:07] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [12:24:07] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [12:24:07] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [12:24:07] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [12:24:07] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [12:24:07] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [12:24:07] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [12:24:07] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [12:24:07] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [12:24:07] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [12:24:07] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [12:24:07] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [12:24:07] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [12:24:07] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [12:24:07] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [12:24:07] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [12:24:07] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [12:24:07] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [12:24:07] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [12:24:07] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [12:24:07] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [12:24:07] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [12:24:07] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [12:24:07] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [12:24:07] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [12:24:07] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [12:24:07] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [12:24:07] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [12:24:07] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [12:24:07] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [12:24:07] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [12:24:07] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [12:24:07] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [12:24:07] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [12:24:07] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [12:24:07] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [12:24:07] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [12:24:07] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [12:24:07] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [12:24:07] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [12:24:07] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [12:24:07] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [12:24:07] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [12:24:07] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [12:24:07] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [12:24:07] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [12:24:07] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [12:24:07] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [12:24:07] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [12:24:07] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [12:24:07] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [12:24:07] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [12:24:07] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [12:24:07] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [12:24:07] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [12:24:07] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [12:24:07] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [12:24:07] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [12:24:07] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [12:24:07] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [12:24:07] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [12:24:07] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [12:24:07] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [12:24:07] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [12:24:07] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [12:24:07] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [12:24:07] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [12:24:07] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [12:24:07] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [12:24:07] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [12:24:07] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [12:24:07] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [12:24:07] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [12:24:07] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [12:24:07] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [12:24:07] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [12:24:07] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [12:24:07] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [12:24:07] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [12:24:07] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [12:24:07] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [12:24:07] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [12:24:07] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [12:24:07] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [12:24:07] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [12:24:07] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [12:24:07] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [12:24:07] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [12:24:07] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [12:24:07] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [12:24:07] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +114: [12:24:07] ------------------------------------- +114: [12:24:07] Test empty molecule BCUT. +107/236 Test #114: testBCUT ............................... Passed 1.55 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: [12:24:07] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [12:24:07] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [12:24:07] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: Elapsed time: 1.32218 s +115: Errors:0 +115: [12:24:07] test on : 500 molecules done +108/236 Test #115: testEEM ................................ Passed 1.43 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 108: ....... 108: ---------------------------------------------------------------------- -108: Ran 21 tests in 1.513s +108: Ran 21 tests in 2.381s 108: 108: OK 108: (Five aromatic carbons And (Not any of Five aromatic carbons)) @@ -24702,228 +24900,68 @@ 108: 1 108: 2 108: running -115: [16:02:44] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [16:02:44] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [16:02:44] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [16:02:44] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [16:02:44] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -74: [16:02:44] Spurious data before the first property will be ignored -74: [16:02:44] Property will be truncated after the first blank line -74: [16:02:44] Property will be truncated after the first blank line -74: [16:02:44] Property will be truncated after the first blank line -115: [16:02:44] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [16:02:44] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [16:02:44] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [16:02:44] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [16:02:44] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [16:02:44] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [16:02:44] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [16:02:44] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [16:02:44] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [16:02:44] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [16:02:44] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -107/236 Test #98: pyChemReactionEnumerations ............. Passed 3.79 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: [16:02:44] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [16:02:44] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [16:02:44] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [16:02:44] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [16:02:44] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [16:02:44] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [16:02:44] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [16:02:44] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [16:02:44] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [16:02:44] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [16:02:44] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [16:02:44] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [16:02:44] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [16:02:44] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [16:02:44] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -108/236 Test #108: pyFilterCatalog ........................ Passed 2.29 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: [16:02:44] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [16:02:44] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [16:02:44] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [16:02:44] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [16:02:44] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -120: [16:02:44] ------------------------------------- -120: [16:02:44] Basic PMI tests. -115: [16:02:44] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [16:02:44] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [16:02:44] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [16:02:44] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [16:02:44] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [16:02:44] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [16:02:44] 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: [16:02:44] test on : 365 molecules done -115: [16:02:44] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [16:02:44] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [16:02:44] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [16:02:44] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [16:02:44] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: 400 -115: [16:02:44] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [16:02:44] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [16:02:44] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [16:02:45] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [16:02:45] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [16:02:45] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [16:02:45] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [16:02:45] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [16:02:45] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [16:02:45] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [16:02:45] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [16:02:45] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [16:02:45] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [16:02:45] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [16:02:45] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [16:02:45] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [16:02:45] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [16:02:45] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [16:02:45] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [16:02:45] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [16:02:45] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [16:02:45] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [16:02:45] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [16:02:45] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [16:02:45] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [16:02:45] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [16:02:45] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [16:02:45] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [16:02:45] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [16:02:45] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [16:02:45] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [16:02:45] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [16:02:45] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -120: [16:02:45] done -120: [16:02:45] ------------------------------------- -120: [16:02:45] More PMI/NPR tests. -115: [16:02:45] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -120: [16:02:45] done -120: [16:02:45] ------------------------------------- -120: [16:02:45] Basic NPR tests. -115: [16:02:45] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [16:02:45] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [16:02:45] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [16:02:45] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [16:02:45] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [16:02:45] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [16:02:45] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [16:02:45] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [16:02:45] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [16:02:45] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [16:02:45] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [16:02:45] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [16:02:45] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [16:02:45] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [16:02:45] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [16:02:45] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [16:02:45] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [16:02:45] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [16:02:45] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [16:02:45] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [16:02:45] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [16:02:45] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [16:02:45] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [16:02:45] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [16:02:45] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [16:02:45] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [16:02:45] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [16:02:45] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [16:02:45] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [16:02:45] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [16:02:45] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [16:02:45] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [16:02:45] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [16:02:45] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [16:02:45] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [16:02:45] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [16:02:45] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [16:02:45] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [16:02:45] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [16:02:45] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [16:02:45] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [16:02:45] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [16:02:45] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [16:02:45] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [16:02:45] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [16:02:45] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [16:02:45] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [16:02:45] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [16:02:45] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [16:02:45] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [16:02:45] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [16:02:45] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [16:02:45] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [16:02:45] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [16:02:45] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [16:02:45] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [16:02:45] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [16:02:45] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [16:02:45] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [16:02:45] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [16:02:45] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [16:02:45] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -120: [16:02:45] done -120: [16:02:45] ------------------------------------- -120: [16:02:45] PMI edge cases. -120: [16:02:45] done -120: [16:02:45] ------------------------------------- -120: [16:02:45] NPR edge cases. -120: [16:02:45] done -120: [16:02:45] ------------------------------------- -120: [16:02:45] 3D descriptors. -115: [16:02:45] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [16:02:45] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [16:02:45] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: Elapsed time: 1.5522 s -115: Errors:0 -115: [16:02:45] test on : 500 molecules done -109/236 Test #115: testEEM ................................ Passed 1.58 sec +74: [12:24:07] Finished: testSmiCorrectness() +74: [12:24:07] ----------------------------------------- +74: +74: [12:24:07] +74: ----------------------------------------- +120: [12:24:07] ------------------------------------- +120: [12:24:07] Basic PMI tests. +74: [12:24:07] Spurious data before the first property will be ignored +74: [12:24:07] Property will be truncated after the first blank line +74: [12:24:07] Property will be truncated after the first blank line +74: [12:24:07] Property will be truncated after the first blank line +109/236 Test #108: pyFilterCatalog ........................ Passed 3.55 sec test 121 Start 121: testWHIM 121: Test command: /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/Descriptors/testWHIM 121: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/Descriptors 121: Test timeout computed to be: 1500 -120: [16:02:45] done -120: [16:02:45] ------------------------------------- -120: [16:02:45] 3D descriptor edge cases. -120: [16:02:45] done -120: [16:02:45] ------------------------------------- -120: [16:02:45] Inertial shape factor. -120: [16:02:45] done -110/236 Test #120: test3D ................................. Passed 0.53 sec +117: =>start test rdf custom +117: [12:24:08] test on : 365 molecules done +120: [12:24:08] done +120: [12:24:08] ------------------------------------- +120: [12:24:08] More PMI/NPR tests. +120: [12:24:08] done +120: [12:24:08] ------------------------------------- +120: [12:24:08] Basic NPR tests. +74: [12:24:08] Finished: testSDCorrectness() +74: [12:24:08] ----------------------------------------- +74: +110/236 Test #74: testMultithreadedMolSupplier ........... Passed 10.12 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 -74: [16:02:45] Finished: testSDCorrectness() -74: [16:02:45] ----------------------------------------- -74: -111/236 Test #74: testMultithreadedMolSupplier ........... Passed 6.48 sec +118: =>start test rdf +118: [12:24:08] test on : 365 molecules done +111/236 Test #118: testRDF ................................ Passed 1.31 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 -118: =>start test rdf -118: [16:02:45] test on : 365 molecules done -112/236 Test #118: testRDF ................................ Passed 0.97 sec +120: [12:24:08] done +120: [12:24:08] ------------------------------------- +120: [12:24:08] PMI edge cases. +120: [12:24:08] done +120: [12:24:08] ------------------------------------- +120: [12:24:08] NPR edge cases. +120: [12:24:08] done +120: [12:24:08] ------------------------------------- +120: [12:24:08] 3D descriptors. +120: [12:24:08] done +120: [12:24:08] ------------------------------------- +120: [12:24:08] 3D descriptor edge cases. +120: [12:24:08] done +120: [12:24:08] ------------------------------------- +120: [12:24:08] Inertial shape factor. +120: [12:24:08] done +112/236 Test #120: test3D ................................. Passed 1.17 sec test 124 Start 124: testCoulombMat @@ -24932,53 +24970,50 @@ 124: Test timeout computed to be: 1500 124: ===================== Testing CoulombMat ======================= 124: CM test 1 mat Done -113/236 Test #124: testCoulombMat ......................... Passed 0.05 sec +113/236 Test #124: testCoulombMat ......................... Passed 0.09 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: 3348666739 -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 -123: =>start test autocorr3D -123: [16:02:45] test on : 365 molecules done -114/236 Test #123: testAUTOCORR3D ......................... Passed 0.41 sec +121: =>start test WHIM +121: [12:24:09] test on : 365 molecules done +114/236 Test #121: testWHIM ............................... Passed 1.16 sec test 126 Start 126: pyMolDescriptors 126: Test command: /usr/bin/python3 "/build/reproducible-path/rdkit-202503.1/Code/GraphMol/Descriptors/Wrap/testMolDescriptors.py" 126: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/Descriptors/Wrap 126: Test timeout computed to be: 1500 -117: =>start test morse custom -117: [16:02:45] test on : 365 molecules done +125: Randomness seeded to: 93055893 125: Warning: Atom Count for residue GLU5A does not match expected count -121: =>start test WHIM -121: [16:02:46] test on : 365 molecules done -115/236 Test #121: testWHIM ............................... Passed 0.67 sec +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 +119: =>start test MORSE +119: =>read file +119: [12:24:09] test on : 365 molecules done +115/236 Test #119: testMORSE .............................. Passed 2.08 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 -119: =>start test MORSE -119: =>read file -119: [16:02:46] test on : 365 molecules done -116/236 Test #119: testMORSE .............................. Passed 1.34 sec +123: =>start test autocorr3D +123: [12:24:09] test on : 365 molecules done +116/236 Test #123: testAUTOCORR3D ......................... Passed 1.15 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 -29: All 191 tests passed +125: Warning: Atom Count for residue GLU5A does not match expected count 128: 128: 128: @@ -25462,145 +25497,358 @@ 128: 128: ------------------- 128: -128: [16:02:46] ------------------------------------- -128: [16:02:46] Test Morgan Fingerprints. -128: [16:02:46] done -128: [16:02:46] ------------------------------------- -128: [16:02:46] Test Morgan Fingerprints using fromAtoms argument. -128: [16:02:46] done -128: [16:02:46] ------------------------------------- -128: [16:02:46] Test Morgan Fingerprints as bit vects. -128: [16:02:46] done -128: [16:02:46] ------------------------------------- -128: [16:02:46] Test Morgan Fingerprints with feature invariants. -128: [16:02:46] done -128: [16:02:46] ------------------------------------- -128: [16:02:46] Test additional Morgan fingerprints options. -128: [16:02:46] done -128: [16:02:46] ------------------------------------- -128: [16:02:46] Test Atom Codes. -128: [16:02:46] done -128: [16:02:46] ------------------------------------- -128: [16:02:46] Test Atom Pairs. -128: [16:02:46] DEPRECATION WARNING: please use AtomPairGenerator -128: [16:02:46] DEPRECATION WARNING: please use AtomPairGenerator -128: [16:02:46] done -128: [16:02:46] ------------------------------------- -128: [16:02:46] Test Atom Pairs part 2. -128: [16:02:46] DEPRECATION WARNING: please use AtomPairGenerator -128: [16:02:46] DEPRECATION WARNING: please use AtomPairGenerator -128: [16:02:46] done -128: [16:02:46] ------------------------------------- -128: [16:02:46] Test Topological Torsions. -128: [16:02:46] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [16:02:46] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [16:02:46] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [16:02:46] done -128: [16:02:46] ------------------------------------- -128: [16:02:46] Test Bulk Topological Torsions. -128: [16:02:46] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [16:02:46] DEPRECATION WARNING: please use TopologicalTorsionGenerator -117: =>start test AUTOCORR3D custom -117: [16:02:46] test on : 365 molecules done -128: [16:02:46] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [16:02:46] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [16:02:46] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [16:02:46] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [16:02:46] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [16:02:46] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [16:02:46] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [16:02:46] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [16:02:46] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [16:02:46] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [16:02:46] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [16:02:46] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [16:02:46] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [16:02:46] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [16:02:46] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [16:02:46] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [16:02:46] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [16:02:46] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [16:02:46] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [16:02:46] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [16:02:46] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [16:02:46] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [16:02:46] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [16:02:46] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [16:02:46] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [16:02:46] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [16:02:46] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [16:02:46] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [16:02:46] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [16:02:46] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [16:02:46] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [16:02:46] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [16:02:46] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [16:02:46] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [16:02:46] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [16:02:46] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [16:02:46] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [16:02:46] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [16:02:46] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [16:02:46] DEPRECATION WARNING: please use TopologicalTorsionGenerator -126: [16:02:46] DEPRECATION WARNING: please use AtomPairGenerator -126: [16:02:46] DEPRECATION WARNING: please use AtomPairGenerator -126: [16:02:46] DEPRECATION WARNING: please use AtomPairGenerator -126: [16:02:46] DEPRECATION WARNING: please use AtomPairGenerator -126: [16:02:46] DEPRECATION WARNING: please use AtomPairGenerator -128: [16:02:46] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [16:02:46] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [16:02:46] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [16:02:46] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [16:02:46] DEPRECATION WARNING: please use TopologicalTorsionGenerator -126: [16:02:46] DEPRECATION WARNING: please use AtomPairGenerator -126: [16:02:46] DEPRECATION WARNING: please use AtomPairGenerator -126: [16:02:46] DEPRECATION WARNING: please use AtomPairGenerator -126: [16:02:46] DEPRECATION WARNING: please use AtomPairGenerator -126: [16:02:46] DEPRECATION WARNING: please use AtomPairGenerator -126: [16:02:46] DEPRECATION WARNING: please use AtomPairGenerator -126: [16:02:46] DEPRECATION WARNING: please use AtomPairGenerator -126: [16:02:46] DEPRECATION WARNING: please use TopologicalTorsionGenerator -126: [16:02:46] DEPRECATION WARNING: please use TopologicalTorsionGenerator -126: [16:02:46] DEPRECATION WARNING: please use TopologicalTorsionGenerator -126: [16:02:46] DEPRECATION WARNING: please use TopologicalTorsionGenerator -126: [16:02:46] DEPRECATION WARNING: please use TopologicalTorsionGenerator -126: [16:02:46] DEPRECATION WARNING: please use TopologicalTorsionGenerator -126: [16:02:46] DEPRECATION WARNING: please use TopologicalTorsionGenerator -126: [16:02:46] DEPRECATION WARNING: please use TopologicalTorsionGenerator -126: [16:02:46] DEPRECATION WARNING: please use TopologicalTorsionGenerator -126: [16:02:46] DEPRECATION WARNING: please use TopologicalTorsionGenerator -126: [16:02:46] DEPRECATION WARNING: please use TopologicalTorsionGenerator -126: [16:02:46] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [16:02:46] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [16:02:46] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [16:02:46] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [16:02:46] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [16:02:46] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [16:02:46] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [16:02:46] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [16:02:46] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [16:02:46] DEPRECATION WARNING: please use TopologicalTorsionGenerator -126: ..[16:02:46] DEPRECATION WARNING: please use AtomPairGenerator -126: [16:02:46] DEPRECATION WARNING: please use AtomPairGenerator -126: [16:02:46] DEPRECATION WARNING: please use AtomPairGenerator -126: [16:02:46] DEPRECATION WARNING: please use AtomPairGenerator -126: [16:02:46] DEPRECATION WARNING: please use AtomPairGenerator -126: [16:02:46] DEPRECATION WARNING: please use AtomPairGenerator -126: .[16:02:46] DEPRECATION WARNING: please use AtomPairGenerator -126: [16:02:46] DEPRECATION WARNING: please use AtomPairGenerator -126: [16:02:46] DEPRECATION WARNING: please use AtomPairGenerator -128: [16:02:46] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [16:02:46] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [16:02:46] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [16:02:46] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [16:02:46] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [16:02:46] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [16:02:46] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [16:02:46] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [16:02:46] DEPRECATION WARNING: please use TopologicalTorsionGenerator -126: ..[16:02:46] +128: [12:24:10] ------------------------------------- +128: [12:24:10] Test Morgan Fingerprints. +128: [12:24:10] done +128: [12:24:10] ------------------------------------- +128: [12:24:10] Test Morgan Fingerprints using fromAtoms argument. +128: [12:24:10] done +128: [12:24:10] ------------------------------------- +128: [12:24:10] Test Morgan Fingerprints as bit vects. +128: [12:24:10] done +128: [12:24:10] ------------------------------------- +128: [12:24:10] Test Morgan Fingerprints with feature invariants. +128: [12:24:10] done +128: [12:24:10] ------------------------------------- +128: [12:24:10] Test additional Morgan fingerprints options. +128: [12:24:10] done +128: [12:24:10] ------------------------------------- +128: [12:24:10] Test Atom Codes. +128: [12:24:10] done +117: =>start test morse custom +117: [12:24:10] test on : 365 molecules done +128: [12:24:10] ------------------------------------- +128: [12:24:10] Test Atom Pairs. +128: [12:24:10] DEPRECATION WARNING: please use AtomPairGenerator +128: [12:24:10] DEPRECATION WARNING: please use AtomPairGenerator +128: [12:24:10] done +128: [12:24:10] ------------------------------------- +128: [12:24:10] Test Atom Pairs part 2. +128: [12:24:10] DEPRECATION WARNING: please use AtomPairGenerator +128: [12:24:10] DEPRECATION WARNING: please use AtomPairGenerator +128: [12:24:10] done +128: [12:24:10] ------------------------------------- +128: [12:24:10] Test Topological Torsions. +128: [12:24:10] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [12:24:10] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [12:24:10] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [12:24:10] done +128: [12:24:10] ------------------------------------- +128: [12:24:10] Test Bulk Topological Torsions. +128: [12:24:10] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [12:24:10] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [12:24:10] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [12:24:10] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [12:24:10] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [12:24:10] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [12:24:10] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [12:24:10] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [12:24:10] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [12:24:10] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [12:24:10] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [12:24:10] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [12:24:10] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [12:24:10] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [12:24:10] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [12:24:10] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [12:24:10] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [12:24:10] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [12:24:10] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [12:24:10] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [12:24:10] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [12:24:10] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [12:24:10] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [12:24:10] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [12:24:10] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [12:24:10] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [12:24:10] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [12:24:10] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [12:24:10] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [12:24:10] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [12:24:10] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [12:24:10] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [12:24:10] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [12:24:10] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [12:24:10] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [12:24:10] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [12:24:10] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [12:24:10] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [12:24:10] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [12:24:10] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [12:24:10] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [12:24:10] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [12:24:10] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [12:24:10] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [12:24:10] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [12:24:10] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [12:24:10] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [12:24:10] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [12:24:10] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [12:24:10] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [12:24:10] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [12:24:10] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [12:24:10] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [12:24:10] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [12:24:10] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [12:24:10] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [12:24:10] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [12:24:10] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [12:24:10] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [12:24:10] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [12:24:10] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [12:24:10] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [12:24:10] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [12:24:10] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [12:24:10] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [12:24:10] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [12:24:10] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [12:24:10] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [12:24:10] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [12:24:10] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [12:24:10] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [12:24:10] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [12:24:10] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [12:24:10] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [12:24:10] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [12:24:10] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [12:24:10] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [12:24:10] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [12:24:10] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [12:24:10] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [12:24:10] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [12:24:10] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [12:24:10] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [12:24:10] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [12:24:10] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [12:24:10] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [12:24:10] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [12:24:10] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [12:24:10] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [12:24:10] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [12:24:10] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [12:24:10] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [12:24:10] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [12:24:10] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [12:24:10] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [12:24:10] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [12:24:10] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [12:24:10] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [12:24:10] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [12:24:10] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [12:24:10] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [12:24:10] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [12:24:10] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [12:24:10] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [12:24:10] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [12:24:10] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [12:24:10] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [12:24:10] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [12:24:10] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [12:24:10] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [12:24:10] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [12:24:10] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [12:24:10] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [12:24:10] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [12:24:10] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [12:24:10] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [12:24:10] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [12:24:10] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [12:24:10] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [12:24:10] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [12:24:10] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [12:24:10] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [12:24:10] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [12:24:10] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [12:24:10] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [12:24:10] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [12:24:10] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [12:24:10] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [12:24:10] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [12:24:10] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [12:24:10] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [12:24:10] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [12:24:10] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [12:24:10] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [12:24:10] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [12:24:10] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [12:24:10] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [12:24:10] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [12:24:10] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [12:24:10] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [12:24:10] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [12:24:10] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [12:24:10] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [12:24:10] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [12:24:10] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [12:24:10] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [12:24:10] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [12:24:10] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [12:24:10] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [12:24:10] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [12:24:10] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [12:24:10] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [12:24:10] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [12:24:10] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [12:24:10] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [12:24:10] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [12:24:10] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [12:24:10] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [12:24:10] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [12:24:10] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [12:24:10] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [12:24:10] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [12:24:10] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [12:24:10] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [12:24:10] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [12:24:10] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [12:24:10] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [12:24:10] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [12:24:10] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [12:24:10] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [12:24:10] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [12:24:10] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [12:24:10] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [12:24:10] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [12:24:10] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [12:24:10] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [12:24:10] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [12:24:10] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [12:24:10] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [12:24:10] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [12:24:10] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [12:24:10] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [12:24:10] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [12:24:10] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [12:24:10] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [12:24:10] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [12:24:10] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [12:24:10] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [12:24:10] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [12:24:10] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [12:24:10] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [12:24:10] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [12:24:10] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [12:24:10] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [12:24:10] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [12:24:10] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [12:24:10] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [12:24:10] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [12:24:10] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [12:24:10] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [12:24:10] done +128: [12:24:10] ------------------------------------- +128: [12:24:10] Test Hashed Atom Pairs. +128: [12:24:10] DEPRECATION WARNING: please use AtomPairGenerator +128: [12:24:10] DEPRECATION WARNING: please use AtomPairGenerator +128: [12:24:10] DEPRECATION WARNING: please use AtomPairGenerator +128: [12:24:10] DEPRECATION WARNING: please use AtomPairGenerator +128: [12:24:10] DEPRECATION WARNING: please use AtomPairGenerator +128: [12:24:10] DEPRECATION WARNING: please use AtomPairGenerator +128: [12:24:10] done +128: [12:24:10] ------------------------------------- +128: [12:24:10] Test Hashed torsions. +128: [12:24:10] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [12:24:10] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [12:24:10] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [12:24:10] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [12:24:10] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [12:24:10] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [12:24:10] done +128: [12:24:10] ------------------------------------- +128: [12:24:10] Test Rooted Atom Pairs. +128: [12:24:10] DEPRECATION WARNING: please use AtomPairGenerator +128: [12:24:10] DEPRECATION WARNING: please use AtomPairGenerator +128: [12:24:10] done +128: [12:24:10] ------------------------------------- +128: [12:24:10] Test ignoring atoms in Atom Pairs. +128: [12:24:10] DEPRECATION WARNING: please use AtomPairGenerator +128: [12:24:10] DEPRECATION WARNING: please use AtomPairGenerator +128: [12:24:10] DEPRECATION WARNING: please use AtomPairGenerator +128: [12:24:10] DEPRECATION WARNING: please use AtomPairGenerator +128: [12:24:10] DEPRECATION WARNING: please use AtomPairGenerator +128: [12:24:10] done +128: [12:24:10] ------------------------------------- +128: [12:24:10] Test Rooted Topological Torsions. +128: [12:24:10] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [12:24:10] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [12:24:10] done +128: [12:24:10] ------------------------------------- +128: [12:24:10] Test ignoring atoms in Topological Torsions. +128: [12:24:10] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [12:24:10] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [12:24:10] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [12:24:10] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [12:24:10] done +128: [12:24:10] ------------------------------------- +128: [12:24:10] Test atom info from morgan fingerprints. +126: [12:24:10] DEPRECATION WARNING: please use AtomPairGenerator +126: [12:24:10] DEPRECATION WARNING: please use AtomPairGenerator +126: [12:24:10] DEPRECATION WARNING: please use AtomPairGenerator +126: [12:24:10] DEPRECATION WARNING: please use AtomPairGenerator +126: [12:24:10] DEPRECATION WARNING: please use AtomPairGenerator +126: [12:24:10] DEPRECATION WARNING: please use AtomPairGenerator +128: [12:24:10] done +128: [12:24:10] ------------------------------------- +128: [12:24:10] Test atom info from morgan fingerprints including Info Redundant Environments. +128: [12:24:10] done +128: [12:24:10] ------------------------------------- +126: [12:24:10] DEPRECATION WARNING: please use AtomPairGenerator +126: [12:24:10] DEPRECATION WARNING: please use AtomPairGenerator +126: [12:24:10] DEPRECATION WARNING: please use AtomPairGenerator +126: [12:24:10] DEPRECATION WARNING: please use AtomPairGenerator +126: [12:24:10] DEPRECATION WARNING: please use AtomPairGenerator +126: [12:24:10] DEPRECATION WARNING: please use AtomPairGenerator +126: [12:24:10] DEPRECATION WARNING: please use TopologicalTorsionGenerator +126: [12:24:10] DEPRECATION WARNING: please use TopologicalTorsionGenerator +126: [12:24:10] DEPRECATION WARNING: please use TopologicalTorsionGenerator +126: [12:24:10] DEPRECATION WARNING: please use TopologicalTorsionGenerator +126: [12:24:10] DEPRECATION WARNING: please use TopologicalTorsionGenerator +126: [12:24:10] DEPRECATION WARNING: please use TopologicalTorsionGenerator +126: [12:24:10] DEPRECATION WARNING: please use TopologicalTorsionGenerator +126: [12:24:10] DEPRECATION WARNING: please use TopologicalTorsionGenerator +126: [12:24:10] DEPRECATION WARNING: please use TopologicalTorsionGenerator +126: [12:24:10] DEPRECATION WARNING: please use TopologicalTorsionGenerator +126: [12:24:10] DEPRECATION WARNING: please use TopologicalTorsionGenerator +126: [12:24:10] DEPRECATION WARNING: please use TopologicalTorsionGenerator +126: ..[12:24:10] DEPRECATION WARNING: please use AtomPairGenerator +126: [12:24:10] DEPRECATION WARNING: please use AtomPairGenerator +126: [12:24:10] DEPRECATION WARNING: please use AtomPairGenerator +126: [12:24:10] DEPRECATION WARNING: please use AtomPairGenerator +126: [12:24:10] DEPRECATION WARNING: please use AtomPairGenerator +126: [12:24:10] DEPRECATION WARNING: please use AtomPairGenerator +126: .[12:24:10] DEPRECATION WARNING: please use AtomPairGenerator +126: [12:24:10] DEPRECATION WARNING: please use AtomPairGenerator +126: [12:24:10] DEPRECATION WARNING: please use AtomPairGenerator +128: [12:24:10] ------------------------------------- +128: [12:24:10] DEPRECATION WARNING: please use AtomPairGenerator +128: [12:24:10] DEPRECATION WARNING: please use AtomPairGenerator +128: [12:24:10] DEPRECATION WARNING: please use AtomPairGenerator +128: [12:24:10] DEPRECATION WARNING: please use AtomPairGenerator +128: [12:24:10] DEPRECATION WARNING: please use AtomPairGenerator +128: [12:24:10] DEPRECATION WARNING: please use AtomPairGenerator +128: [12:24:10] DEPRECATION WARNING: please use AtomPairGenerator +128: [12:24:10] DEPRECATION WARNING: please use AtomPairGenerator +128: [12:24:10] DEPRECATION WARNING: please use AtomPairGenerator +128: [12:24:10] DEPRECATION WARNING: please use AtomPairGenerator +128: [12:24:10] DEPRECATION WARNING: please use AtomPairGenerator +128: [12:24:10] DEPRECATION WARNING: please use AtomPairGenerator +128: [12:24:10] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [12:24:10] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [12:24:10] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [12:24:10] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [12:24:10] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [12:24:10] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [12:24:10] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [12:24:10] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [12:24:10] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [12:24:10] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [12:24:10] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [12:24:10] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [12:24:10] ------------------------------------- +126: ..[12:24:10] 126: 126: **** +128: [12:24:10] ------------------------------------- 126: Pre-condition Violation 126: Number of atom props not equal to number of atoms 126: Violation occurred on line 89 in file ./Code/GraphMol/Descriptors/BCUT.cpp @@ -25610,10 +25858,10 @@ 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# 0x0000FFFF9637D0B8 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdMolDescriptors.so -126: 4# 0x0000FFFF96392370 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdMolDescriptors.so +126: 3# 0x0000FFFF8FB6D0B8 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdMolDescriptors.so +126: 4# 0x0000FFFF8FB82370 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# 0x0000FFFF9A1F2680 in /lib/aarch64-linux-gnu/libboost_python313.so.1.83.0 +126: 6# 0x0000FFFF939E2680 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 @@ -25624,17 +25872,17 @@ 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# 0x0000FFFF987CC320 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so -126: 18# 0x0000FFFF987CC2B8 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so -126: 19# 0x0000FFFF987CC248 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so -126: 20# 0x0000FFFF987CC1E0 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so -126: 21# 0x0000FFFF987CC178 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so +126: 17# 0x0000FFFF91FBC320 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so +126: 18# 0x0000FFFF91FBC2B8 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so +126: 19# 0x0000FFFF91FBC248 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so +126: 20# 0x0000FFFF91FBC1E0 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so +126: 21# 0x0000FFFF91FBC178 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# 0x0000FFFF9A1EF25C in /lib/aarch64-linux-gnu/libboost_python313.so.1.83.0 +126: 27# 0x0000FFFF939DF25C 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# 0x000000000053DD10 in /usr/bin/python3 @@ -25666,577 +25914,361 @@ 126: 56# 0x000000000065F5F0 in /usr/bin/python3 126: 57# Py_RunMain in /usr/bin/python3 126: 58# Py_BytesMain in /usr/bin/python3 -126: 59# 0x0000FFFF9AAF229C in /lib/aarch64-linux-gnu/libc.so.6 +126: 59# 0x0000FFFF942E229C 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: -128: [16:02:46] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [16:02:46] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [16:02:46] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [16:02:46] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [16:02:46] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [12:24:10] ------------------------------------- +128: [12:24:10] ------------------------------------- +128: [12:24:10] Test Atom Pairs including info about chirality. +128: [12:24:10] DEPRECATION WARNING: please use AtomPairGenerator +128: [12:24:10] DEPRECATION WARNING: please use AtomPairGenerator +128: [12:24:10] DEPRECATION WARNING: please use AtomPairGenerator +128: [12:24:10] DEPRECATION WARNING: please use AtomPairGenerator +128: [12:24:10] DEPRECATION WARNING: please use AtomPairGenerator +128: [12:24:10] DEPRECATION WARNING: please use AtomPairGenerator +128: [12:24:10] DEPRECATION WARNING: please use AtomPairGenerator +128: [12:24:10] DEPRECATION WARNING: please use AtomPairGenerator +128: [12:24:10] DEPRECATION WARNING: please use AtomPairGenerator +128: [12:24:10] DEPRECATION WARNING: please use AtomPairGenerator +128: [12:24:10] DEPRECATION WARNING: please use AtomPairGenerator +128: [12:24:10] DEPRECATION WARNING: please use AtomPairGenerator +128: [12:24:10] done +128: [12:24:10] ------------------------------------- +128: [12:24:10] Test Topological Torsions including info about chirality. +128: [12:24:10] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [12:24:10] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [12:24:10] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [12:24:10] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [12:24:10] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [12:24:10] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [12:24:10] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [12:24:10] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [12:24:10] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [12:24:10] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [12:24:10] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [12:24:10] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [12:24:10] done +128: [12:24:10] ------------------------------------- +128: [12:24:10] Test GitHub Issue 25: fingerprint backwards compatibility. +128: [12:24:10] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [12:24:10] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [12:24:10] DEPRECATION WARNING: please use AtomPairGenerator +128: [12:24:10] DEPRECATION WARNING: please use AtomPairGenerator +128: [12:24:10] done +128: [12:24:10] ------------------------------------- +128: [12:24:10] Test GitHub Issue 151: PatternFingerprint problems +128: [12:24:10] done +128: [12:24:10] ------------------------------------- +128: [12:24:10] Test 3D atom pairs. +128: [12:24:10] DEPRECATION WARNING: please use AtomPairGenerator +128: [12:24:10] DEPRECATION WARNING: please use AtomPairGenerator +128: [12:24:10] DEPRECATION WARNING: please use AtomPairGenerator +128: [12:24:10] DEPRECATION WARNING: please use AtomPairGenerator +128: [12:24:10] DEPRECATION WARNING: please use AtomPairGenerator +128: [12:24:10] done +128: [12:24:10] ------------------------------------- +128: [12:24:10] Test GitHub Issue 195: GenMACCSKeys() raises an exception with an empty molecule +128: [12:24:10] done +128: [12:24:10] ------------------------------------- +128: [12:24:10] Test multithreading with the pattern FP +128: reading molecules 126: ...Warning: Atom Count for residue GLU5A does not match expected count +128: pass 1 +128: launch :0 +128: launch :1 +128: launch :2 +128: launch :3 126: 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 -111: [16:02:46] done -111: [16:02:46] ------------------------------------- -111: [16:02:46] Test Issue252: Bad definitions for Crippen atom types. -111: [16:02:46] done -111: [16:02:46] ------------------------------------- -111: [16:02:46] Test calculation of ChiVs. -128: [16:02:46] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [16:02:46] DEPRECATION WARNING: please use TopologicalTorsionGenerator 126: Warning: Atom Count for residue LYS80A does not match expected count -111: [16:02:46] done -111: [16:02:46] ------------------------------------- -111: [16:02:46] Test calculation of ChiNs. -111: [16:02:46] done -111: [16:02:46] ------------------------------------- -111: [16:02:46] Test calculation of HallKierAlpha. -111: [16:02:46] done -111: [16:02:46] ------------------------------------- -111: [16:02:46] Test calculation of Kappa1. -111: [16:02:46] done -111: [16:02:46] ------------------------------------- -111: [16:02:46] Test calculation of Kappa2. -128: [16:02:46] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [16:02:46] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [16:02:46] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [16:02:46] DEPRECATION WARNING: please use TopologicalTorsionGenerator 126: Warning: Atom Count for residue GLU150A does not match expected count 126: Warning: Atom Count for residue ASN157A does not match expected count -111: [16:02:46] done -111: [16:02:46] ------------------------------------- -111: [16:02:46] Test calculation of Kappa3. -111: [16:02:46] done -111: [16:02:46] ------------------------------------- -111: [16:02:46] Test Crippen atom type calculations. -111: [16:02:46] done -111: [16:02:46] ------------------------------------- -111: [16:02:46] Test ring descriptors -128: [16:02:46] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [16:02:46] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [16:02:46] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [16:02:46] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [16:02:46] DEPRECATION WARNING: please use TopologicalTorsionGenerator -111: [16:02:46] done -111: [16:02:46] ------------------------------------- -111: [16:02:46] Test other count descriptors. -111: [16:02:46] done -111: [16:02:46] ------------------------------------- -111: [16:02:46] Test MQN -111: [16:02:46] done -111: [16:02:46] ------------------------------------- -111: [16:02:46] Test GitHub Issue 56. -111: [16:02:46] WARNING: not removing hydrogen atom without neighbors -111: [16:02:46] WARNING: not removing hydrogen atom without neighbors -111: [16:02:46] WARNING: not removing hydrogen atom without neighbors -111: [16:02:46] WARNING: not removing hydrogen atom without neighbors -111: [16:02:46] done -111: [16:02:46] ------------------------------------- -111: [16:02:46] Test Github92: Bad Crippen atom type for pyrrole H. -111: [16:02:46] done -111: [16:02:46] ------------------------------------- -111: [16:02:46] Test Github362: order dependence in Kier-Hall descriptors. -111: [16:02:46] done -111: [16:02:46] ------------------------------------- -111: [16:02:46] Test calculation of spiro and bridgehead counts. -111: [16:02:46] done -111: [16:02:46] ------------------------------------- -111: [16:02:46] Test Github694: ExactMolWt ignoring the mass of the electron -111: [16:02:46] done -111: [16:02:46] ------------------------------------- -111: [16:02:46] Testing Properties and KitchenSink -128: [16:02:46] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [16:02:46] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [16:02:46] DEPRECATION WARNING: please use TopologicalTorsionGenerator -111: [16:02:46] ---Caught keyerror (bad property name)--- -111: [16:02:46] ------------------------------------- -111: [16:02:46] Test USR Descriptor -111: [16:02:46] done -111: [16:02:46] ------------------------------------- -111: [16:02:46] Test Github #1702: AUTOCORR2D.h not installed unless RDK_BUILD_DESCRIPTORS3D but is required -111: [16:02:46] done -111: [16:02:46] ------------------------------------- -111: [16:02:46] Test Github #1973: support P and S terms for TPSA calculation -111: [16:02:46] done -111: [16:02:46] ------------------------------------- -111: [16:02:46] Test Github #2948: Empty molecule has non-zero LabuteASA -111: [16:02:46] done -128: [16:02:46] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [16:02:46] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [16:02:46] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [16:02:46] DEPRECATION WARNING: please use TopologicalTorsionGenerator -117/236 Test #111: testDescriptors ........................ Passed 3.45 sec +126: Warning: Atom Count for residue GLU5A does not match expected count +128: pass 2 +128: launch :0 +128: launch :1 +128: launch :2 +128: launch :3 +125: Warning: Atom Count for residue ASN39A does not match expected count +111: [12:24:11] done +111: [12:24:11] ------------------------------------- +111: [12:24:11] Test Issue252: Bad definitions for Crippen atom types. +111: [12:24:11] done +111: [12:24:11] ------------------------------------- +111: [12:24:11] Test calculation of ChiVs. +111: [12:24:11] done +111: [12:24:11] ------------------------------------- +111: [12:24:11] Test calculation of ChiNs. +111: [12:24:11] done +111: [12:24:11] ------------------------------------- +111: [12:24:11] Test calculation of HallKierAlpha. +111: [12:24:11] done +111: [12:24:11] ------------------------------------- +111: [12:24:11] Test calculation of Kappa1. +111: [12:24:11] done +111: [12:24:11] ------------------------------------- +111: [12:24:11] Test calculation of Kappa2. +111: [12:24:11] done +111: [12:24:11] ------------------------------------- +111: [12:24:11] Test calculation of Kappa3. +111: [12:24:11] done +111: [12:24:11] ------------------------------------- +111: [12:24:11] Test Crippen atom type calculations. +111: [12:24:11] done +111: [12:24:11] ------------------------------------- +111: [12:24:11] Test ring descriptors +111: [12:24:11] done +111: [12:24:11] ------------------------------------- +111: [12:24:11] Test other count descriptors. +111: [12:24:11] done +111: [12:24:11] ------------------------------------- +111: [12:24:11] Test MQN +111: [12:24:11] done +111: [12:24:11] ------------------------------------- +111: [12:24:11] Test GitHub Issue 56. +111: [12:24:11] WARNING: not removing hydrogen atom without neighbors +111: [12:24:11] WARNING: not removing hydrogen atom without neighbors +111: [12:24:11] WARNING: not removing hydrogen atom without neighbors +111: [12:24:11] WARNING: not removing hydrogen atom without neighbors +111: [12:24:11] done +111: [12:24:11] ------------------------------------- +111: [12:24:11] Test Github92: Bad Crippen atom type for pyrrole H. +111: [12:24:11] done +111: [12:24:11] ------------------------------------- +111: [12:24:11] Test Github362: order dependence in Kier-Hall descriptors. +111: [12:24:11] done +111: [12:24:11] ------------------------------------- +111: [12:24:11] Test calculation of spiro and bridgehead counts. +111: [12:24:11] done +111: [12:24:11] ------------------------------------- +111: [12:24:11] Test Github694: ExactMolWt ignoring the mass of the electron +111: [12:24:11] done +111: [12:24:11] ------------------------------------- +111: [12:24:11] Testing Properties and KitchenSink +111: [12:24:11] ---Caught keyerror (bad property name)--- +111: [12:24:11] ------------------------------------- +111: [12:24:11] Test USR Descriptor +111: [12:24:11] done +111: [12:24:11] ------------------------------------- +111: [12:24:11] Test Github #1702: AUTOCORR2D.h not installed unless RDK_BUILD_DESCRIPTORS3D but is required +111: [12:24:11] done +111: [12:24:11] ------------------------------------- +111: [12:24:11] Test Github #1973: support P and S terms for TPSA calculation +111: [12:24:11] done +111: [12:24:11] ------------------------------------- +111: [12:24:11] Test Github #2948: Empty molecule has non-zero LabuteASA +111: [12:24:11] done +117/236 Test #111: testDescriptors ........................ Passed 5.94 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 -128: [16:02:46] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [16:02:46] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [16:02:46] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [16:02:46] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [16:02:46] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [16:02:46] DEPRECATION WARNING: please use TopologicalTorsionGenerator -125: Warning: Atom Count for residue ASN39A does not match expected count -128: [16:02:46] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [16:02:46] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [16:02:46] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [16:02:46] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [16:02:46] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [16:02:46] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [16:02:46] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [16:02:46] DEPRECATION WARNING: please use TopologicalTorsionGenerator -126: Warning: Atom Count for residue GLU5A does not match expected count -117: =>start test 2 WHIM custom -117: [16:02:46] test on : 365 molecules done -128: [16:02:46] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [16:02:46] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [16:02:46] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [16:02:46] DEPRECATION WARNING: please use TopologicalTorsionGenerator -129: [16:02:46] ------------------------------------- -129: [16:02:46] Test MHFP fingerprint encoder initialization -128: [16:02:46] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [16:02:46] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [16:02:46] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [16:02:46] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [16:02:46] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [16:02:46] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [16:02:46] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [16:02:46] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [16:02:46] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [16:02:46] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [16:02:46] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [16:02:46] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [16:02:46] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [16:02:46] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [16:02:46] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [16:02:46] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [16:02:46] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [16:02:46] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [16:02:46] DEPRECATION WARNING: please use TopologicalTorsionGenerator -129: [16:02:46] done -129: [16:02:46] ------------------------------------- -129: [16:02:46] Test MHFP shingling creation -128: [16:02:46] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [16:02:46] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [16:02:46] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [16:02:46] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [16:02:46] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [16:02:46] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [16:02:46] DEPRECATION WARNING: please use TopologicalTorsionGenerator -129: [16:02:46] done -129: [16:02:46] ------------------------------------- -129: [16:02:46] Test MHFP hashing of string and uint arrays -129: [16:02:46] done -129: [16:02:46] ------------------------------------- -129: [16:02:46] Test SECFP fingerprint functionality -128: [16:02:46] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [16:02:46] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [16:02:46] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [16:02:46] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [16:02:46] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [16:02:46] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [16:02:46] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [16:02:46] DEPRECATION WARNING: please use TopologicalTorsionGenerator -129: [16:02:46] done -118/236 Test #129: testMHFPFingerprint .................... Passed 0.12 sec +117: =>start test AUTOCORR3D custom +117: [12:24:11] test on : 365 molecules done +125: Warning: Atom Count for residue GLU53A does not match expected count +129: [12:24:11] ------------------------------------- +129: [12:24:11] Test MHFP fingerprint encoder initialization +129: [12:24:11] done +129: [12:24:11] ------------------------------------- +129: [12:24:11] Test MHFP shingling creation +127: ........ +127: ---------------------------------------------------------------------- +127: Ran 8 tests in 0.497s +127: +127: OK +129: [12:24:11] done +129: [12:24:11] ------------------------------------- +129: [12:24:11] Test MHFP hashing of string and uint arrays +129: [12:24:11] done +129: [12:24:11] ------------------------------------- +129: [12:24:11] Test SECFP fingerprint functionality +129: [12:24:11] done +118/236 Test #129: testMHFPFingerprint .................... Passed 0.18 sec 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 -128: [16:02:46] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [16:02:46] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [16:02:46] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [16:02:46] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [16:02:46] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [16:02:46] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [16:02:46] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [16:02:46] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [16:02:46] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [16:02:46] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [16:02:46] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [16:02:46] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [16:02:46] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [16:02:46] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [16:02:46] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [16:02:46] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [16:02:46] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [16:02:46] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [16:02:46] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [16:02:46] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [16:02:46] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [16:02:46] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [16:02:46] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [16:02:46] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [16:02:46] DEPRECATION WARNING: please use TopologicalTorsionGenerator -127: ........ -127: ---------------------------------------------------------------------- -127: Ran 8 tests in 0.243s -127: -127: OK -128: [16:02:46] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [16:02:46] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [16:02:46] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [16:02:46] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [16:02:46] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [16:02:46] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [16:02:46] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [16:02:46] DEPRECATION WARNING: please use TopologicalTorsionGenerator -126: Warning: Atom Count for residue ASN39A does not match expected count -130: [16:02:46] ------------------------------------- -130: [16:02:46] Test atom-pair fp generator -128: [16:02:46] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [16:02:46] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [16:02:46] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [16:02:46] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [16:02:46] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [16:02:46] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [16:02:46] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [16:02:46] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [16:02:46] DEPRECATION WARNING: please use TopologicalTorsionGenerator -117: =>start test 1 WHIM custom -117: [16:02:46] test on : 365 molecules done -130: [16:02:46] done -128: [16:02:46] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [16:02:46] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [16:02:46] DEPRECATION WARNING: please use TopologicalTorsionGenerator -130: [16:02:46] ------------------------------------- -130: [16:02:46] Test atom-pair fp generator with different arguments -128: [16:02:46] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [16:02:46] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [16:02:46] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [16:02:46] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [16:02:46] DEPRECATION WARNING: please use TopologicalTorsionGenerator -125: Warning: Atom Count for residue GLU53A does not match expected count -128: [16:02:46] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [16:02:46] DEPRECATION WARNING: please use TopologicalTorsionGenerator -119/236 Test #127: pyMolDescriptors3D ..................... Passed 0.61 sec +130: [12:24:11] ------------------------------------- +130: [12:24:11] Test atom-pair fp generator +130: [12:24:11] done +130: [12:24:11] ------------------------------------- +130: [12:24:11] Test atom-pair fp generator with different arguments +130: [12:24:11] done +130: [12:24:11] ------------------------------------- +130: [12:24:11] Test compatibility between atom pair implementation for FingerprintGenerator and old atom pairs implementation +130: [12:24:11] DEPRECATION WARNING: please use AtomPairGenerator +130: [12:24:11] DEPRECATION WARNING: please use AtomPairGenerator +130: [12:24:11] DEPRECATION WARNING: please use AtomPairGenerator +130: [12:24:11] DEPRECATION WARNING: please use AtomPairGenerator +130: [12:24:11] DEPRECATION WARNING: please use AtomPairGenerator +130: [12:24:11] DEPRECATION WARNING: please use AtomPairGenerator +130: [12:24:11] DEPRECATION WARNING: please use AtomPairGenerator +130: [12:24:11] DEPRECATION WARNING: please use AtomPairGenerator +119/236 Test #127: pyMolDescriptors3D ..................... Passed 1.65 sec +130: [12:24:11] DEPRECATION WARNING: please use AtomPairGenerator 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 -128: [16:02:46] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [16:02:46] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [16:02:46] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [16:02:46] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [16:02:46] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [16:02:46] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [16:02:46] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [16:02:46] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [16:02:46] done -130: [16:02:46] done -130: [16:02:46] ------------------------------------- -130: [16:02:46] Test compatibility between atom pair implementation for FingerprintGenerator and old atom pairs implementation -130: [16:02:46] DEPRECATION WARNING: please use AtomPairGenerator -130: [16:02:46] DEPRECATION WARNING: please use AtomPairGenerator -130: [16:02:46] DEPRECATION WARNING: please use AtomPairGenerator -130: [16:02:46] DEPRECATION WARNING: please use AtomPairGenerator -130: [16:02:46] DEPRECATION WARNING: please use AtomPairGenerator -130: [16:02:46] DEPRECATION WARNING: please use AtomPairGenerator -130: [16:02:46] DEPRECATION WARNING: please use AtomPairGenerator -130: [16:02:46] DEPRECATION WARNING: please use AtomPairGenerator -128: [16:02:46] ------------------------------------- -128: [16:02:46] Test Hashed Atom Pairs. -128: [16:02:46] DEPRECATION WARNING: please use AtomPairGenerator -128: [16:02:46] DEPRECATION WARNING: please use AtomPairGenerator -130: [16:02:46] DEPRECATION WARNING: please use AtomPairGenerator -128: [16:02:46] DEPRECATION WARNING: please use AtomPairGenerator -128: [16:02:46] DEPRECATION WARNING: please use AtomPairGenerator -128: [16:02:46] DEPRECATION WARNING: please use AtomPairGenerator -128: [16:02:46] DEPRECATION WARNING: please use AtomPairGenerator -128: [16:02:46] done -128: [16:02:46] ------------------------------------- -128: [16:02:46] Test Hashed torsions. -128: [16:02:46] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [16:02:46] DEPRECATION WARNING: please use TopologicalTorsionGenerator -130: [16:02:46] DEPRECATION WARNING: please use AtomPairGenerator -130: [16:02:46] done -128: [16:02:46] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [16:02:46] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [16:02:46] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [16:02:46] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [16:02:46] done -128: [16:02:46] ------------------------------------- -128: [16:02:46] Test Rooted Atom Pairs. -128: [16:02:46] DEPRECATION WARNING: please use AtomPairGenerator -128: [16:02:46] DEPRECATION WARNING: please use AtomPairGenerator -128: [16:02:46] done -128: [16:02:46] ------------------------------------- -128: [16:02:46] Test ignoring atoms in Atom Pairs. -128: [16:02:46] DEPRECATION WARNING: please use AtomPairGenerator -128: [16:02:46] DEPRECATION WARNING: please use AtomPairGenerator -128: [16:02:46] DEPRECATION WARNING: please use AtomPairGenerator -128: [16:02:46] DEPRECATION WARNING: please use AtomPairGenerator -128: [16:02:46] DEPRECATION WARNING: please use AtomPairGenerator -128: [16:02:46] done -128: [16:02:46] ------------------------------------- -128: [16:02:46] Test Rooted Topological Torsions. -128: [16:02:46] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [16:02:46] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [16:02:46] done -128: [16:02:46] ------------------------------------- -128: [16:02:46] Test ignoring atoms in Topological Torsions. -128: [16:02:46] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [16:02:46] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [16:02:46] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [16:02:46] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [16:02:46] done -128: [16:02:46] ------------------------------------- -130: [16:02:46] ------------------------------------- -130: [16:02:46] Test atom-pair additional output -128: [16:02:46] Test atom info from morgan fingerprints. -128: [16:02:46] done -128: [16:02:46] ------------------------------------- -128: [16:02:46] Test atom info from morgan fingerprints including Info Redundant Environments. -128: [16:02:46] done -128: [16:02:46] ------------------------------------- -130: [16:02:46] done -130: [16:02:46] ------------------------------------- -130: [16:02:46] Test Folded Atom Pairs. -130: [16:02:46] done -130: [16:02:46] ------------------------------------- -130: [16:02:46] Test Rooted Atom Pairs. -130: [16:02:46] done -128: [16:02:46] ------------------------------------- -128: [16:02:46] DEPRECATION WARNING: please use AtomPairGenerator -128: [16:02:46] DEPRECATION WARNING: please use AtomPairGenerator -128: [16:02:46] DEPRECATION WARNING: please use AtomPairGenerator -128: [16:02:46] DEPRECATION WARNING: please use AtomPairGenerator -128: [16:02:46] DEPRECATION WARNING: please use AtomPairGenerator -128: [16:02:46] DEPRECATION WARNING: please use AtomPairGenerator -128: [16:02:46] DEPRECATION WARNING: please use AtomPairGenerator -128: [16:02:46] DEPRECATION WARNING: please use AtomPairGenerator -128: [16:02:46] DEPRECATION WARNING: please use AtomPairGenerator -128: [16:02:46] DEPRECATION WARNING: please use AtomPairGenerator -128: [16:02:46] DEPRECATION WARNING: please use AtomPairGenerator -128: [16:02:46] DEPRECATION WARNING: please use AtomPairGenerator -128: [16:02:46] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [16:02:46] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [16:02:46] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [16:02:46] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [16:02:46] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [16:02:46] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [16:02:46] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [16:02:46] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [16:02:46] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [16:02:46] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [16:02:46] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [16:02:46] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [16:02:46] ------------------------------------- -130: [16:02:46] ------------------------------------- -130: [16:02:46] Test ignoring atoms in Atom Pairs. -130: [16:02:46] done -126: Warning: Atom Count for residue GLU53A does not match expected count -130: [16:02:46] ------------------------------------- -130: [16:02:46] Test Atom Pairs including info about chirality. -130: [16:02:46] done +130: [12:24:11] DEPRECATION WARNING: please use AtomPairGenerator +130: [12:24:11] done +130: [12:24:11] ------------------------------------- +130: [12:24:11] Test atom-pair additional output +130: [12:24:11] done +130: [12:24:11] ------------------------------------- +130: [12:24:11] Test Folded Atom Pairs. +130: [12:24:11] done 125: Warning: Atom Count for residue ARG64A does not match expected count -130: [16:02:46] ------------------------------------- -130: [16:02:46] Test Morgan Fingerprints. -130: [16:02:46] done -130: [16:02:46] ------------------------------------- -130: [16:02:46] Test morgan fp generator -130: [16:02:46] done -130: [16:02:46] ------------------------------------- -130: [16:02:46] Test Morgan Fingerprints using fromAtoms argument. -130: [16:02:46] done -130: [16:02:46] ------------------------------------- -130: [16:02:46] Test Morgan Fingerprints as bit vects. -130: [16:02:46] done -130: [16:02:46] ------------------------------------- -130: [16:02:46] Test Morgan Fingerprints with feature invariants. -128: [16:02:46] ------------------------------------- -128: [16:02:46] ------------------------------------- -130: [16:02:46] done -130: [16:02:46] ------------------------------------- -130: [16:02:46] Test additional Morgan fingerprints options. -130: [16:02:46] done -130: [16:02:46] ------------------------------------- -130: [16:02:46] Test GitHub Issue 695: Include cis/trans stereochemistry when useChirality=true with the morgan fingerprints -130: [16:02:46] done -130: [16:02:46] ------------------------------------- -130: [16:02:46] Single atoms setting radius 1 bits in Morgan fingerprints -130: [16:02:46] done -130: [16:02:46] ------------------------------------- -130: [16:02:46] Test different invariant generator combinations -130: [16:02:46] done -130: [16:02:46] ------------------------------------- -130: [16:02:46] Test invariant overriding -130: [16:02:46] done -130: [16:02:46] ------------------------------------- -130: [16:02:46] Test RDKit fp generator -128: [16:02:46] ------------------------------------- -128: [16:02:46] Test Atom Pairs including info about chirality. -128: [16:02:46] DEPRECATION WARNING: please use AtomPairGenerator -128: [16:02:46] DEPRECATION WARNING: please use AtomPairGenerator -128: [16:02:46] DEPRECATION WARNING: please use AtomPairGenerator -128: [16:02:46] DEPRECATION WARNING: please use AtomPairGenerator -128: [16:02:46] DEPRECATION WARNING: please use AtomPairGenerator -128: [16:02:46] DEPRECATION WARNING: please use AtomPairGenerator -128: [16:02:46] DEPRECATION WARNING: please use AtomPairGenerator -128: [16:02:46] DEPRECATION WARNING: please use AtomPairGenerator -128: [16:02:46] DEPRECATION WARNING: please use AtomPairGenerator -128: [16:02:46] DEPRECATION WARNING: please use AtomPairGenerator -128: [16:02:46] DEPRECATION WARNING: please use AtomPairGenerator -128: [16:02:46] DEPRECATION WARNING: please use AtomPairGenerator -128: [16:02:46] done -128: [16:02:46] ------------------------------------- -128: [16:02:46] Test Topological Torsions including info about chirality. -128: [16:02:46] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [16:02:46] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [16:02:46] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [16:02:46] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [16:02:46] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [16:02:46] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [16:02:46] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [16:02:46] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [16:02:46] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [16:02:46] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [16:02:46] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [16:02:46] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [16:02:46] done -128: [16:02:46] ------------------------------------- -128: [16:02:46] Test GitHub Issue 25: fingerprint backwards compatibility. -128: [16:02:46] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [16:02:46] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [16:02:46] DEPRECATION WARNING: please use AtomPairGenerator -128: [16:02:46] DEPRECATION WARNING: please use AtomPairGenerator -128: [16:02:46] done -128: [16:02:46] ------------------------------------- -128: [16:02:46] Test GitHub Issue 151: PatternFingerprint problems -128: [16:02:46] done -128: [16:02:46] ------------------------------------- -128: [16:02:46] Test 3D atom pairs. -128: [16:02:46] DEPRECATION WARNING: please use AtomPairGenerator -128: [16:02:46] DEPRECATION WARNING: please use AtomPairGenerator -128: [16:02:46] DEPRECATION WARNING: please use AtomPairGenerator -128: [16:02:46] DEPRECATION WARNING: please use AtomPairGenerator -128: [16:02:46] DEPRECATION WARNING: please use AtomPairGenerator -128: [16:02:46] done -128: [16:02:46] ------------------------------------- -128: [16:02:46] Test GitHub Issue 195: GenMACCSKeys() raises an exception with an empty molecule -128: [16:02:46] done -128: [16:02:46] ------------------------------------- -128: [16:02:46] Test multithreading with the pattern FP -128: reading molecules -128: pass 1 -128: launch :0 -128: launch :1 -128: launch :2 -128: launch :3 -126: Warning: Atom Count for residue ARG64A does not match expected count -125: Warning: Atom Count for residue LYS80A 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 -130: [16:02:47] done -130: [16:02:47] ------------------------------------- -130: [16:02:47] Test unfolded version of RDKFP -130: [16:02:47] ------------------------------------- -130: [16:02:47] Test topological torsion fp generator -130: [16:02:47] DEPRECATION WARNING: please use TopologicalTorsionGenerator -130: [16:02:47] DEPRECATION WARNING: please use TopologicalTorsionGenerator -130: [16:02:47] DEPRECATION WARNING: please use TopologicalTorsionGenerator -130: [16:02:47] DEPRECATION WARNING: please use TopologicalTorsionGenerator -130: [16:02:47] DEPRECATION WARNING: please use TopologicalTorsionGenerator -130: [16:02:47] DEPRECATION WARNING: please use TopologicalTorsionGenerator -130: [16:02:47] DEPRECATION WARNING: please use TopologicalTorsionGenerator -130: [16:02:47] DEPRECATION WARNING: please use TopologicalTorsionGenerator -130: [16:02:47] DEPRECATION WARNING: please use TopologicalTorsionGenerator -130: [16:02:47] DEPRECATION WARNING: please use TopologicalTorsionGenerator -130: [16:02:47] done -130: [16:02:47] ------------------------------------- -130: [16:02:47] Test Topological Torsions. -130: [16:02:47] done -130: [16:02:47] ------------------------------------- -130: [16:02:47] Test Folded torsions. -130: [16:02:47] done -130: [16:02:47] ------------------------------------- -130: [16:02:47] Test Bulk Topological Torsions. -131: Randomness seeded to: 839278129 -131: =============================================================================== -131: All tests passed (188 assertions in 16 test cases) -131: -120/236 Test #131: fpTestCatch ............................ Passed 0.62 sec +130: [12:24:11] ------------------------------------- +130: [12:24:11] Test Rooted Atom Pairs. +130: [12:24:11] done +130: [12:24:11] ------------------------------------- +130: [12:24:11] Test ignoring atoms in Atom Pairs. +130: [12:24:11] done +130: [12:24:11] ------------------------------------- +130: [12:24:11] Test Atom Pairs including info about chirality. +130: [12:24:11] done +130: [12:24:11] ------------------------------------- +130: [12:24:11] Test Morgan Fingerprints. +126: Warning: Atom Count for residue ASN39A does not match expected count +130: [12:24:11] done +130: [12:24:11] ------------------------------------- +130: [12:24:11] Test morgan fp generator +130: [12:24:11] done +130: [12:24:11] ------------------------------------- +130: [12:24:11] Test Morgan Fingerprints using fromAtoms argument. +130: [12:24:11] done +130: [12:24:11] ------------------------------------- +130: [12:24:11] Test Morgan Fingerprints as bit vects. +130: [12:24:11] done +130: [12:24:11] ------------------------------------- +130: [12:24:11] Test Morgan Fingerprints with feature invariants. +130: [12:24:11] done +130: [12:24:11] ------------------------------------- +130: [12:24:11] Test additional Morgan fingerprints options. +130: [12:24:11] done +130: [12:24:11] ------------------------------------- +130: [12:24:11] Test GitHub Issue 695: Include cis/trans stereochemistry when useChirality=true with the morgan fingerprints +130: [12:24:11] done +130: [12:24:11] ------------------------------------- +130: [12:24:11] Single atoms setting radius 1 bits in Morgan fingerprints +130: [12:24:11] done +130: [12:24:11] ------------------------------------- +130: [12:24:11] Test different invariant generator combinations +130: [12:24:11] done +130: [12:24:11] ------------------------------------- +130: [12:24:11] Test invariant overriding +130: [12:24:11] done +130: [12:24:11] ------------------------------------- +130: [12:24:11] Test RDKit fp generator +122: =>start test GETAWAY +122: [12:24:11] test on : 365 molecules done +120/236 Test #122: testGETAWAY ............................ Passed 3.08 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 -130: [16:02:47] done -130: [16:02:47] ------------------------------------- -130: [16:02:47] Test Rooted Topological Torsions. -130: [16:02:47] done -130: [16:02:47] ------------------------------------- -130: [16:02:47] Test ignoring atoms in Topological Torsions. -130: [16:02:47] done -130: [16:02:47] ------------------------------------- -130: [16:02:47] ------------------------------------- -130: [16:02:47] Test Topological Torsions including info about chirality. -130: [16:02:47] done -130: [16:02:47] ------------------------------------- -130: [16:02:47] Test GitHub Issue 25: fingerprint backwards compatibility. -130: [16:02:47] done -130: [16:02:47] ------------------------------------- -130: [16:02:47] Test GitHub Issue 334: explicit Hs in SMILES modifies atom pair (and topological torsion) FP. -130: [16:02:47] done -130: [16:02:47] ------------------------------------- -130: [16:02:47] Test GitHub Issue 811: rooted atom fingerprint non identical for the same molecules #811 -130: [16:02:47] done -130: [16:02:47] ------------------------------------- -130: [16:02:47] Test convenience and bulk fp calculation functions -29: -29: Computing MMFF94 energies for /build/reproducible-path/rdkit-202503.1/Code/ForceField/MMFF/test_data/MMFF94_hypervalent.sdf... -126: Warning: Atom Count for residue GLU150A does not match expected count -126: Warning: Atom Count for residue ASN157A does not match expected count -125: Warning: Atom Count for residue GLU150A does not match expected count -132: Randomness seeded to: 1476839770 -132: =============================================================================== -132: All tests passed (2737 assertions in 7 test cases) -132: -121/236 Test #132: fpGenTestCatch ......................... Passed 0.49 sec +117: =>start test 2 WHIM custom +117: [12:24:11] test on : 365 molecules done +126: Warning: Atom Count for residue GLU53A does not match expected count +125: Warning: Atom Count for residue LYS80A does not match expected count +131: Randomness seeded to: 4096039341 +131: =============================================================================== +131: All tests passed (188 assertions in 16 test cases) +131: +121/236 Test #131: fpTestCatch ............................ Passed 0.50 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 -125: Warning: Atom Count for residue ASN157A does not match expected count -130: [16:02:47] done -130: [16:02:47] ------------------------------------- -130: [16:02:47] Test GitHub Issue #6958 -130: [16:02:47] DEPRECATION WARNING: please use AtomPairGenerator -122/236 Test #130: testFingerprintGenerators .............. Passed 1.43 sec +126: Warning: Atom Count for residue ARG64A does not match expected count +132: Randomness seeded to: 3446845473 +132: =============================================================================== +132: All tests passed (2737 assertions in 7 test cases) +132: +122/236 Test #132: fpGenTestCatch ......................... Passed 0.62 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 -122: =>start test GETAWAY -122: [16:02:48] test on : 365 molecules done -123/236 Test #122: testGETAWAY ............................ Passed 3.06 sec +130: [12:24:12] done +130: [12:24:12] ------------------------------------- +130: [12:24:12] Test unfolded version of RDKFP +130: [12:24:12] ------------------------------------- +130: [12:24:12] Test topological torsion fp generator +130: [12:24:12] DEPRECATION WARNING: please use TopologicalTorsionGenerator +130: [12:24:12] DEPRECATION WARNING: please use TopologicalTorsionGenerator +130: [12:24:12] DEPRECATION WARNING: please use TopologicalTorsionGenerator +130: [12:24:12] DEPRECATION WARNING: please use TopologicalTorsionGenerator +130: [12:24:12] DEPRECATION WARNING: please use TopologicalTorsionGenerator +130: [12:24:12] DEPRECATION WARNING: please use TopologicalTorsionGenerator +130: [12:24:12] DEPRECATION WARNING: please use TopologicalTorsionGenerator +130: [12:24:12] DEPRECATION WARNING: please use TopologicalTorsionGenerator +130: [12:24:12] DEPRECATION WARNING: please use TopologicalTorsionGenerator +130: [12:24:12] DEPRECATION WARNING: please use TopologicalTorsionGenerator +130: [12:24:12] done +130: [12:24:12] ------------------------------------- +130: [12:24:12] Test Topological Torsions. +130: [12:24:12] done +130: [12:24:12] ------------------------------------- +130: [12:24:12] Test Folded torsions. +130: [12:24:12] done +130: [12:24:12] ------------------------------------- +130: [12:24:12] Test Bulk Topological Torsions. +117: =>start test 1 WHIM custom +117: [12:24:12] test on : 365 molecules done +126: Warning: Atom Count for residue LYS80A does not match expected count +130: [12:24:12] done +130: [12:24:12] ------------------------------------- +130: [12:24:12] Test Rooted Topological Torsions. +130: [12:24:12] done +130: [12:24:12] ------------------------------------- +130: [12:24:12] Test ignoring atoms in Topological Torsions. +130: [12:24:12] done +130: [12:24:12] ------------------------------------- +130: [12:24:12] ------------------------------------- +130: [12:24:12] Test Topological Torsions including info about chirality. +130: [12:24:12] done +130: [12:24:12] ------------------------------------- +130: [12:24:12] Test GitHub Issue 25: fingerprint backwards compatibility. +130: [12:24:12] done +130: [12:24:12] ------------------------------------- +130: [12:24:12] Test GitHub Issue 334: explicit Hs in SMILES modifies atom pair (and topological torsion) FP. +130: [12:24:12] done +130: [12:24:12] ------------------------------------- +130: [12:24:12] Test GitHub Issue 811: rooted atom fingerprint non identical for the same molecules #811 +130: [12:24:12] done +130: [12:24:12] ------------------------------------- +130: [12:24:12] Test convenience and bulk fp calculation functions +134: .. +134: ---------------------------------------------------------------------- +134: Ran 2 tests in 0.076s +134: +134: OK +123/236 Test #134: pyTestMHFP ............................. Passed 1.13 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 -124/236 Test #135: testPartialCharges ..................... Passed 0.04 sec +124/236 Test #135: testPartialCharges ..................... Passed 0.06 sec test 136 Start 136: pyPartialCharges @@ -26245,10 +26277,14 @@ 136: Test timeout computed to be: 1500 133: .............. 133: ---------------------------------------------------------------------- -133: Ran 14 tests in 0.437s +133: Ran 14 tests in 0.510s 133: 133: OK -125/236 Test #133: pyTestGenerator ........................ Passed 0.91 sec +130: [12:24:13] done +130: [12:24:13] ------------------------------------- +130: [12:24:13] Test GitHub Issue #6958 +130: [12:24:13] DEPRECATION WARNING: please use AtomPairGenerator +125/236 Test #130: testFingerprintGenerators .............. Passed 2.12 sec test 137 Start 137: testMolTransforms @@ -26285,83 +26321,77 @@ 137: testWeightedCentroid 137: 137: *********************************************************** -126/236 Test #137: testMolTransforms ...................... Passed 0.13 sec +126/236 Test #137: testMolTransforms ...................... Passed 0.17 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 -134: .. -134: ---------------------------------------------------------------------- -134: Ran 2 tests in 0.119s -134: -134: OK -138: Randomness seeded to: 3935533011 -138: =============================================================================== -138: All tests passed (4 assertions in 1 test case) -138: -127/236 Test #138: molTransformsTestCatch ................. Passed 0.16 sec +125: Warning: Atom Count for residue GLU150A does not match expected count +127/236 Test #133: pyTestGenerator ........................ Passed 1.81 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 -117: =>start test GETAWAY custom -117: [16:02:49] test on : 365 molecules done -128/236 Test #117: testRDFcustom .......................... Passed 4.73 sec +29: Checking against /build/reproducible-path/rdkit-202503.1/Code/ForceField/MMFF/test_data/MMFF94_reference.log... +125: Warning: Atom Count for residue ASN157A does not match expected count +138: Randomness seeded to: 2289108302 +138: =============================================================================== +138: All tests passed (4 assertions in 1 test case) +138: +128/236 Test #138: molTransformsTestCatch ................. Passed 0.46 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 -129/236 Test #134: pyTestMHFP ............................. Passed 1.04 sec +29: All 191 tests passed +126: Warning: Atom Count for residue GLU150A does not match expected count +29: +136: ....... +136: ---------------------------------------------------------------------- +136: Ran 7 tests in 0.315s +136: +136: OK +29: Computing MMFF94 energies for /build/reproducible-path/rdkit-202503.1/Code/ForceField/MMFF/test_data/MMFF94_hypervalent.smi... +126: Warning: Atom Count for residue ASN157A does not match expected count +129/236 Test #136: pyPartialCharges ....................... Passed 1.12 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: [16:02:49] ------------------------------------- -141: [16:02:49] Test MMFF atom types. -141: [16:02:49] done -141: [16:02:49] ------------------------------------- -141: [16:02:49] Testing MMFF builder tools. -141: [16:02:49] done -141: [16:02:49] ------------------------------------- -141: [16:02:49] Testing MMFF builder+minimization. -136: ....... -136: ---------------------------------------------------------------------- -136: Ran 7 tests in 0.295s -136: -136: OK -130/236 Test #136: pyPartialCharges ....................... Passed 0.73 sec +140: Randomness seeded to: 3580643042 +140: =============================================================================== +140: All tests passed (17 assertions in 2 test cases) +140: +130/236 Test #140: forceFieldHelpersCatch ................. Passed 0.45 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 -141: [16:02:49] done -141: [16:02:49] ------------------------------------- -141: [16:02:49] Testing Issue239. -142: [16:02:49] ------------------------------------- -142: [16:02:49] Test MMFF multithreading -141: [16:02:49] done -141: [16:02:49] ------------------------------------- -141: [16:02:49] Testing calcEnergy with passed coords. -141: [16:02:49] done -141: [16:02:49] ------------------------------------- -141: [16:02:49] Testing calcGrad. -141: [16:02:49] done -141: [16:02:49] ------------------------------------- -141: [16:02:49] Testing Issue242. -140: Randomness seeded to: 2386378411 -140: =============================================================================== -140: All tests passed (17 assertions in 2 test cases) -140: +141: [12:24:14] ------------------------------------- +141: [12:24:14] Test MMFF atom types. +141: [12:24:14] done +141: [12:24:14] ------------------------------------- +141: [12:24:14] Testing MMFF builder tools. +142: [12:24:14] ------------------------------------- +142: [12:24:14] Test MMFF multithreading +141: [12:24:14] done +141: [12:24:14] ------------------------------------- +141: [12:24:14] Testing MMFF builder+minimization. +139: ........ +139: ---------------------------------------------------------------------- +139: Ran 8 tests in 0.246s +139: +139: OK 142: processing 142: launch :0 142: launch :1 @@ -26387,515 +26417,543 @@ 142: launch :21 142: launch :22 142: launch :23 -131/236 Test #140: forceFieldHelpersCatch ................. Passed 0.43 sec +141: [12:24:14] done +141: [12:24:14] ------------------------------------- +141: [12:24:14] Testing Issue239. +131/236 Test #139: pyMolTransforms ........................ Passed 1.08 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: [16:02:49] done -141: [16:02:49] ------------------------------------- -141: [16:02:49] Testing github 308: crash during MMFF parameterization . -141: [16:02:49] ------------------------------------- -141: [16:02:49] Testing SFIssue1653802. -139: ........ -139: ---------------------------------------------------------------------- -139: Ran 8 tests in 0.247s -139: -139: OK -141: [16:02:49] done -141: [16:02:49] ------------------------------------- -141: [16:02:49] Testing SFIssue2378119. -141: [16:02:49] done -141: [16:02:49] ------------------------------------- -141: [16:02:49] Test MMFF force-field parameter getters. -141: [16:02:49] ------------------------------------- -141: [16:02:49] Test MMFF multithreading -80: =============================================================================== -80: All tests passed (1596 assertions in 100 test cases) -80: -132/236 Test #80: fileParsersCatchTest ................... Passed 10.18 sec +141: [12:24:14] done +141: [12:24:14] ------------------------------------- +141: [12:24:14] Testing calcEnergy with passed coords. +141: [12:24:14] done +141: [12:24:14] ------------------------------------- +141: [12:24:14] Testing calcGrad. +143: [12:24:14] ------------------------------------- +143: [12:24:14] Test UFF atom labels. +141: [12:24:14] done +141: [12:24:14] ------------------------------------- +141: [12:24:14] Testing Issue242. +143: [12:24:15] done +143: [12:24:15] ------------------------------------- +143: [12:24:15] Test UFF atom typer. +143: [12:24:15] done +141: [12:24:15] done +143: [12:24:15] ------------------------------------- +143: [12:24:15] Testing UFF builder tools. +141: [12:24:15] ------------------------------------- +141: [12:24:15] Testing github 308: crash during MMFF parameterization . +141: [12:24:15] ------------------------------------- +141: [12:24:15] Testing SFIssue1653802. +141: [12:24:15] done +141: [12:24:15] ------------------------------------- +141: [12:24:15] Testing SFIssue2378119. +143: [12:24:15] done +143: [12:24:15] ------------------------------------- +143: [12:24:15] Testing UFF builder+minimization. +141: [12:24:15] done +141: [12:24:15] ------------------------------------- +141: [12:24:15] Test MMFF force-field parameter getters. +141: [12:24:15] ------------------------------------- +141: [12:24:15] Test MMFF multithreading +141: generating reference data +142: done +142: [12:24:15] done +132/236 Test #142: testMMFFForceFieldHelpersMultiThread ... Passed 0.68 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 -141: generating reference data -143: [16:02:49] ------------------------------------- -143: [16:02:49] Test UFF atom labels. -143: [16:02:49] done -143: [16:02:49] ------------------------------------- -143: [16:02:49] Test UFF atom typer. -143: [16:02:49] done -143: [16:02:49] ------------------------------------- -143: [16:02:49] Testing UFF builder tools. +143: [12:24:15] done 144: ------------------------------------- 144: Test CrystalFF torsional term. -143: [16:02:49] done -143: [16:02:49] ------------------------------------- -143: [16:02:49] Testing UFF builder+minimization. -133/236 Test #139: pyMolTransforms ........................ Passed 0.59 sec +143: [12:24:15] ------------------------------------- +143: [12:24:15] Testing UFF special cases. +143: [12:24:15] UFFTYPER: Unrecognized charge state for atom: 0 +143: [12:24:15] done +143: [12:24:15] ------------------------------------- +143: [12:24:15] Testing Issue239. +143: [12:24:15] done +143: [12:24:15] ------------------------------------- +143: [12:24:15] Testing calcEnergy with passed coords. +143: [12:24:15] done +143: [12:24:15] ------------------------------------- +143: [12:24:15] Testing calcGrad. +143: [12:24:15] done +143: [12:24:15] ------------------------------------- +143: [12:24:15] Testing SFIssue1653802. +143: [12:24:15] done +143: [12:24:15] ------------------------------------- +143: [12:24:15] Testing SFIssue2378119. +143: [12:24:15] done +143: [12:24:15] ------------------------------------- +143: [12:24:15] Test UFF force-field parameter getters. +143: [12:24:15] ------------------------------------- +143: [12:24:15] Testing handling missing parameters. +143: [12:24:15] UFFTYPER: Unrecognized hybridization for atom: 0 +143: [12:24:15] UFFTYPER: Unrecognized atom type: Cu+1 (0) +143: [12:24:15] UFFTYPER: Unrecognized hybridization for atom: 0 +143: [12:24:15] UFFTYPER: Unrecognized atom type: Cu+1 (0) +143: [12:24:15] done +143: [12:24:15] ------------------------------------- +143: [12:24:15] Testing SFIssue3009337. +143: [12:24:15] done +143: [12:24:15] ------------------------------------- +143: [12:24:15] Test UFF multithreading +143: generating reference data +133/236 Test #144: testCrystalForceField .................. Passed 0.33 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 -134/236 Test #144: testCrystalForceField .................. Passed 0.20 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 -143: [16:02:49] done -143: [16:02:49] ------------------------------------- -143: [16:02:49] Testing UFF special cases. -143: [16:02:49] UFFTYPER: Unrecognized charge state for atom: 0 -143: [16:02:49] done -143: [16:02:49] ------------------------------------- -143: [16:02:49] Testing Issue239. -143: [16:02:49] done -143: [16:02:49] ------------------------------------- -143: [16:02:49] Testing calcEnergy with passed coords. -143: [16:02:49] done -143: [16:02:49] ------------------------------------- -143: [16:02:49] Testing calcGrad. -142: done -143: [16:02:49] done -143: [16:02:49] ------------------------------------- -143: [16:02:49] Testing SFIssue1653802. -143: [16:02:49] done -143: [16:02:49] ------------------------------------- -143: [16:02:49] Testing SFIssue2378119. -142: [16:02:49] done -143: [16:02:49] done -143: [16:02:49] ------------------------------------- -143: [16:02:49] Test UFF force-field parameter getters. -143: [16:02:49] ------------------------------------- -143: [16:02:49] Testing handling missing parameters. -143: [16:02:49] UFFTYPER: Unrecognized hybridization for atom: 0 -143: [16:02:49] UFFTYPER: Unrecognized atom type: Cu+1 (0) -146: [16:02:49] ******************************************************** -146: [16:02:49] Testing DistGeomHelpers -146: [16:02:49] --------------------------------- -146: [16:02:49] test2 -146: -146: go -143: [16:02:49] UFFTYPER: Unrecognized hybridization for atom: 0 -143: [16:02:49] UFFTYPER: Unrecognized atom type: Cu+1 (0) -135/236 Test #142: testMMFFForceFieldHelpersMultiThread ... Passed 0.62 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 -143: [16:02:49] done -143: [16:02:49] ------------------------------------- -143: [16:02:49] Testing SFIssue3009337. -146: ------------------------------------- -146: -143: [16:02:49] done -143: [16:02:49] ------------------------------------- -143: [16:02:49] Test UFF multithreading -143: generating reference data 141: processing 141: launch :0 141: launch :1 141: launch :2 141: launch :3 -141: [16:02:50] Rep: 0 Mol:0 -141: [16:02:50] Rep: 0 Mol:3 -141: [16:02:50] Rep: 0 Mol:1 -141: [16:02:50] Rep: 0 Mol:5 -141: [16:02:50] Rep: 0 Mol:4 -141: [16:02:50] Rep: 0 Mol:9 -141: [16:02:50] Rep: 0 Mol:2 -141: [16:02:50] Rep: 0 Mol:13 -141: [16:02:50] Rep: 0 Mol:17 -141: [16:02:50] Rep: 0 Mol:6 -141: [16:02:50] Rep: 0 Mol:8 -141: [16:02:50] Rep: 0 Mol:21 -141: [16:02:50] Rep: 0 Mol:25 -145: [16:02:50] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -145: [16:02:50] Molecule does not have explicit Hs. Consider calling AddHs() -141: [16:02:50] Rep: 0 Mol:10 -141: [16:02:50] Rep: 0 Mol:12 -141: [16:02:50] Rep: 0 Mol:16 -145: [16:02:50] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -145: [16:02:50] Molecule does not have explicit Hs. Consider calling AddHs() -145: [16:02:50] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -145: [16:02:50] Molecule does not have explicit Hs. Consider calling AddHs() -145: [16:02:50] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -145: [16:02:50] Molecule does not have explicit Hs. Consider calling AddHs() -145: [16:02:50] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -145: [16:02:50] Molecule does not have explicit Hs. Consider calling AddHs() -141: [16:02:50] Rep: 0 Mol:29 -141: [16:02:50] Rep: 0 Mol:7 -141: [16:02:50] Rep: 0 Mol:11 -141: [16:02:50] Rep: 0 Mol:15 -141: [16:02:50] Rep: 0 Mol:20 -141: [16:02:50] Rep: 0 Mol:19 -141: [16:02:50] Rep: 0 Mol:24 -141: [16:02:50] Rep: 0 Mol:23 -141: [16:02:50] Rep: 0 Mol:27 -141: [16:02:50] Rep: 0 Mol:31 -141: [16:02:50] Rep: 0 Mol:28 -145: ..[16:02:50] Molecule does not have explicit Hs. Consider calling AddHs() -145: [16:02:50] Molecule does not have explicit Hs. Consider calling AddHs() -145: .[16:02:50] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -145: [16:02:50] Molecule does not have explicit Hs. Consider calling AddHs() -141: [16:02:50] Rep: 0 Mol:14 -145: .[16:02:50] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -145: [16:02:50] Molecule does not have explicit Hs. Consider calling AddHs() -141: [16:02:50] Rep: 0 Mol:18 -141: [16:02:50] Rep: 0 Mol:22 -141: [16:02:50] Rep: 0 Mol:26 -141: [16:02:50] Rep: 0 Mol:30 -145: .[16:02:50] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -145: [16:02:50] 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: .[16:02:50] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -145: [16:02:50] Molecule does not have explicit Hs. Consider calling AddHs() -141: [16:02:50] Rep: 20 Mol:3 -141: [16:02:50] Rep: 20 Mol:7 -141: [16:02:50] Rep: 20 Mol:11 -141: [16:02:50] Rep: 20 Mol:15 -141: [16:02:50] Rep: 20 Mol:19 -141: [16:02:50] Rep: 20 Mol:23 -141: [16:02:50] Rep: 20 Mol:27 -141: [16:02:50] Rep: 20 Mol:31 -141: [16:02:50] Rep: 20 Mol:1 -141: [16:02:50] Rep: 20 Mol:5 -141: [16:02:50] Rep: 20 Mol:9 -141: [16:02:50] Rep: 20 Mol:13 -141: [16:02:50] Rep: 20 Mol:17 -141: [16:02:50] Rep: 20 Mol:21 -141: [16:02:50] Rep: 20 Mol:25 -141: [16:02:50] Rep: 20 Mol:29 -145: .[16:02:50] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -145: [16:02:50] Molecule does not have explicit Hs. Consider calling AddHs() -145: .[16:02:50] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -145: [16:02:50] Molecule does not have explicit Hs. Consider calling AddHs() -145: .[16:02:50] UFFTYPER: Unrecognized hybridization for atom: 0 -145: [16:02:50] UFFTYPER: Unrecognized atom type: Cu+1 (0) -141: [16:02:50] Rep: 20 Mol:0 -145: .[16:02:50] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -145: [16:02:50] Molecule does not have explicit Hs. Consider calling AddHs() -145: [16:02:50] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -145: [16:02:50] Molecule does not have explicit Hs. Consider calling AddHs() -145: [16:02:50] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -145: [16:02:50] Molecule does not have explicit Hs. Consider calling AddHs() -145: [16:02:50] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -145: [16:02:50] Molecule does not have explicit Hs. Consider calling AddHs() -145: [16:02:50] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -145: [16:02:50] Molecule does not have explicit Hs. Consider calling AddHs() -141: [16:02:50] Rep: 20 Mol:4 -141: [16:02:50] Rep: 20 Mol:8 -141: [16:02:50] Rep: 20 Mol:12 -141: [16:02:50] Rep: 20 Mol:16 -141: [16:02:50] Rep: 20 Mol:20 -141: [16:02:50] Rep: 20 Mol:24 -141: [16:02:50] Rep: 20 Mol:28 -145: .[16:02:50] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -145: [16:02:50] Molecule does not have explicit Hs. Consider calling AddHs() -145: .[16:02:50] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -145: [16:02:50] Molecule does not have explicit Hs. Consider calling AddHs() -145: .[16:02:50] Molecule does not have explicit Hs. Consider calling AddHs() -145: [16:02:50] Molecule does not have explicit Hs. Consider calling AddHs() -145: ...[16:02:50] Molecule does not have explicit Hs. Consider calling AddHs() -145: [16:02:50] Molecule does not have explicit Hs. Consider calling AddHs() -29: All 191 tests passed -145: [16:02:50] Molecule does not have explicit Hs. Consider calling AddHs() -141: [16:02:50] Rep: 40 Mol:3 -141: [16:02:50] Rep: 40 Mol:7 -141: [16:02:50] Rep: 40 Mol:11 -141: [16:02:50] Rep: 40 Mol:15 -141: [16:02:50] Rep: 40 Mol:19 -141: [16:02:50] Rep: 40 Mol:23 -141: [16:02:50] Rep: 40 Mol:27 -141: [16:02:50] Rep: 40 Mol:31 +141: [12:24:16] Rep: 0 Mol:3 +141: [12:24:16] Rep: 0 Mol:2 +141: [12:24:16] Rep: 0 Mol:1 +141: [12:24:16] Rep: 0 Mol:0 +141: [12:24:16] Rep: 0 Mol:4 +141: [12:24:16] Rep: 0 Mol:5 +141: [12:24:16] Rep: 0 Mol:9 +141: [12:24:16] Rep: 0 Mol:13 +141: [12:24:16] Rep: 0 Mol:17 143: processing 143: launch :0 143: launch :1 143: launch :2 143: launch :3 -143: [16:02:50] Rep: 0 Mol:0 -143: [16:02:50] Rep: 0 Mol:1 -143: [16:02:50] Rep: 0 Mol:5 -143: [16:02:50] Rep: 0 Mol:9 -143: [16:02:50] Rep: 0 Mol:4 -143: [16:02:50] Rep: 0 Mol:2 -141: [16:02:50] Rep: 20 Mol:2 -141: [16:02:50] Rep: 20 Mol:6 -141: [16:02:50] Rep: 20 Mol:10 +141: [12:24:16] Rep: 0 Mol:8 +143: [12:24:16] Rep: 0 Mol:3 +143: [12:24:16] Rep: 0 Mol:1 +141: [12:24:16] Rep: 0 Mol:6 +141: [12:24:16] Rep: 0 Mol:10 +143: [12:24:16] Rep: 0 Mol:0 +143: [12:24:16] Rep: 0 Mol:4 +143: [12:24:16] Rep: 0 Mol:2 +143: [12:24:16] Rep: 0 Mol:5 +143: [12:24:16] Rep: 0 Mol:9 +141: [12:24:16] Rep: 0 Mol:12 +141: [12:24:16] Rep: 0 Mol:16 +143: [12:24:16] Rep: 0 Mol:13 +143: [12:24:16] Rep: 0 Mol:7 +143: [12:24:16] Rep: 0 Mol:11 +143: [12:24:16] Rep: 0 Mol:15 +143: [12:24:16] Rep: 0 Mol:17 +143: [12:24:16] Rep: 0 Mol:6 +143: [12:24:16] Rep: 0 Mol:10 +141: [12:24:16] Rep: 0 Mol:21 +141: [12:24:16] Rep: 0 Mol:7 +141: [12:24:16] Rep: 0 Mol:11 +141: [12:24:16] Rep: 0 Mol:20 +141: [12:24:16] Rep: 0 Mol:15 +143: [12:24:16] Rep: 0 Mol:19 +143: [12:24:16] Rep: 0 Mol:23 +143: [12:24:16] Rep: 0 Mol:27 +141: [12:24:16] Rep: 0 Mol:25 +143: [12:24:16] Rep: 0 Mol:8 +141: [12:24:16] Rep: 0 Mol:29 +141: [12:24:16] Rep: 0 Mol:19 +141: [12:24:16] Rep: 0 Mol:23 +141: [12:24:16] Rep: 0 Mol:27 +143: [12:24:16] Rep: 0 Mol:31 +141: [12:24:16] Rep: 0 Mol:24 +143: [12:24:16] Rep: 0 Mol:12 +143: [12:24:16] Rep: 0 Mol:16 +141: [12:24:16] Rep: 0 Mol:28 +141: [12:24:16] Rep: 0 Mol:31 +143: [12:24:16] Rep: 0 Mol:21 +143: [12:24:16] Rep: 0 Mol:25 +143: [12:24:16] Rep: 0 Mol:20 +141: [12:24:16] Rep: 0 Mol:14 +143: [12:24:16] Rep: 0 Mol:14 +143: [12:24:16] Rep: 0 Mol:29 +143: [12:24:16] Rep: 0 Mol:24 +143: [12:24:16] Rep: 0 Mol:28 +143: [12:24:16] Rep: 0 Mol:18 +141: [12:24:16] Rep: 0 Mol:18 +145: [12:24:16] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +145: [12:24:16] Molecule does not have explicit Hs. Consider calling AddHs() +145: [12:24:16] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +145: [12:24:16] Molecule does not have explicit Hs. Consider calling AddHs() +145: [12:24:16] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +145: [12:24:16] Molecule does not have explicit Hs. Consider calling AddHs() +145: [12:24:16] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +145: [12:24:16] Molecule does not have explicit Hs. Consider calling AddHs() +145: [12:24:16] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +145: [12:24:16] Molecule does not have explicit Hs. Consider calling AddHs() +143: [12:24:16] Rep: 0 Mol:22 +143: [12:24:16] Rep: 0 Mol:26 +141: [12:24:16] Rep: 0 Mol:22 +145: ..[12:24:16] Molecule does not have explicit Hs. Consider calling AddHs() +145: [12:24:16] Molecule does not have explicit Hs. Consider calling AddHs() +145: .[12:24:16] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +145: [12:24:16] Molecule does not have explicit Hs. Consider calling AddHs() +143: [12:24:16] Rep: 0 Mol:30 +141: [12:24:16] Rep: 0 Mol:26 +145: .[12:24:16] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +145: [12:24:16] Molecule does not have explicit Hs. Consider calling AddHs() +141: [12:24:16] Rep: 0 Mol:30 +145: .[12:24:16] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +145: [12:24:16] Molecule does not have explicit Hs. Consider calling AddHs() +145: .[12:24:16] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +145: [12:24:16] Molecule does not have explicit Hs. Consider calling AddHs() +145: .[12:24:16] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +145: [12:24:16] Molecule does not have explicit Hs. Consider calling AddHs() +145: .[12:24:16] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +145: [12:24:16] Molecule does not have explicit Hs. Consider calling AddHs() +145: .[12:24:16] UFFTYPER: Unrecognized hybridization for atom: 0 +145: [12:24:16] UFFTYPER: Unrecognized atom type: Cu+1 (0) +145: .[12:24:16] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +145: [12:24:16] Molecule does not have explicit Hs. Consider calling AddHs() +145: [12:24:16] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +145: [12:24:16] Molecule does not have explicit Hs. Consider calling AddHs() +145: [12:24:16] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +145: [12:24:16] Molecule does not have explicit Hs. Consider calling AddHs() +145: [12:24:16] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +145: [12:24:16] Molecule does not have explicit Hs. Consider calling AddHs() +145: [12:24:16] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +145: [12:24:16] Molecule does not have explicit Hs. Consider calling AddHs() +141: [12:24:16] Rep: 20 Mol:3 +141: [12:24:16] Rep: 20 Mol:7 +141: [12:24:16] Rep: 20 Mol:11 +141: [12:24:16] Rep: 20 Mol:15 +141: [12:24:16] Rep: 20 Mol:19 +141: [12:24:16] Rep: 20 Mol:23 +141: [12:24:16] Rep: 20 Mol:27 +141: [12:24:16] Rep: 20 Mol:31 +145: .[12:24:16] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +145: [12:24:16] Molecule does not have explicit Hs. Consider calling AddHs() +145: .[12:24:16] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +145: [12:24:16] Molecule does not have explicit Hs. Consider calling AddHs() +145: .[12:24:16] Molecule does not have explicit Hs. Consider calling AddHs() +145: [12:24:16] Molecule does not have explicit Hs. Consider calling AddHs() +145: ...[12:24:16] Molecule does not have explicit Hs. Consider calling AddHs() +145: [12:24:16] Molecule does not have explicit Hs. Consider calling AddHs() +141: [12:24:16] Rep: 20 Mol:0 +141: [12:24:16] Rep: 20 Mol:4 +141: [12:24:16] Rep: 20 Mol:8 +141: [12:24:16] Rep: 20 Mol:12 +141: [12:24:16] Rep: 20 Mol:16 +141: [12:24:16] Rep: 20 Mol:20 +141: [12:24:16] Rep: 20 Mol:24 +141: [12:24:16] Rep: 20 Mol:28 +145: [12:24:16] Molecule does not have explicit Hs. Consider calling AddHs() +141: [12:24:16] Rep: 20 Mol:1 +141: [12:24:16] Rep: 20 Mol:5 +141: [12:24:16] Rep: 20 Mol:9 +141: [12:24:16] Rep: 20 Mol:13 +141: [12:24:16] Rep: 20 Mol:17 +141: [12:24:16] Rep: 20 Mol:21 +141: [12:24:16] Rep: 20 Mol:25 +141: [12:24:16] Rep: 20 Mol:29 145: ... 145: ---------------------------------------------------------------------- -145: Ran 19 tests in 0.387s +145: Ran 19 tests in 0.460s 145: 145: OK -143: [16:02:50] Rep: 0 Mol:3 -141: [16:02:50] Rep: 20 Mol:14 -141: [16:02:50] Rep: 20 Mol:18 -141: [16:02:50] Rep: 20 Mol:22 -141: [16:02:50] Rep: 20 Mol:26 -141: [16:02:50] Rep: 20 Mol:30 -147: Randomness seeded to: 1813174504 -143: [16:02:50] Rep: 0 Mol:6 -143: [16:02:50] Rep: 0 Mol:13 -143: [16:02:50] Rep: 0 Mol:10 -143: [16:02:50] Rep: 0 Mol:8 -143: [16:02:50] Rep: 0 Mol:12 -143: [16:02:50] Rep: 0 Mol:16 -143: [16:02:50] Rep: 0 Mol:20 -143: [16:02:50] Rep: 0 Mol:7 -143: [16:02:50] Rep: 0 Mol:11 -143: [16:02:50] Rep: 0 Mol:17 -143: [16:02:50] Rep: 0 Mol:15 -143: [16:02:50] Rep: 0 Mol:24 -143: [16:02:50] Rep: 0 Mol:14 -143: [16:02:50] Rep: 0 Mol:28 -143: [16:02:50] Rep: 0 Mol:19 -143: [16:02:50] Rep: 0 Mol:18 -143: [16:02:50] Rep: 0 Mol:23 -143: [16:02:50] Rep: 0 Mol:27 -141: [16:02:50] Rep: 40 Mol:0 -141: [16:02:50] Rep: 40 Mol:4 -141: [16:02:50] Rep: 40 Mol:8 -141: [16:02:50] Rep: 40 Mol:12 -141: [16:02:50] Rep: 40 Mol:16 -143: [16:02:50] Rep: 0 Mol:22 -143: [16:02:50] Rep: 0 Mol:26 -143: [16:02:50] Rep: 0 Mol:21 -143: [16:02:50] Rep: 0 Mol:31 -143: [16:02:50] Rep: 0 Mol:30 -141: [16:02:50] Rep: 40 Mol:20 -141: [16:02:50] Rep: 40 Mol:24 -141: [16:02:50] Rep: 40 Mol:28 -141: [16:02:50] Rep: 40 Mol:1 -141: [16:02:50] Rep: 40 Mol:5 -141: [16:02:50] Rep: 40 Mol:9 -141: [16:02:50] Rep: 40 Mol:13 -141: [16:02:50] Rep: 40 Mol:17 -141: [16:02:50] Rep: 40 Mol:21 -29: -29: Computing MMFF94 energies for /build/reproducible-path/rdkit-202503.1/Code/ForceField/MMFF/test_data/MMFF94_dative.smi... -141: [16:02:50] Rep: 60 Mol:3 -141: [16:02:50] Rep: 60 Mol:7 -141: [16:02:50] Rep: 60 Mol:11 -141: [16:02:50] Rep: 60 Mol:15 -141: [16:02:50] Rep: 60 Mol:19 -141: [16:02:50] Rep: 60 Mol:23 -141: [16:02:50] Rep: 60 Mol:27 -141: [16:02:50] Rep: 60 Mol:31 -143: [16:02:50] Rep: 0 Mol:25 -147: [16:02:50] [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: [16:02:50] [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: [16:02:50] [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: [16:02:50] [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: [16:02:50] [!#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: [16:02:50] [!#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: [16:02:50] [!#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: [16:02:50] [!#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: [16:02:50] [!#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: [16:02:50] [!#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: [16:02:50] [!#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: [16:02:50] [!#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: [16:02:50] [!#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: [16:02:50] [!#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: [16:02:50] [!#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: [16:02:50] [!#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: [16:02:50] [!#1:1][CX4:2]!@;-[CX4:3][!#1:4]: 96 97 98 99, [(1 0), (1 0), (1 7), (1 0), (1 0), (1 0)] -141: [16:02:50] Rep: 40 Mol:25 -141: [16:02:50] Rep: 40 Mol:29 -143: [16:02:50] Rep: 0 Mol:29 -147: [16:02:50] [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: [16:02:50] [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: [16:02:50] [*: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: [16:02:50] [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: [16:02:50] [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: [16:02:50] [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: [16:02:50] [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: [16:02:50] [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: [16:02:50] [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: [16:02:50] [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: [16:02:50] [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: [16:02:50] [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: [16:02:50] [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: [16:02:50] [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: [16:02:50] [$([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: [16:02:50] [$(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: [16:02:50] [$(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: [16:02:50] [$(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: [16:02:50] [$(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: [16:02:50] [$(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: [16:02:50] [$(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: [16:02:50] [$(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: [16:02:50] [$(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: [16:02:50] [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: [16:02:50] [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: [16:02:50] [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: [16:02:50] [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: [16:02:50] [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: [16:02:50] 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: [16:02:50] [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: [16:02:50] [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: [16:02:50] [!#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: [16:02:50] [!#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: [16:02:50] [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: [16:02:50] [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: [16:02:50] [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: [16:02:50] [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: [16:02:50] [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: [16:02:50] [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: [16:02:50] [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: [16:02:50] [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)] -136/236 Test #145: pyForceFieldHelpers .................... Passed 1.09 sec +141: [12:24:16] Rep: 40 Mol:3 +141: [12:24:16] Rep: 40 Mol:7 +141: [12:24:16] Rep: 40 Mol:11 +141: [12:24:16] Rep: 40 Mol:15 +141: [12:24:16] Rep: 40 Mol:19 +141: [12:24:16] Rep: 40 Mol:23 +141: [12:24:16] Rep: 40 Mol:27 +141: [12:24:16] Rep: 40 Mol:31 +134/236 Test #145: pyForceFieldHelpers .................... Passed 1.36 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: [12:24:16] Rep: 20 Mol:2 +141: [12:24:16] Rep: 20 Mol:6 +141: [12:24:16] Rep: 20 Mol:10 +141: [12:24:16] Rep: 20 Mol:14 +141: [12:24:16] Rep: 20 Mol:18 +141: [12:24:16] Rep: 20 Mol:22 +141: [12:24:16] Rep: 20 Mol:26 +141: [12:24:16] Rep: 20 Mol:30 +141: [12:24:16] Rep: 40 Mol:0 +141: [12:24:16] Rep: 40 Mol:4 +141: [12:24:16] Rep: 40 Mol:8 +141: [12:24:16] Rep: 40 Mol:12 +141: [12:24:16] Rep: 40 Mol:16 +141: [12:24:16] Rep: 40 Mol:20 +141: [12:24:16] Rep: 40 Mol:24 +141: [12:24:16] Rep: 40 Mol:28 +117: =>start test GETAWAY custom +117: [12:24:16] test on : 365 molecules done +141: [12:24:16] Rep: 40 Mol:1 +141: [12:24:16] Rep: 40 Mol:5 +141: [12:24:16] Rep: 40 Mol:9 +141: [12:24:16] Rep: 40 Mol:13 +141: [12:24:16] Rep: 40 Mol:17 +141: [12:24:16] Rep: 40 Mol:21 +141: [12:24:16] Rep: 40 Mol:25 +141: [12:24:16] Rep: 40 Mol:29 +135/236 Test #117: testRDFcustom .......................... Passed 10.10 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: [12:24:17] Rep: 60 Mol:3 +141: [12:24:17] Rep: 60 Mol:7 +146: [12:24:17] ******************************************************** +146: [12:24:17] Testing DistGeomHelpers +146: [12:24:17] --------------------------------- +146: [12:24:17] test2 +146: +146: go +141: [12:24:17] Rep: 60 Mol:11 +141: [12:24:17] Rep: 60 Mol:15 +141: [12:24:17] Rep: 60 Mol:19 +141: [12:24:17] Rep: 60 Mol:23 +141: [12:24:17] Rep: 60 Mol:27 +141: [12:24:17] Rep: 60 Mol:31 +80: =============================================================================== +80: All tests passed (1596 assertions in 100 test cases) +80: +146: ------------------------------------- +146: +136/236 Test #80: fileParsersCatchTest ................... Passed 18.20 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 +143: [12:24:17] Rep: 100 Mol:3 +143: [12:24:17] Rep: 100 Mol:7 +143: [12:24:17] Rep: 100 Mol:11 +143: [12:24:17] Rep: 100 Mol:15 +143: [12:24:17] Rep: 100 Mol:19 +143: [12:24:17] Rep: 100 Mol:23 +143: [12:24:17] Rep: 100 Mol:27 +143: [12:24:17] Rep: 100 Mol:31 +141: [12:24:17] Rep: 80 Mol:3 +141: [12:24:17] Rep: 80 Mol:7 +141: [12:24:17] Rep: 80 Mol:11 +141: [12:24:17] Rep: 80 Mol:15 +141: [12:24:17] Rep: 80 Mol:19 +141: [12:24:17] Rep: 80 Mol:23 +141: [12:24:17] Rep: 80 Mol:27 +141: [12:24:17] Rep: 80 Mol:31 +141: [12:24:17] Rep: 60 Mol:0 +141: [12:24:17] Rep: 60 Mol:4 +141: [12:24:17] Rep: 60 Mol:8 +141: [12:24:17] Rep: 60 Mol:12 +141: [12:24:17] Rep: 60 Mol:16 +141: [12:24:17] Rep: 60 Mol:20 +141: [12:24:17] Rep: 60 Mol:24 +141: [12:24:17] Rep: 60 Mol:28 +141: [12:24:17] Rep: 60 Mol:1 +141: [12:24:17] Rep: 60 Mol:5 +147: Randomness seeded to: 3779698105 +141: [12:24:17] Rep: 60 Mol:9 +141: [12:24:17] Rep: 60 Mol:13 +141: [12:24:17] Rep: 60 Mol:17 +141: [12:24:17] Rep: 60 Mol:21 +141: [12:24:17] Rep: 60 Mol:25 +141: [12:24:17] Rep: 60 Mol:29 +141: [12:24:17] Rep: 40 Mol:2 +141: [12:24:17] Rep: 40 Mol:6 +141: [12:24:17] Rep: 40 Mol:10 +141: [12:24:17] Rep: 40 Mol:14 +141: [12:24:17] Rep: 40 Mol:18 +141: [12:24:17] Rep: 40 Mol:22 +141: [12:24:17] Rep: 40 Mol:26 +141: [12:24:17] Rep: 40 Mol:30 +147: [12:24:17] [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: [12:24:17] [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: [12:24:17] [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: [12:24:17] [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: [12:24:17] [!#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: [12:24:17] [!#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: [12:24:17] [!#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: [12:24:17] [!#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: [12:24:17] [!#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: [12:24:17] [!#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: [12:24:17] [!#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: [12:24:17] [!#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: [12:24:17] [!#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: [12:24:17] [!#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: [12:24:17] [!#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: [12:24:17] [!#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: [12:24:17] [!#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: [12:24:17] [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)] +143: [12:24:17] Rep: 100 Mol:0 +143: [12:24:17] Rep: 100 Mol:4 +143: [12:24:17] Rep: 100 Mol:8 +143: [12:24:17] Rep: 100 Mol:12 +143: [12:24:17] Rep: 100 Mol:16 +143: [12:24:17] Rep: 100 Mol:20 +143: [12:24:17] Rep: 100 Mol:24 +147: [12:24:17] [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: [12:24:17] [*: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: [12:24:17] [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: [12:24:17] [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: [12:24:17] [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: [12:24:17] [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: [12:24:17] [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: [12:24:17] [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: [12:24:17] [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: [12:24:17] [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: [12:24:17] [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: [12:24:17] [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: [12:24:17] [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: [12:24:17] [$([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: [12:24:17] [$(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: [12:24:17] [$(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: [12:24:17] [$(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: [12:24:17] [$(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: [12:24:17] [$(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: [12:24:17] [$(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: [12:24:17] [$(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: [12:24:17] [$(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)] +143: [12:24:17] Rep: 100 Mol:28 +147: [12:24:17] [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: [12:24:17] [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: [12:24:17] [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: [12:24:17] [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: [12:24:17] [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: [12:24:17] 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: [12:24:17] [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: [12:24:17] [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: [12:24:17] [!#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: [12:24:17] [!#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: [12:24:17] [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: [12:24:17] [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: [12:24:17] [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: [12:24:17] [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: [12:24:17] [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: [12:24:17] [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: [12:24:17] [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: [12:24:17] [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: [16:02:50] [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: [16:02:50] [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: [16:02:50] [$([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: [16:02:50] [$([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: [16:02:50] [$(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: [16:02:50] [$(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: [16:02:50] [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: [16:02:50] [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: [16:02:50] 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: [16:02:50] 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: [16:02:50] [!#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: [16:02:50] [!#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: [16:02:50] [!#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: [16:02:50] [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: [16:02:50] [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: [12:24:17] [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: [12:24:17] [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: [12:24:17] [$([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: [12:24:17] [$([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: [12:24:17] [$(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: [12:24:17] [$(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: [12:24:17] [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: [12:24:17] [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: [12:24:17] 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: [12:24:17] 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: [12:24:17] [!#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: [12:24:17] [!#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: [12:24:17] [!#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: [12:24:17] [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: [12:24:17] [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)] +141: [12:24:17] Rep: 80 Mol:0 +141: [12:24:17] Rep: 80 Mol:4 +141: [12:24:17] Rep: 80 Mol:8 147: ----------- -147: [16:02:50] [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: [16:02:50] [$([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: [16:02:50] [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: [16:02:50] 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: [12:24:17] [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: [12:24:17] [$([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: [12:24:17] [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: [12:24:17] 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: ----------- +141: [12:24:17] Rep: 80 Mol:12 +141: [12:24:17] Rep: 80 Mol:16 +141: [12:24:17] Rep: 80 Mol:20 +141: [12:24:17] Rep: 80 Mol:24 +141: [12:24:17] Rep: 80 Mol:28 147: ----------- -147: [16:02:50] [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: [16:02:50] [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: [16:02:50] [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: [16:02:50] [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: [16:02:50] [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: [16:02:50] [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: [16:02:50] [$(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: [16:02:50] [$(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: [16:02:50] [$(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: [16:02:50] [$(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: [16:02:50] [$(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: [16:02:50] [$(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: [16:02:50] [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: [16:02:50] [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: [16:02:50] [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: [16:02:50] [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: [16:02:50] [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: [16:02:50] [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: [16:02:50] Rep: 80 Mol:3 -141: [16:02:50] Rep: 80 Mol:7 -141: [16:02:50] Rep: 80 Mol:11 -141: [16:02:50] Rep: 80 Mol:15 -141: [16:02:50] Rep: 40 Mol:2 -141: [16:02:50] Rep: 40 Mol:6 -141: [16:02:50] Rep: 40 Mol:10 -141: [16:02:50] Rep: 80 Mol:19 -141: [16:02:50] Rep: 80 Mol:23 -141: [16:02:50] Rep: 80 Mol:27 -141: [16:02:50] Rep: 80 Mol:31 -141: [16:02:50] Rep: 40 Mol:14 -141: [16:02:50] Rep: 40 Mol:18 -141: [16:02:50] Rep: 40 Mol:22 -141: [16:02:50] Rep: 40 Mol:26 -141: [16:02:50] Rep: 40 Mol:30 -141: [16:02:50] Rep: 60 Mol:1 -141: [16:02:50] Rep: 60 Mol:5 -141: [16:02:50] Rep: 60 Mol:9 -141: [16:02:50] Rep: 60 Mol:13 -141: [16:02:50] Rep: 60 Mol:17 -141: [16:02:50] Rep: 60 Mol:21 -141: [16:02:50] Rep: 60 Mol:25 -141: [16:02:50] Rep: 60 Mol:29 -141: [16:02:50] Rep: 60 Mol:0 -141: [16:02:50] Rep: 60 Mol:4 -141: [16:02:50] Rep: 60 Mol:8 -141: [16:02:50] Rep: 60 Mol:12 -141: [16:02:50] Rep: 60 Mol:16 -141: [16:02:50] Rep: 60 Mol:20 -141: [16:02:50] Rep: 60 Mol:24 -141: [16:02:50] Rep: 60 Mol:28 -147: [16:02:50] UFFTYPER: Unrecognized atom type: Pt5+2 (1) -147: [16:02:51] UFFTYPER: Unrecognized charge state for atom: 1 -147: [16:02:51] UFFTYPER: Unrecognized charge state for atom: 1 -147: [16:02:51] UFFTYPER: Unrecognized charge state for atom: 1 -128: [16:02:51] done -128: [16:02:51] ------------------------------------- -128: [16:02:51] Test GitHub Issue 258: Bad pattern fingerprint for query molecule -141: [16:02:51] Rep: 60 Mol:2 -141: [16:02:51] Rep: 60 Mol:6 -141: [16:02:51] Rep: 60 Mol:10 -141: [16:02:51] Rep: 60 Mol:14 -141: [16:02:51] Rep: 60 Mol:18 -141: [16:02:51] Rep: 60 Mol:22 -141: [16:02:51] Rep: 60 Mol:26 -143: [16:02:51] Rep: 100 Mol:3 -143: [16:02:51] Rep: 100 Mol:7 -143: [16:02:51] Rep: 100 Mol:11 -143: [16:02:51] Rep: 100 Mol:15 -143: [16:02:51] Rep: 100 Mol:19 -143: [16:02:51] Rep: 100 Mol:23 -143: [16:02:51] Rep: 100 Mol:27 -143: [16:02:51] Rep: 100 Mol:31 -148: .[16:02:51] Molecule does not have explicit Hs. Consider calling AddHs() -141: [16:02:51] Rep: 80 Mol:0 -128: [16:02:51] done -128: [16:02:51] ------------------------------------- -128: [16:02:51] Test GitHub Issue 334: explicit Hs in SMILES modifies atom pair (and topological torsion) FP. -128: [16:02:51] DEPRECATION WARNING: please use AtomPairGenerator -128: [16:02:51] DEPRECATION WARNING: please use AtomPairGenerator -141: [16:02:51] Rep: 80 Mol:4 -141: [16:02:51] Rep: 80 Mol:8 -141: [16:02:51] Rep: 80 Mol:12 -141: [16:02:51] Rep: 80 Mol:16 -141: [16:02:51] Rep: 80 Mol:20 -141: [16:02:51] Rep: 80 Mol:24 -141: [16:02:51] Rep: 80 Mol:28 -128: [16:02:51] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [16:02:51] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [16:02:51] done -128: [16:02:51] ------------------------------------- -128: [16:02:51] Test GitHub Issue 695: Include cis/trans stereochemistry when useChirality=true with the morgan fingerprints -128: [16:02:51] done -141: [16:02:51] Rep: 80 Mol:1 -141: [16:02:51] Rep: 80 Mol:5 -141: [16:02:51] Rep: 80 Mol:9 -141: [16:02:51] Rep: 80 Mol:13 -141: [16:02:51] Rep: 80 Mol:17 -141: [16:02:51] Rep: 80 Mol:21 -141: [16:02:51] Rep: 80 Mol:25 -141: [16:02:51] Rep: 80 Mol:29 -141: [16:02:51] Rep: 60 Mol:30 -128: [16:02:51] ------------------------------------- -128: [16:02:51] Test GitHub Issue 811: rooted atom fingerprint non identical for the same molecules #811 -128: [16:02:51] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [16:02:51] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [16:02:51] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [16:02:51] done -128: [16:02:51] ------------------------------------- -128: [16:02:51] Test unfolded version of RDKFP -148: [16:02:51] Molecule does not have explicit Hs. Consider calling AddHs() -148: [16:02:51] Molecule does not have explicit Hs. Consider calling AddHs() -128: [16:02:51] ------------------------------------- -128: [16:02:51] Test bitinfo of RDKFP +147: [12:24:17] [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: [12:24:17] [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: [12:24:17] [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: [12:24:17] [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: [12:24:17] [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: [12:24:17] [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: [12:24:17] [$(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: [12:24:17] [$(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: [12:24:17] [$(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: [12:24:17] [$(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: [12:24:17] [$(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: [12:24:17] [$(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)] +143: [12:24:17] Rep: 100 Mol:1 +143: [12:24:17] Rep: 100 Mol:5 +143: [12:24:17] Rep: 100 Mol:9 +143: [12:24:17] Rep: 100 Mol:13 +143: [12:24:17] Rep: 100 Mol:17 +143: [12:24:17] Rep: 100 Mol:21 +143: [12:24:17] Rep: 100 Mol:25 +143: [12:24:17] Rep: 100 Mol:29 +147: [12:24:17] [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: [12:24:17] [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: [12:24:17] [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: [12:24:17] [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: [12:24:17] [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: [12:24:17] [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: [12:24:17] Rep: 80 Mol:1 +141: [12:24:17] Rep: 80 Mol:5 +141: [12:24:17] Rep: 80 Mol:9 +141: [12:24:17] Rep: 80 Mol:13 +141: [12:24:17] Rep: 80 Mol:17 +141: [12:24:17] Rep: 80 Mol:21 +141: [12:24:17] Rep: 80 Mol:25 +141: [12:24:17] Rep: 80 Mol:29 +147: [12:24:17] UFFTYPER: Unrecognized atom type: Pt5+2 (1) +147: [12:24:17] UFFTYPER: Unrecognized charge state for atom: 1 +147: [12:24:17] UFFTYPER: Unrecognized charge state for atom: 1 +143: [12:24:17] Rep: 100 Mol:2 +143: [12:24:17] Rep: 100 Mol:6 +143: [12:24:17] Rep: 100 Mol:10 +143: [12:24:17] Rep: 100 Mol:14 +147: [12:24:17] UFFTYPER: Unrecognized charge state for atom: 1 +143: [12:24:17] Rep: 100 Mol:18 +143: [12:24:17] Rep: 100 Mol:22 +143: [12:24:17] Rep: 100 Mol:26 +143: [12:24:17] Rep: 100 Mol:30 +141: [12:24:17] Rep: 60 Mol:2 +141: [12:24:17] Rep: 60 Mol:6 +141: [12:24:17] Rep: 60 Mol:10 +141: [12:24:17] Rep: 60 Mol:14 +141: [12:24:17] Rep: 60 Mol:18 +141: [12:24:17] Rep: 60 Mol:22 +141: [12:24:17] Rep: 60 Mol:26 +141: [12:24:17] Rep: 60 Mol:30 +148: .[12:24:18] Molecule does not have explicit Hs. Consider calling AddHs() +128: [12:24:18] done +128: [12:24:18] ------------------------------------- +128: [12:24:18] Test GitHub Issue 258: Bad pattern fingerprint for query molecule +128: [12:24:18] done +128: [12:24:18] ------------------------------------- +128: [12:24:18] Test GitHub Issue 334: explicit Hs in SMILES modifies atom pair (and topological torsion) FP. +128: [12:24:18] DEPRECATION WARNING: please use AtomPairGenerator +128: [12:24:18] DEPRECATION WARNING: please use AtomPairGenerator +128: [12:24:18] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [12:24:18] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [12:24:18] done +128: [12:24:18] ------------------------------------- +128: [12:24:18] Test GitHub Issue 695: Include cis/trans stereochemistry when useChirality=true with the morgan fingerprints +147: [12:24:18] UFFTYPER: Unrecognized charge state for atom: 5 +128: [12:24:18] done +128: [12:24:18] ------------------------------------- +128: [12:24:18] Test GitHub Issue 811: rooted atom fingerprint non identical for the same molecules #811 +128: [12:24:18] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [12:24:18] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [12:24:18] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [12:24:18] done +128: [12:24:18] ------------------------------------- +128: [12:24:18] Test unfolded version of RDKFP +128: [12:24:18] ------------------------------------- +128: [12:24:18] Test bitinfo of RDKFP 128: 562: [ 2 ], 128: 709: [ 0 1 ], 128: 1118: [ 0 1 2 ], @@ -26907,133 +26965,129 @@ 128: 1772: [ 0 ], [ 1 ], 128: 1813: [ 0 1 ], 128: ------------ -128: [16:02:51] ------------------------------------- -128: [16:02:51] Single atoms setting radius 1 bits in Morgan fingerprints -128: [16:02:51] done -128: [16:02:51] ------------------------------------- -128: [16:02:51] Github #879: Pattern fingerprint should set bits for single-atom fragments. -148: [16:02:51] Molecule does not have explicit Hs. Consider calling AddHs() -148: ..[16:02:51] Molecule does not have explicit Hs. Consider calling AddHs() -128: [16:02:51] done -128: [16:02:51] ------------------------------------- -128: [16:02:51] Github #1496: Pattern fingerprint setting bad bits for degree zero atoms -128: [16:02:51] done -128: [16:02:51] ------------------------------------- -128: [16:02:51] Github #1793: Fingerprint segfaults with branchedPaths=False and useHs=False -128: [16:02:51] done -128: [16:02:51] ------------------------------------- -128: [16:02:51] Github #1993: fingerprinters that use R/S labels should force a call to assignStereochemistry() if it hasn't already been called -148: [16:02:51] Molecule does not have explicit Hs. Consider calling AddHs() -148: [16:02:51] Molecule does not have explicit Hs. Consider calling AddHs() -148: [16:02:51] Molecule does not have explicit Hs. Consider calling AddHs() -148: [16:02:51] Molecule does not have explicit Hs. Consider calling AddHs() -148: [16:02:51] Molecule does not have explicit Hs. Consider calling AddHs() -148: [16:02:51] Molecule does not have explicit Hs. Consider calling AddHs() -148: [16:02:51] Molecule does not have explicit Hs. Consider calling AddHs() -148: [16:02:51] Molecule does not have explicit Hs. Consider calling AddHs() -148: [16:02:51] Molecule does not have explicit Hs. Consider calling AddHs() -148: [16:02:51] Molecule does not have explicit Hs. Consider calling AddHs() -128: [16:02:51] DEPRECATION WARNING: please use AtomPairGenerator -128: [16:02:51] DEPRECATION WARNING: please use AtomPairGenerator -128: [16:02:51] DEPRECATION WARNING: please use AtomPairGenerator -128: [16:02:51] DEPRECATION WARNING: please use AtomPairGenerator -128: [16:02:51] DEPRECATION WARNING: please use AtomPairGenerator -128: [16:02:51] DEPRECATION WARNING: please use AtomPairGenerator -128: [16:02:51] DEPRECATION WARNING: please use AtomPairGenerator -128: [16:02:51] DEPRECATION WARNING: please use AtomPairGenerator -128: [16:02:51] DEPRECATION WARNING: please use AtomPairGenerator -128: [16:02:51] DEPRECATION WARNING: please use AtomPairGenerator -128: [16:02:51] DEPRECATION WARNING: please use AtomPairGenerator -128: [16:02:51] DEPRECATION WARNING: please use AtomPairGenerator -128: [16:02:51] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [16:02:51] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [16:02:51] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [16:02:51] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [16:02:51] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [16:02:51] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [16:02:51] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [16:02:51] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [16:02:51] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [16:02:51] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [16:02:51] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [16:02:51] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [16:02:51] done -128: [16:02:51] ------------------------------------- -128: [16:02:51] Github #2115: BitInfo not complete for RDKFingerprint -128: [16:02:51] done -128: [16:02:51] ------------------------------------- -128: [16:02:51] Github #3723: Fingerprint crash for mols with Zero order bonds -128: [16:02:51] done -137/236 Test #128: testFingerprints ....................... Passed 5.14 sec +128: [12:24:18] ------------------------------------- +128: [12:24:18] Single atoms setting radius 1 bits in Morgan fingerprints +128: [12:24:18] done +128: [12:24:18] ------------------------------------- +128: [12:24:18] Github #879: Pattern fingerprint should set bits for single-atom fragments. +128: [12:24:18] done +128: [12:24:18] ------------------------------------- +128: [12:24:18] Github #1496: Pattern fingerprint setting bad bits for degree zero atoms +128: [12:24:18] done +128: [12:24:18] ------------------------------------- +128: [12:24:18] Github #1793: Fingerprint segfaults with branchedPaths=False and useHs=False +128: [12:24:18] done +128: [12:24:18] ------------------------------------- +128: [12:24:18] Github #1993: fingerprinters that use R/S labels should force a call to assignStereochemistry() if it hasn't already been called +128: [12:24:18] DEPRECATION WARNING: please use AtomPairGenerator +128: [12:24:18] DEPRECATION WARNING: please use AtomPairGenerator +128: [12:24:18] DEPRECATION WARNING: please use AtomPairGenerator +128: [12:24:18] DEPRECATION WARNING: please use AtomPairGenerator +128: [12:24:18] DEPRECATION WARNING: please use AtomPairGenerator +128: [12:24:18] DEPRECATION WARNING: please use AtomPairGenerator +128: [12:24:18] DEPRECATION WARNING: please use AtomPairGenerator +128: [12:24:18] DEPRECATION WARNING: please use AtomPairGenerator +128: [12:24:18] DEPRECATION WARNING: please use AtomPairGenerator +128: [12:24:18] DEPRECATION WARNING: please use AtomPairGenerator +128: [12:24:18] DEPRECATION WARNING: please use AtomPairGenerator +128: [12:24:18] DEPRECATION WARNING: please use AtomPairGenerator +128: [12:24:18] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [12:24:18] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [12:24:18] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [12:24:18] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [12:24:18] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [12:24:18] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [12:24:18] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [12:24:18] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [12:24:18] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [12:24:18] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [12:24:18] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [12:24:18] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [12:24:18] done +128: [12:24:18] ------------------------------------- +128: [12:24:18] Github #2115: BitInfo not complete for RDKFingerprint +128: [12:24:18] done +128: [12:24:18] ------------------------------------- +128: [12:24:18] Github #3723: Fingerprint crash for mols with Zero order bonds +128: [12:24:18] done +137/236 Test #128: testFingerprints ....................... Passed 8.27 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 -147: [16:02:51] UFFTYPER: Unrecognized charge state for atom: 5 -147: [16:02:51] UFFTYPER: Unrecognized charge state for atom: 5 -148: ..[16:02:51] Molecule does not have explicit Hs. Consider calling AddHs() -148: .[16:02:51] Molecule does not have explicit Hs. Consider calling AddHs() -148: [16:02:51] Molecule does not have explicit Hs. Consider calling AddHs() -148: [16:02:51] Molecule does not have explicit Hs. Consider calling AddHs() -148: [16:02:51] Molecule does not have explicit Hs. Consider calling AddHs() -143: [16:02:51] Rep: 100 Mol:0 -143: [16:02:51] Rep: 100 Mol:4 -143: [16:02:51] Rep: 100 Mol:8 -143: [16:02:51] Rep: 100 Mol:12 -143: [16:02:51] Rep: 100 Mol:16 -143: [16:02:51] Rep: 100 Mol:20 -143: [16:02:51] Rep: 100 Mol:24 -143: [16:02:51] Rep: 100 Mol:28 -148: [16:02:51] Molecule does not have explicit Hs. Consider calling AddHs() -148: [16:02:51] Molecule does not have explicit Hs. Consider calling AddHs() -147: [16:02:51] UFFTYPER: Unrecognized charge state for atom: 5 -148: [16:02:51] Molecule does not have explicit Hs. Consider calling AddHs() -148: [16:02:51] Molecule does not have explicit Hs. Consider calling AddHs() -148: [16:02:51] Molecule does not have explicit Hs. Consider calling AddHs() -148: [16:02:51] Molecule does not have explicit Hs. Consider calling AddHs() -148: [16:02:51] Molecule does not have explicit Hs. Consider calling AddHs() -148: [16:02:51] Molecule does not have explicit Hs. Consider calling AddHs() -148: [16:02:51] Molecule does not have explicit Hs. Consider calling AddHs() -148: [16:02:51] Molecule does not have explicit Hs. Consider calling AddHs() -148: [16:02:51] Molecule does not have explicit Hs. Consider calling AddHs() -148: [16:02:51] Molecule does not have explicit Hs. Consider calling AddHs() -148: [16:02:51] Molecule does not have explicit Hs. Consider calling AddHs() -143: [16:02:51] Rep: 100 Mol:1 -148: [16:02:51] Molecule does not have explicit Hs. Consider calling AddHs() -148: [16:02:51] Molecule does not have explicit Hs. Consider calling AddHs() -148: [16:02:51] Molecule does not have explicit Hs. Consider calling AddHs() -148: [16:02:51] Molecule does not have explicit Hs. Consider calling AddHs() -148: [16:02:51] Molecule does not have explicit Hs. Consider calling AddHs() -148: [16:02:51] Molecule does not have explicit Hs. Consider calling AddHs() -148: [16:02:51] Molecule does not have explicit Hs. Consider calling AddHs() -143: [16:02:51] Rep: 100 Mol:5 -143: [16:02:51] Rep: 100 Mol:9 -143: [16:02:51] Rep: 100 Mol:13 -143: [16:02:51] Rep: 100 Mol:17 -143: [16:02:51] Rep: 100 Mol:21 -143: [16:02:51] Rep: 100 Mol:25 -143: [16:02:51] Rep: 100 Mol:29 -148: [16:02:51] Molecule does not have explicit Hs. Consider calling AddHs() -148: [16:02:51] Molecule does not have explicit Hs. Consider calling AddHs() -148: [16:02:51] Molecule does not have explicit Hs. Consider calling AddHs() -148: [16:02:51] Molecule does not have explicit Hs. Consider calling AddHs() -148: [16:02:51] Molecule does not have explicit Hs. Consider calling AddHs() -148: [16:02:51] Molecule does not have explicit Hs. Consider calling AddHs() -148: [16:02:51] Molecule does not have explicit Hs. Consider calling AddHs() -148: [16:02:51] Molecule does not have explicit Hs. Consider calling AddHs() -148: [16:02:51] Molecule does not have explicit Hs. Consider calling AddHs() -148: [16:02:51] Molecule does not have explicit Hs. Consider calling AddHs() -148: [16:02:51] Molecule does not have explicit Hs. Consider calling AddHs() -148: [16:02:51] Molecule does not have explicit Hs. Consider calling AddHs() -148: [16:02:51] Molecule does not have explicit Hs. Consider calling AddHs() -148: [16:02:51] Molecule does not have explicit Hs. Consider calling AddHs() -148: [16:02:51] Molecule does not have explicit Hs. Consider calling AddHs() -148: [16:02:51] Molecule does not have explicit Hs. Consider calling AddHs() -148: [16:02:51] Molecule does not have explicit Hs. Consider calling AddHs() -148: [16:02:51] Molecule does not have explicit Hs. Consider calling AddHs() -148: [16:02:51] Molecule does not have explicit Hs. Consider calling AddHs() +147: [12:24:18] UFFTYPER: Unrecognized charge state for atom: 5 +147: [12:24:18] UFFTYPER: Unrecognized charge state for atom: 5 +148: [12:24:18] Molecule does not have explicit Hs. Consider calling AddHs() +148: [12:24:18] Molecule does not have explicit Hs. Consider calling AddHs() +148: [12:24:18] Molecule does not have explicit Hs. Consider calling AddHs() +148: ..[12:24:18] Molecule does not have explicit Hs. Consider calling AddHs() +148: [12:24:18] Molecule does not have explicit Hs. Consider calling AddHs() +148: [12:24:18] Molecule does not have explicit Hs. Consider calling AddHs() +148: [12:24:18] Molecule does not have explicit Hs. Consider calling AddHs() +148: [12:24:18] Molecule does not have explicit Hs. Consider calling AddHs() +148: [12:24:18] Molecule does not have explicit Hs. Consider calling AddHs() +148: [12:24:18] Molecule does not have explicit Hs. Consider calling AddHs() +148: [12:24:18] Molecule does not have explicit Hs. Consider calling AddHs() +148: [12:24:18] Molecule does not have explicit Hs. Consider calling AddHs() +148: [12:24:18] Molecule does not have explicit Hs. Consider calling AddHs() +148: [12:24:18] Molecule does not have explicit Hs. Consider calling AddHs() +148: ..[12:24:18] Molecule does not have explicit Hs. Consider calling AddHs() +148: .[12:24:18] Molecule does not have explicit Hs. Consider calling AddHs() +148: [12:24:18] Molecule does not have explicit Hs. Consider calling AddHs() +148: [12:24:18] Molecule does not have explicit Hs. Consider calling AddHs() +148: [12:24:18] Molecule does not have explicit Hs. Consider calling AddHs() +148: [12:24:18] Molecule does not have explicit Hs. Consider calling AddHs() +148: [12:24:18] Molecule does not have explicit Hs. Consider calling AddHs() +148: [12:24:18] Molecule does not have explicit Hs. Consider calling AddHs() +148: [12:24:18] Molecule does not have explicit Hs. Consider calling AddHs() +148: [12:24:18] Molecule does not have explicit Hs. Consider calling AddHs() +148: [12:24:18] Molecule does not have explicit Hs. Consider calling AddHs() +148: [12:24:18] Molecule does not have explicit Hs. Consider calling AddHs() +148: [12:24:18] Molecule does not have explicit Hs. Consider calling AddHs() +148: [12:24:18] Molecule does not have explicit Hs. Consider calling AddHs() +148: [12:24:18] Molecule does not have explicit Hs. Consider calling AddHs() +148: [12:24:18] Molecule does not have explicit Hs. Consider calling AddHs() +148: [12:24:18] Molecule does not have explicit Hs. Consider calling AddHs() +148: [12:24:18] Molecule does not have explicit Hs. Consider calling AddHs() +148: [12:24:18] Molecule does not have explicit Hs. Consider calling AddHs() +148: [12:24:18] Molecule does not have explicit Hs. Consider calling AddHs() +148: [12:24:18] Molecule does not have explicit Hs. Consider calling AddHs() +147: [12:24:18] UFFTYPER: Unrecognized charge state for atom: 6 +148: [12:24:18] Molecule does not have explicit Hs. Consider calling AddHs() +148: [12:24:18] Molecule does not have explicit Hs. Consider calling AddHs() +148: [12:24:18] Molecule does not have explicit Hs. Consider calling AddHs() +141: [12:24:18] Rep: 80 Mol:2 +141: [12:24:18] Rep: 80 Mol:6 +141: [12:24:18] Rep: 80 Mol:10 +148: [12:24:18] Molecule does not have explicit Hs. Consider calling AddHs() +148: [12:24:18] Molecule does not have explicit Hs. Consider calling AddHs() +147: [12:24:18] UFFTYPER: Unrecognized charge state for atom: 6 +141: [12:24:18] Rep: 80 Mol:14 +141: [12:24:18] Rep: 80 Mol:18 +141: [12:24:18] Rep: 80 Mol:22 +141: [12:24:18] Rep: 80 Mol:26 +141: [12:24:18] Rep: 80 Mol:30 +148: [12:24:18] Molecule does not have explicit Hs. Consider calling AddHs() +148: [12:24:18] Molecule does not have explicit Hs. Consider calling AddHs() +148: [12:24:18] Molecule does not have explicit Hs. Consider calling AddHs() +148: [12:24:18] Molecule does not have explicit Hs. Consider calling AddHs() +148: [12:24:18] Molecule does not have explicit Hs. Consider calling AddHs() +148: [12:24:18] Molecule does not have explicit Hs. Consider calling AddHs() +148: [12:24:18] Molecule does not have explicit Hs. Consider calling AddHs() +148: [12:24:18] Molecule does not have explicit Hs. Consider calling AddHs() +148: [12:24:18] Molecule does not have explicit Hs. Consider calling AddHs() +148: [12:24:18] Molecule does not have explicit Hs. Consider calling AddHs() +148: [12:24:18] Molecule does not have explicit Hs. Consider calling AddHs() +148: [12:24:18] Molecule does not have explicit Hs. Consider calling AddHs() +148: [12:24:18] Molecule does not have explicit Hs. Consider calling AddHs() +148: [12:24:18] Molecule does not have explicit Hs. Consider calling AddHs() +147: [12:24:18] UFFTYPER: Unrecognized charge state for atom: 6 +148: [12:24:18] Molecule does not have explicit Hs. Consider calling AddHs() +148: [12:24:18] Molecule does not have explicit Hs. Consider calling AddHs() +148: [12:24:18] Molecule does not have explicit Hs. Consider calling AddHs() +148: [12:24:18] Molecule does not have explicit Hs. Consider calling AddHs() 149: *********************************************************** 149: Testing MolAlign 149: --------------------------------- @@ -27055,360 +27109,264 @@ 149: testIssue241 149: 149: *********************************************************** -138/236 Test #149: testMolAlign ........................... Passed 0.19 sec +138/236 Test #149: testMolAlign ........................... Passed 0.41 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: [16:02:51] Molecule does not have explicit Hs. Consider calling AddHs() -148: [16:02:51] Molecule does not have explicit Hs. Consider calling AddHs() -141: [16:02:51] Rep: 80 Mol:2 -141: [16:02:51] Rep: 80 Mol:6 -141: [16:02:51] Rep: 80 Mol:10 -141: [16:02:51] Rep: 80 Mol:14 -141: [16:02:51] Rep: 80 Mol:18 -141: [16:02:51] Rep: 80 Mol:22 -141: [16:02:51] Rep: 80 Mol:26 -141: [16:02:51] Rep: 80 Mol:30 -148: [16:02:51] Molecule does not have explicit Hs. Consider calling AddHs() -143: [16:02:51] Rep: 100 Mol:2 -143: [16:02:51] Rep: 100 Mol:6 -143: [16:02:51] Rep: 100 Mol:10 -143: [16:02:51] Rep: 100 Mol:14 -143: [16:02:51] Rep: 100 Mol:18 -143: [16:02:51] Rep: 100 Mol:22 -143: [16:02:51] Rep: 100 Mol:26 -143: [16:02:51] Rep: 100 Mol:30 -147: [16:02:51] UFFTYPER: Unrecognized charge state for atom: 6 -148: [16:02:51] Molecule does not have explicit Hs. Consider calling AddHs() -147: [16:02:51] UFFTYPER: Unrecognized charge state for atom: 6 -148: [16:02:51] Molecule does not have explicit Hs. Consider calling AddHs() -147: [16:02:51] UFFTYPER: Unrecognized charge state for atom: 6 -148: [16:02:51] Molecule does not have explicit Hs. Consider calling AddHs() -148: [16:02:51] Molecule does not have explicit Hs. Consider calling AddHs() -148: [16:02:51] Molecule does not have explicit Hs. Consider calling AddHs() -148: [16:02:51] Molecule does not have explicit Hs. Consider calling AddHs() -148: [16:02:51] Molecule does not have explicit Hs. Consider calling AddHs() -148: [16:02:51] Molecule does not have explicit Hs. Consider calling AddHs() -141: [16:02:51] done -141: [16:02:51] ------------------------------------- -141: [16:02:51] Test MMFF multithreading2 -148: [16:02:51] Molecule does not have explicit Hs. Consider calling AddHs() -148: [16:02:51] Molecule does not have explicit Hs. Consider calling AddHs() -148: [16:02:51] Molecule does not have explicit Hs. Consider calling AddHs() -148: [16:02:51] Molecule does not have explicit Hs. Consider calling AddHs() -148: [16:02:51] Molecule does not have explicit Hs. Consider calling AddHs() -148: [16:02:51] Molecule does not have explicit Hs. Consider calling AddHs() -148: [16:02:51] Molecule does not have explicit Hs. Consider calling AddHs() -148: [16:02:51] Molecule does not have explicit Hs. Consider calling AddHs() -148: .[16:02:51] Molecule does not have explicit Hs. Consider calling AddHs() -146: [16:02:49] --------------------------------- -146: [16:02:49] test3 +148: [12:24:18] Molecule does not have explicit Hs. Consider calling AddHs() +148: [12:24:18] Molecule does not have explicit Hs. Consider calling AddHs() +148: [12:24:18] Molecule does not have explicit Hs. Consider calling AddHs() +148: [12:24:18] Molecule does not have explicit Hs. Consider calling AddHs() +148: [12:24:18] Molecule does not have explicit Hs. Consider calling AddHs() +148: [12:24:18] Molecule does not have explicit Hs. Consider calling AddHs() +141: [12:24:18] done +141: [12:24:18] ------------------------------------- +141: [12:24:18] Test MMFF multithreading2 +148: [12:24:18] Molecule does not have explicit Hs. Consider calling AddHs() +148: [12:24:18] Molecule does not have explicit Hs. Consider calling AddHs() +148: [12:24:18] Molecule does not have explicit Hs. Consider calling AddHs() +148: [12:24:19] Molecule does not have explicit Hs. Consider calling AddHs() +148: [12:24:19] Molecule does not have explicit Hs. Consider calling AddHs() +148: [12:24:19] Molecule does not have explicit Hs. Consider calling AddHs() +143: [12:24:19] done +143: [12:24:19] ------------------------------------- +143: [12:24:19] Test UFF multithreading2 +148: [12:24:19] Molecule does not have explicit Hs. Consider calling AddHs() +148: [12:24:19] Molecule does not have explicit Hs. Consider calling AddHs() +148: [12:24:19] Molecule does not have explicit Hs. Consider calling AddHs() +148: [12:24:19] Molecule does not have explicit Hs. Consider calling AddHs() +148: [12:24:19] Molecule does not have explicit Hs. Consider calling AddHs() +148: [12:24:19] Molecule does not have explicit Hs. Consider calling AddHs() +95: 0,0 0 +95: 0,1 0 +95: 1,0 0 +95: 1,1 0 +95: 2,0 0 +95: 2,1 0 +139/236 Test #95: testEnumeration ........................ Passed 17.78 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: [12:24:19] Molecule does not have explicit Hs. Consider calling AddHs() +148: .[12:24:19] Molecule does not have explicit Hs. Consider calling AddHs() +141: [12:24:19] done +141: [12:24:19] ------------------------------------- +141: [12:24:19] Test MMFF multithreading3 +148: [12:24:19] Molecule does not have explicit Hs. Consider calling AddHs() +151: Randomness seeded to: 1667628562 +151: 85591353 +151: 89037095 +146: [12:24:17] --------------------------------- +146: [12:24:17] test3 146: -146: [16:02:50] --------------------------------- -146: [16:02:50] test4 +146: [12:24:17] --------------------------------- +146: [12:24:17] test4 146: -146: [16:02:50] --------------------------------- -146: [16:02:50] test5 +146: [12:24:17] --------------------------------- +146: [12:24:17] test5 146: -146: [16:02:51] --------------------------------- -146: [16:02:51] test6 +146: [12:24:19] --------------------------------- +146: [12:24:19] test6 146: -146: [16:02:51] --------------------------------- -146: [16:02:51] test15Dists +146: [12:24:19] --------------------------------- +146: [12:24:19] test15Dists 146: -146: [16:02:51] --------------------------------- -146: [16:02:51] test Issue 215 +146: [12:24:19] --------------------------------- +146: [12:24:19] test Issue 215 146: -146: [16:02:51] --------------------------------- -146: [16:02:51] testMultipleConfs +146: [12:24:19] --------------------------------- +146: [12:24:19] testMultipleConfs 146: -146: [16:02:51] --------------------------------- -146: [16:02:51] testMultipleConfsExpTors +146: [12:24:19] --------------------------------- +146: [12:24:19] testMultipleConfsExpTors 146: -146: [16:02:51] --------------------------------- -146: [16:02:51] testIssue227 +146: [12:24:20] --------------------------------- +146: [12:24:20] testIssue227 146: -146: [16:02:51] --------------------------------- -146: [16:02:51] testIssue236 +146: [12:24:20] --------------------------------- +146: [12:24:20] testIssue236 146: -146: [16:02:51] --------------------------------- -146: [16:02:51] testOrdering +146: [12:24:20] --------------------------------- +146: [12:24:20] testOrdering 146: -146: [16:02:51] --------------------------------- -146: [16:02:51] testIssue244 +146: [12:24:20] --------------------------------- +146: [12:24:20] testIssue244 146: -146: [16:02:51] --------------------------------- -146: [16:02:51] testIssue251 +146: [12:24:20] --------------------------------- +146: [12:24:20] testIssue251 146: -146: [16:02:51] --------------------------------- -146: [16:02:51] testIssue276 -146: [16:02:51] --------------------------------- -146: [16:02:51] testIssue284 +146: [12:24:20] --------------------------------- +146: [12:24:20] testIssue276 +146: [12:24:20] --------------------------------- +146: [12:24:20] testIssue284 146: -146: [16:02:51] --------------------------------- -146: [16:02:51] testIssue285 +146: [12:24:20] --------------------------------- +146: [12:24:20] testIssue285 146: -146: [16:02:51] --------------------------------- -146: [16:02:51] testIssue355 +146: [12:24:20] --------------------------------- +146: [12:24:20] testIssue355 146: -146: [16:02:52] --------------------------------- -146: [16:02:52] testRandomCoords +146: [12:24:20] --------------------------------- +146: [12:24:20] testRandomCoords 146: -146: [16:02:52] --------------------------------- -146: [16:02:52] test sf.net issue 1989539 +146: [12:24:20] --------------------------------- +146: [12:24:20] test sf.net issue 1989539 146: -146: [16:02:52] --------------------------------- -146: [16:02:52] test sf.net issue 2091864 +146: [12:24:20] --------------------------------- +146: [12:24:20] test sf.net issue 2091864 146: -146: [16:02:52] --------------------------------- -146: [16:02:52] test constrained embedding +146: [12:24:20] --------------------------------- +146: [12:24:20] test constrained embedding 146: -146: [16:02:52] ssd: 0.0752641 -146: [16:02:52] ssd: 0.0659363 -146: [16:02:52] --------------------------------- -146: [16:02:52] test sf.net issue 2091974 +146: [12:24:20] ssd: 0.0752641 +146: [12:24:20] ssd: 0.0659363 +143: [12:24:20] done +143: [12:24:20] ------------------------------------- +143: [12:24:20] Test UFF multithreading3 +148: [12:24:20] Molecule does not have explicit Hs. Consider calling AddHs() +146: [12:24:20] --------------------------------- +146: [12:24:20] test sf.net issue 2091974 146: -146: [16:02:52] --------------------------------- -146: [16:02:52] test sf.net issue 2835784 +146: [12:24:20] --------------------------------- +146: [12:24:20] test sf.net issue 2835784 146: -146: [16:02:52] --------------------------------- -146: [16:02:52] test sf.net issue 3019283 +146: [12:24:20] --------------------------------- +146: [12:24:20] test sf.net issue 3019283 146: -146: [16:02:52] --------------------------------- -146: [16:02:52] test sf.net issue 3238580 +146: [12:24:20] --------------------------------- +146: [12:24:20] test sf.net issue 3238580 146: -146: [16:02:52] --------------------------------- -146: [16:02:52] test sf.net issue 3483968 +146: [12:24:20] --------------------------------- +146: [12:24:20] test sf.net issue 3483968 146: -146: [16:02:52] --------------------------------- -146: [16:02:52] test github issue 55 +146: [12:24:20] --------------------------------- +146: [12:24:20] test github issue 55 146: -146: [16:02:52] --------------------------------- -146: [16:02:52] test1 +146: [12:24:20] --------------------------------- +146: [12:24:20] test1 146: -146: [16:02:52] --------------------------------- -146: [16:02:52] test multi-threading +146: [12:24:20] --------------------------------- +146: [12:24:20] test multi-threading 146: 146: building molecules 146: generating reference data -95: 0,0 0 -95: 0,1 0 -95: 1,0 0 -95: 1,1 0 -95: 2,0 0 -95: 2,1 0 -139/236 Test #95: testEnumeration ........................ Passed 11.73 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: [16:02:52] Molecule does not have explicit Hs. Consider calling AddHs() -143: [16:02:52] done -143: [16:02:52] ------------------------------------- -143: [16:02:52] Test UFF multithreading2 -141: [16:02:52] done -141: [16:02:52] ------------------------------------- -141: [16:02:52] Test MMFF multithreading3 -148: [16:02:52] Molecule does not have explicit Hs. Consider calling AddHs() -151: Randomness seeded to: 3465441300 -151: 177471520 -151: 120371840 -148: [16:02:52] Molecule does not have explicit Hs. Consider calling AddHs() -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 -126: .[16:02:53] DEPRECATION WARNING: please use MorganGenerator -126: .[16:02:53] DEPRECATION WARNING: please use MorganGenerator -126: ..[16:02:53] DEPRECATION WARNING: please use AtomPairGenerator -126: [16:02:53] DEPRECATION WARNING: please use AtomPairGenerator -126: [16:02:53] DEPRECATION WARNING: please use AtomPairGenerator -126: [16:02:53] DEPRECATION WARNING: please use AtomPairGenerator -126: [16:02:53] DEPRECATION WARNING: please use AtomPairGenerator -126: [16:02:53] DEPRECATION WARNING: please use AtomPairGenerator -126: .[16:02:53] DEPRECATION WARNING: please use TopologicalTorsionGenerator -126: [16:02:53] DEPRECATION WARNING: please use TopologicalTorsionGenerator -126: ...[16:02:53] DEPRECATION WARNING: please use MorganGenerator -126: [16:02:53] DEPRECATION WARNING: please use MorganGenerator -126: [16:02:53] DEPRECATION WARNING: please use MorganGenerator -126: [16:02:53] DEPRECATION WARNING: please use MorganGenerator -126: [16:02:53] DEPRECATION WARNING: please use MorganGenerator -126: [16:02:53] DEPRECATION WARNING: please use MorganGenerator -126: [16:02:53] DEPRECATION WARNING: please use MorganGenerator -126: [16:02:53] DEPRECATION WARNING: please use MorganGenerator -126: [16:02:53] DEPRECATION WARNING: please use MorganGenerator -126: [16:02:53] DEPRECATION WARNING: please use MorganGenerator -126: [16:02:53] DEPRECATION WARNING: please use MorganGenerator -126: [16:02:53] DEPRECATION WARNING: please use MorganGenerator -126: [16:02:53] DEPRECATION WARNING: please use MorganGenerator -126: [16:02:53] DEPRECATION WARNING: please use MorganGenerator -126: [16:02:53] DEPRECATION WARNING: please use MorganGenerator -126: [16:02:53] DEPRECATION WARNING: please use MorganGenerator -126: [16:02:53] DEPRECATION WARNING: please use MorganGenerator -126: [16:02:53] DEPRECATION WARNING: please use MorganGenerator -126: [16:02:53] DEPRECATION WARNING: please use MorganGenerator -126: [16:02:53] DEPRECATION WARNING: please use MorganGenerator -126: [16:02:53] DEPRECATION WARNING: please use MorganGenerator -126: [16:02:53] DEPRECATION WARNING: please use MorganGenerator -126: ....[16:02:53] DEPRECATION WARNING: please use AtomPairGenerator -126: [16:02:53] DEPRECATION WARNING: please use AtomPairGenerator -148: [16:02:53] Molecule does not have explicit Hs. Consider calling AddHs() -126: ....[16:02:53] DEPRECATION WARNING: please use AtomPairGenerator -126: [16:02:53] DEPRECATION WARNING: please use AtomPairGenerator -126: .[16:02:53] DEPRECATION WARNING: please use TopologicalTorsionGenerator -126: [16:02:53] DEPRECATION WARNING: please use TopologicalTorsionGenerator -126: [16:02:53] DEPRECATION WARNING: please use TopologicalTorsionGenerator -126: [16:02:53] DEPRECATION WARNING: please use TopologicalTorsionGenerator -126: [16:02:53] DEPRECATION WARNING: please use TopologicalTorsionGenerator -126: ..[16:02:53] DEPRECATION WARNING: please use TopologicalTorsionGenerator -126: [16:02:53] DEPRECATION WARNING: please use TopologicalTorsionGenerator -126: [16:02:53] DEPRECATION WARNING: please use TopologicalTorsionGenerator -126: [16:02:53] DEPRECATION WARNING: please use TopologicalTorsionGenerator -126: [16:02:53] DEPRECATION WARNING: please use TopologicalTorsionGenerator -126: [16:02:53] DEPRECATION WARNING: please use TopologicalTorsionGenerator -126: .[16:02:53] DEPRECATION WARNING: please use TopologicalTorsionGenerator -126: [16:02:53] DEPRECATION WARNING: please use TopologicalTorsionGenerator -126: ... -126: ---------------------------------------------------------------------- -126: Ran 31 tests in 6.905s -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 -140/236 Test #126: pyMolDescriptors ....................... Passed 7.52 sec +141: [12:24:20] done +141: [12:24:20] ------------------------------------- +141: [12:24:20] Testing github 162: Incorrect SMILES after MMFF parameterization . +141: [12:24:20] done +141: [12:24:20] ------------------------------------- +141: [12:24:20] Testing github 224: crash during MMFF parameterization . +141: [12:24:20] done +141: [12:24:20] ------------------------------------- +141: [12:24:20] Testing github6728: crash due to missing stretch-bend params. +140/236 Test #141: testMMFFForceFieldHelpers .............. Passed 6.33 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 -148: [16:02:53] Molecule does not have explicit Hs. Consider calling AddHs() -143: [16:02:53] done -143: [16:02:53] ------------------------------------- -143: [16:02:53] Test UFF multithreading3 -141: [16:02:53] done -141: [16:02:53] ------------------------------------- -141: [16:02:53] Testing github 162: Incorrect SMILES after MMFF parameterization . -141: [16:02:53] done -141: [16:02:53] ------------------------------------- -141: [16:02:53] Testing github 224: crash during MMFF parameterization . -141: [16:02:53] done -141: [16:02:53] ------------------------------------- -141: [16:02:53] Testing github6728: crash due to missing stretch-bend params. -141/236 Test #141: testMMFFForceFieldHelpers .............. Passed 4.56 sec +147: [12:24:20] UFFTYPER: Warning: hybridization set to SP3 for atom 6 +148: [12:24:21] Molecule does not have explicit Hs. Consider calling AddHs() +147: [12:24:21] UFFTYPER: Warning: hybridization set to SP3 for atom 6 +147: [12:24:21] UFFTYPER: Warning: hybridization set to SP3 for atom 6 +143: [12:24:21] done +143: [12:24:21] ------------------------------------- +143: [12:24:21] Testing GitHubIssue62. +143: [12:24:21] beta-lactam 39.6387 +143: [12:24:21] cyclopropanone 174.698 +143: [12:24:21] aziridine 337.986 +143: [12:24:21] aziridinone 115.248 +143: [12:24:21] isobutene 2.48217 +143: [12:24:21] acetone 1.91788 +143: [12:24:21] cyclopentanone 10.1648 +143: [12:24:21] cyclopropene 99.4921 +143: [12:24:21] cyclobutene 41.0156 +143: [12:24:21] cyclopropane 267.236 +143: [12:24:21] gamma-lactam 15.7471 +147: [12:24:21] UFFTYPER: Warning: hybridization set to SP3 for atom 11 +147: [12:24:21] UFFTYPER: Warning: hybridization set to SP3 for atom 11 +147: [12:24:21] UFFTYPER: Warning: hybridization set to SP3 for atom 11 +143: [12:24:21] trans-2,3-diphenylcyclopropan-1-one 203.398 +143: [12:24:21] cis-2,3-diphenylcyclopropan-1-one 206.852 +143: [12:24:21] 2,3-diphenylcyclopropa-2-en-1-one 20.0443 +143: [12:24:21] cyclopropylidencyclobutane 218.879 +143: [12:24:21] diphenylmethylidencyclobutane 79.6139 +143: [12:24:21] done +143: [12:24:21] ------------------------------------- +143: [12:24:21] Test Github Issue 613: UFF Atom type not properly assigned to lanthanides. +143: [12:24:21] done +143: [12:24:21] ------------------------------------- +143: [12:24:21] Test square planar complexes +143: [12:24:21] done +143: [12:24:21] ------------------------------------- +143: [12:24:21] Test octahedral complexes +143: [12:24:21] done +141/236 Test #143: testUFFForceFieldHelpers ............... Passed 6.79 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: [16:02:53] ------------------------------------- -153: [16:02:53] AtomType parser testing. -147: [16:02:53] UFFTYPER: Warning: hybridization set to SP3 for atom 6 -153: [16:02:53] SMARTS Parse Error: syntax error while parsing: [$([!$([NH0])_100;N,O,$([S])_101,$([N,O)_102])_103] -153: [16:02:53] 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: [16:02:53] done -153: [16:02:53] ------------------------------------- -153: [16:02:53] FeatureDefinition parser testing. -147: [16:02:53] UFFTYPER: Warning: hybridization set to SP3 for atom 6 -153: [16:02:53] done -153: [16:02:53] ------------------------------------- -153: [16:02:53] Test pulling feat defs from a string. -153: [16:02:53] done -153: [16:02:53] ------------------------------------- -153: [16:02:53] FeatureDef functionality testing. -153: [16:02:53] done -153: [16:02:53] ------------------------------------- -153: [16:02:53] FeatureFactory testing. -153: [16:02:53] 1 -153: [16:02:53] 2 -153: [16:02:53] 3 -153: [16:02:53] 4 -153: [16:02:53] 5 -153: [16:02:53] 6 -153: [16:02:53] done -153: [16:02:53] ------------------------------------- -153: [16:02:53] Feature Location testing. -153: [16:02:53] done -153: [16:02:53] ------------------------------------- -153: [16:02:53] Test building a FeatureFactory from a file -153: [16:02:53] done -153: [16:02:53] ------------------------------------- -153: [16:02:53] Testing Issue 224. -153: [16:02:53] done -147: [16:02:53] UFFTYPER: Warning: hybridization set to SP3 for atom 6 -153: [16:02:53] ------------------------------------- -153: [16:02:53] Testing Issue 225. -153: [16:02:53] done -153: [16:02:53] ------------------------------------- -153: [16:02:53] Test Issue346 -153: [16:02:53] done -153: [16:02:53] ------------------------------------- -153: [16:02:53] Test Issue347 -153: [16:02:53] done -153: [16:02:53] ------------------------------------- -153: [16:02:53] Testing Issue 348. -153: [16:02:53] SMARTS Parse Error: syntax error while parsing: [C[C] -153: [16:02:53] SMARTS Parse Error: Failed parsing SMARTS '[C[C]' for input: '[C[C]' -153: [16:02:53] ------------------------------------- -153: [16:02:53] Testing Nested AtomType definitions. +153: [12:24:21] ------------------------------------- +153: [12:24:21] AtomType parser testing. +153: [12:24:21] SMARTS Parse Error: syntax error while parsing: [$([!$([NH0])_100;N,O,$([S])_101,$([N,O)_102])_103] +153: [12:24:21] 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: [12:24:21] done +153: [12:24:21] ------------------------------------- +153: [12:24:21] FeatureDefinition parser testing. +153: [12:24:21] done +153: [12:24:21] ------------------------------------- +153: [12:24:21] Test pulling feat defs from a string. +153: [12:24:21] done +153: [12:24:21] ------------------------------------- +153: [12:24:21] FeatureDef functionality testing. +153: [12:24:21] done +153: [12:24:21] ------------------------------------- +153: [12:24:21] FeatureFactory testing. +153: [12:24:21] 1 +153: [12:24:21] 2 +153: [12:24:21] 3 +153: [12:24:21] 4 +153: [12:24:21] 5 +153: [12:24:21] 6 +153: [12:24:21] done +153: [12:24:21] ------------------------------------- +153: [12:24:21] Feature Location testing. +153: [12:24:21] done +153: [12:24:21] ------------------------------------- +153: [12:24:21] Test building a FeatureFactory from a file +153: [12:24:21] done +153: [12:24:21] ------------------------------------- +153: [12:24:21] Testing Issue 224. +153: [12:24:21] done +153: [12:24:21] ------------------------------------- +153: [12:24:21] Testing Issue 225. +153: [12:24:21] done +153: [12:24:21] ------------------------------------- +153: [12:24:21] Test Issue346 +153: [12:24:21] done +153: [12:24:21] ------------------------------------- +153: [12:24:21] Test Issue347 +153: [12:24:21] done +153: [12:24:21] ------------------------------------- +153: [12:24:21] Testing Issue 348. +153: [12:24:21] SMARTS Parse Error: syntax error while parsing: [C[C] +153: [12:24:21] SMARTS Parse Error: Failed parsing SMARTS '[C[C]' for input: '[C[C]' +153: [12:24:21] ------------------------------------- +153: [12:24:21] Testing Nested AtomType definitions. 153: [$([$([$([C;!$(C=[O,N,P,S]);!$(C#N)]),c]);R])] -153: [16:02:53] ------------------------------------- -153: [16:02:53] Testing Github Issue #252: crash when calling getPos() with no conformer. -153: [16:02:53] expect a precondition failure message below -153: [16:02:53] +153: [12:24:21] ------------------------------------- +153: [12:24:21] Testing Github Issue #252: crash when calling getPos() with no conformer. +153: [12:24:21] expect a precondition failure message below +153: [12:24:21] 153: 153: **** 153: Pre-condition Violation @@ -27421,25 +27379,29 @@ 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# 0x0000AAAADF741AB0 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/MolChemicalFeatures/testFeatures -153: 5# 0x0000AAAADF734568 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/MolChemicalFeatures/testFeatures -153: 6# 0x0000FFFF8928229C in /lib/aarch64-linux-gnu/libc.so.6 +153: 4# 0x0000AAAAE2951AB0 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/MolChemicalFeatures/testFeatures +153: 5# 0x0000AAAAE2944568 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/MolChemicalFeatures/testFeatures +153: 6# 0x0000FFFF8EE5229C in /lib/aarch64-linux-gnu/libc.so.6 153: 7# __libc_start_main in /lib/aarch64-linux-gnu/libc.so.6 -153: 8# 0x0000AAAADF734730 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/MolChemicalFeatures/testFeatures +153: 8# 0x0000AAAAE2944730 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/MolChemicalFeatures/testFeatures 153: ---------- 153: **** 153: -153: [16:02:53] Done -153: [16:02:53] ------------------------------------- -153: [16:02:53] Testing github 2077: add confId argument to MolChemicalFeatureFactor::getFeaturesForMol() -153: [16:02:53] done -142/236 Test #153: testFeatures ........................... Passed 0.22 sec +153: [12:24:21] Done +153: [12:24:21] ------------------------------------- +153: [12:24:21] Testing github 2077: add confId argument to MolChemicalFeatureFactor::getFeaturesForMol() +153: [12:24:21] done +142/236 Test #153: testFeatures ........................... Passed 0.19 sec test 154 Start 154: pyChemicalFeatures 154: Test command: /usr/bin/python3 "/build/reproducible-path/rdkit-202503.1/Code/GraphMol/MolChemicalFeatures/Wrap/testChemicalFeatures.py" 154: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/MolChemicalFeatures/Wrap 154: Test timeout computed to be: 1500 +148: [12:24:21] Molecule does not have explicit Hs. Consider calling AddHs() +148: [12:24:22] Molecule does not have explicit Hs. Consider calling AddHs() +154: .[12:24:22] Molecule does not have explicit Hs. Consider calling AddHs() +154: .[12:24:22] 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 @@ -27447,19 +27409,25 @@ 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 -147: [16:02:53] UFFTYPER: Warning: hybridization set to SP3 for atom 11 +154: ..[12:24:22] Molecule does not have explicit Hs. Consider calling AddHs() +154: .[12:24:22] Molecule does not have explicit Hs. Consider calling AddHs() +154: .[12:24:22] SMARTS Parse Error: syntax error while parsing: [N,O;!HQ] +154: [12:24:22] SMARTS Parse Error: Failed parsing SMARTS '[N,O;!HQ]' for input: '[N,O;!HQ]' +154: ... +154: ---------------------------------------------------------------------- +154: Ran 9 tests in 0.243s +154: +154: OK 125: =============================================================================== 125: All tests passed (515 assertions in 10 test cases) 125: -143/236 Test #125: descriptorsTestCatch ................... Passed 8.45 sec +143/236 Test #125: descriptorsTestCatch ................... Passed 13.52 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 -147: [16:02:54] UFFTYPER: Warning: hybridization set to SP3 for atom 11 -147: [16:02:54] UFFTYPER: Warning: hybridization set to SP3 for atom 11 155: *********************************************************** 155: Testing ShapeHelpers 155: --------------------------------- @@ -27472,147 +27440,186 @@ 155: testGithub4364 155: 155: *********************************************************** -144/236 Test #155: testShapeHelpers ....................... Passed 0.10 sec +144/236 Test #155: testShapeHelpers ....................... Passed 0.09 sec test 156 Start 156: pyShapeHelpers 156: Test command: /usr/bin/python3 "/build/reproducible-path/rdkit-202503.1/Code/GraphMol/ShapeHelpers/Wrap/testShapeHelpers.py" 156: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/ShapeHelpers/Wrap 156: Test timeout computed to be: 1500 -154: .[16:02:54] Molecule does not have explicit Hs. Consider calling AddHs() -154: .[16:02:54] Molecule does not have explicit Hs. Consider calling AddHs() -148: [16:02:54] Molecule does not have explicit Hs. Consider calling AddHs() -148: [16:02:54] Molecule does not have explicit Hs. Consider calling AddHs() -154: ..[16:02:54] Molecule does not have explicit Hs. Consider calling AddHs() -154: .[16:02:54] Molecule does not have explicit Hs. Consider calling AddHs() -154: .[16:02:54] SMARTS Parse Error: syntax error while parsing: [N,O;!HQ] -154: [16:02:54] SMARTS Parse Error: Failed parsing SMARTS '[N,O;!HQ]' for input: '[N,O;!HQ]' -154: ... -154: ---------------------------------------------------------------------- -154: Ran 9 tests in 0.209s -154: -154: OK -143: [16:02:54] done -143: [16:02:54] ------------------------------------- -143: [16:02:54] Testing GitHubIssue62. -143: [16:02:54] beta-lactam 39.6387 -143: [16:02:54] cyclopropanone 174.698 -143: [16:02:54] aziridine 337.986 -143: [16:02:54] aziridinone 115.248 -143: [16:02:54] isobutene 2.48217 -143: [16:02:54] acetone 1.91788 -143: [16:02:54] cyclopentanone 10.1648 -143: [16:02:54] cyclopropene 99.4921 -143: [16:02:54] cyclobutene 41.0156 -143: [16:02:54] cyclopropane 267.236 -143: [16:02:54] gamma-lactam 15.7471 -148: [16:02:54] Molecule does not have explicit Hs. Consider calling AddHs() -143: [16:02:54] trans-2,3-diphenylcyclopropan-1-one 203.398 -156: . -156: ---------------------------------------------------------------------- -156: Ran 1 test in 0.059s -156: -156: OK -156: Testing Shape Helpers wrapper -145/236 Test #154: pyChemicalFeatures ..................... Passed 0.72 sec +145/236 Test #154: pyChemicalFeatures ..................... Passed 0.93 sec test 157 Start 157: testMolCatalog 157: Test command: /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/MolCatalog/testMolCatalog 157: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/MolCatalog 157: Test timeout computed to be: 1500 -143: [16:02:54] cis-2,3-diphenylcyclopropan-1-one 206.852 -148: [16:02:54] Molecule does not have explicit Hs. Consider calling AddHs() -143: [16:02:54] 2,3-diphenylcyclopropa-2-en-1-one 20.0443 -146/236 Test #156: pyShapeHelpers ......................... Passed 0.50 sec +146/236 Test #157: testMolCatalog ......................... Passed 0.14 sec test 158 Start 158: pyMolCatalog 158: Test command: /usr/bin/python3 "/build/reproducible-path/rdkit-202503.1/Code/GraphMol/MolCatalog/Wrap/rough_test.py" 158: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/MolCatalog/Wrap 158: Test timeout computed to be: 1500 -143: [16:02:54] cyclopropylidencyclobutane 218.879 -143: [16:02:54] diphenylmethylidencyclobutane 79.6139 -143: [16:02:54] done -143: [16:02:54] ------------------------------------- -143: [16:02:54] Test Github Issue 613: UFF Atom type not properly assigned to lanthanides. -143: [16:02:54] done -143: [16:02:54] ------------------------------------- -143: [16:02:54] Test square planar complexes -143: [16:02:54] done -143: [16:02:54] ------------------------------------- -143: [16:02:54] Test octahedral complexes -143: [16:02:54] done -147/236 Test #143: testUFFForceFieldHelpers ............... Passed 5.21 sec +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 +126: .[12:24:22] DEPRECATION WARNING: please use MorganGenerator +126: .[12:24:23] DEPRECATION WARNING: please use MorganGenerator +126: ..[12:24:23] DEPRECATION WARNING: please use AtomPairGenerator +126: [12:24:23] DEPRECATION WARNING: please use AtomPairGenerator +126: [12:24:23] DEPRECATION WARNING: please use AtomPairGenerator +126: [12:24:23] DEPRECATION WARNING: please use AtomPairGenerator +126: [12:24:23] DEPRECATION WARNING: please use AtomPairGenerator +126: [12:24:23] DEPRECATION WARNING: please use AtomPairGenerator +126: .[12:24:23] DEPRECATION WARNING: please use TopologicalTorsionGenerator +126: [12:24:23] DEPRECATION WARNING: please use TopologicalTorsionGenerator +126: ...[12:24:23] DEPRECATION WARNING: please use MorganGenerator +126: [12:24:23] DEPRECATION WARNING: please use MorganGenerator +126: [12:24:23] DEPRECATION WARNING: please use MorganGenerator +126: [12:24:23] DEPRECATION WARNING: please use MorganGenerator +126: [12:24:23] DEPRECATION WARNING: please use MorganGenerator +126: [12:24:23] DEPRECATION WARNING: please use MorganGenerator +126: [12:24:23] DEPRECATION WARNING: please use MorganGenerator +126: [12:24:23] DEPRECATION WARNING: please use MorganGenerator +126: [12:24:23] DEPRECATION WARNING: please use MorganGenerator +126: [12:24:23] DEPRECATION WARNING: please use MorganGenerator +126: [12:24:23] DEPRECATION WARNING: please use MorganGenerator +126: [12:24:23] DEPRECATION WARNING: please use MorganGenerator +126: [12:24:23] DEPRECATION WARNING: please use MorganGenerator +126: [12:24:23] DEPRECATION WARNING: please use MorganGenerator +126: [12:24:23] DEPRECATION WARNING: please use MorganGenerator +126: [12:24:23] DEPRECATION WARNING: please use MorganGenerator +126: [12:24:23] DEPRECATION WARNING: please use MorganGenerator +126: [12:24:23] DEPRECATION WARNING: please use MorganGenerator +126: [12:24:23] DEPRECATION WARNING: please use MorganGenerator +126: [12:24:23] DEPRECATION WARNING: please use MorganGenerator +126: [12:24:23] DEPRECATION WARNING: please use MorganGenerator +126: [12:24:23] DEPRECATION WARNING: please use MorganGenerator +126: ....[12:24:23] DEPRECATION WARNING: please use AtomPairGenerator +126: [12:24:23] DEPRECATION WARNING: please use AtomPairGenerator +126: ....[12:24:23] DEPRECATION WARNING: please use AtomPairGenerator +126: [12:24:23] DEPRECATION WARNING: please use AtomPairGenerator +126: .[12:24:23] DEPRECATION WARNING: please use TopologicalTorsionGenerator +126: [12:24:23] DEPRECATION WARNING: please use TopologicalTorsionGenerator +126: [12:24:23] DEPRECATION WARNING: please use TopologicalTorsionGenerator +126: [12:24:23] DEPRECATION WARNING: please use TopologicalTorsionGenerator +126: [12:24:23] DEPRECATION WARNING: please use TopologicalTorsionGenerator +126: ..[12:24:23] DEPRECATION WARNING: please use TopologicalTorsionGenerator +126: [12:24:23] DEPRECATION WARNING: please use TopologicalTorsionGenerator +126: [12:24:23] DEPRECATION WARNING: please use TopologicalTorsionGenerator +126: [12:24:23] DEPRECATION WARNING: please use TopologicalTorsionGenerator +126: [12:24:23] DEPRECATION WARNING: please use TopologicalTorsionGenerator +126: [12:24:23] DEPRECATION WARNING: please use TopologicalTorsionGenerator +126: .[12:24:23] DEPRECATION WARNING: please use TopologicalTorsionGenerator +126: [12:24:23] DEPRECATION WARNING: please use TopologicalTorsionGenerator +156: . +156: ---------------------------------------------------------------------- +156: Ran 1 test in 0.063s +156: +156: OK +156: Testing Shape Helpers wrapper +126: ... +126: ---------------------------------------------------------------------- +126: Ran 31 tests in 12.787s +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 +147/236 Test #156: pyShapeHelpers ......................... Passed 0.55 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 -148/236 Test #157: testMolCatalog ......................... Passed 0.12 sec +159: ----------------- Test 1 +151: 3098432453 +148/236 Test #126: pyMolDescriptors ....................... Passed 14.18 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 -159: ----------------- Test 1 -146: validating reference data -148: [16:02:54] Molecule does not have explicit Hs. Consider calling AddHs() -160: Randomness seeded to: 1174488290 -160: file contourMol_1.svg gave hash 4125787245U not the expected 3634867913U -160: file contourMol_2.svg gave hash 2761342533U not the expected 1815941817U -160: file contourMol_3.svg gave hash 1333854566U not the expected 2579392727U -160: file contourMol_4.svg gave hash 4249475618U not the expected 2914799663U -160: file contourMol_5.svg gave hash 3376179346U not the expected 3792684719U -51: Randomness seeded to: 417442151 -51: =============================================================================== -51: All tests passed (14835 assertions in 14 test cases) -51: -149/236 Test #51: canonTestsCatch ........................ Passed 18.52 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 test1_6.svg gave hash 1109656969U not the expected 2635907956U 159: Done 159: ----------------- Test 2 -161: ----------------- Test 1 -160: file testGithub3226_1.png gave hash 632134109U not the expected 3165135374U 159: file test2_1.png gave hash 2467931916U not the expected 638584804U -160: file testGithub3226_2.png gave hash 1790248804U not the expected 643975155U -148: [16:02:54] Molecule does not have explicit Hs. Consider calling AddHs() 159: file test2_2.png gave hash 3737953282U not the expected 610424244U -160: file testGithub3226_3.png gave hash 1296655029U not the expected 3119571946U -161: file rxn_test1_1.png gave hash 2332294744U not the expected 801892091U 159: file test2_3.png gave hash 2294574389U not the expected 2179746375U 159: Done 159: ----------------- Test 4 -160: file testPNGMetadata_1.png gave hash 2053548476U not the expected 997629701U -161: file rxn_test1_2.png gave hash 3186000742U not the expected 507435337U 159: file test4_1.png gave hash 516573244U not the expected 3993974247U 159: Done 159: ----------------- Test 5 -161: file rxn_test1_3.png gave hash 2120547110U not the expected 1590809137U +160: Randomness seeded to: 4126484580 +160: file contourMol_1.svg gave hash 4125787245U not the expected 3634867913U 159: file test5_1.png gave hash 2590128341U not the expected 571291290U -151: 2200296040 +160: file contourMol_2.svg gave hash 2761342533U not the expected 1815941817U 159: file test5_2.png gave hash 2869651309U not the expected 97265124U -161: file rxn_test1_4.png gave hash 59268109U not the expected 1766700542U -160: file testPNGMetadata_2.png gave hash 1147517534U not the expected 1797853056U -161: file rxn_test1_5.png gave hash 3733738372U not the expected 2552100594U +158: . +158: ---------------------------------------------------------------------- +158: Ran 1 test in 0.038s +158: +158: OK +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: file test5_3.png gave hash 4285469383U not the expected 606188176U 159: Done 159: ----------------- Test 6 (atom labels) +160: file contourMol_5.svg gave hash 3376179346U not the expected 3792684719U +29: Checking against /build/reproducible-path/rdkit-202503.1/Code/ForceField/MMFF/test_data/MMFF94_reference.log... 159: Done 159: ----------------- Test 7 (backgrounds) -158: . -158: ---------------------------------------------------------------------- -158: Ran 1 test in 0.039s -158: -158: OK 159: file test7_1.png gave hash 3445382333U not the expected 1322246680U 159: file test7_2.png gave hash 4080486780U not the expected 1499012715U 159: Done @@ -27620,78 +27627,129 @@ 159: Done 159: ----------------- Test multi-threaded drawing 159: reading molecules -161: file rxn_test1_6.png gave hash 2102224395U not the expected 3791582903U +149/236 Test #158: pyMolCatalog ........................... Passed 0.93 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: generating reference drawings +148: [12:24:23] Molecule does not have explicit Hs. Consider calling AddHs() +161: ----------------- Test 1 +160: file testGithub3226_1.png gave hash 632134109U not the expected 3165135374U +160: file testGithub3226_2.png gave hash 1790248804U not the expected 643975155U +161: file rxn_test1_1.png gave hash 2332294744U not the expected 801892091U +160: file testGithub3226_3.png gave hash 1296655029U not the expected 3119571946U +161: file rxn_test1_2.png gave hash 3186000742U not the expected 507435337U +160: file testPNGMetadata_1.png gave hash 2053548476U not the expected 997629701U +29: All 191 tests passed +29: done +29: ------------------------------------- +29: Unit tests for all MMFF constraint terms. +161: file rxn_test1_3.png gave hash 2120547110U not the expected 1590809137U +159: processing +159: launch :0 +159: launch :1 +159: launch :2 +159: launch :3 +161: file rxn_test1_4.png gave hash 59268109U not the expected 1766700542U +160: file testPNGMetadata_2.png gave hash 1147517534U not the expected 1797853056U +161: file rxn_test1_5.png gave hash 3733738372U not the expected 2552100594U +29: 10.0003 +161: file rxn_test1_6.png gave hash 2102224395U not the expected 3791582903U +29: done +29: ------------------------------------- +29: Unit test for MMFF TorsionConstraint close to 0 degrees. +29: done +29: ------------------------------------- +29: Unit tests for copying MMFF ForceFields. 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 -150/236 Test #158: pyMolCatalog ........................... Passed 0.54 sec +148: [12:24:24] Molecule does not have explicit Hs. Consider calling AddHs() +29: done +29: ------------------------------------- +29: Unit test for MMFF butane scan. +161: file rxn_test2_1.png gave hash 2631413446U not the expected 3551633840U +151: 907272180 +151: =============================================================================== +151: All tests passed (73 assertions in 3 test cases) +151: +150/236 Test #151: molAlignCatchTest ...................... Passed 4.89 sec 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_test2_1.png gave hash 2631413446U not the expected 3551633840U 161: 3 [cH:1]1[cH:2][cH:3][c:4][cH:5][cH:6]1>>CC(C)[c:1]1[cH:2][cH:3][c:4][cH:5][cH:6]1 CN1CCC(CC1)N(C)S(=O)(=O)c2ccccc2 CC(C)c1ccc(cc1)S(=O)(=O)N(C)C2CCN(CC2)C +160: [12:24:24] Font file /build/reproducible-path/rdkit-202503.1/Data/Fonts/ComicNeue-Regular.ttf not found. +160: [12:24:24] Falling back to original font file /build/reproducible-path/rdkit-202503.1/Data/Fonts/Telex-Regular.ttf. +160: file testHandDrawn-1.svg gave hash 1143910631U not the expected 2253418236U +160: [12:24:24] Font file /build/reproducible-path/rdkit-202503.1/Data/Fonts/ComicNeue-Regular.ttf not found. +160: [12:24:24] Falling back to original font file /build/reproducible-path/rdkit-202503.1/Data/Fonts/Telex-Regular.ttf. 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 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: [16:02:55] Font file /build/reproducible-path/rdkit-202503.1/Data/Fonts/ComicNeue-Regular.ttf not found. -160: [16:02:55] 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 -159: processing -159: launch :0 -159: launch :1 -159: launch :2 -159: launch :3 +160: file testHandDrawn-1.png gave hash 1854123184U not the expected 3894611804U 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: [16:02:55] Font file /build/reproducible-path/rdkit-202503.1/Data/Fonts/ComicNeue-Regular.ttf not found. -160: [16:02:55] 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 161: Done 161: ----------------- Test 3: test reactant highlighting -160: file testHandDrawn-1.png gave hash 1854123184U not the expected 3894611804U 161: file rxn_test3_1.png gave hash 3254654119U not the expected 4189980366U +160: [12:24:24] Font file /build/reproducible-path/rdkit-202503.1/Data/Fonts/ComicNeue-Regular.ttf not found. +160: [12:24:24] Falling back to original font file /build/reproducible-path/rdkit-202503.1/Data/Fonts/Telex-Regular.ttf. 161: Done 161: ----------------- Test 4: some examples from SMARTS in testing 161: draw! -161: file rxn_test4_1.png gave hash 4262495936U not the expected 2745201873U -161: done -160: [16:02:55] Font file /build/reproducible-path/rdkit-202503.1/Data/Fonts/ComicNeue-Regular.ttf not found. -160: [16:02:55] 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: [16:02:55] Font file /build/reproducible-path/rdkit-202503.1/Data/Fonts/ComicNeue-Regular.ttf not found. -160: [16:02:55] Falling back to original font file /build/reproducible-path/rdkit-202503.1/Data/Fonts/Telex-Regular.ttf. +160: [12:24:24] Font file /build/reproducible-path/rdkit-202503.1/Data/Fonts/ComicNeue-Regular.ttf not found. +160: [12:24:24] 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 160: file testHandDrawn-2.png gave hash 3861646972U not the expected 1443443188U -160: [16:02:55] Font file /build/reproducible-path/rdkit-202503.1/Data/Fonts/ComicNeue-Regular.ttf not found. -160: [16:02:55] Falling back to original font file /build/reproducible-path/rdkit-202503.1/Data/Fonts/Telex-Regular.ttf. -161: file rxn_test4_2.png gave hash 2281531937U not the expected 3094925886U +160: [12:24:24] Font file /build/reproducible-path/rdkit-202503.1/Data/Fonts/ComicNeue-Regular.ttf not found. +160: [12:24:24] Falling back to original font file /build/reproducible-path/rdkit-202503.1/Data/Fonts/Telex-Regular.ttf. +161: done 160: file testHandDrawn-3.svg gave hash 2359787964U not the expected 3982694296U -160: [16:02:55] Font file /build/reproducible-path/rdkit-202503.1/Data/Fonts/ComicNeue-Regular.ttf not found. -160: [16:02:55] Falling back to original font file /build/reproducible-path/rdkit-202503.1/Data/Fonts/Telex-Regular.ttf. +160: [12:24:24] Font file /build/reproducible-path/rdkit-202503.1/Data/Fonts/ComicNeue-Regular.ttf not found. +160: [12:24:24] Falling back to original font file /build/reproducible-path/rdkit-202503.1/Data/Fonts/Telex-Regular.ttf. +148: [12:24:24] Molecule does not have explicit Hs. Consider calling AddHs() +160: file testHandDrawn-3.png gave hash 2744546773U not the expected 865629432U +160: [12:24:24] Font file /build/reproducible-path/rdkit-202503.1/Data/Fonts/ComicNeue-Regular.ttf not found. +160: [12:24:24] 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: [12:24:24] Font file /build/reproducible-path/rdkit-202503.1/Data/Fonts/ComicNeue-Regular.ttf not found. +160: [12:24:24] 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 -151/236 Test #161: moldraw2DRxnTest1 ...................... Passed 0.57 sec +151/236 Test #161: moldraw2DRxnTest1 ...................... Passed 0.93 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 -160: file testHandDrawn-3.png gave hash 2744546773U not the expected 865629432U -160: [16:02:55] Font file /build/reproducible-path/rdkit-202503.1/Data/Fonts/ComicNeue-Regular.ttf not found. -160: [16:02:55] 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: [16:02:55] Font file /build/reproducible-path/rdkit-202503.1/Data/Fonts/ComicNeue-Regular.ttf not found. -160: [16:02:55] 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 -162: ...[16:02:55] Font file /build/reproducible-path/rdkit-202503.1/Code/GraphMol/MolDraw2D/Amadeus.ttf not found. -162: [16:02:55] Falling back to original font file /build/reproducible-path/rdkit-202503.1/Data/Fonts/Telex-Regular.ttf. -162: ..........[16:02:55] +148: [12:24:24] Molecule does not have explicit Hs. Consider calling AddHs() +146: validating reference data +29: done +152/236 Test #29: testMMFFForceField ..................... Passed 32.52 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 +148: [12:24:25] Molecule does not have explicit Hs. Consider calling AddHs() +162: ...[12:24:25] Font file /build/reproducible-path/rdkit-202503.1/Code/GraphMol/MolDraw2D/Amadeus.ttf not found. +162: [12:24:25] Falling back to original font file /build/reproducible-path/rdkit-202503.1/Data/Fonts/Telex-Regular.ttf. +148: [12:24:25] Molecule does not have explicit Hs. Consider calling AddHs() +162: ..........[12:24:25] 162: 162: **** 162: Pre-condition Violation @@ -27705,7 +27763,7 @@ 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# 0x0000FFFF91AD2680 in /lib/aarch64-linux-gnu/libboost_python313.so.1.83.0 +162: 5# 0x0000FFFF963B2680 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 @@ -27716,17 +27774,17 @@ 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# 0x0000FFFF910EC320 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so -162: 17# 0x0000FFFF910EC2B8 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so -162: 18# 0x0000FFFF910EC248 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so -162: 19# 0x0000FFFF910EC1E0 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so -162: 20# 0x0000FFFF910EC178 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so +162: 16# 0x0000FFFF959CC320 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so +162: 17# 0x0000FFFF959CC2B8 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so +162: 18# 0x0000FFFF959CC248 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so +162: 19# 0x0000FFFF959CC1E0 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so +162: 20# 0x0000FFFF959CC178 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# 0x0000FFFF91ACF25C in /lib/aarch64-linux-gnu/libboost_python313.so.1.83.0 +162: 26# 0x0000FFFF963AF25C 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# 0x000000000053DD10 in /usr/bin/python3 @@ -27758,31 +27816,19 @@ 162: 55# 0x000000000065F5F0 in /usr/bin/python3 162: 56# Py_RunMain in /usr/bin/python3 162: 57# Py_BytesMain in /usr/bin/python3 -162: 58# 0x0000FFFF933F229C in /lib/aarch64-linux-gnu/libc.so.6 +162: 58# 0x0000FFFF97CD229C 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: .[16:02:55] Molecule does not have explicit Hs. Consider calling AddHs() -151: 717096280 -151: =============================================================================== -151: All tests passed (73 assertions in 3 test cases) -151: -152/236 Test #151: molAlignCatchTest ...................... Passed 3.49 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 162: ...................... 162: ---------------------------------------------------------------------- -162: Ran 35 tests in 0.286s +162: Ran 35 tests in 0.558s 162: 162: OK 162: json lasso -153/236 Test #162: pyMolDraw2D ............................ Passed 0.89 sec +153/236 Test #162: pyMolDraw2D ............................ Passed 1.78 sec test 165 Start 165: FMCStest @@ -29754,55 +29800,46 @@ 165: 165: testFileSDF_RandomSet(): benchmark/chembl13_threshold_90.smi 165: ERROR: RDKit could not load input file -154/236 Test #165: FMCStest ............................... Passed 0.05 sec +154/236 Test #165: FMCStest ............................... Passed 0.24 sec test 166 Start 166: molHashCatchTest 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 -166: Randomness seeded to: 1319000495 +148: .[12:24:26] Molecule does not have explicit Hs. Consider calling AddHs() +160: file testHandDrawn-5a.svg gave hash 2796249138U not the expected 1567781555U +160: [12:24:26] Font file /build/reproducible-path/rdkit-202503.1/Data/Fonts/ComicNeue-Regular.ttf not found. +160: [12:24:26] Falling back to original font file /build/reproducible-path/rdkit-202503.1/Data/Fonts/Telex-Regular.ttf. +51: Randomness seeded to: 2036497351 +51: =============================================================================== +51: All tests passed (14835 assertions in 14 test cases) +51: +166: Randomness seeded to: 592798428 166: =============================================================================== 166: All tests passed (363 assertions in 14 test cases) 166: -155/236 Test #166: molHashCatchTest ....................... Passed 0.68 sec +155/236 Test #51: canonTestsCatch ........................ Passed 32.39 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 -160: file testHandDrawn-5a.svg gave hash 2796249138U not the expected 1567781555U -160: [16:02:56] Font file /build/reproducible-path/rdkit-202503.1/Data/Fonts/ComicNeue-Regular.ttf not found. -160: [16:02:56] Falling back to original font file /build/reproducible-path/rdkit-202503.1/Data/Fonts/Telex-Regular.ttf. +156/236 Test #166: molHashCatchTest ....................... Passed 0.71 sec 160: file testHandDrawn-5b.svg gave hash 4043231252U not the expected 66354106U -160: [16:02:56] Font file /build/reproducible-path/rdkit-202503.1/Data/Fonts/ComicNeue-Regular.ttf not found. -160: [16:02:56] Falling back to original font file /build/reproducible-path/rdkit-202503.1/Data/Fonts/Telex-Regular.ttf. -160: file testHandDrawn-5.png gave hash 2095603616U not the expected 828378555U -160: file testBrackets-5a.svg gave hash 279553678U not the expected 1447240271U -160: file testPositionVariation-1b.svg gave hash 3055422087U not the expected 3269244452U -167: .... -167: ---------------------------------------------------------------------- -167: Ran 4 tests in 0.024s -167: -167: OK -146: processing -146: launch :0 -146: launch :1 -146: launch :2 -146: launch :3 -160: [16:02:57] unrecognized bond typefile testGithub4238_1.png gave hash 3445079665U not the expected 2623427676U -156/236 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 -160: file testGithub4323_1.png gave hash 1102454531U not the expected 3075787867U +160: [12:24:27] Font file /build/reproducible-path/rdkit-202503.1/Data/Fonts/ComicNeue-Regular.ttf not found. +160: [12:24:27] Falling back to original font file /build/reproducible-path/rdkit-202503.1/Data/Fonts/Telex-Regular.ttf. +160: file testHandDrawn-5.png gave hash 2095603616U not the expected 828378555U 168: 168: TEST mol: Case1 Cc1ccccc1NC(=O)[C:7](C)[NH+]1CCCC1 Case1 -168: Time elapsed 0.002276 seconds +168: Time elapsed 0.002291 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 @@ -29839,11 +29876,12 @@ 168: 17: NOREF. Reference data NOT LISTED in test case. 168: 18: res= NULL,C1CC[NH+]([*:1])C1.Cc1ccccc1NC(=O)[C:2](C)[*:1] 168: 18: NOREF. Reference data NOT LISTED in test case. +160: file testBrackets-5a.svg gave hash 279553678U not the expected 1447240271U 168: 168: --- UNMATCHED Reference RESULTS: --- 168: 1: Cc1ccccc1NC(=O)[C:7](C)[NH+]1CCCC1,Case1,[*:1][C:7]([*:2])[*:3],C1CC[NH+]([*:3])C1.C[*:2].Cc1ccccc1NC(=O)[*:1] 168: ----------------------------------- -168: Time elapsed 0.002094 seconds +168: Time elapsed 0.002092 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 @@ -29885,7 +29923,7 @@ 168: ----------------------------------- 168: 168: TEST mol: ZINC21984717 Cc1c(C(=O)NCCO)[n+](=O)c2ccccc2n1[O-] ZINC21984717 -168: Time elapsed 0.010136 seconds +168: Time elapsed 0.001990 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] @@ -29925,7 +29963,7 @@ 168: ----------------------------------- 168: 168: TEST mol: Case1-SIMPLE CC(N1CC1)C(=O) Case1-SIMPLE -168: Time elapsed 0.000541 seconds +168: Time elapsed 0.000552 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] @@ -29947,7 +29985,7 @@ 168: ----------------------------------- 168: 168: TEST mol: Case1 Cc1ccccc1NC(=O)[C:7](C)[NH+]1CCCC1 Case1 -168: Time elapsed 0.002209 seconds +168: Time elapsed 0.014336 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 @@ -29984,43 +30022,13 @@ 168: 17: NOREF. Reference data NOT LISTED in test case. 168: 18: res= NULL,C1CC[NH+]([*:1])C1.Cc1ccccc1NC(=O)[C:2](C)[*:1] 168: 18: NOREF. Reference data NOT LISTED in test case. -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 168: 168: --- UNMATCHED Reference RESULTS: --- 168: 1: Cc1ccccc1NC(=O)[C:7](C)[NH+]1CCCC1,Case1,[*:1][C:7]([*:2])[*:3],C1CC[NH+]([*:3])C1.C[*:2].Cc1ccccc1NC(=O)[*:1] 168: ----------------------------------- 168: 168: TEST mol: Case2 O=C(OCc1ccccc1)C(O)c1ccccc1 Case2 -168: Time elapsed 0.010545 seconds +168: Time elapsed 0.002322 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 @@ -30043,6 +30051,7 @@ 168: 10: NOREF. Reference data NOT LISTED in test case. 168: 11: res= O=C(OC[*:1])C(O)[*:2],c1ccc([*:1])cc1.c1ccc([*:2])cc1 168: 11: NOREF. Reference data NOT LISTED in test case. +160: file testPositionVariation-1b.svg gave hash 3055422087U not the expected 3269244452U 168: 12: res= NULL,O=C(OCc1ccccc1)[*:1].OC(c1ccccc1)[*:1] 168: 12: NOREF. Reference data NOT LISTED in test case. 168: 13: res= c1ccc(C([*:1])[*:2])cc1,O=C(OCc1ccccc1)[*:1].O[*:2] @@ -30061,19 +30070,63 @@ 168: --- ALL PASSED --- 168: ----------------------------------- 168: 5 TEST CASES FAILED -157/236 Test #168: testMMPA ............................... Passed 0.29 sec +157/236 Test #168: testMMPA ............................... Passed 0.35 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 +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: [12:24:27] 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 +167: .... +167: ---------------------------------------------------------------------- +167: Ran 4 tests in 0.047s +167: +167: OK +158/236 Test #167: pyMolHash .............................. Passed 1.17 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 163: MCS: [#6]-[#6]1-[#6]-[#6]-[#6]-[#6]-[#6]-1 7 atoms, 7 bonds -163: Time elapsed 0.000 seconds +163: Time elapsed 0.120 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 0.071 seconds +163: Time elapsed 0.104 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 @@ -30081,27 +30134,27 @@ 163: 163: test3() 163: MCS: [#6]1:[#6]:[#6]:[#6]:[#6]:[#6]:1-[#6]-[#6](=[#8])-[#7]-[#6]-[#6]-[#6]-[#6] 14 atoms, 14 bonds -163: Time elapsed 0.015 seconds +163: 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 0.116 seconds +163: Time elapsed 0.226 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 0.104 seconds +163: Time elapsed 0.223 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 0.120 seconds +163: Time elapsed 0.258 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 0.160 seconds +163: Time elapsed 0.266 seconds 163: 163: testSegFault() 163: MCS: [#6]1:&@[#6]:&@[#6]:&@[#6]:&@[#6]:&@[#6]:&@1 6 atoms, 6 bonds -163: Time elapsed 0.021 seconds +163: Time elapsed 0.041 seconds 163: MCS MatchFusedRings: [#6]1:&@[#6]:&@[#6]:&@[#6]:&@[#6]:&@[#6]:&@1 6 atoms, 6 bonds -163: Time elapsed 0.007 seconds +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 0.027 seconds +163: Time elapsed 0.035 seconds 163: 163: testThreshold() 163: MCS: [#6]-[#6]-[#6] 3 atoms, 2 bonds @@ -30109,11 +30162,11 @@ 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 0.564 seconds +163: Time elapsed 0.818 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 0.414 seconds +163: Time elapsed 0.767 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 0.798 seconds +163: Time elapsed 0.797 seconds 163: 163: testAtomCompareIsotopes() 163: MCS: [0*]-[0*]-[13*] 3 atoms, 2 bonds @@ -30125,7 +30178,7 @@ 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: Time elapsed 0.005 seconds 163: 163: testAtomCompareAnyAtom() 163: MCS: [#1]-[#6]1:[#6]:[#6]:[#6]:[#6]:[#6]:1-[#6,#8] 8 atoms, 8 bonds @@ -30137,8 +30190,13 @@ 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 0.025 seconds +163: Time elapsed 0.017 seconds 163: MCS: [#6]-[#6]-[#8]-[#6]1:[#6](:[#6](:[#6]:[#6](:[#7]:1)-[#7]-[#6](=[#8])-[#6]-[#6]1:[#6]:[#6]:[#6]:[#6](:[#6]:1)-[#6,#8])-[#7])-[#6]#[#7] *c1cccc(CC(=O)Nc2cc(N)c(C#N)c(OCC)n2)c1 23 atoms, 24 bonds +146: processing +146: launch :0 +146: launch :1 +146: launch :2 +146: launch :3 163: Time elapsed 0.001 seconds 163: 163: test18() @@ -30149,15 +30207,15 @@ 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 0.205 seconds +163: Time elapsed 0.252 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 0.050 seconds +163: Time elapsed 0.091 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: 1 Seeds:1 MCS 25 atoms, 28 bonds for 0.0009 seconds. bond[0]=6 163: STATISTICS: -163: Total Growing Steps = 1, MCS found on 1 step, for 0.0008 seconds +163: Total Growing Steps = 1, MCS found on 1 step, for 0.0009 seconds 163: Initial Seeds = 1, Mismatched 0 163: Inspected Seeds = 2 163: Rejected by BestSize = 0 @@ -30272,62 +30330,33 @@ 163: res sub = 1 size=3 163: MCS: [#6]-[#6]-[#6] 3 atoms, 2 bonds 163: done +160: file testGithub4323_3.png gave hash 2734641420U not the expected 381907253U +160: [12:24:30] FIELDDISP info not found for DAT SGroup which isn't associated with an atom. SGroup will not be rendered. 150: processing 150: launch :0 150: launch :1 150: launch :2 150: launch :3 -29: Checking against /build/reproducible-path/rdkit-202503.1/Code/ForceField/MMFF/test_data/MMFF94_reference.log... -29: All 191 tests passed -29: -29: Computing MMFF94 energies for /build/reproducible-path/rdkit-202503.1/Code/ForceField/MMFF/test_data/MMFF94_hypervalent.smi... -169: ......... -169: ---------------------------------------------------------------------- -169: Ran 9 tests in 2.771s -169: -169: OK -158/236 Test #169: pyMMPA ................................. Passed 3.38 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 -163: [16:03:01] The provided InitialSeed is not an MCS and will be ignored -160: file testGithub4323_3.png gave hash 2734641420U not the expected 381907253U -160: [16:03:01] FIELDDISP info not found for DAT SGroup which isn't associated with an atom. SGroup will not be rendered. -164: ........................................[16:03:01] The provided InitialSeed is not an MCS and will be ignored -164: [16:03:01] The provided InitialSeed is not an MCS and will be ignored -164: [16:03:01] The provided InitialSeed is not an MCS and will be ignored -164: .[16:03:01] The provided InitialSeed is not an MCS and will be ignored -164: [16:03:01] The provided InitialSeed is not an MCS and will be ignored -164: [16:03:01] The provided InitialSeed is not an MCS and will be ignored -164: .[16:03:01] The provided InitialSeed is not an MCS and will be ignored -164: [16:03:01] The provided InitialSeed is not an MCS and will be ignored -164: [16:03:01] The provided InitialSeed is not an MCS and will be ignored -164: .[16:03:02] The provided InitialSeed is not an MCS and will be ignored -164: [16:03:02] The provided InitialSeed is not an MCS and will be ignored -164: [16:03:02] The provided InitialSeed is not an MCS and will be ignored -164: ................. -164: ---------------------------------------------------------------------- -164: Ran 60 tests in 6.056s -164: -164: OK 160: file testFlexiCanvas.2a.png gave hash 1840424214U not the expected 2609920321U 160: file testFlexiCanvas.2b.png gave hash 3366044980U not the expected 3615599154U 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 -159/236 Test #164: pyFMCS ................................. Passed 6.59 sec +160: file testGithub4764.sz1.png gave hash 3992785979U not the expected 2179222277U +160: file testGithub4764.sz2.png gave hash 3438062002U not the expected 444262090U +160: file testGithub4764.sz3.png gave hash 850758438U not the expected 3567162200U +169: ......... +169: ---------------------------------------------------------------------- +169: Ran 9 tests in 3.531s +169: +169: OK +159/236 Test #169: pyMMPA ................................. Passed 4.33 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.png gave hash 3992785979U not the expected 2179222277U -160: file testGithub4764.sz2.png gave hash 3438062002U not the expected 444262090U -160: file testGithub4764.sz3.png gave hash 850758438U not the expected 3567162200U 160: file github5383_1.svg gave hash 2761342533U not the expected 1815941817U 160: file github5383_2.svg gave hash 2560846108U not the expected 0U 160: file github5383_1.png gave hash 482266761U not the expected 2893520928U @@ -30336,10 +30365,11 @@ 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: [16:03:02] 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: [12:24:31] 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 +163: [12:24:32] The provided InitialSeed is not an MCS and will be ignored 160: file github6336_1.png gave hash 1930712448U not the expected 2958833204U 160: file AtropManyChiralsEnhanced.svg gave hash 643650995U not the expected 2256768013U 160: file testWedgingShouldBeOnSingleBond.svg gave hash 2637422009U not the expected 1002741488U @@ -30352,13 +30382,38 @@ 160: =============================================================================== 160: All tests passed (6857 assertions in 116 test cases) 160: -160/236 Test #160: moldraw2DTestCatch ..................... Passed 9.65 sec +160/236 Test #160: moldraw2DTestCatch ..................... Passed 11.09 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 +164: ........................................[12:24:36] The provided InitialSeed is not an MCS and will be ignored +164: [12:24:36] The provided InitialSeed is not an MCS and will be ignored +164: [12:24:36] The provided InitialSeed is not an MCS and will be ignored +164: .[12:24:36] The provided InitialSeed is not an MCS and will be ignored +164: [12:24:36] The provided InitialSeed is not an MCS and will be ignored +164: [12:24:36] The provided InitialSeed is not an MCS and will be ignored +164: .[12:24:36] The provided InitialSeed is not an MCS and will be ignored +164: [12:24:36] The provided InitialSeed is not an MCS and will be ignored +164: [12:24:36] The provided InitialSeed is not an MCS and will be ignored +164: .[12:24:36] The provided InitialSeed is not an MCS and will be ignored +164: [12:24:36] The provided InitialSeed is not an MCS and will be ignored +164: [12:24:36] The provided InitialSeed is not an MCS and will be ignored +172: ..........[12:24:36] Too many matching bond pairs (1032) so can't continue. +164: ................. +164: ---------------------------------------------------------------------- +164: Ran 60 tests in 10.215s +164: +164: OK +161/236 Test #164: pyFMCS ................................. Passed 11.64 sec +test 173 + Start 173: testSynthonSpaceSubstructureSearch + +173: Test command: /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/SynthonSpaceSearch/testSynthonSpaceSubstructureSearch +173: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/SynthonSpaceSearch +173: Test timeout computed to be: 1500 159: Done 159: ----------------- Test Github #781: Rendering single-atom molecules 159: Done @@ -30376,6 +30431,11 @@ 159: Done 159: ----------------- Test Github774: upside-down drawings 159: file test774_1.png gave hash 4271933551U not the expected 428322245U +172: .... +172: ---------------------------------------------------------------------- +172: Ran 14 tests in 3.322s +172: +172: OK 159: file test774_2.png gave hash 3001633592U not the expected 4095288521U 159: Done 159: ----------------- Test 9 (molecule legends) @@ -30383,7 +30443,6 @@ 159: Done 159: ----------------- Test Github852: Lines used to wedge bonds are too thick 159: file test852_1.png gave hash 172981142U not the expected 271517011U -172: ..........[16:03:05] Too many matching bond pairs (1032) so can't continue. 159: file test852_2.png gave hash 330355316U not the expected 967452082U 159: ---------------- 159: ---------------- @@ -30391,7 +30450,14 @@ 159: ---------------- 159: Done 159: ----------------- Test Github860: Atom symbols in wrong order if bond comes from right +162/236 Test #172: pyRascalMCES ........................... Passed 4.71 sec 159: file test860_1.png gave hash 3780999807U not the expected 2835587240U +test 174 + Start 174: testSynthonSpaceRascalSearch + +174: Test command: /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/SynthonSpaceSearch/testSynthonSpaceRascalSearch +174: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/SynthonSpaceSearch +174: Test timeout computed to be: 1500 159: file test860_2.png gave hash 3452704378U not the expected 1116015475U 159: file test860_3.png gave hash 391459872U not the expected 1872467868U 159: Done @@ -30454,6 +30520,8 @@ 159: file test20_1.png gave hash 2819944294U not the expected 200877868U 159: file test20_2.png gave hash 3331636090U not the expected 1651164846U 159: file test20_3.png gave hash 4024902774U not the expected 1463603076U +170: Randomness seeded to: 2675303144 +170: [12:24:39] Timed out after 11 seconds. 159: file test20_4.png gave hash 2389521325U not the expected 1714613205U 159: Done 159: ----------------- Test 21 - different font @@ -30465,6 +30533,8 @@ 159: ----------------- Test Github 3305 - change and scale line widths. 159: file testGithub3305_1.png gave hash 3457577365U not the expected 3303791649U 159: file testGithub3305_2.png gave hash 3436809982U not the expected 4003267433U +173: Randomness seeded to: 3636648354 +173: [12:24:40] Writing the enumerated file may take quite some time and result in a large file. 159: file testGithub3305_3.png gave hash 1717897897U not the expected 273338209U 159: file testGithub3305_4.png gave hash 268184992U not the expected 3842605920U 159: file testGithub3305_4.svg gave hash 3625812711U not the expected 300865579U @@ -30472,7 +30542,6 @@ 159: file testGithub3305_5.svg gave hash 3310590632U not the expected 1335449325U 159: file testGithub3305_6.png gave hash 1460538730U not the expected 613418460U 159: file testGithub3305_7.png gave hash 2902968538U not the expected 2835747678U -29: Checking against /build/reproducible-path/rdkit-202503.1/Code/ForceField/MMFF/test_data/MMFF94_reference.log... 159: Done 159: ----------------- Test Github 3391 - maxFontSize interacting badly with DrawMolecules. 159: Done @@ -30484,60 +30553,26 @@ 159: Done 159: ----------------- Test AND queries 159: Done -161/236 Test #159: moldraw2DTest1 ......................... Passed 11.59 sec -test 173 - Start 173: testSynthonSpaceSubstructureSearch - -173: Test command: /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/SynthonSpaceSearch/testSynthonSpaceSubstructureSearch -173: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/SynthonSpaceSearch -173: Test timeout computed to be: 1500 -29: All 191 tests passed -29: done -29: ------------------------------------- -29: Unit tests for all MMFF constraint terms. -29: 10.0003 -29: done -29: ------------------------------------- -29: Unit test for MMFF TorsionConstraint close to 0 degrees. -29: done -29: ------------------------------------- -29: Unit tests for copying MMFF ForceFields. -29: done -29: ------------------------------------- -29: Unit test for MMFF butane scan. -29: done -162/236 Test #29: testMMFFForceField ..................... Passed 32.47 sec -test 174 - Start 174: testSynthonSpaceRascalSearch - -174: Test command: /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/SynthonSpaceSearch/testSynthonSpaceRascalSearch -174: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/SynthonSpaceSearch -174: Test timeout computed to be: 1500 -172: .... -172: ---------------------------------------------------------------------- -172: Ran 14 tests in 1.970s -172: -172: OK -163/236 Test #172: pyRascalMCES ........................... Passed 2.77 sec +163/236 Test #159: moldraw2DTest1 ......................... Passed 17.30 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: 1755494230 -175: [16:03:07] non kekulizable aromatic bond being treated as bond order 1 -175: [16:03:07] non kekulizable aromatic bond being treated as bond order 1 -175: [16:03:07] non kekulizable aromatic bond being treated as bond order 1 -175: [16:03:07] non kekulizable aromatic bond being treated as bond order 1 -175: [16:03:07] non kekulizable aromatic bond being treated as bond order 1 -175: [16:03:07] non kekulizable aromatic bond being treated as bond order 1 -175: [16:03:07] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored -175: [16:03:07] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored +175: Randomness seeded to: 919881500 +175: [12:24:40] non kekulizable aromatic bond being treated as bond order 1 +175: [12:24:40] non kekulizable aromatic bond being treated as bond order 1 +175: [12:24:40] non kekulizable aromatic bond being treated as bond order 1 +175: [12:24:40] non kekulizable aromatic bond being treated as bond order 1 +175: [12:24:40] non kekulizable aromatic bond being treated as bond order 1 +175: [12:24:40] non kekulizable aromatic bond being treated as bond order 1 +175: [12:24:40] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored +175: [12:24:40] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored 175: =============================================================================== 175: All tests passed (6577 assertions in 19 test cases) 175: -164/236 Test #175: testCIPLabeler ......................... Passed 0.19 sec +164/236 Test #175: testCIPLabeler ......................... Passed 0.58 sec test 176 Start 176: pyCIPLabelsWrapTest @@ -30546,33 +30581,20 @@ 176: Test timeout computed to be: 1500 176: .... 176: ---------------------------------------------------------------------- -176: Ran 4 tests in 0.077s +176: Ran 4 tests in 0.052s 176: 176: OK -165/236 Test #176: pyCIPLabelsWrapTest .................... Passed 0.31 sec +165/236 Test #176: pyCIPLabelsWrapTest .................... Passed 1.03 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: Randomness seeded to: 111216352 -173: [16:03:08] Writing the enumerated file may take quite some time and result in a large file. -152: .............[16:03:11] Molecule does not have explicit Hs. Consider calling AddHs() -173: [16:03:11] Building the fingerprints may take some time. -170: Randomness seeded to: 1628136223 -170: [16:03:11] Timed out after 11 seconds. -152: [16:03:12] Molecule does not have explicit Hs. Consider calling AddHs() -152: [16:03:12] Molecule does not have explicit Hs. Consider calling AddHs() -152: [16:03:12] Molecule does not have explicit Hs. Consider calling AddHs() -152: [16:03:12] Molecule does not have explicit Hs. Consider calling AddHs() -152: [16:03:12] Molecule does not have explicit Hs. Consider calling AddHs() -152: [16:03:12] Molecule does not have explicit Hs. Consider calling AddHs() -152: [16:03:12] Molecule does not have explicit Hs. Consider calling AddHs() -152: [16:03:12] Molecule does not have explicit Hs. Consider calling AddHs() -152: [16:03:12] Molecule does not have explicit Hs. Consider calling AddHs() -152: [16:03:12] Molecule does not have explicit Hs. Consider calling AddHs() -173: [16:03:12] +171: Randomness seeded to: 4179973074 +171: /build/reproducible-path/rdkit-202503.1/Code/GraphMol/RascalMCES/data/chembl_1907596.smi +173: [12:24:45] Building the fingerprints may take some time. +173: [12:24:46] 173: 173: **** 173: Invariant Violation @@ -30588,60 +30610,69 @@ 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# 0x0000AAAAE703DB50 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/SynthonSpaceSearch/testSynthonSpaceSubstructureSearch -173: 8# 0x0000AAAAE70866EC in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/SynthonSpaceSearch/testSynthonSpaceSubstructureSearch -173: 9# 0x0000AAAAE70870A0 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/SynthonSpaceSearch/testSynthonSpaceSubstructureSearch -173: 10# 0x0000AAAAE70874D4 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/SynthonSpaceSearch/testSynthonSpaceSubstructureSearch -173: 11# 0x0000AAAAE705A958 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/SynthonSpaceSearch/testSynthonSpaceSubstructureSearch -173: 12# 0x0000AAAAE705AEA4 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/SynthonSpaceSearch/testSynthonSpaceSubstructureSearch -173: 13# 0x0000AAAAE703CC10 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/SynthonSpaceSearch/testSynthonSpaceSubstructureSearch -173: 14# 0x0000FFFFA0B0229C in /lib/aarch64-linux-gnu/libc.so.6 +173: 7# 0x0000AAAACC24DB50 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/SynthonSpaceSearch/testSynthonSpaceSubstructureSearch +173: 8# 0x0000AAAACC2966EC in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/SynthonSpaceSearch/testSynthonSpaceSubstructureSearch +173: 9# 0x0000AAAACC2970A0 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/SynthonSpaceSearch/testSynthonSpaceSubstructureSearch +173: 10# 0x0000AAAACC2974D4 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/SynthonSpaceSearch/testSynthonSpaceSubstructureSearch +173: 11# 0x0000AAAACC26A958 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/SynthonSpaceSearch/testSynthonSpaceSubstructureSearch +173: 12# 0x0000AAAACC26AEA4 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/SynthonSpaceSearch/testSynthonSpaceSubstructureSearch +173: 13# 0x0000AAAACC24CC10 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/SynthonSpaceSearch/testSynthonSpaceSubstructureSearch +173: 14# 0x0000FFFF961D229C in /lib/aarch64-linux-gnu/libc.so.6 173: 15# __libc_start_main in /lib/aarch64-linux-gnu/libc.so.6 -173: 16# 0x0000AAAAE703CCF0 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/SynthonSpaceSearch/testSynthonSpaceSubstructureSearch +173: 16# 0x0000AAAACC24CCF0 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/SynthonSpaceSearch/testSynthonSpaceSubstructureSearch 173: ---------- 173: **** 173: -173: [16:03:12] Error:: in reaction amide-1 :: building molecule from synthons : 1-1 (c1cc[1*]ccc1C(=O)[1*]) and 2-1 ([1*]N1CCCC1) +173: [12:24:46] 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: [16:03:12] Explicit valence for atom # 4 C, 5, is greater than permitted -173: [16:03:12] Error:: in reaction error-1 :: building molecule from synthons : 1-1 (C(=[2*])=CC=[1*]) and 2-1 (ClC([2*])=CN=[1*]) +173: [12:24:46] Explicit valence for atom # 4 C, 5, is greater than permitted +173: [12:24:46] 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: [16:03:12] Complex queries can be slow. -173: [16:03:12] Complex queries can be slow. -173: [16:03:12] Complex queries can be slow. -173: [16:03:12] Complex queries can be slow. -173: [16:03:13] Complex queries can be slow. -173: [16:03:13] Complex queries can be slow. -173: [16:03:13] Complex queries can be slow. -171: Randomness seeded to: 793126968 -171: /build/reproducible-path/rdkit-202503.1/Code/GraphMol/RascalMCES/data/chembl_1907596.smi -173: [16:03:13] Complex queries can be slow. -173: [16:03:13] Complex queries can be slow. -173: [16:03:13] Complex queries can be slow. -173: [16:03:14] Complex queries can be slow. -152: ...[16:03:16] Molecule does not have explicit Hs. Consider calling AddHs() -152: [16:03:16] Molecule does not have explicit Hs. Consider calling AddHs() -152: [16:03:16] Molecule does not have explicit Hs. Consider calling AddHs() -152: [16:03:16] Molecule does not have explicit Hs. Consider calling AddHs() -152: [16:03:16] Molecule does not have explicit Hs. Consider calling AddHs() +173: [12:24:46] Complex queries can be slow. +173: [12:24:46] Complex queries can be slow. +152: .............[12:24:46] Molecule does not have explicit Hs. Consider calling AddHs() +173: [12:24:46] Complex queries can be slow. +152: [12:24:47] Molecule does not have explicit Hs. Consider calling AddHs() +152: [12:24:47] Molecule does not have explicit Hs. Consider calling AddHs() +152: [12:24:47] Molecule does not have explicit Hs. Consider calling AddHs() +152: [12:24:47] Molecule does not have explicit Hs. Consider calling AddHs() +152: [12:24:47] Molecule does not have explicit Hs. Consider calling AddHs() +152: [12:24:47] Molecule does not have explicit Hs. Consider calling AddHs() +173: [12:24:47] Complex queries can be slow. +152: [12:24:47] Molecule does not have explicit Hs. Consider calling AddHs() +152: [12:24:47] Molecule does not have explicit Hs. Consider calling AddHs() +152: [12:24:47] Molecule does not have explicit Hs. Consider calling AddHs() +152: [12:24:47] Molecule does not have explicit Hs. Consider calling AddHs() +173: [12:24:47] Complex queries can be slow. +173: [12:24:47] Complex queries can be slow. +173: [12:24:48] Complex queries can be slow. +173: [12:24:48] Complex queries can be slow. +173: [12:24:49] Complex queries can be slow. +173: [12:24:49] Complex queries can be slow. +173: [12:24:50] Complex queries can be slow. +152: ...[12:24:50] Molecule does not have explicit Hs. Consider calling AddHs() +152: [12:24:50] Molecule does not have explicit Hs. Consider calling AddHs() +152: [12:24:50] Molecule does not have explicit Hs. Consider calling AddHs() +152: [12:24:50] Molecule does not have explicit Hs. Consider calling AddHs() +152: [12:24:50] Molecule does not have explicit Hs. Consider calling AddHs() 152: ... 152: ---------------------------------------------------------------------- -152: Ran 19 tests in 22.800s +152: Ran 19 tests in 29.333s 152: 152: OK 152: Testing MolAlign Wrappers -166/236 Test #152: pyMolAlign ............................. Passed 23.75 sec +166/236 Test #152: pyMolAlign ............................. Passed 30.67 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: 1205512191 +178: Randomness seeded to: 1236098269 178: =============================================================================== 178: All tests passed (111 assertions in 3 test cases) 178: -167/236 Test #178: deprotectTest .......................... Passed 0.11 sec +167/236 Test #178: deprotectTest .......................... Passed 0.64 sec test 179 Start 179: pyDeprotect @@ -30650,7 +30681,7 @@ 179: Test timeout computed to be: 1500 179: ..... 179: ---------------------------------------------------------------------- -179: Ran 5 tests in 0.057s +179: Ran 5 tests in 0.135s 179: 179: OK 179: Testing tert-butyldimethylsilyl @@ -30703,7 +30734,7 @@ 179: Testing acetamide 179: Testing carbobenzyloxy 179: Testing Acetal/Ketal -168/236 Test #179: pyDeprotect ............................ Passed 0.51 sec +168/236 Test #179: pyDeprotect ............................ Passed 1.39 sec test 180 Start 180: testReducedGraphs @@ -30728,7 +30759,7 @@ 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: -169/236 Test #180: testReducedGraphs ...................... Passed 0.07 sec +169/236 Test #180: testReducedGraphs ...................... Passed 0.16 sec test 181 Start 181: pyReducedGraphs @@ -30737,71 +30768,46 @@ 181: Test timeout computed to be: 1500 181: ..... 181: ---------------------------------------------------------------------- -181: Ran 5 tests in 0.025s +181: Ran 5 tests in 0.034s 181: 181: OK -170/236 Test #181: pyReducedGraphs ........................ Passed 0.59 sec +170/236 Test #181: pyReducedGraphs ........................ Passed 1.23 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 -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 23.15 seconds -171/236 Test #163: testFMCS ............................... Passed 23.20 sec +171/236 Test #182: trajectoryTest ......................... Passed 0.88 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: [16:03:18] ------------------------------------- -183: [16:03:18] Test1 -172/236 Test #182: trajectoryTest ......................... Passed 0.49 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: [16:03:19] done -183: [16:03:19] ------------------------------------- -183: [16:03:19] Test2 -183: [16:03:19] done -183: [16:03:19] ------------------------------------- -183: [16:03:19] Test3 (stereo options) -183: [16:03:19] Done (stereo options) -183: [16:03:19] ------------------------------------- -183: [16:03:19] Test4 (trusted smiles) -183: [16:03:19] Done (trusted smiles) -183: [16:03:19] ------------------------------------- -183: [16:03:19] Testing C++ docs -183: [16:03:19] Done (C++ doc tests) -183: [16:03:19] ------------------------------------- -183: [16:03:19] Testing C++ ring query: PatternHolder -183: [16:03:19] Done (C++ ring query tests) -183: [16:03:19] ------------------------------------- -183: [16:03:19] Testing C++ ring query: TautomerPatternHolder -183: [16:03:19] Done (C++ ring query tests) -183: [16:03:19] ------------------------------------- -183: [16:03:19] Add Patterns -184: Randomness seeded to: 3265264185 -184: =============================================================================== -184: All tests passed (171 assertions in 5 test cases) -184: -173/236 Test #184: substructLibraryCatchTest .............. Passed 1.41 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 +183: [12:24:55] ------------------------------------- +183: [12:24:55] Test1 +183: [12:24:56] done +183: [12:24:56] ------------------------------------- +183: [12:24:56] Test2 +183: [12:24:57] done +183: [12:24:57] ------------------------------------- +183: [12:24:57] Test3 (stereo options) +183: [12:24:57] Done (stereo options) +183: [12:24:57] ------------------------------------- +183: [12:24:57] Test4 (trusted smiles) +183: [12:24:57] Done (trusted smiles) +183: [12:24:57] ------------------------------------- +183: [12:24:57] Testing C++ docs +183: [12:24:57] Done (C++ doc tests) +183: [12:24:57] ------------------------------------- +183: [12:24:57] Testing C++ ring query: PatternHolder +183: [12:24:57] Done (C++ ring query tests) +183: [12:24:57] ------------------------------------- +183: [12:24:57] Testing C++ ring query: TautomerPatternHolder +183: [12:24:57] Done (C++ ring query tests) +183: [12:24:57] ------------------------------------- +183: [12:24:57] Add Patterns 177: VS001: PASSED 177: VS002: PASSED 177: VS003: PASSED @@ -31104,15 +31110,24 @@ 177: VS300: PASSED 177: Check finished: 0 molecules failed. 177: Failed: -174/236 Test #177: pyCIPLabelsValidation .................. Passed 13.09 sec -test 186 - Start 186: testRGroupDecomp +172/236 Test #177: pyCIPLabelsValidation .................. Passed 17.36 sec +test 184 + Start 184: substructLibraryCatchTest -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: [16:03:22] Non terminal R group defined. To allow set allowNonTerminalRGroups in RGroupDecompositionParameters -186: [16:03:22] WARNING: not removing hydrogen atom with dummy atom neighbors +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 +184: Randomness seeded to: 1337239633 +184: =============================================================================== +184: All tests passed (171 assertions in 5 test cases) +184: +173/236 Test #184: substructLibraryCatchTest .............. Passed 2.29 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 150: --------------------------------- 150: test O3A multithreading bug 150: @@ -31120,1182 +31135,1196 @@ 150: testCrippenO3A multithreading 150: 150: generating reference data -148: .........[16:03:24] Molecule does not have explicit Hs. Consider calling AddHs() -148: .[16:03:24] Molecule does not have explicit Hs. Consider calling AddHs() -148: [16:03:24] Molecule does not have explicit Hs. Consider calling AddHs() -148: [16:03:24] Molecule does not have explicit Hs. Consider calling AddHs() -148: [16:03:24] Molecule does not have explicit Hs. Consider calling AddHs() -148: [16:03:24] Molecule does not have explicit Hs. Consider calling AddHs() -148: [16:03:24] Molecule does not have explicit Hs. Consider calling AddHs() -148: [16:03:24] Molecule does not have explicit Hs. Consider calling AddHs() -148: [16:03:24] Molecule does not have explicit Hs. Consider calling AddHs() -148: [16:03:24] Molecule does not have explicit Hs. Consider calling AddHs() -148: [16:03:24] Molecule does not have explicit Hs. Consider calling AddHs() -148: .[16:03:24] Molecule does not have explicit Hs. Consider calling AddHs() -148: [16:03:24] Molecule does not have explicit Hs. Consider calling AddHs() -148: [16:03:24] Molecule does not have explicit Hs. Consider calling AddHs() -148: [16:03:24] Molecule does not have explicit Hs. Consider calling AddHs() -148: [16:03:24] Molecule does not have explicit Hs. Consider calling AddHs() -148: [16:03:24] Molecule does not have explicit Hs. Consider calling AddHs() -148: [16:03:24] Molecule does not have explicit Hs. Consider calling AddHs() -148: [16:03:24] Molecule does not have explicit Hs. Consider calling AddHs() -148: [16:03:24] Molecule does not have explicit Hs. Consider calling AddHs() -148: [16:03:24] Molecule does not have explicit Hs. Consider calling AddHs() +183: [12:25:04] ------------------------------------- +183: [12:25:04] testing PatternHolder +183: [12:25:04] ------------------------------------- +183: [12:25:04] testing TautomerPatternHolder 150: processing 150: launch :0 150: launch :1 150: launch :2 150: launch :3 -173: [16:03:26] Complex queries can be slow. -173: [16:03:26] Complex queries can be slow. -173: [16:03:26] Complex queries can be slow. -173: [16:03:26] Complex queries can be slow. -173: [16:03:26] Complex queries can be slow. -173: [16:03:27] Complex queries can be slow. -183: [16:03:27] ------------------------------------- -183: [16:03:27] testing PatternHolder +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 40.41 seconds +183: [12:25:05] ------------------------------------- +183: [12:25:05] testSegFaultInHolder +183: [12:25:05] SMILES Parse Error: syntax error while parsing: dsafsdf +183: [12:25:05] SMILES Parse Error: check for mistakes around position 1: +183: [12:25:05] dsafsdf +183: [12:25:05] ^ +183: [12:25:05] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +183: [12:25:05] SMILES Parse Error: syntax error while parsing: dsafsdf +183: [12:25:05] SMILES Parse Error: check for mistakes around position 1: +183: [12:25:05] dsafsdf +183: [12:25:05] ^ +183: [12:25:05] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +183: [12:25:05] SMILES Parse Error: syntax error while parsing: dsafsdf +183: [12:25:05] SMILES Parse Error: check for mistakes around position 1: +183: [12:25:05] dsafsdf +183: [12:25:05] ^ +183: [12:25:05] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +183: [12:25:05] SMILES Parse Error: syntax error while parsing: dsafsdf +183: [12:25:05] SMILES Parse Error: check for mistakes around position 1: +183: [12:25:05] dsafsdf +183: [12:25:05] ^ +183: [12:25:05] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +183: [12:25:05] SMILES Parse Error: syntax error while parsing: dsafsdf +183: [12:25:05] SMILES Parse Error: check for mistakes around position 1: +183: [12:25:05] dsafsdf +183: [12:25:05] ^ +183: [12:25:05] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +183: [12:25:05] SMILES Parse Error: syntax error while parsing: dsafsdf +183: [12:25:05] SMILES Parse Error: check for mistakes around position 1: +183: [12:25:05] dsafsdf +183: [12:25:05] ^ +183: [12:25:05] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +183: [12:25:05] SMILES Parse Error: syntax error while parsing: dsafsdf +183: [12:25:05] SMILES Parse Error: check for mistakes around position 1: +183: [12:25:05] dsafsdf +183: [12:25:05] ^ +183: [12:25:05] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +183: [12:25:05] SMILES Parse Error: syntax error while parsing: dsafsdf +183: [12:25:05] SMILES Parse Error: check for mistakes around position 1: +183: [12:25:05] dsafsdf +183: [12:25:05] ^ +183: [12:25:05] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +183: [12:25:05] SMILES Parse Error: syntax error while parsing: dsafsdf +183: [12:25:05] SMILES Parse Error: check for mistakes around position 1: +183: [12:25:05] dsafsdf +183: [12:25:05] ^ +183: [12:25:05] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +183: [12:25:05] SMILES Parse Error: syntax error while parsing: dsafsdf +183: [12:25:05] SMILES Parse Error: check for mistakes around position 1: +183: [12:25:05] dsafsdf +183: [12:25:05] ^ +183: [12:25:05] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +183: [12:25:05] SMILES Parse Error: syntax error while parsing: dsafsdf +183: [12:25:05] SMILES Parse Error: check for mistakes around position 1: +183: [12:25:05] dsafsdf +183: [12:25:05] ^ +183: [12:25:05] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +183: [12:25:05] SMILES Parse Error: syntax error while parsing: dsafsdf +183: [12:25:05] SMILES Parse Error: check for mistakes around position 1: +183: [12:25:05] dsafsdf +183: [12:25:05] ^ +183: [12:25:05] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +183: [12:25:05] SMILES Parse Error: syntax error while parsing: dsafsdf +183: [12:25:05] SMILES Parse Error: check for mistakes around position 1: +183: [12:25:05] dsafsdf +183: [12:25:05] ^ +183: [12:25:05] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +183: [12:25:05] SMILES Parse Error: syntax error while parsing: dsafsdf +183: [12:25:05] SMILES Parse Error: check for mistakes around position 1: +183: [12:25:05] dsafsdf +183: [12:25:05] ^ +183: [12:25:05] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +183: [12:25:05] SMILES Parse Error: syntax error while parsing: dsafsdf +183: [12:25:05] SMILES Parse Error: check for mistakes around position 1: +183: [12:25:05] dsafsdf +183: [12:25:05] ^ +183: [12:25:05] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +183: [12:25:05] SMILES Parse Error: syntax error while parsing: dsafsdf +183: [12:25:05] SMILES Parse Error: check for mistakes around position 1: +183: [12:25:05] dsafsdf +183: [12:25:05] ^ +183: [12:25:05] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +183: [12:25:05] SMILES Parse Error: syntax error while parsing: dsafsdf +183: [12:25:05] SMILES Parse Error: check for mistakes around position 1: +183: [12:25:05] dsafsdf +183: [12:25:05] ^ +183: [12:25:05] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +183: [12:25:05] SMILES Parse Error: syntax error while parsing: dsafsdf +183: [12:25:05] SMILES Parse Error: check for mistakes around position 1: +183: [12:25:05] dsafsdf +183: [12:25:05] ^ +183: [12:25:05] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +183: [12:25:05] SMILES Parse Error: syntax error while parsing: dsafsdf +183: [12:25:05] SMILES Parse Error: check for mistakes around position 1: +183: [12:25:05] dsafsdf +183: [12:25:05] ^ +183: [12:25:05] SMILES Parse Error: syntax error while parsing: dsafsdf +183: [12:25:05] SMILES Parse Error: check for mistakes around position 1: +183: [12:25:05] [12:25:05] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +183: [12:25:05] SMILES Parse Error: syntax error while parsing: dsafsdf +183: [12:25:05] SMILES Parse Error: check for mistakes around position 1: +183: [12:25:05] dsafsdf +183: [12:25:05] ^ +183: [12:25:05] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +183: [12:25:05] SMILES Parse Error: syntax error while parsing: dsafsdf +183: [12:25:05] SMILES Parse Error: check for mistakes around position 1: +183: [12:25:05] dsafsdf +183: [12:25:05] ^ +183: [12:25:05] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +183: [12:25:05] SMILES Parse Error: syntax error while parsing: dsafsdf +183: [12:25:05] SMILES Parse Error: syntax error while parsing: dsafsdf +183: [12:25:05] SMILES Parse Error: check for mistakes around position 1: +183: [12:25:05] dsafsdf +183: [12:25:05] ^ +183: [12:25:05] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +183: [12:25:05] SMILES Parse Error: syntax error while parsing: dsafsdf +183: [12:25:05] SMILES Parse Error: check for mistakes around position 1: +183: [12:25:05] dsafsdf +183: [12:25:05] ^ +183: [12:25:05] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +183: [12:25:05] SMILES Parse Error: syntax error while parsing: dsafsdf +183: [12:25:05] SMILES Parse Error: check for mistakes around position 1: +183: [12:25:05] dsafsdf +183: [12:25:05] ^ +183: [12:25:05] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +183: [12:25:05] SMILES Parse Error: syntax error while parsing: dsafsdf +183: [12:25:05] SMILES Parse Error: check for mistakes around position 1: +183: [12:25:05] dsafsdf +183: [12:25:05] ^ +183: [12:25:05] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +183: [12:25:05] SMILES Parse Error: syntax error while parsing: dsafsdf +183: [12:25:05] SMILES Parse Error: check for mistakes around position 1: +183: [12:25:05] dsafsdf +183: [12:25:05] ^ +183: [12:25:05] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +183: dsafsdf +183: [12:25:05] ^ +183: [12:25:05] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +183: [12:25:05] SMILES Parse Error: syntax error while parsing: dsafsdf +183: [12:25:05] SMILES Parse Error: check for mistakes around position 1: +183: [12:25:05] dsafsdf +183: [12:25:05] ^ +183: [12:25:05] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +183: [12:25:05] SMILES Parse Error: syntax error while parsing: dsafsdf +183: [12:25:05] SMILES Parse Error: check for mistakes around position 1: +183: [12:25:05] dsafsdf +183: [12:25:05] ^ +183: [12:25:05] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +183: [12:25:05] SMILES Parse Error: syntax error while parsing: dsafsdf +183: [12:25:05] SMILES Parse Error: check for mistakes around position 1: +183: [12:25:05] dsafsdf +183: [12:25:05] ^ +183: [12:25:05] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +183: [12:25:05] SMILES Parse Error: syntax error while parsing: dsafsdf +183: [12:25:05] SMILES Parse Error: check for mistakes around position 1: +183: [12:25:05] dsafsdf +183: [12:25:05] ^ +183: [12:25:05] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +183: [12:25:05] SMILES Parse Error: syntax error while parsing: dsafsdf +183: [12:25:05] SMILES Parse Error: check for mistakes around position 1: +183: [12:25:05] dsafsdf +183: [12:25:05] ^ +183: [12:25:05] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +183: [12:25:05] SMILES Parse Error: syntax error while parsing: dsafsdf +183: [12:25:05] SMILES Parse Error: check for mistakes around position 1: +183: [12:25:05] dsafsdf +183: [12:25:05] ^ +183: [12:25:05] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +183: [12:25:05] SMILES Parse Error: syntax error while parsing: dsafsdf +183: [12:25:05] SMILES Parse Error: check for mistakes around position 1: +183: [12:25:05] dsafsdf +183: [12:25:05] ^ +183: [12:25:05] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +183: [12:25:05] SMILES Parse Error: syntax error while parsing: dsafsdf +183: [12:25:05] SMILES Parse Error: check for mistakes around position 1: +183: [12:25:05] dsafsdf +183: [12:25:05] ^ +183: [12:25:05] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +183: [12:25:05] SMILES Parse Error: syntax error while parsing: dsafsdf +183: [12:25:05] SMILES Parse Error: check for mistakes around position 1: +183: [12:25:05] dsafsdf +183: [12:25:05] ^ +183: [12:25:05] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +183: [12:25:05] SMILES Parse Error: syntax error while parsing: dsafsdf +183: [12:25:05] SMILES Parse Error: check for mistakes around position 1: +183: [12:25:05] dsafsdf +183: [12:25:05] ^ +183: [12:25:05] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +183: [12:25:05] SMILES Parse Error: syntax error while parsing: dsafsdf +183: [12:25:05] SMILES Parse Error: check for mistakes around position 1: +183: [12:25:05] dsafsdf +183: [12:25:05] ^ +183: [12:25:05] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +183: [12:25:05] SMILES Parse Error: syntax error while parsing: dsafsdf +183: [12:25:05] SMILES Parse Error: check for mistakes around position 1: +183: [12:25:05] dsafsdf +183: [12:25:05] ^ +183: [12:25:05] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +183: [12:25:05] SMILES Parse Error: syntax error while parsing: dsafsdf +183: [12:25:05] SMILES Parse Error: check for mistakes around position 1: +183: [12:25:05] dsafsdf +183: [12:25:05] ^ +183: [12:25:05] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +183: [12:25:05] SMILES Parse Error: check for mistakes around position 1: +183: [12:25:05] dsafsdf +183: [12:25:05] ^ +183: [12:25:05] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +183: [12:25:05] SMILES Parse Error: syntax error while parsing: dsafsdf +183: [12:25:05] SMILES Parse Error: check for mistakes around position 1: +183: [12:25:05] dsafsdf +183: [12:25:05] ^ +183: [12:25:05] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +183: [12:25:05] SMILES Parse Error: syntax error while parsing: dsafsdf +183: [12:25:05] SMILES Parse Error: check for mistakes around position 1: +183: [12:25:05] dsafsdf +183: [12:25:05] ^ +183: [12:25:05] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +183: [12:25:05] SMILES Parse Error: syntax error while parsing: dsafsdf +183: [12:25:05] SMILES Parse Error: check for mistakes around position 1: +183: [12:25:05] dsafsdf +183: [12:25:05] ^ +183: [12:25:05] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +183: [12:25:05] SMILES Parse Error: syntax error while parsing: dsafsdf +183: [12:25:05] SMILES Parse Error: check for mistakes around position 1: +183: [12:25:05] dsafsdf +183: [12:25:05] ^ +183: [12:25:05] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +183: [12:25:05] SMILES Parse Error: syntax error while parsing: dsafsdf +183: [12:25:05] SMILES Parse Error: check for mistakes around position 1: +183: [12:25:05] dsafsdf +183: [12:25:05] ^ +183: [12:25:05] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +183: [12:25:05] SMILES Parse Error: syntax error while parsing: dsafsdf +183: [12:25:05] SMILES Parse Error: check for mistakes around position 1: +183: [12:25:05] dsafsdf +183: [12:25:05] ^ +183: [12:25:05] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +183: [12:25:05] SMILES Parse Error: syntax error while parsing: dsafsdf +183: [12:25:05] SMILES Parse Error: check for mistakes around position 1: +183: [12:25:05] dsafsdf +183: [12:25:05] ^ +183: [12:25:05] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +183: [12:25:05] SMILES Parse Error: syntax error while parsing: dsafsdf +183: [12:25:05] SMILES Parse Error: check for mistakes around position 1: +183: [12:25:05] dsafsdf +183: [12:25:05] ^ +183: [12:25:05] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +183: [12:25:05] SMILES Parse Error: syntax error while parsing: dsafsdf +183: [12:25:05] SMILES Parse Error: check for mistakes around position 1: +183: [12:25:05] dsafsdf +183: [12:25:05] ^ +183: [12:25:05] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +183: [12:25:05] SMILES Parse Error: syntax error while parsing: dsafsdf +183: [12:25:05] SMILES Parse Error: check for mistakes around position 1: +183: [12:25:05] dsafsdf +183: [12:25:05] ^ +183: [12:25:05] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +183: [12:25:05] SMILES Parse Error: syntax error while parsing: dsafsdf +183: [12:25:05] SMILES Parse Error: check for mistakes around position 1: +183: [12:25:05] dsafsdf +183: [12:25:05] ^ +183: [12:25:05] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +183: [12:25:05] SMILES Parse Error: syntax error while parsing: dsafsdf +183: [12:25:05] SMILES Parse Error: check for mistakes around position 1: +183: [12:25:05] dsafsdf +183: [12:25:05] ^ +183: [12:25:05] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +183: [12:25:05] SMILES Parse Error: syntax error while parsing: dsafsdf +183: [12:25:05] SMILES Parse Error: check for mistakes around position 1: +183: [12:25:05] dsafsdf +183: [12:25:05] ^ +183: [12:25:05] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +183: [12:25:05] SMILES Parse Error: syntax error while parsing: dsafsdf +183: [12:25:05] SMILES Parse Error: check for mistakes around position 1: +183: [12:25:05] dsafsdf +183: [12:25:05] ^ +183: [12:25:05] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +183: [12:25:05] SMILES Parse Error: syntax error while parsing: dsafsdf +183: [12:25:05] SMILES Parse Error: check for mistakes around position 1: +183: [12:25:05] dsafsdf +183: [12:25:05] ^ +183: [12:25:05] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +183: [12:25:05] SMILES Parse Error: syntax error while parsing: dsafsdf +183: [12:25:05] SMILES Parse Error: check for mistakes around position 1: +183: [12:25:05] dsafsdf +183: [12:25:05] ^ +183: [12:25:05] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +183: [12:25:05] SMILES Parse Error: syntax error while parsing: dsafsdf +183: [12:25:05] SMILES Parse Error: check for mistakes around position 1: +183: [12:25:05] dsafsdf +183: [12:25:05] ^ +183: [12:25:05] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +183: [12:25:05] SMILES Parse Error: syntax error while parsing: dsafsdf +183: [12:25:05] SMILES Parse Error: check for mistakes around position 1: +183: [12:25:05] dsafsdf +183: [12:25:05] ^ +183: [12:25:05] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +183: [12:25:05] SMILES Parse Error: syntax error while parsing: dsafsdf +183: [12:25:05] SMILES Parse Error: check for mistakes around position 1: +183: [12:25:05] dsafsdf +183: [12:25:05] ^ +183: [12:25:05] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +183: [12:25:05] SMILES Parse Error: syntax error while parsing: dsafsdf +183: [12:25:05] SMILES Parse Error: check for mistakes around position 1: +183: [12:25:05] dsafsdf +183: [12:25:05] ^ +183: [12:25:05] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +183: [12:25:05] SMILES Parse Error: syntax error while parsing: dsafsdf +183: [12:25:05] SMILES Parse Error: check for mistakes around position 1: +183: [12:25:05] dsafsdf +183: [12:25:05] ^ +183: [12:25:05] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +183: [12:25:05] SMILES Parse Error: syntax error while parsing: dsafsdf +183: [12:25:05] SMILES Parse Error: check for mistakes around position 1: +183: [12:25:05] dsafsdf +183: [12:25:05] ^ +183: [12:25:05] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +183: [12:25:05] SMILES Parse Error: syntax error while parsing: dsafsdf +183: [12:25:05] SMILES Parse Error: check for mistakes around position 1: +183: [12:25:05] dsafsdf +183: [12:25:05] ^ +183: [12:25:05] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +183: [12:25:05] SMILES Parse Error: syntax error while parsing: dsafsdf +183: [12:25:05] SMILES Parse Error: check for mistakes around position 1: +183: [12:25:05] dsafsdf +183: [12:25:05] ^ +183: [12:25:05] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +183: [12:25:05] SMILES Parse Error: syntax error while parsing: dsafsdf +183: [12:25:05] SMILES Parse Error: check for mistakes around position 1: +183: [12:25:05] dsafsdf +183: [12:25:05] ^ +183: [12:25:05] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +183: [12:25:05] SMILES Parse Error: syntax error while parsing: dsafsdf +183: [12:25:05] SMILES Parse Error: check for mistakes around position 1: +183: [12:25:05] dsafsdf +183: [12:25:05] ^ +183: [12:25:05] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +183: [12:25:05] SMILES Parse Error: syntax error while parsing: dsafsdf +183: [12:25:05] SMILES Parse Error: check for mistakes around position 1: +183: [12:25:05] dsafsdf +183: [12:25:05] ^ +183: [12:25:05] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +183: [12:25:05] SMILES Parse Error: syntax error while parsing: dsafsdf +183: [12:25:05] SMILES Parse Error: check for mistakes around position 1: +183: [12:25:05] dsafsdf +183: [12:25:05] ^ +183: [12:25:05] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +183: [12:25:05] SMILES Parse Error: syntax error while parsing: dsafsdf +183: [12:25:05] SMILES Parse Error: check for mistakes around position 1: +183: [12:25:05] dsafsdf +183: [12:25:05] ^ +183: [12:25:05] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +183: [12:25:05] SMILES Parse Error: syntax error while parsing: dsafsdf +183: [12:25:05] SMILES Parse Error: check for mistakes around position 1: +183: [12:25:05] dsafsdf +183: [12:25:05] ^ +183: [12:25:05] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +183: [12:25:05] SMILES Parse Error: syntax error while parsing: dsafsdf +183: [12:25:05] SMILES Parse Error: check for mistakes around position 1: +183: [12:25:05] dsafsdf +183: [12:25:05] ^ +183: [12:25:05] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +183: [12:25:05] SMILES Parse Error: syntax error while parsing: dsafsdf +183: [12:25:05] SMILES Parse Error: check for mistakes around position 1: +183: [12:25:05] dsafsdf +183: [12:25:05] ^ +183: [12:25:05] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +183: [12:25:05] SMILES Parse Error: syntax error while parsing: dsafsdf +183: [12:25:05] SMILES Parse Error: check for mistakes around position 1: +183: [12:25:05] dsafsdf +183: [12:25:05] ^ +183: [12:25:05] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +183: [12:25:05] SMILES Parse Error: syntax error while parsing: dsafsdf +183: [12:25:05] SMILES Parse Error: check for mistakes around position 1: +183: [12:25:05] dsafsdf +183: [12:25:05] ^ +183: [12:25:05] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +183: [12:25:05] SMILES Parse Error: syntax error while parsing: dsafsdf +183: [12:25:05] SMILES Parse Error: check for mistakes around position 1: +183: [12:25:05] dsafsdf +183: [12:25:05] ^ +183: [12:25:05] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +183: [12:25:05] SMILES Parse Error: syntax error while parsing: dsafsdf +183: [12:25:05] SMILES Parse Error: check for mistakes around position 1: +183: [12:25:05] dsafsdf +183: [12:25:05] ^ +183: [12:25:05] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +183: [12:25:05] SMILES Parse Error: syntax error while parsing: dsafsdf +183: [12:25:05] SMILES Parse Error: check for mistakes around position 1: +183: [12:25:05] dsafsdf +183: [12:25:05] ^ +183: [12:25:05] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +183: [12:25:05] SMILES Parse Error: syntax error while parsing: dsafsdf +183: [12:25:05] SMILES Parse Error: check for mistakes around position 1: +183: [12:25:05] dsafsdf +183: [12:25:05] ^ +183: [12:25:05] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +183: [12:25:05] SMILES Parse Error: syntax error while parsing: dsafsdf +183: [12:25:05] SMILES Parse Error: check for mistakes around position 1: +183: [12:25:05] dsafsdf +183: [12:25:05] ^ +183: [12:25:05] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +183: [12:25:05] SMILES Parse Error: syntax error while parsing: dsafsdf +183: [12:25:05] SMILES Parse Error: check for mistakes around position 1: +183: [12:25:05] dsafsdf +183: [12:25:05] ^ +183: [12:25:05] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +183: [12:25:05] SMILES Parse Error: syntax error while parsing: dsafsdf +183: [12:25:05] SMILES Parse Error: check for mistakes around position 1: +183: [12:25:05] dsafsdf +183: [12:25:05] ^ +183: [12:25:05] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +183: [12:25:05] SMILES Parse Error: syntax error while parsing: dsafsdf +183: [12:25:05] SMILES Parse Error: check for mistakes around position 1: +183: [12:25:05] dsafsdf +183: [12:25:05] ^ +183: [12:25:05] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +183: [12:25:05] SMILES Parse Error: syntax error while parsing: dsafsdf +183: [12:25:05] SMILES Parse Error: check for mistakes around position 1: +183: [12:25:05] dsafsdf +183: [12:25:05] ^ +183: [12:25:05] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +183: [12:25:05] SMILES Parse Error: syntax error while parsing: dsafsdf +183: [12:25:05] SMILES Parse Error: check for mistakes around position 1: +183: [12:25:05] dsafsdf +183: [12:25:05] ^ +183: [12:25:05] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +183: [12:25:05] SMILES Parse Error: syntax error while parsing: dsafsdf +183: [12:25:05] SMILES Parse Error: check for mistakes around position 1: +183: [12:25:05] dsafsdf +183: [12:25:05] ^ +183: [12:25:05] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +183: [12:25:05] SMILES Parse Error: syntax error while parsing: dsafsdf +183: [12:25:05] SMILES Parse Error: check for mistakes around position 1: +183: [12:25:05] dsafsdf +183: [12:25:05] ^ +183: [12:25:05] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +183: [12:25:05] SMILES Parse Error: syntax error while parsing: dsafsdf +183: [12:25:05] SMILES Parse Error: check for mistakes around position 1: +183: [12:25:05] dsafsdf +183: [12:25:05] ^ +183: [12:25:05] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +183: [12:25:05] SMILES Parse Error: syntax error while parsing: dsafsdf +183: [12:25:05] SMILES Parse Error: check for mistakes around position 1: +183: [12:25:05] dsafsdf +183: [12:25:05] ^ +183: [12:25:05] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +183: [12:25:05] SMILES Parse Error: syntax error while parsing: dsafsdf +183: [12:25:05] SMILES Parse Error: check for mistakes around position 1: +183: [12:25:05] dsafsdf +183: [12:25:05] ^ +183: [12:25:05] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +183: [12:25:05] SMILES Parse Error: syntax error while parsing: dsafsdf +183: [12:25:05] SMILES Parse Error: check for mistakes around position 1: +183: [12:25:05] dsafsdf +183: [12:25:05] ^ +183: [12:25:05] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +183: [12:25:05] SMILES Parse Error: syntax error while parsing: dsafsdf +183: [12:25:05] SMILES Parse Error: check for mistakes around position 1: +183: [12:25:05] dsafsdf +183: [12:25:05] ^ +183: [12:25:05] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +183: [12:25:05] SMILES Parse Error: syntax error while parsing: dsafsdf +183: [12:25:05] SMILES Parse Error: check for mistakes around position 1: +183: [12:25:05] dsafsdf +183: [12:25:05] ^ +183: [12:25:05] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +183: [12:25:05] SMILES Parse Error: syntax error while parsing: dsafsdf +183: [12:25:05] SMILES Parse Error: check for mistakes around position 1: +183: [12:25:05] dsafsdf +183: [12:25:05] ^ +183: [12:25:05] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +183: [12:25:05] SMILES Parse Error: syntax error while parsing: dsafsdf +183: [12:25:05] SMILES Parse Error: check for mistakes around position 1: +183: [12:25:05] dsafsdf +183: [12:25:05] ^ +183: [12:25:05] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +183: [12:25:05] SMILES Parse Error: syntax error while parsing: dsafsdf +183: [12:25:05] SMILES Parse Error: check for mistakes around position 1: +183: [12:25:05] dsafsdf +183: [12:25:05] ^ +183: [12:25:05] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +183: [12:25:05] SMILES Parse Error: syntax error while parsing: dsafsdf +183: [12:25:05] SMILES Parse Error: check for mistakes around position 1: +183: [12:25:05] dsafsdf +183: [12:25:05] ^ +183: [12:25:05] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +183: [12:25:05] SMILES Parse Error: syntax error while parsing: dsafsdf +183: [12:25:05] SMILES Parse Error: check for mistakes around position 1: +183: [12:25:05] dsafsdf +183: [12:25:05] ^ +183: [12:25:05] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +183: [12:25:05] SMILES Parse Error: syntax error while parsing: dsafsdf +183: [12:25:05] SMILES Parse Error: check for mistakes around position 1: +183: [12:25:05] dsafsdf +183: [12:25:05] ^ +183: [12:25:05] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +183: [12:25:05] SMILES Parse Error: syntax error while parsing: dsafsdf +183: [12:25:05] SMILES Parse Error: check for mistakes around position 1: +183: [12:25:05] dsafsdf +183: [12:25:05] ^ +183: [12:25:05] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +183: [12:25:05] SMILES Parse Error: syntax error while parsing: dsafsdf +183: [12:25:05] SMILES Parse Error: check for mistakes around position 1: +183: [12:25:05] dsafsdf +183: [12:25:05] ^ +183: [12:25:05] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +183: [12:25:05] SMILES Parse Error: syntax error while parsing: dsafsdf +183: [12:25:05] SMILES Parse Error: check for mistakes around position 1: +183: [12:25:05] dsafsdf +183: [12:25:05] ^ +183: [12:25:05] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +183: [12:25:05] SMILES Parse Error: syntax error while parsing: dsafsdf +183: [12:25:05] SMILES Parse Error: check for mistakes around position 1: +183: [12:25:05] dsafsdf +183: [12:25:05] ^ +183: [12:25:05] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +183: [12:25:05] SMILES Parse Error: syntax error while parsing: dsafsdf +183: [12:25:05] SMILES Parse Error: check for mistakes around position 1: +183: [12:25:05] dsafsdf +183: [12:25:05] ^ +183: [12:25:05] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +183: [12:25:05] SMILES Parse Error: syntax error while parsing: dsafsdf +183: [12:25:05] SMILES Parse Error: check for mistakes around position 1: +183: [12:25:05] dsafsdf +183: [12:25:05] ^ +183: [12:25:05] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +183: [12:25:05] SMILES Parse Error: syntax error while parsing: dsafsdf +183: [12:25:05] SMILES Parse Error: check for mistakes around position 1: +183: [12:25:05] dsafsdf +183: [12:25:05] ^ +183: [12:25:05] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +183: [12:25:05] SMILES Parse Error: syntax error while parsing: dsafsdf +183: [12:25:05] SMILES Parse Error: check for mistakes around position 1: +183: [12:25:05] dsafsdf +183: [12:25:05] ^ +183: [12:25:05] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +183: [12:25:05] SMILES Parse Error: syntax error while parsing: dsafsdf +183: [12:25:05] SMILES Parse Error: check for mistakes around position 1: +183: [12:25:05] dsafsdf +183: [12:25:05] ^ +183: [12:25:05] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +183: [12:25:05] SMILES Parse Error: syntax error while parsing: dsafsdf +183: [12:25:05] SMILES Parse Error: check for mistakes around position 1: +183: [12:25:05] dsafsdf +183: [12:25:05] ^ +183: [12:25:05] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +183: [12:25:05] SMILES Parse Error: syntax error while parsing: dsafsdf +183: [12:25:05] SMILES Parse Error: check for mistakes around position 1: +183: [12:25:05] dsafsdf +183: [12:25:05] ^ +183: [12:25:05] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +183: [12:25:05] SMILES Parse Error: syntax error while parsing: dsafsdf +183: [12:25:05] SMILES Parse Error: check for mistakes around position 1: +183: [12:25:05] dsafsdf +183: [12:25:05] ^ +183: [12:25:05] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +183: [12:25:05] SMILES Parse Error: syntax error while parsing: dsafsdf +183: [12:25:05] SMILES Parse Error: check for mistakes around position 1: +183: [12:25:05] dsafsdf +183: [12:25:05] ^ +183: [12:25:05] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +183: [12:25:05] SMILES Parse Error: syntax error while parsing: dsafsdf +183: [12:25:05] SMILES Parse Error: check for mistakes around position 1: +183: [12:25:05] dsafsdf +183: [12:25:05] ^ +183: [12:25:05] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +183: [12:25:05] SMILES Parse Error: syntax error while parsing: dsafsdf +183: [12:25:05] SMILES Parse Error: check for mistakes around position 1: +183: [12:25:05] dsafsdf +183: [12:25:05] ^ +183: [12:25:05] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +183: [12:25:05] SMILES Parse Error: syntax error while parsing: dsafsdf +183: [12:25:05] SMILES Parse Error: check for mistakes around position 1: +183: [12:25:05] dsafsdf +183: [12:25:05] ^ +183: [12:25:05] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +183: [12:25:05] SMILES Parse Error: syntax error while parsing: dsafsdf +183: [12:25:05] SMILES Parse Error: check for mistakes around position 1: +183: [12:25:05] dsafsdf +183: [12:25:05] ^ +183: [12:25:05] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +183: [12:25:05] SMILES Parse Error: syntax error while parsing: dsafsdf +183: [12:25:05] SMILES Parse Error: check for mistakes around position 1: +183: [12:25:05] dsafsdf +183: [12:25:05] ^ +183: [12:25:05] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +183: [12:25:05] SMILES Parse Error: syntax error while parsing: dsafsdf +183: [12:25:05] SMILES Parse Error: check for mistakes around position 1: +183: [12:25:05] dsafsdf +183: [12:25:05] ^ +183: [12:25:05] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +183: [12:25:05] SMILES Parse Error: syntax error while parsing: dsafsdf +183: [12:25:05] SMILES Parse Error: check for mistakes around position 1: +183: [12:25:05] dsafsdf +183: [12:25:05] ^ +183: [12:25:05] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +183: [12:25:05] SMILES Parse Error: syntax error while parsing: dsafsdf +183: [12:25:05] SMILES Parse Error: check for mistakes around position 1: +183: [12:25:05] dsafsdf +183: [12:25:05] ^ +183: [12:25:05] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +183: [12:25:05] SMILES Parse Error: syntax error while parsing: dsafsdf +183: [12:25:05] SMILES Parse Error: check for mistakes around position 1: +183: [12:25:05] dsafsdf +183: [12:25:05] ^ +183: [12:25:05] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +183: [12:25:05] SMILES Parse Error: syntax error while parsing: dsafsdf +183: [12:25:05] SMILES Parse Error: check for mistakes around position 1: +183: [12:25:05] dsafsdf +183: [12:25:05] ^ +183: [12:25:05] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +183: [12:25:05] SMILES Parse Error: syntax error while parsing: dsafsdf +183: [12:25:05] SMILES Parse Error: check for mistakes around position 1: +183: [12:25:05] dsafsdf +183: [12:25:05] ^ +183: [12:25:05] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +183: [12:25:05] SMILES Parse Error: syntax error while parsing: dsafsdf +183: [12:25:05] SMILES Parse Error: check for mistakes around position 1: +183: [12:25:05] dsafsdf +183: [12:25:05] ^ +183: [12:25:05] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +183: [12:25:05] SMILES Parse Error: syntax error while parsing: dsafsdf +183: [12:25:05] SMILES Parse Error: check for mistakes around position 1: +183: [12:25:05] dsafsdf +183: [12:25:05] ^ +183: [12:25:05] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +183: [12:25:05] SMILES Parse Error: syntax error while parsing: dsafsdf +183: [12:25:05] SMILES Parse Error: check for mistakes around position 1: +183: [12:25:05] dsafsdf +183: [12:25:05] ^ +183: [12:25:05] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +183: [12:25:05] SMILES Parse Error: syntax error while parsing: dsafsdf +183: [12:25:05] SMILES Parse Error: check for mistakes around position 1: +183: [12:25:05] dsafsdf +183: [12:25:05] ^ +183: [12:25:05] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +183: [12:25:05] SMILES Parse Error: syntax error while parsing: dsafsdf +183: [12:25:05] SMILES Parse Error: check for mistakes around position 1: +183: [12:25:05] dsafsdf +183: [12:25:05] ^ +183: [12:25:05] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +183: [12:25:05] SMILES Parse Error: syntax error while parsing: dsafsdf +183: [12:25:05] SMILES Parse Error: check for mistakes around position 1: +183: [12:25:05] dsafsdf +183: [12:25:05] ^ +183: [12:25:05] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +183: [12:25:05] SMILES Parse Error: syntax error while parsing: dsafsdf +183: [12:25:05] SMILES Parse Error: check for mistakes around position 1: +183: [12:25:05] dsafsdf +183: [12:25:05] ^ +183: [12:25:05] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +183: [12:25:05] SMILES Parse Error: syntax error while parsing: dsafsdf +183: [12:25:05] SMILES Parse Error: check for mistakes around position 1: +183: [12:25:05] dsafsdf +183: [12:25:05] ^ +183: [12:25:05] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +183: [12:25:05] SMILES Parse Error: syntax error while parsing: dsafsdf +183: [12:25:05] SMILES Parse Error: check for mistakes around position 1: +183: [12:25:05] dsafsdf +183: [12:25:05] ^ +183: [12:25:05] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +183: [12:25:05] SMILES Parse Error: syntax error while parsing: dsafsdf +183: [12:25:05] SMILES Parse Error: check for mistakes around position 1: +183: [12:25:05] dsafsdf +183: [12:25:05] ^ +183: [12:25:05] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +183: [12:25:05] SMILES Parse Error: syntax error while parsing: dsafsdf +183: [12:25:05] SMILES Parse Error: check for mistakes around position 1: +183: [12:25:05] dsafsdf +183: [12:25:05] ^ +183: [12:25:05] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +183: [12:25:05] SMILES Parse Error: syntax error while parsing: dsafsdf +183: [12:25:05] SMILES Parse Error: check for mistakes around position 1: +183: [12:25:05] dsafsdf +183: [12:25:05] ^ +183: [12:25:05] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +183: [12:25:05] SMILES Parse Error: syntax error while parsing: dsafsdf +183: [12:25:05] SMILES Parse Error: check for mistakes around position 1: +183: [12:25:05] dsafsdf +183: [12:25:05] ^ +183: [12:25:05] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +183: [12:25:05] SMILES Parse Error: syntax error while parsing: dsafsdf +183: [12:25:05] SMILES Parse Error: check for mistakes around position 1: +183: [12:25:05] dsafsdf +183: [12:25:05] ^ +183: [12:25:05] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +183: [12:25:05] SMILES Parse Error: syntax error while parsing: dsafsdf +183: [12:25:05] SMILES Parse Error: check for mistakes around position 1: +183: [12:25:05] dsafsdf +183: [12:25:05] ^ +183: [12:25:05] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +183: [12:25:05] SMILES Parse Error: syntax error while parsing: dsafsdf +183: [12:25:05] SMILES Parse Error: check for mistakes around position 1: +183: [12:25:05] dsafsdf +183: [12:25:05] ^ +183: [12:25:05] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +183: [12:25:05] SMILES Parse Error: syntax error while parsing: dsafsdf +183: [12:25:05] SMILES Parse Error: check for mistakes around position 1: +183: [12:25:05] dsafsdf +183: [12:25:05] ^ +183: [12:25:05] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +183: [12:25:05] SMILES Parse Error: syntax error while parsing: dsafsdf +183: [12:25:05] SMILES Parse Error: check for mistakes around position 1: +183: [12:25:05] dsafsdf +183: [12:25:05] ^ +183: [12:25:05] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +183: [12:25:05] SMILES Parse Error: syntax error while parsing: dsafsdf +183: [12:25:05] SMILES Parse Error: check for mistakes around position 1: +183: [12:25:05] dsafsdf +183: [12:25:05] ^ +183: [12:25:05] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +183: [12:25:05] SMILES Parse Error: syntax error while parsing: dsafsdf +183: [12:25:05] SMILES Parse Error: check for mistakes around position 1: +183: [12:25:05] dsafsdf +183: [12:25:05] ^ +183: [12:25:05] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +183: [12:25:05] SMILES Parse Error: syntax error while parsing: dsafsdf +183: [12:25:05] SMILES Parse Error: check for mistakes around position 1: +183: [12:25:05] dsafsdf +183: [12:25:05] ^ +183: [12:25:05] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +183: [12:25:05] SMILES Parse Error: syntax error while parsing: dsafsdf +183: [12:25:05] SMILES Parse Error: check for mistakes around position 1: +183: [12:25:05] dsafsdf +183: [12:25:05] ^ +183: [12:25:05] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +183: [12:25:05] SMILES Parse Error: syntax error while parsing: dsafsdf +183: [12:25:05] SMILES Parse Error: check for mistakes around position 1: +183: [12:25:05] dsafsdf +183: [12:25:05] ^ +183: [12:25:05] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +183: [12:25:05] SMILES Parse Error: syntax error while parsing: dsafsdf +183: [12:25:05] SMILES Parse Error: check for mistakes around position 1: +183: [12:25:05] dsafsdf +183: [12:25:05] ^ +183: [12:25:05] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +183: [12:25:05] SMILES Parse Error: syntax error while parsing: dsafsdf +183: [12:25:05] SMILES Parse Error: check for mistakes around position 1: +183: [12:25:05] dsafsdf +183: [12:25:05] ^ +183: [12:25:05] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +183: [12:25:05] SMILES Parse Error: syntax error while parsing: dsafsdf +183: [12:25:05] SMILES Parse Error: check for mistakes around position 1: +183: [12:25:05] dsafsdf +183: [12:25:05] ^ +183: [12:25:05] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +183: [12:25:05] SMILES Parse Error: syntax error while parsing: dsafsdf +183: [12:25:05] SMILES Parse Error: check for mistakes around position 1: +183: [12:25:05] dsafsdf +183: [12:25:05] ^ +183: [12:25:05] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +174/236 Test #163: testFMCS ............................... Passed 40.66 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 +183: [12:25:05] SMILES Parse Error: syntax error while parsing: dsafsdf +183: [12:25:05] SMILES Parse Error: check for mistakes around position 1: +183: [12:25:05] dsafsdf +183: [12:25:05] ^ +183: [12:25:05] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +183: [12:25:05] SMILES Parse Error: syntax error while parsing: dsafsdf +183: [12:25:05] SMILES Parse Error: check for mistakes around position 1: +183: [12:25:05] dsafsdf +183: [12:25:05] ^ +183: [12:25:05] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +183: [12:25:05] SMILES Parse Error: syntax error while parsing: dsafsdf +183: [12:25:05] SMILES Parse Error: check for mistakes around position 1: +183: [12:25:05] dsafsdf +183: [12:25:05] ^ +183: [12:25:05] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +183: [12:25:05] SMILES Parse Error: syntax error while parsing: dsafsdf +183: [12:25:05] SMILES Parse Error: check for mistakes around position 1: +183: [12:25:05] dsafsdf +183: [12:25:05] ^ +183: [12:25:05] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +183: [12:25:05] SMILES Parse Error: syntax error while parsing: dsafsdf +183: [12:25:05] SMILES Parse Error: check for mistakes around position 1: +183: [12:25:05] dsafsdf +183: [12:25:05] ^ +183: [12:25:05] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +183: [12:25:05] SMILES Parse Error: syntax error while parsing: dsafsdf +183: [12:25:05] SMILES Parse Error: check for mistakes around position 1: +183: [12:25:05] dsafsdf +183: [12:25:05] ^ +183: [12:25:05] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +183: [12:25:05] SMILES Parse Error: syntax error while parsing: dsafsdf +183: [12:25:05] SMILES Parse Error: check for mistakes around position 1: +183: [12:25:05] dsafsdf +183: [12:25:05] ^ +183: [12:25:05] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +183: [12:25:05] SMILES Parse Error: syntax error while parsing: dsafsdf +183: [12:25:05] SMILES Parse Error: check for mistakes around position 1: +183: [12:25:05] dsafsdf +183: [12:25:05] ^ +183: [12:25:05] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +183: [12:25:05] SMILES Parse Error: syntax error while parsing: dsafsdf +183: [12:25:05] SMILES Parse Error: check for mistakes around position 1: +183: [12:25:05] dsafsdf +183: [12:25:05] ^ +183: [12:25:05] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +183: [12:25:05] SMILES Parse Error: syntax error while parsing: dsafsdf +183: [12:25:05] SMILES Parse Error: check for mistakes around position 1: +183: [12:25:05] dsafsdf +183: [12:25:05] ^ +183: [12:25:05] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +183: [12:25:05] SMILES Parse Error: syntax error while parsing: dsafsdf +183: [12:25:05] SMILES Parse Error: check for mistakes around position 1: +183: [12:25:05] dsafsdf +183: [12:25:05] ^ +183: [12:25:05] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +183: [12:25:05] SMILES Parse Error: syntax error while parsing: dsafsdf +183: [12:25:05] SMILES Parse Error: check for mistakes around position 1: +183: [12:25:05] dsafsdf +183: [12:25:05] ^ +183: [12:25:05] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +183: [12:25:05] SMILES Parse Error: syntax error while parsing: dsafsdf +183: [12:25:05] SMILES Parse Error: check for mistakes around position 1: +183: [12:25:05] dsafsdf +183: [12:25:05] ^ +183: [12:25:05] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +183: [12:25:05] SMILES Parse Error: syntax error while parsing: dsafsdf +183: [12:25:05] SMILES Parse Error: check for mistakes around position 1: +183: [12:25:05] dsafsdf +183: [12:25:05] ^ +183: [12:25:05] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +183: [12:25:05] SMILES Parse Error: syntax error while parsing: dsafsdf +183: [12:25:05] SMILES Parse Error: check for mistakes around position 1: +183: [12:25:05] dsafsdf +183: [12:25:05] ^ +183: [12:25:05] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +183: [12:25:05] SMILES Parse Error: syntax error while parsing: dsafsdf +183: [12:25:05] SMILES Parse Error: check for mistakes around position 1: +183: [12:25:05] dsafsdf +183: [12:25:05] ^ +183: [12:25:05] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +183: [12:25:05] SMILES Parse Error: syntax error while parsing: dsafsdf +183: [12:25:05] SMILES Parse Error: check for mistakes around position 1: +183: [12:25:05] dsafsdf +183: [12:25:05] ^ +183: [12:25:05] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +183: [12:25:05] SMILES Parse Error: syntax error while parsing: dsafsdf +183: [12:25:05] SMILES Parse Error: check for mistakes around position 1: +183: [12:25:05] dsafsdf +183: [12:25:05] ^ +183: [12:25:05] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +183: [12:25:05] SMILES Parse Error: syntax error while parsing: dsafsdf +183: [12:25:05] SMILES Parse Error: check for mistakes around position 1: +183: [12:25:05] dsafsdf +183: [12:25:05] ^ +183: [12:25:05] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +183: [12:25:05] SMILES Parse Error: syntax error while parsing: dsafsdf +183: [12:25:05] SMILES Parse Error: check for mistakes around position 1: +183: [12:25:05] dsafsdf +183: [12:25:05] ^ +183: [12:25:05] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +183: [12:25:05] SMILES Parse Error: syntax error while parsing: dsafsdf +183: [12:25:05] SMILES Parse Error: check for mistakes around position 1: +183: [12:25:05] dsafsdf +183: [12:25:05] ^ +183: [12:25:05] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +183: [12:25:05] SMILES Parse Error: syntax error while parsing: dsafsdf +183: [12:25:05] SMILES Parse Error: check for mistakes around position 1: +183: [12:25:05] dsafsdf +183: [12:25:05] ^ +183: [12:25:05] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +183: [12:25:05] SMILES Parse Error: syntax error while parsing: dsafsdf +183: [12:25:05] SMILES Parse Error: check for mistakes around position 1: +183: [12:25:05] dsafsdf +183: [12:25:05] ^ +183: [12:25:05] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +183: [12:25:05] SMILES Parse Error: syntax error while parsing: dsafsdf +183: [12:25:05] SMILES Parse Error: check for mistakes around position 1: +183: [12:25:05] dsafsdf +183: [12:25:05] ^ +183: [12:25:05] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +183: [12:25:05] SMILES Parse Error: syntax error while parsing: dsafsdf +183: [12:25:05] SMILES Parse Error: check for mistakes around position 1: +183: [12:25:05] dsafsdf +183: [12:25:05] ^ +183: [12:25:05] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +183: [12:25:05] SMILES Parse Error: syntax error while parsing: dsafsdf +183: [12:25:05] SMILES Parse Error: check for mistakes around position 1: +183: [12:25:05] dsafsdf +183: [12:25:05] ^ +183: [12:25:05] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +183: [12:25:05] SMILES Parse Error: syntax error while parsing: dsafsdf +183: [12:25:05] SMILES Parse Error: check for mistakes around position 1: +183: [12:25:05] dsafsdf +183: [12:25:05] ^ +183: [12:25:05] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +183: [12:25:05] SMILES Parse Error: syntax error while parsing: dsafsdf +183: [12:25:05] SMILES Parse Error: check for mistakes around position 1: +183: [12:25:05] dsafsdf +183: [12:25:05] ^ +183: [12:25:05] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +183: [12:25:05] SMILES Parse Error: syntax error while parsing: dsafsdf +183: [12:25:05] SMILES Parse Error: check for mistakes around position 1: +183: [12:25:05] dsafsdf +183: [12:25:05] ^ +183: [12:25:05] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +183: [12:25:05] SMILES Parse Error: syntax error while parsing: dsafsdf +183: [12:25:05] SMILES Parse Error: check for mistakes around position 1: +183: [12:25:05] dsafsdf +183: [12:25:05] ^ +183: [12:25:05] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +183: [12:25:05] SMILES Parse Error: syntax error while parsing: dsafsdf +183: [12:25:05] SMILES Parse Error: check for mistakes around position 1: +183: [12:25:05] dsafsdf +183: [12:25:05] ^ +183: [12:25:05] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +183: [12:25:05] SMILES Parse Error: syntax error while parsing: dsafsdf +183: [12:25:05] SMILES Parse Error: check for mistakes around position 1: +183: [12:25:05] dsafsdf +183: [12:25:05] ^ +183: [12:25:05] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +183: [12:25:05] SMILES Parse Error: syntax error while parsing: dsafsdf +183: [12:25:05] SMILES Parse Error: check for mistakes around position 1: +183: [12:25:05] dsafsdf +183: [12:25:05] ^ +183: [12:25:05] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +183: [12:25:05] SMILES Parse Error: syntax error while parsing: dsafsdf +183: [12:25:05] SMILES Parse Error: check for mistakes around position 1: +183: [12:25:05] dsafsdf +183: [12:25:05] ^ +183: [12:25:05] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +183: [12:25:05] SMILES Parse Error: syntax error while parsing: dsafsdf +183: [12:25:05] SMILES Parse Error: check for mistakes around position 1: +183: [12:25:05] dsafsdf +183: [12:25:05] ^ +183: [12:25:05] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +183: [12:25:05] SMILES Parse Error: syntax error while parsing: dsafsdf +183: [12:25:05] SMILES Parse Error: check for mistakes around position 1: +183: [12:25:05] dsafsdf +183: [12:25:05] ^ +183: [12:25:05] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +183: [12:25:05] SMILES Parse Error: syntax error while parsing: dsafsdf +183: [12:25:05] SMILES Parse Error: check for mistakes around position 1: +183: [12:25:05] dsafsdf +183: [12:25:05] ^ +183: [12:25:05] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +183: [12:25:05] SMILES Parse Error: syntax error while parsing: dsafsdf +183: [12:25:05] SMILES Parse Error: check for mistakes around position 1: +183: [12:25:05] dsafsdf +183: [12:25:05] ^ +183: [12:25:05] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +183: [12:25:05] SMILES Parse Error: syntax error while parsing: dsafsdf +183: [12:25:05] SMILES Parse Error: check for mistakes around position 1: +183: [12:25:05] dsafsdf +183: [12:25:05] ^ +183: [12:25:05] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +183: [12:25:05] SMILES Parse Error: syntax error while parsing: dsafsdf +183: [12:25:05] SMILES Parse Error: check for mistakes around position 1: +183: [12:25:05] dsafsdf +183: [12:25:05] ^ +183: [12:25:05] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +183: [12:25:05] SMILES Parse Error: syntax error while parsing: dsafsdf +183: [12:25:05] SMILES Parse Error: check for mistakes around position 1: +183: [12:25:05] dsafsdf +183: [12:25:05] ^ +183: [12:25:05] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +183: [12:25:05] SMILES Parse Error: syntax error while parsing: dsafsdf +183: [12:25:05] SMILES Parse Error: check for mistakes around position 1: +183: [12:25:05] dsafsdf +183: [12:25:05] ^ +183: [12:25:05] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +183: [12:25:05] SMILES Parse Error: syntax error while parsing: dsafsdf +183: [12:25:05] SMILES Parse Error: check for mistakes around position 1: +183: [12:25:05] dsafsdf +183: [12:25:05] ^ +183: [12:25:05] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +183: [12:25:05] SMILES Parse Error: syntax error while parsing: dsafsdf +183: [12:25:05] SMILES Parse Error: check for mistakes around position 1: +183: [12:25:05] dsafsdf +183: [12:25:05] ^ +183: [12:25:05] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +183: [12:25:05] SMILES Parse Error: syntax error while parsing: dsafsdf +183: [12:25:05] SMILES Parse Error: check for mistakes around position 1: +183: [12:25:05] dsafsdf +183: [12:25:05] ^ +183: [12:25:05] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +183: [12:25:05] SMILES Parse Error: syntax error while parsing: dsafsdf +183: [12:25:05] SMILES Parse Error: check for mistakes around position 1: +183: [12:25:05] dsafsdf +183: [12:25:05] ^ +183: [12:25:05] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +183: [12:25:05] SMILES Parse Error: syntax error while parsing: dsafsdf +183: [12:25:05] SMILES Parse Error: check for mistakes around position 1: +183: [12:25:05] dsafsdf +183: [12:25:05] ^ +183: [12:25:05] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +183: [12:25:05] SMILES Parse Error: syntax error while parsing: dsafsdf +183: [12:25:05] SMILES Parse Error: check for mistakes around position 1: +183: [12:25:05] dsafsdf +183: [12:25:05] ^ +183: [12:25:05] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +183: [12:25:05] SMILES Parse Error: syntax error while parsing: dsafsdf +183: [12:25:05] SMILES Parse Error: check for mistakes around position 1: +183: [12:25:05] dsafsdf +183: [12:25:05] ^ +183: [12:25:05] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +183: [12:25:05] SMILES Parse Error: syntax error while parsing: dsafsdf +183: [12:25:05] SMILES Parse Error: check for mistakes around position 1: +183: [12:25:05] dsafsdf +183: [12:25:05] ^ +183: [12:25:05] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +183: [12:25:05] ------------------------------------- +183: [12:25:05] Results do not depend on numThreads +148: .........[12:25:05] Molecule does not have explicit Hs. Consider calling AddHs() +148: .[12:25:05] Molecule does not have explicit Hs. Consider calling AddHs() +148: [12:25:05] Molecule does not have explicit Hs. Consider calling AddHs() +148: [12:25:05] Molecule does not have explicit Hs. Consider calling AddHs() +148: [12:25:05] Molecule does not have explicit Hs. Consider calling AddHs() +148: [12:25:05] Molecule does not have explicit Hs. Consider calling AddHs() +148: [12:25:05] Molecule does not have explicit Hs. Consider calling AddHs() +148: [12:25:05] Molecule does not have explicit Hs. Consider calling AddHs() +148: [12:25:05] Molecule does not have explicit Hs. Consider calling AddHs() +148: [12:25:05] Molecule does not have explicit Hs. Consider calling AddHs() +148: [12:25:05] Molecule does not have explicit Hs. Consider calling AddHs() +148: .[12:25:05] Molecule does not have explicit Hs. Consider calling AddHs() +148: [12:25:05] Molecule does not have explicit Hs. Consider calling AddHs() +148: [12:25:05] Molecule does not have explicit Hs. Consider calling AddHs() +148: [12:25:05] Molecule does not have explicit Hs. Consider calling AddHs() +148: [12:25:05] Molecule does not have explicit Hs. Consider calling AddHs() +148: [12:25:05] Molecule does not have explicit Hs. Consider calling AddHs() +148: [12:25:05] Molecule does not have explicit Hs. Consider calling AddHs() +148: [12:25:05] Molecule does not have explicit Hs. Consider calling AddHs() +148: [12:25:05] Molecule does not have explicit Hs. Consider calling AddHs() +148: [12:25:05] Molecule does not have explicit Hs. Consider calling AddHs() +186: [12:25:06] Non terminal R group defined. To allow set allowNonTerminalRGroups in RGroupDecompositionParameters +186: [12:25:06] WARNING: not removing hydrogen atom with dummy atom neighbors +173: [12:25:09] Complex queries can be slow. +173: [12:25:09] Complex queries can be slow. +173: [12:25:09] Complex queries can be slow. +173: [12:25:10] Complex queries can be slow. +173: [12:25:10] Complex queries can be slow. +173: [12:25:10] Complex queries can be slow. +173: [12:25:11] Complex queries can be slow. +173: [12:25:11] Complex queries can be slow. 186: iterative -183: [16:03:27] ------------------------------------- -183: [16:03:27] testing TautomerPatternHolder -173: [16:03:27] Complex queries can be slow. -183: [16:03:27] ------------------------------------- -183: [16:03:27] testSegFaultInHolder -183: [16:03:27] SMILES Parse Error: syntax error while parsing: dsafsdf -183: [16:03:27] SMILES Parse Error: check for mistakes around position 1: -183: [16:03:27] dsafsdf -183: [16:03:27] ^ -183: [16:03:27] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -183: [16:03:27] SMILES Parse Error: syntax error while parsing: dsafsdf -183: [16:03:27] SMILES Parse Error: check for mistakes around position 1: -183: [16:03:27] dsafsdf -183: [16:03:27] ^ -183: [16:03:27] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -183: [16:03:27] SMILES Parse Error: syntax error while parsing: dsafsdf -183: [16:03:27] SMILES Parse Error: check for mistakes around position 1: -183: [16:03:27] dsafsdf -183: [16:03:27] ^ -183: [16:03:27] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -183: [16:03:27] SMILES Parse Error: syntax error while parsing: dsafsdf -183: [16:03:27] SMILES Parse Error: check for mistakes around position 1: -183: [16:03:27] dsafsdf -183: [16:03:27] ^ -183: [16:03:27] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -183: [16:03:27] SMILES Parse Error: syntax error while parsing: dsafsdf -183: [16:03:27] SMILES Parse Error: check for mistakes around position 1: -183: [16:03:27] dsafsdf -183: [16:03:27] ^ -183: [16:03:27] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -183: [16:03:27] SMILES Parse Error: syntax error while parsing: dsafsdf -183: [16:03:27] SMILES Parse Error: check for mistakes around position 1: -183: [16:03:27] dsafsdf -183: [16:03:27] ^ -183: [16:03:27] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -183: [16:03:27] SMILES Parse Error: syntax error while parsing: dsafsdf -183: [16:03:27] SMILES Parse Error: check for mistakes around position 1: -183: [16:03:27] dsafsdf -183: [16:03:27] ^ -183: [16:03:27] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -183: [16:03:27] SMILES Parse Error: syntax error while parsing: dsafsdf -183: [16:03:27] SMILES Parse Error: check for mistakes around position 1: -183: [16:03:27] dsafsdf -183: [16:03:27] ^ -183: [16:03:27] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -183: [16:03:27] SMILES Parse Error: syntax error while parsing: dsafsdf -183: [16:03:27] SMILES Parse Error: check for mistakes around position 1: -183: [16:03:27] dsafsdf -183: [16:03:27] ^ -183: [16:03:27] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -183: [16:03:27] SMILES Parse Error: syntax error while parsing: dsafsdf -183: [16:03:27] SMILES Parse Error: check for mistakes around position 1: -183: [16:03:27] dsafsdf -183: [16:03:27] ^ -183: [16:03:27] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -183: [16:03:27] SMILES Parse Error: syntax error while parsing: dsafsdf -183: [16:03:27] SMILES Parse Error: check for mistakes around position 1: -183: [16:03:27] dsafsdf -183: [16:03:27] ^ -183: [16:03:27] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -183: [16:03:27] SMILES Parse Error: syntax error while parsing: dsafsdf -183: [16:03:27] SMILES Parse Error: check for mistakes around position 1: -183: [16:03:27] dsafsdf -183: [16:03:27] ^ -183: [16:03:27] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -183: [16:03:27] SMILES Parse Error: syntax error while parsing: dsafsdf -183: [16:03:27] SMILES Parse Error: check for mistakes around position 1: -183: [16:03:27] dsafsdf -183: [16:03:27] ^ -183: [16:03:27] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -183: [16:03:27] SMILES Parse Error: syntax error while parsing: dsafsdf -183: [16:03:27] SMILES Parse Error: check for mistakes around position 1: -183: [16:03:27] dsafsdf -183: [16:03:27] ^ -183: [16:03:27] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -183: [16:03:27] SMILES Parse Error: syntax error while parsing: dsafsdf -183: [16:03:27] SMILES Parse Error: check for mistakes around position 1: -183: [16:03:27] dsafsdf -183: [16:03:27] ^ -183: [16:03:27] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -183: [16:03:27] SMILES Parse Error: syntax error while parsing: dsafsdf -183: [16:03:27] SMILES Parse Error: check for mistakes around position 1: -183: [16:03:27] dsafsdf -183: [16:03:27] ^ -183: [16:03:27] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -183: [16:03:27] SMILES Parse Error: syntax error while parsing: dsafsdf -183: [16:03:27] SMILES Parse Error: check for mistakes around position 1: -183: [16:03:27] dsafsdf -183: [16:03:27] ^ -183: [16:03:27] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -183: [16:03:27] SMILES Parse Error: syntax error while parsing: dsafsdf -183: [16:03:27] SMILES Parse Error: check for mistakes around position 1: -183: [16:03:27] dsafsdf -183: [16:03:27] ^ -183: [16:03:27] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -183: [16:03:27] SMILES Parse Error: syntax error while parsing: dsafsdf -183: [16:03:27] SMILES Parse Error: check for mistakes around position 1: -183: [16:03:27] dsafsdf -183: [16:03:27] ^ -183: [16:03:27] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -183: [16:03:27] SMILES Parse Error: syntax error while parsing: dsafsdf -183: [16:03:27] SMILES Parse Error: check for mistakes around position 1: -183: [16:03:27] dsafsdf -183: [16:03:27] ^ -183: [16:03:27] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -183: [16:03:27] SMILES Parse Error: syntax error while parsing: dsafsdf -183: [16:03:27] SMILES Parse Error: check for mistakes around position 1: -183: [16:03:27] dsafsdf -183: [16:03:27] ^ -183: [16:03:27] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -183: [16:03:27] SMILES Parse Error: syntax error while parsing: dsafsdf -183: [16:03:27] SMILES Parse Error: check for mistakes around position 1: -183: [16:03:27] dsafsdf -183: [16:03:27] ^ -183: [16:03:27] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -183: [16:03:27] SMILES Parse Error: syntax error while parsing: dsafsdf -183: [16:03:27] SMILES Parse Error: check for mistakes around position 1: -183: [16:03:27] dsafsdf -183: [16:03:27] ^ -183: [16:03:27] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -183: [16:03:27] SMILES Parse Error: syntax error while parsing: dsafsdf -183: [16:03:27] SMILES Parse Error: check for mistakes around position 1: -183: [16:03:27] dsafsdf -183: [16:03:27] ^ -183: [16:03:27] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -183: [16:03:27] SMILES Parse Error: syntax error while parsing: dsafsdf -183: [16:03:27] SMILES Parse Error: check for mistakes around position 1: -183: [16:03:27] dsafsdf -183: [16:03:27] ^ -183: [16:03:27] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -183: [16:03:27] SMILES Parse Error: syntax error while parsing: dsafsdf -183: [16:03:27] SMILES Parse Error: check for mistakes around position 1: -183: [16:03:27] dsafsdf -183: [16:03:27] ^ -183: [16:03:27] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -183: [16:03:27] SMILES Parse Error: syntax error while parsing: dsafsdf -183: [16:03:27] SMILES Parse Error: check for mistakes around position 1: -183: [16:03:27] dsafsdf -183: [16:03:27] ^ -183: [16:03:27] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -183: [16:03:27] SMILES Parse Error: syntax error while parsing: dsafsdf -183: [16:03:27] SMILES Parse Error: check for mistakes around position 1: -183: [16:03:27] dsafsdf -183: [16:03:27] ^ -183: [16:03:27] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -183: [16:03:27] SMILES Parse Error: syntax error while parsing: dsafsdf -183: [16:03:27] SMILES Parse Error: check for mistakes around position 1: -183: [16:03:27] dsafsdf -183: [16:03:27] ^ -183: [16:03:27] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -183: [16:03:27] SMILES Parse Error: syntax error while parsing: dsafsdf -183: [16:03:27] SMILES Parse Error: check for mistakes around position 1: -183: [16:03:27] dsafsdf -183: [16:03:27] ^ -183: [16:03:27] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -183: [16:03:27] SMILES Parse Error: syntax error while parsing: dsafsdf -183: [16:03:27] SMILES Parse Error: check for mistakes around position 1: -183: [16:03:27] dsafsdf -183: [16:03:27] ^ -183: [16:03:27] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -183: [16:03:27] SMILES Parse Error: syntax error while parsing: dsafsdf -183: [16:03:27] SMILES Parse Error: check for mistakes around position 1: -183: [16:03:27] dsafsdf -183: [16:03:27] ^ -183: [16:03:27] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -183: [16:03:27] SMILES Parse Error: syntax error while parsing: dsafsdf -183: [16:03:27] SMILES Parse Error: check for mistakes around position 1: -183: [16:03:27] dsafsdf -183: [16:03:27] ^ -183: [16:03:27] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -183: [16:03:27] SMILES Parse Error: syntax error while parsing: dsafsdf -183: [16:03:27] SMILES Parse Error: check for mistakes around position 1: -183: [16:03:27] dsafsdf -183: [16:03:27] ^ -183: [16:03:27] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -183: [16:03:27] SMILES Parse Error: syntax error while parsing: dsafsdf -183: [16:03:27] SMILES Parse Error: check for mistakes around position 1: -183: [16:03:27] dsafsdf -183: [16:03:27] ^ -183: [16:03:27] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -183: [16:03:27] SMILES Parse Error: syntax error while parsing: dsafsdf -183: [16:03:27] SMILES Parse Error: check for mistakes around position 1: -183: [16:03:27] dsafsdf -183: [16:03:27] ^ -183: [16:03:27] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -183: [16:03:27] SMILES Parse Error: syntax error while parsing: dsafsdf -183: [16:03:27] SMILES Parse Error: check for mistakes around position 1: -183: [16:03:27] dsafsdf -183: [16:03:27] ^ -183: [16:03:27] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -183: [16:03:27] SMILES Parse Error: syntax error while parsing: dsafsdf -183: [16:03:27] SMILES Parse Error: check for mistakes around position 1: -183: [16:03:27] dsafsdf -183: [16:03:27] ^ -183: [16:03:27] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -183: [16:03:27] SMILES Parse Error: syntax error while parsing: dsafsdf -183: [16:03:27] SMILES Parse Error: check for mistakes around position 1: -183: [16:03:27] dsafsdf -183: [16:03:27] ^ -183: [16:03:27] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -183: [16:03:27] SMILES Parse Error: syntax error while parsing: dsafsdf -183: [16:03:27] SMILES Parse Error: check for mistakes around position 1: -183: [16:03:27] dsafsdf -183: [16:03:27] ^ -183: [16:03:27] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -183: [16:03:27] SMILES Parse Error: syntax error while parsing: dsafsdf -183: [16:03:27] SMILES Parse Error: check for mistakes around position 1: -183: [16:03:27] dsafsdf -183: [16:03:27] ^ -183: [16:03:27] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -183: [16:03:27] SMILES Parse Error: syntax error while parsing: dsafsdf -183: [16:03:27] SMILES Parse Error: check for mistakes around position 1: -183: [16:03:27] dsafsdf -183: [16:03:27] ^ -183: [16:03:27] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -183: [16:03:27] SMILES Parse Error: syntax error while parsing: dsafsdf -183: [16:03:27] SMILES Parse Error: check for mistakes around position 1: -183: [16:03:27] dsafsdf -183: [16:03:27] ^ -183: [16:03:27] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -183: [16:03:27] SMILES Parse Error: syntax error while parsing: dsafsdf -183: [16:03:27] SMILES Parse Error: check for mistakes around position 1: -183: [16:03:27] dsafsdf -183: [16:03:27] ^ -183: [16:03:27] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -183: [16:03:27] SMILES Parse Error: syntax error while parsing: dsafsdf -183: [16:03:27] SMILES Parse Error: check for mistakes around position 1: -183: [16:03:27] dsafsdf -183: [16:03:27] ^ -183: [16:03:27] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -183: [16:03:27] SMILES Parse Error: syntax error while parsing: dsafsdf -183: [16:03:27] SMILES Parse Error: check for mistakes around position 1: -183: [16:03:27] dsafsdf -183: [16:03:27] ^ -183: [16:03:27] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -183: [16:03:27] SMILES Parse Error: syntax error while parsing: dsafsdf -183: [16:03:27] SMILES Parse Error: check for mistakes around position 1: -183: [16:03:27] dsafsdf -183: [16:03:27] ^ -183: [16:03:27] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -183: [16:03:27] SMILES Parse Error: syntax error while parsing: dsafsdf -183: [16:03:27] SMILES Parse Error: check for mistakes around position 1: -183: [16:03:27] dsafsdf -183: [16:03:27] ^ -183: [16:03:27] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -183: [16:03:27] SMILES Parse Error: syntax error while parsing: dsafsdf -183: [16:03:27] SMILES Parse Error: check for mistakes around position 1: -183: [16:03:27] dsafsdf -183: [16:03:27] ^ -183: [16:03:27] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -183: [16:03:27] SMILES Parse Error: syntax error while parsing: dsafsdf -183: [16:03:27] SMILES Parse Error: check for mistakes around position 1: -183: [16:03:27] dsafsdf -183: [16:03:27] ^ -183: [16:03:27] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -183: [16:03:27] SMILES Parse Error: syntax error while parsing: dsafsdf -183: [16:03:27] SMILES Parse Error: check for mistakes around position 1: -183: [16:03:27] dsafsdf -183: [16:03:27] ^ -183: [16:03:27] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -183: [16:03:27] SMILES Parse Error: syntax error while parsing: dsafsdf -183: [16:03:27] SMILES Parse Error: check for mistakes around position 1: -183: [16:03:27] dsafsdf -183: [16:03:27] ^ -183: [16:03:27] [16:03:27] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -183: [16:03:27] SMILES Parse Error: syntax error while parsing: dsafsdf -183: [16:03:27] SMILES Parse Error: check for mistakes around position 1: -183: [16:03:27] dsafsdf -183: [16:03:27] ^ -183: [16:03:27] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -183: [16:03:27] SMILES Parse Error: syntax error while parsing: dsafsdf -183: [16:03:27] SMILES Parse Error: check for mistakes around position 1: -183: [16:03:27] dsafsdf -183: [16:03:27] ^ -183: [16:03:27] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -183: [16:03:27] SMILES Parse Error: syntax error while parsing: dsafsdf -183: [16:03:27] SMILES Parse Error: check for mistakes around position 1: -183: [16:03:27] dsafsdf -183: [16:03:27] ^ -183: [16:03:27] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -183: [16:03:27] SMILES Parse Error: syntax error while parsing: dsafsdf -183: [16:03:27] SMILES Parse Error: check for mistakes around position 1: -183: [16:03:27] dsafsdf -183: [16:03:27] ^ -183: [16:03:27] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -183: [16:03:27] SMILES Parse Error: syntax error while parsing: dsafsdf -183: [16:03:27] SMILES Parse Error: check for mistakes around position 1: -183: [16:03:27] dsafsdf -183: [16:03:27] ^ -183: [16:03:27] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -183: [16:03:27] SMILES Parse Error: syntax error while parsing: dsafsdf -183: [16:03:27] SMILES Parse Error: check for mistakes around position 1: -183: [16:03:27] dsafsdf -183: [16:03:27] ^ -183: [16:03:27] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -183: [16:03:27] SMILES Parse Error: syntax error while parsing: dsafsdf -183: [16:03:27] SMILES Parse Error: check for mistakes around position 1: -183: [16:03:27] dsafsdf -183: [16:03:27] ^ -183: [16:03:27] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -183: [16:03:27] SMILES Parse Error: syntax error while parsing: dsafsdf -183: [16:03:27] SMILES Parse Error: check for mistakes around position 1: -183: [16:03:27] dsafsdf -183: [16:03:27] ^ -183: [16:03:27] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -183: [16:03:27] SMILES Parse Error: syntax error while parsing: dsafsdf -183: [16:03:27] SMILES Parse Error: check for mistakes around position 1: -183: [16:03:27] dsafsdf -183: [16:03:27] ^ -183: [16:03:27] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -183: [16:03:27] SMILES Parse Error: syntax error while parsing: dsafsdf -183: [16:03:27] SMILES Parse Error: check for mistakes around position 1: -183: [16:03:27] dsafsdf -183: [16:03:27] ^ -183: [16:03:27] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -183: [16:03:27] SMILES Parse Error: syntax error while parsing: dsafsdf -183: [16:03:27] SMILES Parse Error: check for mistakes around position 1: -183: [16:03:27] dsafsdf -183: [16:03:27] ^ -183: [16:03:27] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -183: [16:03:27] SMILES Parse Error: syntax error while parsing: dsafsdf -183: [16:03:27] SMILES Parse Error: check for mistakes around position 1: -183: [16:03:27] dsafsdf -183: [16:03:27] ^ -183: [16:03:27] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -183: SMILES Parse Error: syntax error while parsing: dsafsdf -183: [16:03:27] SMILES Parse Error: check for mistakes around position 1: -183: [16:03:27] dsafsdf -183: [16:03:27] ^ -183: [16:03:27] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -183: [16:03:27] SMILES Parse Error: syntax error while parsing: dsafsdf -183: [16:03:27] SMILES Parse Error: check for mistakes around position 1: -183: [16:03:27] dsafsdf -183: [16:03:27] ^ -183: [16:03:27] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -183: [16:03:27] SMILES Parse Error: syntax error while parsing: dsafsdf -183: [16:03:27] SMILES Parse Error: check for mistakes around position 1: -183: [16:03:27] dsafsdf -183: [16:03:27] ^ -183: [16:03:27] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -183: [16:03:27] SMILES Parse Error: syntax error while parsing: dsafsdf -183: [16:03:27] SMILES Parse Error: check for mistakes around position 1: -183: [16:03:27] dsafsdf -183: [16:03:27] ^ -183: [16:03:27] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -183: [16:03:27] SMILES Parse Error: syntax error while parsing: dsafsdf -183: [16:03:27] SMILES Parse Error: check for mistakes around position 1: -183: [16:03:27] dsafsdf -183: [16:03:27] ^ -183: [16:03:27] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -183: [16:03:27] SMILES Parse Error: syntax error while parsing: dsafsdf -183: [16:03:27] SMILES Parse Error: check for mistakes around position 1: -183: [16:03:27] dsafsdf -183: [16:03:27] ^ -183: [16:03:27] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -183: [16:03:27] SMILES Parse Error: syntax error while parsing: dsafsdf -183: [16:03:27] SMILES Parse Error: check for mistakes around position 1: -183: [16:03:27] dsafsdf -183: [16:03:27] ^ -183: [16:03:27] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -183: [16:03:27] SMILES Parse Error: syntax error while parsing: dsafsdf -183: [16:03:27] SMILES Parse Error: check for mistakes around position 1: -183: [16:03:27] dsafsdf -183: [16:03:27] ^ -183: [16:03:27] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -183: [16:03:27] SMILES Parse Error: syntax error while parsing: dsafsdf -183: [16:03:27] SMILES Parse Error: check for mistakes around position 1: -183: [16:03:27] dsafsdf -183: [16:03:27] ^ -183: [16:03:27] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -183: [16:03:27] SMILES Parse Error: syntax error while parsing: dsafsdf -183: [16:03:27] SMILES Parse Error: check for mistakes around position 1: -183: [16:03:27] dsafsdf -183: [16:03:27] ^ -183: [16:03:27] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -183: [16:03:27] SMILES Parse Error: syntax error while parsing: dsafsdf -183: [16:03:27] SMILES Parse Error: check for mistakes around position 1: -183: [16:03:27] dsafsdf -183: [16:03:27] ^ -183: [16:03:27] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -183: [16:03:27] SMILES Parse Error: syntax error while parsing: dsafsdf -183: [16:03:27] SMILES Parse Error: check for mistakes around position 1: -183: [16:03:27] dsafsdf -183: [16:03:27] ^ -183: [16:03:27] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -183: [16:03:27] SMILES Parse Error: syntax error while parsing: dsafsdf -183: [16:03:27] SMILES Parse Error: check for mistakes around position 1: -183: [16:03:27] dsafsdf -183: [16:03:27] ^ -183: [16:03:27] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -183: [16:03:27] SMILES Parse Error: syntax error while parsing: dsafsdf -183: [16:03:27] SMILES Parse Error: check for mistakes around position 1: -183: [16:03:27] dsafsdf -183: [16:03:27] ^ -183: [16:03:27] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -183: [16:03:27] SMILES Parse Error: syntax error while parsing: dsafsdf -183: [16:03:27] SMILES Parse Error: check for mistakes around position 1: -183: [16:03:27] dsafsdf -183: [16:03:27] ^ -183: [16:03:27] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -183: [16:03:27] SMILES Parse Error: syntax error while parsing: dsafsdf -183: [16:03:27] SMILES Parse Error: check for mistakes around position 1: -183: [16:03:27] dsafsdf -183: [16:03:27] ^ -183: [16:03:27] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -183: [16:03:27] SMILES Parse Error: syntax error while parsing: dsafsdf -183: [16:03:27] SMILES Parse Error: check for mistakes around position 1: -183: [16:03:27] dsafsdf -183: [16:03:27] ^ -183: [16:03:27] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -183: [16:03:27] SMILES Parse Error: syntax error while parsing: dsafsdf -183: [16:03:27] SMILES Parse Error: check for mistakes around position 1: -183: [16:03:27] dsafsdf -183: [16:03:27] ^ -183: [16:03:27] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -183: [16:03:27] SMILES Parse Error: syntax error while parsing: dsafsdf -183: [16:03:27] SMILES Parse Error: check for mistakes around position 1: -183: [16:03:27] dsafsdf -183: [16:03:27] ^ -183: [16:03:27] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -183: [16:03:27] SMILES Parse Error: syntax error while parsing: dsafsdf -183: [16:03:27] SMILES Parse Error: check for mistakes around position 1: -183: [16:03:27] dsafsdf -183: [16:03:27] ^ -183: [16:03:27] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -183: [16:03:27] SMILES Parse Error: syntax error while parsing: dsafsdf -183: [16:03:27] SMILES Parse Error: check for mistakes around position 1: -183: [16:03:27] dsafsdf -183: [16:03:27] ^ -183: [16:03:27] SMILES Parse Error: syntax error while parsing: dsafsdf[16:03:27] SMILES -183: [16:03:27] SMILES Parse Error: check for mistakes around position 1: -183: [16:03:27] dsafsdf -183: [16:03:27] ^ -183: [16:03:27] SMILES Parse Error: syntax error while parsing: dsafsdf -183: [16:03:27] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -183: [16:03:27] SMILES Parse Error: syntax error while parsing: dsafsdf -183: [16:03:27] SMILES Parse Error: check for mistakes around position 1: -183: [16:03:27] dsafsdf -183: [16:03:27] ^ -183: [16:03:27] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -183: [16:03:27] SMILES Parse Error: syntax error while parsing: dsafsdf -183: [16:03:27] SMILES Parse Error: check for mistakes around position 1: -183: [16:03:27] dsafsdf -183: [16:03:27] ^ -183: [16:03:27] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -183: [16:03:27] SMILES Parse Error: syntax error while parsing: dsafsdf -183: [16:03:27] SMILES Parse Error: check for mistakes around position 1: -183: [16:03:27] dsafsdf -183: [16:03:27] ^ -183: [16:03:27] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -183: [16:03:27] SMILES Parse Error: syntax error while parsing: dsafsdf -183: [16:03:27] SMILES Parse Error: check for mistakes around position 1: -183: [16:03:27] dsafsdf -183: [16:03:27] ^ -183: [16:03:27] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -183: Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -183: [16:03:27] SMILES Parse Error: syntax error while parsing: dsafsdf -183: [16:03:27] SMILES Parse Error: check for mistakes around position 1: -183: [16:03:27] dsafsdf -183: [16:03:27] ^ -183: [16:03:27] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -183: [16:03:27] SMILES Parse Error: syntax error while parsing: dsafsdf -183: [16:03:27] SMILES Parse Error: check for mistakes around position 1: -183: [16:03:27] dsafsdf -183: [16:03:27] ^ -183: [16:03:27] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -183: [16:03:27] SMILES Parse Error: syntax error while parsing: dsafsdf -183: [16:03:27] SMILES Parse Error: check for mistakes around position 1: -183: [16:03:27] dsafsdf -183: [16:03:27] ^ -183: [16:03:27] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -183: [16:03:27] SMILES Parse Error: check for mistakes around position 1: -183: [16:03:27] dsafsdf -183: [16:03:27] ^ -183: [16:03:27] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -183: [16:03:27] SMILES Parse Error: syntax error while parsing: dsafsdf -183: [16:03:27] SMILES Parse Error: check for mistakes around position 1: -183: [16:03:27] dsafsdf -183: [16:03:27] ^ -183: [16:03:27] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -183: [16:03:27] SMILES Parse Error: syntax error while parsing: dsafsdf -183: [16:03:27] SMILES Parse Error: check for mistakes around position 1: -183: [16:03:27] dsafsdf -183: [16:03:27] ^ -183: [16:03:27] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -183: [16:03:27] SMILES Parse Error: syntax error while parsing: dsafsdf -183: [16:03:27] SMILES Parse Error: check for mistakes around position 1: -183: [16:03:27] dsafsdf -183: [16:03:27] ^ -183: [16:03:27] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -183: [16:03:27] SMILES Parse Error: syntax error while parsing: dsafsdf -183: [16:03:27] SMILES Parse Error: check for mistakes around position 1: -183: [16:03:27] dsafsdf -183: [16:03:27] ^ -183: [16:03:27] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -183: [16:03:27] SMILES Parse Error: syntax error while parsing: dsafsdf -183: [16:03:27] SMILES Parse Error: check for mistakes around position 1: -183: [16:03:27] dsafsdf -183: [16:03:27] ^ -183: [16:03:27] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -183: [16:03:27] SMILES Parse Error: syntax error while parsing: dsafsdf -183: [16:03:27] SMILES Parse Error: check for mistakes around position 1: -183: [16:03:27] dsafsdf -183: [16:03:27] ^ -183: [16:03:27] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -183: [16:03:27] SMILES Parse Error: syntax error while parsing: dsafsdf -183: [16:03:27] SMILES Parse Error: check for mistakes around position 1: -183: [16:03:27] dsafsdf -183: [16:03:27] ^ -183: [16:03:27] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -183: [16:03:27] SMILES Parse Error: syntax error while parsing: dsafsdf -183: [16:03:27] SMILES Parse Error: check for mistakes around position 1: -183: [16:03:27] dsafsdf -183: [16:03:27] ^ -183: [16:03:27] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -183: [16:03:27] SMILES Parse Error: syntax error while parsing: dsafsdf -183: [16:03:27] SMILES Parse Error: check for mistakes around position 1: -183: [16:03:27] dsafsdf -183: [16:03:27] ^ -183: [16:03:27] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -183: [16:03:27] SMILES Parse Error: syntax error while parsing: dsafsdf -183: [16:03:27] SMILES Parse Error: check for mistakes around position 1: -183: [16:03:27] dsafsdf -183: [16:03:27] ^ -183: [16:03:27] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -183: [16:03:27] SMILES Parse Error: syntax error while parsing: dsafsdf -183: [16:03:27] SMILES Parse Error: check for mistakes around position 1: -183: [16:03:27] dsafsdf -183: [16:03:27] ^ -183: [16:03:27] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -183: [16:03:27] SMILES Parse Error: syntax error while parsing: dsafsdf -183: [16:03:27] SMILES Parse Error: check for mistakes around position 1: -183: [16:03:27] dsafsdf -183: [16:03:27] ^ -183: [16:03:27] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -183: [16:03:27] SMILES Parse Error: syntax error while parsing: dsafsdf -183: [16:03:27] SMILES Parse Error: check for mistakes around position 1: -183: [16:03:27] dsafsdf -183: [16:03:27] ^ -183: [16:03:27] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -183: [16:03:27] SMILES Parse Error: syntax error while parsing: dsafsdf -183: [16:03:27] SMILES Parse Error: check for mistakes around position 1: -183: [16:03:27] dsafsdf -183: [16:03:27] ^ -183: [16:03:27] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -183: [16:03:27] SMILES Parse Error: syntax error while parsing: dsafsdf -183: [16:03:27] SMILES Parse Error: check for mistakes around position 1: -183: [16:03:27] dsafsdf -183: [16:03:27] ^ -183: [16:03:27] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -183: [16:03:27] SMILES Parse Error: syntax error while parsing: dsafsdf -183: [16:03:27] SMILES Parse Error: check for mistakes around position 1: -183: [16:03:27] dsafsdf -183: [16:03:27] ^ -183: [16:03:27] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -183: [16:03:27] SMILES Parse Error: syntax error while parsing: dsafsdf -183: [16:03:27] SMILES Parse Error: check for mistakes around position 1: -183: [16:03:27] dsafsdf -183: [16:03:27] ^ -183: [16:03:27] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -183: [16:03:27] SMILES Parse Error: syntax error while parsing: dsafsdf -183: [16:03:27] SMILES Parse Error: check for mistakes around position 1: -183: [16:03:27] dsafsdf -183: [16:03:27] ^ -183: [16:03:27] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -183: [16:03:27] SMILES Parse Error: syntax error while parsing: dsafsdf -183: [16:03:27] SMILES Parse Error: check for mistakes around position 1: -183: [16:03:27] dsafsdf -183: [16:03:27] ^ -183: [16:03:27] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -183: [16:03:27] SMILES Parse Error: syntax error while parsing: dsafsdf -183: [16:03:27] SMILES Parse Error: check for mistakes around position 1: -183: [16:03:27] dsafsdf -183: [16:03:27] ^ -183: [16:03:27] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -183: [16:03:27] SMILES Parse Error: syntax error while parsing: dsafsdf -183: [16:03:27] SMILES Parse Error: check for mistakes around position 1: -183: [16:03:27] dsafsdf -183: [16:03:27] ^ -183: [16:03:27] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -183: [16:03:27] SMILES Parse Error: syntax error while parsing: dsafsdf -183: [16:03:27] SMILES Parse Error: check for mistakes around position 1: -183: [16:03:27] dsafsdf -183: [16:03:27] ^ -183: [16:03:27] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -183: [16:03:27] SMILES Parse Error: syntax error while parsing: dsafsdf -183: [16:03:27] SMILES Parse Error: check for mistakes around position 1: -183: [16:03:27] dsafsdf -183: [16:03:27] ^ -183: [16:03:27] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -183: [16:03:27] SMILES Parse Error: syntax error while parsing: dsafsdf -183: [16:03:27] SMILES Parse Error: check for mistakes around position 1: -183: [16:03:27] dsafsdf -183: [16:03:27] ^ -183: [16:03:27] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -183: [16:03:27] SMILES Parse Error: syntax error while parsing: dsafsdf -183: [16:03:27] SMILES Parse Error: check for mistakes around position 1: -183: [16:03:27] dsafsdf -183: [16:03:27] ^ -183: [16:03:27] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -183: [16:03:27] SMILES Parse Error: syntax error while parsing: dsafsdf -183: [16:03:27] SMILES Parse Error: check for mistakes around position 1: -183: [16:03:27] dsafsdf -183: [16:03:27] ^ -183: [16:03:27] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -183: [16:03:27] SMILES Parse Error: syntax error while parsing: dsafsdf -183: [16:03:27] SMILES Parse Error: check for mistakes around position 1: -183: [16:03:27] dsafsdf -183: [16:03:27] ^ -183: [16:03:27] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -183: [16:03:27] SMILES Parse Error: syntax error while parsing: dsafsdf -183: [16:03:27] SMILES Parse Error: check for mistakes around position 1: -183: [16:03:27] dsafsdf -183: [16:03:27] ^ -183: [16:03:27] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -183: [16:03:27] SMILES Parse Error: syntax error while parsing: dsafsdf -183: [16:03:27] SMILES Parse Error: check for mistakes around position 1: -183: [16:03:27] dsafsdf -183: [16:03:27] ^ -183: [16:03:27] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -183: [16:03:27] SMILES Parse Error: syntax error while parsing: dsafsdf -183: [16:03:27] SMILES Parse Error: check for mistakes around position 1: -183: [16:03:27] dsafsdf -183: [16:03:27] ^ -183: [16:03:27] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -183: [16:03:27] SMILES Parse Error: syntax error while parsing: dsafsdf -183: [16:03:27] SMILES Parse Error: check for mistakes around position 1: -183: [16:03:27] dsafsdf -183: [16:03:27] ^ -183: [16:03:27] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -183: [16:03:27] SMILES Parse Error: syntax error while parsing: dsafsdf -183: [16:03:27] SMILES Parse Error: check for mistakes around position 1: -183: [16:03:27] dsafsdf -183: [16:03:27] ^ -183: [16:03:27] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -183: [16:03:27] SMILES Parse Error: syntax error while parsing: dsafsdf -183: [16:03:27] SMILES Parse Error: check for mistakes around position 1: -183: [16:03:27] dsafsdf -183: [16:03:27] ^ -183: [16:03:27] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -183: [16:03:27] SMILES Parse Error: syntax error while parsing: dsafsdf -183: [16:03:27] SMILES Parse Error: check for mistakes around position 1: -183: [16:03:27] dsafsdf -183: [16:03:27] ^ -183: [16:03:27] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -183: [16:03:27] SMILES Parse Error: syntax error while parsing: dsafsdf -183: [16:03:27] SMILES Parse Error: check for mistakes around position 1: -183: [16:03:27] dsafsdf -183: [16:03:27] ^ -183: [16:03:27] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -183: [16:03:27] SMILES Parse Error: syntax error while parsing: dsafsdf -183: [16:03:27] SMILES Parse Error: check for mistakes around position 1: -183: [16:03:27] dsafsdf -183: [16:03:27] ^ -183: [16:03:27] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -183: [16:03:27] SMILES Parse Error: syntax error while parsing: dsafsdf -183: [16:03:27] SMILES Parse Error: check for mistakes around position 1: -183: [16:03:27] dsafsdf -183: [16:03:27] ^ -183: [16:03:27] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -183: [16:03:27] SMILES Parse Error: syntax error while parsing: dsafsdf -183: [16:03:27] SMILES Parse Error: check for mistakes around position 1: -183: [16:03:27] dsafsdf -183: [16:03:27] ^ -183: [16:03:27] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -183: [16:03:27] SMILES Parse Error: syntax error while parsing: dsafsdf -183: [16:03:27] SMILES Parse Error: check for mistakes around position 1: -183: [16:03:27] dsafsdf -183: [16:03:27] ^ -183: [16:03:27] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -183: [16:03:27] SMILES Parse Error: syntax error while parsing: dsafsdf -183: [16:03:27] SMILES Parse Error: check for mistakes around position 1: -183: [16:03:27] dsafsdf -183: [16:03:27] ^ -183: [16:03:27] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -183: [16:03:27] SMILES Parse Error: syntax error while parsing: dsafsdf -183: [16:03:27] SMILES Parse Error: check for mistakes around position 1: -183: [16:03:27] dsafsdf -183: [16:03:27] ^ -183: [16:03:27] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -183: [16:03:27] SMILES Parse Error: syntax error while parsing: dsafsdf -183: [16:03:27] SMILES Parse Error: check for mistakes around position 1: -183: [16:03:27] dsafsdf -183: [16:03:27] ^ -183: [16:03:27] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -183: [16:03:27] SMILES Parse Error: syntax error while parsing: dsafsdf -183: [16:03:27] SMILES Parse Error: check for mistakes around position 1: -183: [16:03:27] dsafsdf -183: [16:03:27] ^ -183: [16:03:27] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -183: [16:03:27] SMILES Parse Error: syntax error while parsing: dsafsdf -183: [16:03:27] SMILES Parse Error: check for mistakes around position 1: -183: [16:03:27] dsafsdf -183: [16:03:27] ^ -183: [16:03:27] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -183: [16:03:27] SMILES Parse Error: syntax error while parsing: dsafsdf -183: [16:03:27] SMILES Parse Error: check for mistakes around position 1: -183: [16:03:27] dsafsdf -183: [16:03:27] ^ -183: [16:03:27] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -183: [16:03:27] SMILES Parse Error: syntax error while parsing: dsafsdf -183: [16:03:27] SMILES Parse Error: check for mistakes around position 1: -183: [16:03:27] dsafsdf -183: [16:03:27] ^ -183: [16:03:27] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -183: [16:03:27] SMILES Parse Error: syntax error while parsing: dsafsdf -183: [16:03:27] SMILES Parse Error: check for mistakes around position 1: -183: [16:03:27] dsafsdf -183: [16:03:27] ^ -183: [16:03:27] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -183: [16:03:27] SMILES Parse Error: syntax error while parsing: dsafsdf -183: [16:03:27] SMILES Parse Error: check for mistakes around position 1: -183: [16:03:27] dsafsdf -183: [16:03:27] ^ -183: [16:03:27] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -183: [16:03:27] SMILES Parse Error: syntax error while parsing: dsafsdf -183: [16:03:27] SMILES Parse Error: check for mistakes around position 1: -183: [16:03:27] dsafsdf -183: [16:03:27] ^ -183: [16:03:27] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -183: [16:03:27] SMILES Parse Error: syntax error while parsing: dsafsdf -183: [16:03:27] SMILES Parse Error: check for mistakes around position 1: -183: [16:03:27] dsafsdf -183: [16:03:27] ^ -183: [16:03:27] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -183: [16:03:27] SMILES Parse Error: syntax error while parsing: dsafsdf -183: [16:03:27] SMILES Parse Error: check for mistakes around position 1: -183: [16:03:27] dsafsdf -183: [16:03:27] ^ -183: [16:03:27] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -183: [16:03:27] SMILES Parse Error: syntax error while parsing: dsafsdf -183: [16:03:27] SMILES Parse Error: check for mistakes around position 1: -183: [16:03:27] dsafsdf -183: [16:03:27] ^ -183: [16:03:27] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -183: [16:03:27] SMILES Parse Error: syntax error while parsing: dsafsdf -183: [16:03:27] SMILES Parse Error: check for mistakes around position 1: -183: [16:03:27] dsafsdf -183: [16:03:27] ^ -183: [16:03:27] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -183: [16:03:27] SMILES Parse Error: syntax error while parsing: dsafsdf -183: [16:03:27] SMILES Parse Error: check for mistakes around position 1: -183: [16:03:27] dsafsdf -183: [16:03:27] ^ -183: [16:03:27] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -183: [16:03:27] SMILES Parse Error: syntax error while parsing: dsafsdf -183: [16:03:27] SMILES Parse Error: check for mistakes around position 1: -183: [16:03:27] dsafsdf -183: [16:03:27] ^ -183: [16:03:27] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -183: [16:03:27] SMILES Parse Error: syntax error while parsing: dsafsdf -183: [16:03:27] SMILES Parse Error: check for mistakes around position 1: -183: [16:03:27] dsafsdf -183: [16:03:27] ^ -183: [16:03:27] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -183: [16:03:27] SMILES Parse Error: syntax error while parsing: dsafsdf -183: [16:03:27] SMILES Parse Error: check for mistakes around position 1: -183: [16:03:27] dsafsdf -183: [16:03:27] ^ -183: [16:03:27] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -183: [16:03:27] SMILES Parse Error: syntax error while parsing: dsafsdf -183: [16:03:27] SMILES Parse Error: check for mistakes around position 1: -183: [16:03:27] dsafsdf -183: [16:03:27] ^ -183: [16:03:27] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -183: [16:03:27] SMILES Parse Error: syntax error while parsing: dsafsdf -183: [16:03:27] SMILES Parse Error: check for mistakes around position 1: -183: [16:03:27] dsafsdf -183: [16:03:27] ^ -183: [16:03:27] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -183: [16:03:27] SMILES Parse Error: syntax error while parsing: dsafsdf -183: [16:03:27] SMILES Parse Error: check for mistakes around position 1: -183: [16:03:27] dsafsdf -183: [16:03:27] ^ -183: [16:03:27] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -183: [16:03:27] SMILES Parse Error: syntax error while parsing: dsafsdf -183: [16:03:27] SMILES Parse Error: check for mistakes around position 1: -183: [16:03:27] dsafsdf -183: [16:03:27] ^ -183: [16:03:27] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -183: [16:03:27] SMILES Parse Error: syntax error while parsing: dsafsdf -183: [16:03:27] SMILES Parse Error: check for mistakes around position 1: -183: [16:03:27] dsafsdf -183: [16:03:27] ^ -183: [16:03:27] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -183: [16:03:27] SMILES Parse Error: syntax error while parsing: dsafsdf -183: [16:03:27] SMILES Parse Error: check for mistakes around position 1: -183: [16:03:27] dsafsdf -183: [16:03:27] ^ -183: [16:03:27] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -183: [16:03:27] SMILES Parse Error: syntax error while parsing: dsafsdf -183: [16:03:27] SMILES Parse Error: check for mistakes around position 1: -183: [16:03:27] dsafsdf -183: [16:03:27] ^ -183: [16:03:27] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -183: [16:03:27] SMILES Parse Error: syntax error while parsing: dsafsdf -183: [16:03:27] SMILES Parse Error: check for mistakes around position 1: -183: [16:03:27] dsafsdf -183: [16:03:27] ^ -183: [16:03:27] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -183: [16:03:27] SMILES Parse Error: syntax error while parsing: dsafsdf -183: [16:03:27] SMILES Parse Error: check for mistakes around position 1: -183: [16:03:27] dsafsdf -183: [16:03:27] ^ -183: [16:03:27] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -183: [16:03:27] SMILES Parse Error: syntax error while parsing: dsafsdf -183: [16:03:27] SMILES Parse Error: check for mistakes around position 1: -183: [16:03:27] dsafsdf -183: [16:03:27] ^ -183: [16:03:27] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -183: [16:03:27] SMILES Parse Error: syntax error while parsing: dsafsdf -183: [16:03:27] SMILES Parse Error: check for mistakes around position 1: -183: [16:03:27] dsafsdf -183: [16:03:27] ^ -183: [16:03:27] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -183: [16:03:27] SMILES Parse Error: syntax error while parsing: dsafsdf -183: [16:03:27] SMILES Parse Error: check for mistakes around position 1: -183: [16:03:27] dsafsdf -183: [16:03:27] ^ -183: [16:03:27] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -183: [16:03:27] SMILES Parse Error: syntax error while parsing: dsafsdf -183: [16:03:27] SMILES Parse Error: check for mistakes around position 1: -183: [16:03:27] dsafsdf -183: [16:03:27] ^ -183: [16:03:27] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -183: [16:03:27] SMILES Parse Error: syntax error while parsing: dsafsdf -183: [16:03:27] SMILES Parse Error: check for mistakes around position 1: -183: [16:03:27] dsafsdf -183: [16:03:27] ^ -183: [16:03:27] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -183: [16:03:27] SMILES Parse Error: syntax error while parsing: dsafsdf -183: [16:03:27] SMILES Parse Error: check for mistakes around position 1: -183: [16:03:27] dsafsdf -183: [16:03:27] ^ -183: [16:03:27] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -183: [16:03:27] SMILES Parse Error: syntax error while parsing: dsafsdf -183: [16:03:27] SMILES Parse Error: check for mistakes around position 1: -183: [16:03:27] dsafsdf -183: [16:03:27] ^ -183: [16:03:27] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -183: [16:03:27] SMILES Parse Error: syntax error while parsing: dsafsdf -183: [16:03:27] SMILES Parse Error: check for mistakes around position 1: -183: [16:03:27] dsafsdf -183: [16:03:27] ^ -183: [16:03:27] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -183: [16:03:27] SMILES Parse Error: syntax error while parsing: dsafsdf -183: [16:03:27] SMILES Parse Error: check for mistakes around position 1: -183: [16:03:27] dsafsdf -183: [16:03:27] ^ -183: [16:03:27] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -183: [16:03:27] SMILES Parse Error: syntax error while parsing: dsafsdf -183: [16:03:27] SMILES Parse Error: check for mistakes around position 1: -183: [16:03:27] dsafsdf -183: [16:03:27] ^ -183: [16:03:27] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -183: [16:03:27] SMILES Parse Error: syntax error while parsing: dsafsdf -183: [16:03:27] SMILES Parse Error: check for mistakes around position 1: -183: [16:03:27] dsafsdf -183: [16:03:27] ^ -183: [16:03:27] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -183: [16:03:27] SMILES Parse Error: syntax error while parsing: dsafsdf -183: [16:03:27] SMILES Parse Error: check for mistakes around position 1: -183: [16:03:27] dsafsdf -183: [16:03:27] ^ -183: [16:03:27] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -183: [16:03:27] SMILES Parse Error: syntax error while parsing: dsafsdf -183: [16:03:27] SMILES Parse Error: check for mistakes around position 1: -183: [16:03:27] dsafsdf -183: [16:03:27] ^ -183: [16:03:27] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -183: [16:03:27] SMILES Parse Error: syntax error while parsing: dsafsdf -183: [16:03:27] SMILES Parse Error: check for mistakes around position 1: -183: [16:03:27] dsafsdf -183: [16:03:27] ^ -183: [16:03:27] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -183: [16:03:27] SMILES Parse Error: syntax error while parsing: dsafsdf -183: [16:03:27] SMILES Parse Error: check for mistakes around position 1: -183: [16:03:27] dsafsdf -183: [16:03:27] ^ -183: [16:03:27] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -183: [16:03:27] SMILES Parse Error: syntax error while parsing: dsafsdf -183: [16:03:27] SMILES Parse Error: check for mistakes around position 1: -183: [16:03:27] dsafsdf -183: [16:03:27] ^ -183: [16:03:27] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -183: [16:03:27] SMILES Parse Error: syntax error while parsing: dsafsdf -183: [16:03:27] SMILES Parse Error: check for mistakes around position 1: -183: [16:03:27] dsafsdf -183: [16:03:27] ^ -183: [16:03:27] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -183: [16:03:27] SMILES Parse Error: syntax error while parsing: dsafsdf -183: [16:03:27] SMILES Parse Error: check for mistakes around position 1: -183: [16:03:27] dsafsdf -183: [16:03:27] ^ -183: [16:03:27] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -183: [16:03:27] SMILES Parse Error: syntax error while parsing: dsafsdf -183: [16:03:27] SMILES Parse Error: check for mistakes around position 1: -183: [16:03:27] dsafsdf -183: [16:03:27] ^ -183: [16:03:27] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -183: [16:03:27] SMILES Parse Error: syntax error while parsing: dsafsdf -183: [16:03:27] SMILES Parse Error: check for mistakes around position 1: -183: [16:03:27] dsafsdf -183: [16:03:27] ^ -183: [16:03:27] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -183: [16:03:27] SMILES Parse Error: syntax error while parsing: dsafsdf -183: [16:03:27] SMILES Parse Error: check for mistakes around position 1: -183: [16:03:27] dsafsdf -183: [16:03:27] ^ -183: [16:03:27] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -183: [16:03:27] SMILES Parse Error: syntax error while parsing: dsafsdf -183: [16:03:27] SMILES Parse Error: check for mistakes around position 1: -183: [16:03:27] dsafsdf -183: [16:03:27] ^ -183: [16:03:27] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -183: [16:03:27] SMILES Parse Error: syntax error while parsing: dsafsdf -183: [16:03:27] SMILES Parse Error: check for mistakes around position 1: -183: [16:03:27] dsafsdf -183: [16:03:27] ^ -183: [16:03:27] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -183: [16:03:27] SMILES Parse Error: syntax error while parsing: dsafsdf -183: [16:03:27] SMILES Parse Error: check for mistakes around position 1: -183: [16:03:27] dsafsdf -183: [16:03:27] ^ -183: [16:03:27] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -183: [16:03:27] SMILES Parse Error: syntax error while parsing: dsafsdf -183: [16:03:27] SMILES Parse Error: check for mistakes around position 1: -183: [16:03:27] dsafsdf -183: [16:03:27] ^ -183: [16:03:27] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -183: [16:03:27] SMILES Parse Error: syntax error while parsing: dsafsdf -183: [16:03:27] SMILES Parse Error: check for mistakes around position 1: -183: [16:03:27] dsafsdf -183: [16:03:27] ^ -183: [16:03:27] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -183: [16:03:27] SMILES Parse Error: syntax error while parsing: dsafsdf -183: [16:03:27] SMILES Parse Error: check for mistakes around position 1: -183: [16:03:27] dsafsdf -183: [16:03:27] ^ -183: [16:03:27] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -183: [16:03:27] SMILES Parse Error: syntax error while parsing: dsafsdf -183: [16:03:27] SMILES Parse Error: check for mistakes around position 1: -183: [16:03:27] dsafsdf -183: [16:03:27] ^ -183: [16:03:27] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -183: [16:03:27] SMILES Parse Error: syntax error while parsing: dsafsdf -183: [16:03:27] SMILES Parse Error: check for mistakes around position 1: -183: [16:03:27] dsafsdf -183: [16:03:27] ^ -183: [16:03:27] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -183: [16:03:27] SMILES Parse Error: syntax error while parsing: dsafsdf -183: [16:03:27] SMILES Parse Error: check for mistakes around position 1: -183: [16:03:27] dsafsdf -183: [16:03:27] ^ -183: [16:03:27] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -183: [16:03:27] SMILES Parse Error: syntax error while parsing: dsafsdf -183: [16:03:27] SMILES Parse Error: check for mistakes around position 1: -183: [16:03:27] dsafsdf -183: [16:03:27] ^ -183: [16:03:27] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -183: [16:03:27] SMILES Parse Error: syntax error while parsing: dsafsdf -183: [16:03:27] SMILES Parse Error: check for mistakes around position 1: -183: [16:03:27] dsafsdf -183: [16:03:27] ^ -183: [16:03:27] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -183: [16:03:27] SMILES Parse Error: syntax error while parsing: dsafsdf -183: [16:03:27] SMILES Parse Error: check for mistakes around position 1: -183: [16:03:27] dsafsdf -183: [16:03:27] ^ -183: [16:03:27] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -183: [16:03:27] SMILES Parse Error: syntax error while parsing: dsafsdf -183: [16:03:27] SMILES Parse Error: check for mistakes around position 1: -183: [16:03:27] dsafsdf -183: [16:03:27] ^ -183: [16:03:27] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -183: [16:03:27] SMILES Parse Error: syntax error while parsing: dsafsdf -183: [16:03:27] SMILES Parse Error: check for mistakes around position 1: -183: [16:03:27] dsafsdf -183: [16:03:27] ^ -183: [16:03:27] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -183: [16:03:27] SMILES Parse Error: syntax error while parsing: dsafsdf -183: [16:03:27] SMILES Parse Error: check for mistakes around position 1: -183: [16:03:27] dsafsdf -183: [16:03:27] ^ -183: [16:03:27] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -183: [16:03:27] SMILES Parse Error: syntax error while parsing: dsafsdf -183: [16:03:27] SMILES Parse Error: check for mistakes around position 1: -183: [16:03:27] dsafsdf -183: [16:03:27] ^ -183: [16:03:27] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -183: [16:03:27] SMILES Parse Error: syntax error while parsing: dsafsdf -183: [16:03:27] SMILES Parse Error: check for mistakes around position 1: -183: [16:03:27] dsafsdf -183: [16:03:27] ^ -183: [16:03:27] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -183: [16:03:27] SMILES Parse Error: syntax error while parsing: dsafsdf -183: [16:03:27] SMILES Parse Error: check for mistakes around position 1: -183: [16:03:27] dsafsdf -183: [16:03:27] ^ -183: [16:03:27] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -183: [16:03:27] SMILES Parse Error: syntax error while parsing: dsafsdf -183: [16:03:27] SMILES Parse Error: check for mistakes around position 1: -183: [16:03:27] dsafsdf -183: [16:03:27] ^ -183: [16:03:27] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -183: [16:03:27] ------------------------------------- -183: [16:03:27] Results do not depend on numThreads -173: [16:03:28] Complex queries can be slow. -173: [16:03:28] Complex queries can be slow. -173: [16:03:28] Complex queries can be slow. -173: [16:03:28] Complex queries can be slow. -173: [16:03:28] Complex queries can be slow. -173: [16:03:28] Complex queries can be slow. -173: [16:03:28] Complex queries can be slow. -173: [16:03:28] Complex queries can be slow. -173: [16:03:29] Complex queries can be slow. -173: [16:03:29] Complex queries can be slow. -173: [16:03:29] Complex queries can be slow. -173: [16:03:29] Complex queries can be slow. -148: ... -148: ---------------------------------------------------------------------- -148: Ran 22 tests in 38.677s -148: -148: OK -173: =============================================================================== -173: All tests passed (121 assertions in 17 test cases) -173: -175/236 Test #173: testSynthonSpaceSubstructureSearch ..... Passed 23.59 sec +173: [12:25:11] Complex queries can be slow. +173: [12:25:12] Complex queries can be slow. +183: [12:25:12] ------------------------------------- +183: [12:25:12] Results do not depend on numThreads (all same) +173: [12:25:12] Complex queries can be slow. +183: [12:25:12] ------------------------------------- +183: [12:25:12] testTautomerQueries +183: [12:25:12] Pattern fingerprints for tautomersearch aren't tautomer fingerprints, ignoring... +183: [12:25:12] ------------------------------------- +183: [12:25:12] github3881 recursive smarts with rings +175/236 Test #183: substructLibraryTest ................... Passed 16.73 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: [16:03:29] WARNING: not removing hydrogen atom with dummy atom neighbors -187: [16:03:29] WARNING: not removing hydrogen atom with dummy atom neighbors -187: [16:03:29] WARNING: not removing hydrogen atom with dummy atom neighbors -187: [16:03:29] WARNING: not removing hydrogen atom with dummy atom neighbors -187: [16:03:29] WARNING: not removing hydrogen atom with dummy atom neighbors -187: [16:03:29] WARNING: not removing hydrogen atom with dummy atom neighbors -187: [16:03:29] WARNING: not removing hydrogen atom with dummy atom neighbors -187: [16:03:29] WARNING: not removing hydrogen atom with dummy atom neighbors -187: [16:03:29] WARNING: not removing hydrogen atom with dummy atom neighbors -187: [16:03:29] WARNING: not removing hydrogen atom with dummy atom neighbors -187: [16:03:29] WARNING: not removing hydrogen atom with dummy atom neighbors -187: [16:03:29] WARNING: not removing hydrogen atom with dummy atom neighbors -187: [16:03:29] WARNING: not removing hydrogen atom with dummy atom neighbors -187: [16:03:29] WARNING: not removing hydrogen atom with dummy atom neighbors -187: [16:03:29] WARNING: not removing hydrogen atom with dummy atom neighbors -187: [16:03:29] WARNING: not removing hydrogen atom with dummy atom neighbors -187: [16:03:29] WARNING: not removing hydrogen atom with dummy atom neighbors -187: [16:03:29] WARNING: not removing hydrogen atom with dummy atom neighbors -187: [16:03:29] WARNING: not removing hydrogen atom with dummy atom neighbors -187: [16:03:29] WARNING: not removing hydrogen atom with dummy atom neighbors -187: [16:03:29] WARNING: not removing hydrogen atom with dummy atom neighbors -176/236 Test #187: testRGroupDecompInternals .............. Passed 0.11 sec +187: [12:25:12] WARNING: not removing hydrogen atom with dummy atom neighbors +187: [12:25:12] WARNING: not removing hydrogen atom with dummy atom neighbors +187: [12:25:12] WARNING: not removing hydrogen atom with dummy atom neighbors +187: [12:25:12] WARNING: not removing hydrogen atom with dummy atom neighbors +187: [12:25:12] WARNING: not removing hydrogen atom with dummy atom neighbors +187: [12:25:12] WARNING: not removing hydrogen atom with dummy atom neighbors +187: [12:25:12] WARNING: not removing hydrogen atom with dummy atom neighbors +187: [12:25:12] WARNING: not removing hydrogen atom with dummy atom neighbors +187: [12:25:12] WARNING: not removing hydrogen atom with dummy atom neighbors +187: [12:25:12] WARNING: not removing hydrogen atom with dummy atom neighbors +187: [12:25:12] WARNING: not removing hydrogen atom with dummy atom neighbors +187: [12:25:12] WARNING: not removing hydrogen atom with dummy atom neighbors +187: [12:25:12] WARNING: not removing hydrogen atom with dummy atom neighbors +187: [12:25:12] WARNING: not removing hydrogen atom with dummy atom neighbors +187: [12:25:12] WARNING: not removing hydrogen atom with dummy atom neighbors +187: [12:25:12] WARNING: not removing hydrogen atom with dummy atom neighbors +187: [12:25:12] WARNING: not removing hydrogen atom with dummy atom neighbors +187: [12:25:12] WARNING: not removing hydrogen atom with dummy atom neighbors +187: [12:25:12] WARNING: not removing hydrogen atom with dummy atom neighbors +187: [12:25:12] WARNING: not removing hydrogen atom with dummy atom neighbors +187: [12:25:12] WARNING: not removing hydrogen atom with dummy atom neighbors +176/236 Test #187: testRGroupDecompInternals .............. Passed 0.13 sec test 188 Start 188: rgroupCatchTests 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 -177/236 Test #148: pyDistGeomHelpers ...................... Passed 39.37 sec +173: [12:25:12] Complex queries can be slow. +173: [12:25:13] Complex queries can be slow. +173: [12:25:13] Complex queries can be slow. +186: bulk +188: Randomness seeded to: 2566824897 +188: =============================================================================== +188: All tests passed (1475 assertions in 14 test cases) +188: +177/236 Test #188: rgroupCatchTests ....................... Passed 1.05 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 -186: bulk -188: Randomness seeded to: 4286026811 -188: =============================================================================== -188: All tests passed (1475 assertions in 14 test cases) -188: -178/236 Test #188: rgroupCatchTests ....................... Passed 0.62 sec +148: ... +148: ---------------------------------------------------------------------- +148: Ran 22 tests in 55.887s +148: +148: OK +178/236 Test #148: pyDistGeomHelpers ...................... Passed 57.16 sec test 190 Start 190: molInterchangeTest1 190: Test command: /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/MolInterchange/molInterchangeTest1 190: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/MolInterchange 190: Test timeout computed to be: 1500 -190: [16:03:30] test1: basics -190: [16:03:30] done -190: [16:03:30] test2: basic writing +173: [12:25:14] Complex queries can be slow. +190: [12:25:14] test1: basics +190: [12:25:14] done +190: [12:25:14] test2: basic writing 190: {"rdkitjson":{"version":11},"defaults":{"atom":{"z":6,"impHs":0,"chg":0,"nRad":0,"isotope":0,"stereo":"unspecified"},"bond":{"bo":1,"stereo":"unspecified"}},"molecules":[{"name":"mol1 name","atoms":[{"impHs":3},{"impHs":3}],"bonds":[{"atoms":[0,1]}],"extensions":[{"name":"rdkitRepresentation","formatVersion":2,"toolkitVersion":"2025.03.1","cipRanks":[0,0]}]}]} 190: {"rdkitjson":{"version":11},"defaults":{"atom":{"z":6,"impHs":0,"chg":0,"nRad":0,"isotope":0,"stereo":"unspecified"},"bond":{"bo":1,"stereo":"unspecified"}},"molecules":[{"name":"test mol","atoms":[{"z":9},{"stereo":"cw"},{"z":17},{"z":8,"impHs":1},{"impHs":3}],"bonds":[{"atoms":[0,1]},{"atoms":[1,2]},{"atoms":[1,3]},{"atoms":[1,4]}],"extensions":[{"name":"rdkitRepresentation","formatVersion":2,"toolkitVersion":"2025.03.1","cipRanks":[3,1,4,2,0],"cipCodes":[[1,"S"]]}]}]} 190: {"rdkitjson":{"version":11},"defaults":{"atom":{"z":6,"impHs":0,"chg":0,"nRad":0,"isotope":0,"stereo":"unspecified"},"bond":{"bo":1,"stereo":"unspecified"}},"molecules":[{"name":"test mol","atoms":[{"impHs":1},{"impHs":1},{"impHs":1},{"impHs":1},{"impHs":1},{"impHs":1}],"bonds":[{"bo":2,"atoms":[0,1]},{"atoms":[1,2]},{"bo":2,"atoms":[2,3]},{"atoms":[3,4]},{"bo":2,"atoms":[4,5]},{"atoms":[5,0]}],"extensions":[{"name":"rdkitRepresentation","formatVersion":2,"toolkitVersion":"2025.03.1","aromaticAtoms":[0,1,2,3,4,5],"aromaticBonds":[0,1,2,3,4,5],"cipRanks":[0,0,0,0,0,0],"atomRings":[[0,5,4,3,2,1]]}]}]} 190: {"rdkitjson":{"version":11},"defaults":{"atom":{"z":6,"impHs":0,"chg":0,"nRad":0,"isotope":0,"stereo":"unspecified"},"bond":{"bo":1,"stereo":"unspecified"}},"molecules":[{"name":"test mol","atoms":[{"impHs":3},{"impHs":2},{},{},{"z":7,"impHs":2},{"impHs":1},{},{"impHs":3},{"z":7},{"impHs":1}],"bonds":[{"atoms":[0,1]},{"atoms":[1,2]},{"bo":2,"atoms":[2,3]},{"atoms":[3,4]},{"atoms":[3,5]},{"bo":2,"atoms":[5,6]},{"atoms":[6,7]},{"atoms":[6,8]},{"bo":2,"atoms":[8,9]},{"atoms":[9,2]}],"extensions":[{"name":"rdkitRepresentation","formatVersion":2,"toolkitVersion":"2025.03.1","aromaticAtoms":[2,3,5,6,8,9],"aromaticBonds":[2,4,5,7,8,9],"cipRanks":[0,2,4,5,8,3,7,1,9,6],"atomRings":[[2,9,8,6,5,3]]}]}]} -190: [16:03:30] done -190: [16:03:30] test3: writing conformers +190: [12:25:14] done +190: [12:25:14] test3: writing conformers 190: {"rdkitjson":{"version":11},"defaults":{"atom":{"z":6,"impHs":0,"chg":0,"nRad":0,"isotope":0,"stereo":"unspecified"},"bond":{"bo":1,"stereo":"unspecified"}},"molecules":[{"name":"example 2","atoms":[{"z":8},{"stereo":"cw"},{"z":17,"isotope":35},{"z":9},{"z":1},{"z":1}],"bonds":[{"atoms":[0,1]},{"atoms":[1,2]},{"atoms":[1,3]},{"atoms":[0,4]},{"atoms":[1,5]}],"conformers":[{"dim":2,"coords":[[-1.1988,-0.0452],[-0.3332,0.4556],[0.166,1.322],[0.5332,-0.0438],[-2.0652,0.4542],[-0.834,1.3212]]},{"dim":3,"coords":[[0.9554,-0.3743,-0.4679],[-0.3616,-0.1311,-0.0795],[-0.5097,1.6256,0.1706],[-0.5779,-0.792,1.1042],[1.5277,0.1064,0.1628],[-1.0339,-0.4346,-0.8902]]}],"extensions":[{"name":"rdkitRepresentation","formatVersion":2,"toolkitVersion":"2025.03.1","cipCodes":[[1,"S"]]},{"name":"partialCharges","generator":"RDKit","formatVersion":10,"generatorVersion":"2025.03.1","values":[-0.352,0.273,-0.055,-0.198,0.215,0.117]}]}]} -190: [16:03:30] done -190: [16:03:30] test4: writing properties +190: [12:25:14] done +190: [12:25:14] test4: writing properties 190: {"rdkitjson":{"version":11},"defaults":{"atom":{"z":6,"impHs":0,"chg":0,"nRad":0,"isotope":0,"stereo":"unspecified"},"bond":{"bo":1,"stereo":"unspecified"}},"molecules":[{"atoms":[{"impHs":3},{"impHs":3}],"bonds":[{"atoms":[0,1]}],"properties":{"foo_string":"bar","foo_int":1,"foo_double":1.2},"extensions":[{"name":"rdkitRepresentation","formatVersion":2,"toolkitVersion":"2025.03.1","cipRanks":[0,0]}]}]} -190: [16:03:30] done -190: [16:03:30] test5: writing partial charges +190: [12:25:14] done +190: [12:25:14] test5: writing partial charges 190: {"rdkitjson":{"version":11},"defaults":{"atom":{"z":6,"impHs":0,"chg":0,"nRad":0,"isotope":0,"stereo":"unspecified"},"bond":{"bo":1,"stereo":"unspecified"}},"molecules":[{"atoms":[{"impHs":3},{"z":8,"impHs":1}],"bonds":[{"atoms":[0,1]}],"extensions":[{"name":"rdkitRepresentation","formatVersion":2,"toolkitVersion":"2025.03.1","cipRanks":[0,1]},{"name":"partialCharges","generator":"RDKit","formatVersion":10,"generatorVersion":"2025.03.1","values":[0.5,-0.5]}]}]} -190: [16:03:30] testing parse options -190: [16:03:30] done -190: [16:03:30] testing github #2046: CIPRank values from JSONDataToMols are not unsigned +190: [12:25:14] testing parse options +190: [12:25:14] done +190: [12:25:14] testing github #2046: CIPRank values from JSONDataToMols are not unsigned 190: {"rdkitjson":{"version":11},"defaults":{"atom":{"z":6,"impHs":0,"chg":0,"nRad":0,"isotope":0,"stereo":"unspecified"},"bond":{"bo":1,"stereo":"unspecified"}},"molecules":[{"name":"test mol","atoms":[{"impHs":2},{"impHs":2},{"impHs":2},{"z":8},{"impHs":1,"stereo":"cw"},{"z":9}],"bonds":[{"atoms":[0,1]},{"atoms":[1,2]},{"atoms":[2,3]},{"atoms":[3,4]},{"atoms":[4,5]},{"atoms":[4,0]}],"extensions":[{"name":"rdkitRepresentation","formatVersion":2,"toolkitVersion":"2025.03.1","cipRanks":[1,0,2,4,3,5],"cipCodes":[[4,"S"]],"atomRings":[[0,1,2,3,4]]}]}]} -190: [16:03:30] done -190: [16:03:30] testing 'either' stereochemistry -190: [16:03:30] done -179/236 Test #190: molInterchangeTest1 .................... Passed 0.22 sec +190: [12:25:14] done +190: [12:25:14] testing 'either' stereochemistry +190: [12:25:14] done +179/236 Test #190: molInterchangeTest1 .................... Passed 0.30 sec test 191 Start 191: molInterchangeCatchTest 191: Test command: /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/MolInterchange/molInterchangeCatchTest 191: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/MolInterchange 191: Test timeout computed to be: 1500 -191: Randomness seeded to: 467208560 -191: [16:03:31] unrecognized bond type 12 set to zero while writing -191: [16:03:31] unrecognized bond type 0 set to zero while writing +173: [12:25:14] Complex queries can be slow. +191: Randomness seeded to: 1846522210 +191: [12:25:14] unrecognized bond type 12 set to zero while writing +191: [12:25:15] unrecognized bond type 0 set to zero while writing 191: =============================================================================== 191: All tests passed (125 assertions in 7 test cases) 191: -180/236 Test #191: molInterchangeCatchTest ................ Passed 0.47 sec +180/236 Test #191: molInterchangeCatchTest ................ Passed 0.57 sec test 192 Start 192: pyMolInterchange 192: Test command: /usr/bin/python3 "/build/reproducible-path/rdkit-202503.1/Code/GraphMol/MolInterchange/Wrap/testMolInterchange.py" 192: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/MolInterchange/Wrap 192: Test timeout computed to be: 1500 +173: [12:25:15] Complex queries can be slow. 192: .. 192: ---------------------------------------------------------------------- -192: Ran 2 tests in 0.035s +192: Ran 2 tests in 0.007s 192: 192: OK -181/236 Test #192: pyMolInterchange ....................... Passed 1.06 sec +181/236 Test #192: pyMolInterchange ....................... Passed 0.50 sec test 193 Start 193: testSLNParse 193: Test command: /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/SLNParse/testSLNParse 193: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/SLNParse 193: Test timeout computed to be: 1500 -189: .................... -189: ---------------------------------------------------------------------- -189: Ran 20 tests in 2.143s -189: -189: OK +186: bulk, no symmetry 193: Atoms: 193: 0 6 C chg: 1 deg: 5 exp: N/A imp: 0 hyb: 193: 1 1 H chg: 0 deg: 1 exp: N/A imp: N/A hyb: @@ -32309,62 +32338,77 @@ 193: 2 0->3 order: 1 193: 3 0->4 order: 1 193: 4 0->5 order: 1 -193: [16:03:32] SLN Parse Error: syntax error while parsing: CH4[I=13] -193: [16:03:32] Failed parsing SLN 'CH4[I=13]' -193: [16:03:32] SLN Parser error: Atom ID 1 appears *after* its ring closure. -193: [16:03:32] SLN Parser error: Ring closure 1 does not have a corresponding opener. -193: [16:03:32] SLN Parse Error: syntax error while parsing: CH2(C@1H2)CH2(CH2CH2C[1]H2) -193: [16:03:32] Failed parsing SLN 'CH2(C@1H2)CH2(CH2CH2C[1]H2)' -193: [16:03:32] SLN Parse Error: syntax error while parsing: CH2(CH2[1])CH2(CH2CH2CH2@1) -193: [16:03:32] Failed parsing SLN 'CH2(CH2[1])CH2(CH2CH2CH2@1)' -182/236 Test #189: pyRGroupDecomposition .................. Passed 2.59 sec +193: [12:25:15] SLN Parse Error: syntax error while parsing: CH4[I=13] +193: [12:25:15] Failed parsing SLN 'CH4[I=13]' +173: [12:25:15] Complex queries can be slow. +193: [12:25:15] SLN Parser error: Atom ID 1 appears *after* its ring closure. +193: [12:25:15] SLN Parser error: Ring closure 1 does not have a corresponding opener. +193: [12:25:15] SLN Parse Error: syntax error while parsing: CH2(C@1H2)CH2(CH2CH2C[1]H2) +193: [12:25:15] Failed parsing SLN 'CH2(C@1H2)CH2(CH2CH2C[1]H2)' +193: [12:25:15] SLN Parse Error: syntax error while parsing: CH2(CH2[1])CH2(CH2CH2CH2@1) +193: [12:25:15] Failed parsing SLN 'CH2(CH2[1])CH2(CH2CH2CH2@1)' +193: [12:25:15] SLN Parse Error: syntax error while parsing: CH4 fff +193: [12:25:15] Failed parsing SLN 'CH4 fff' +193: [12:25:15] SLN Parse Error: syntax error while parsing: C[charge=+1] foo +193: [12:25:15] Failed parsing SLN 'C[charge=+1] foo' +193: [12:25:16] Query property 'is' ignored on non-query atom +193: [12:25:16] Query property 'is' ignored on non-query atom +182/236 Test #193: testSLNParse ........................... Passed 0.42 sec test 194 Start 194: pySLNParse 194: Test command: /usr/bin/python3 "/build/reproducible-path/rdkit-202503.1/Code/GraphMol/SLNParse/Wrap/testSLN.py" 194: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/SLNParse/Wrap 194: Test timeout computed to be: 1500 -193: [16:03:32] SLN Parse Error: syntax error while parsing: CH4 fff -193: [16:03:32] Failed parsing SLN 'CH4 fff' -193: [16:03:32] SLN Parse Error: syntax error while parsing: C[charge=+1] foo -193: [16:03:32] Failed parsing SLN 'C[charge=+1] foo' -193: [16:03:32] Query property 'is' ignored on non-query atom -193: [16:03:32] Query property 'is' ignored on non-query atom -183/236 Test #193: testSLNParse ........................... Passed 0.34 sec +173: [12:25:16] Complex queries can be slow. +194: .. +194: ---------------------------------------------------------------------- +194: Ran 2 tests in 0.026s +194: +194: OK +183/236 Test #194: pySLNParse ............................. Passed 0.69 sec test 195 Start 195: pyGraphMolWrap 195: Test command: /usr/bin/python3 "/build/reproducible-path/rdkit-202503.1/Code/GraphMol/Wrap/rough_test.py" 195: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/Wrap 195: Test timeout computed to be: 1500 -183: [16:03:33] ------------------------------------- -183: [16:03:33] Results do not depend on numThreads (all same) -194: .. -194: ---------------------------------------------------------------------- -194: Ran 2 tests in 0.046s -194: -194: OK -186: bulk, no symmetry -184/236 Test #194: pySLNParse ............................. Passed 0.62 sec +189: .................... +189: ---------------------------------------------------------------------- +189: Ran 20 tests in 2.195s +189: +189: OK +173: =============================================================================== +173: All tests passed (121 assertions in 17 test cases) +173: +184/236 Test #173: testSynthonSpaceSubstructureSearch ..... Passed 40.18 sec test 196 Start 196: pyTestConformerWrap 196: Test command: /usr/bin/python3 "/build/reproducible-path/rdkit-202503.1/Code/GraphMol/Wrap/testConformer.py" 196: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/Wrap 196: Test timeout computed to be: 1500 -183: [16:03:33] ------------------------------------- -183: [16:03:33] testTautomerQueries -183: [16:03:33] Pattern fingerprints for tautomersearch aren't tautomer fingerprints, ignoring... -183: [16:03:33] ------------------------------------- -183: [16:03:33] github3881 recursive smarts with rings -185/236 Test #183: substructLibraryTest ................... Passed 14.83 sec +185/236 Test #189: pyRGroupDecomposition .................. Passed 3.21 sec test 197 Start 197: pyTestTrajectory 197: Test command: /usr/bin/python3 "/build/reproducible-path/rdkit-202503.1/Code/GraphMol/Wrap/testTrajectory.py" 197: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/Wrap 197: Test timeout computed to be: 1500 -197: [16:03:34] +186: [12:25:17] Relabelling existing label +196: ...... +196: ---------------------------------------------------------------------- +196: Ran 6 tests in 0.065s +196: +196: OK +186/236 Test #196: pyTestConformerWrap .................... Passed 1.15 sec +test 198 + Start 198: pyTestSGroups + +198: Test command: /usr/bin/python3 "/build/reproducible-path/rdkit-202503.1/Code/GraphMol/Wrap/testSGroups.py" +198: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/Wrap +198: Test timeout computed to be: 1500 +197: [12:25:18] 197: 197: **** 197: Pre-condition Violation @@ -32378,23 +32422,23 @@ 197: 2# RDKit::Trajectory::addConformersToMol(RDKit::ROMol&, int, int) in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu//lib/libRDKitTrajectory.so.1 197: 3# boost::python::objects::caller_py_function_impl > >::operator()(_object*, _object*) in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdtrajectory.so 197: 4# boost::python::objects::function::call(_object*, _object*) const in /lib/aarch64-linux-gnu/libboost_python313.so.1.83.0 -197: 5# 0x0000FFFFABB42680 in /lib/aarch64-linux-gnu/libboost_python313.so.1.83.0 +197: 5# 0x0000FFFF809A2680 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/rdmolfiles.so 197: 8# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdmolfiles.so 197: 9# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdCIPLabeler.so 197: 10# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so -197: 11# 0x0000FFFFAA11C320 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so -197: 12# 0x0000FFFFAA11C2B8 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so -197: 13# 0x0000FFFFAA11C248 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so -197: 14# 0x0000FFFFAA11C1E0 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so -197: 15# 0x0000FFFFAA11C178 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so +197: 11# 0x0000FFFF7EF7C320 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so +197: 12# 0x0000FFFF7EF7C2B8 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so +197: 13# 0x0000FFFF7EF7C248 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so +197: 14# 0x0000FFFF7EF7C1E0 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so +197: 15# 0x0000FFFF7EF7C178 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so 197: 16# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/rdBase.so 197: 17# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/rdBase.so 197: 18# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/rdBase.so 197: 19# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/rdBase.so 197: 20# boost::python::handle_exception_impl(boost::function0) in /lib/aarch64-linux-gnu/libboost_python313.so.1.83.0 -197: 21# 0x0000FFFFABB3F25C in /lib/aarch64-linux-gnu/libboost_python313.so.1.83.0 +197: 21# 0x0000FFFF8099F25C in /lib/aarch64-linux-gnu/libboost_python313.so.1.83.0 197: 22# _PyObject_MakeTpCall in /usr/bin/python3 197: 23# _PyEval_EvalFrameDefault in /usr/bin/python3 197: 24# 0x000000000053DD10 in /usr/bin/python3 @@ -32426,13 +32470,13 @@ 197: 50# 0x000000000065F5F0 in /usr/bin/python3 197: 51# Py_RunMain in /usr/bin/python3 197: 52# Py_BytesMain in /usr/bin/python3 -197: 53# 0x0000FFFFAC32229C in /lib/aarch64-linux-gnu/libc.so.6 +197: 53# 0x0000FFFF8118229C in /lib/aarch64-linux-gnu/libc.so.6 197: 54# __libc_start_main in /lib/aarch64-linux-gnu/libc.so.6 197: 55# _start in /usr/bin/python3 197: ---------- 197: **** 197: -197: .[16:03:34] +197: .[12:25:18] 197: 197: **** 197: Pre-condition Violation @@ -32446,23 +32490,23 @@ 197: 2# RDKit::Trajectory::addConformersToMol(RDKit::ROMol&, int, int) in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu//lib/libRDKitTrajectory.so.1 197: 3# boost::python::objects::caller_py_function_impl > >::operator()(_object*, _object*) in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdtrajectory.so 197: 4# boost::python::objects::function::call(_object*, _object*) const in /lib/aarch64-linux-gnu/libboost_python313.so.1.83.0 -197: 5# 0x0000FFFFABB42680 in /lib/aarch64-linux-gnu/libboost_python313.so.1.83.0 +197: 5# 0x0000FFFF809A2680 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/rdmolfiles.so 197: 8# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdmolfiles.so 197: 9# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdCIPLabeler.so 197: 10# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so -197: 11# 0x0000FFFFAA11C320 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so -197: 12# 0x0000FFFFAA11C2B8 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so -197: 13# 0x0000FFFFAA11C248 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so -197: 14# 0x0000FFFFAA11C1E0 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so -197: 15# 0x0000FFFFAA11C178 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so +197: 11# 0x0000FFFF7EF7C320 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so +197: 12# 0x0000FFFF7EF7C2B8 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so +197: 13# 0x0000FFFF7EF7C248 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so +197: 14# 0x0000FFFF7EF7C1E0 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so +197: 15# 0x0000FFFF7EF7C178 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so 197: 16# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/rdBase.so 197: 17# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/rdBase.so 197: 18# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/rdBase.so 197: 19# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/rdBase.so 197: 20# boost::python::handle_exception_impl(boost::function0) in /lib/aarch64-linux-gnu/libboost_python313.so.1.83.0 -197: 21# 0x0000FFFFABB3F25C in /lib/aarch64-linux-gnu/libboost_python313.so.1.83.0 +197: 21# 0x0000FFFF8099F25C in /lib/aarch64-linux-gnu/libboost_python313.so.1.83.0 197: 22# _PyObject_MakeTpCall in /usr/bin/python3 197: 23# _PyEval_EvalFrameDefault in /usr/bin/python3 197: 24# 0x000000000053DD10 in /usr/bin/python3 @@ -32494,13 +32538,209 @@ 197: 50# 0x000000000065F5F0 in /usr/bin/python3 197: 51# Py_RunMain in /usr/bin/python3 197: 52# Py_BytesMain in /usr/bin/python3 -197: 53# 0x0000FFFFAC32229C in /lib/aarch64-linux-gnu/libc.so.6 +197: 53# 0x0000FFFF8118229C in /lib/aarch64-linux-gnu/libc.so.6 197: 54# __libc_start_main in /lib/aarch64-linux-gnu/libc.so.6 197: 55# _start in /usr/bin/python3 197: ---------- 197: **** 197: -197: .[16:03:34] +195: ..............[12:25:18] SMARTS Parse Error: syntax error while parsing: fiib +195: [12:25:18] SMARTS Parse Error: Failed parsing SMARTS 'fiib' for input: 'fiib' +195: ....[12:25:18] ERROR: Problems encountered parsing data fields +195: [12:25:18] ERROR: moving to the beginning of the next molecule +195: [12:25:18] ERROR: Problems encountered parsing data fields +195: [12:25:18] ERROR: moving to the beginning of the next molecule +195: [12:25:18] Spurious data before the first property will be ignored +195: [12:25:18] Property will be truncated after the first blank line +195: [12:25:18] Property will be truncated after the first blank line +195: [12:25:18] Property will be truncated after the first blank line +195: [12:25:18] ERROR: Problems encountered parsing data fields +195: [12:25:18] ERROR: moving to the beginning of the next molecule +195: [12:25:18] ERROR: Problems encountered parsing data fields +195: [12:25:18] ERROR: moving to the beginning of the next molecule +195: [12:25:18] Spurious data before the first property will be ignored +195: [12:25:18] Property will be truncated after the first blank line +195: [12:25:18] Property will be truncated after the first blank line +195: [12:25:18] Property will be truncated after the first blank line +195: [12:25:18] ERROR: Problems encountered parsing data fields +195: [12:25:18] ERROR: moving to the beginning of the next molecule +195: [12:25:18] Property will be truncated after the first blank line +195: [12:25:18] ERROR: Problems encountered parsing data fields +195: [12:25:18] ERROR: moving to the beginning of the next molecule +195: [12:25:18] Property will be truncated after the first blank line +195: .[12:25:18] SMILES Parse Error: syntax error while parsing: fail +195: [12:25:18] SMILES Parse Error: check for mistakes around position 1: +195: [12:25:18] fail +195: [12:25:18] ^ +195: [12:25:18] SMILES Parse Error: Failed parsing SMILES 'fail' for input: 'fail' +195: [12:25:18] ERROR: Smiles parse error on line 2 +195: [12:25:18] ERROR: Cannot create molecule from : 'fail' +195: >>> This may result in an infinite loop. It should finish almost instantly +195: <<< OK, it finished. +195: ............[12:25:18] Explicit valence for atom # 1 C, 5, is greater than permitted +195: ......[12:25:18] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +195: [12:25:18] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +195: [12:25:18] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +195: [12:25:18] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +195: .inWedges: [H]C12C3([H])C4([H])C1([H])C1([H])C2([H])C3([H])C41[H] |(-0.612,-0.6446,0.635;0.0021,-0.0041,0.002;-0.0187,1.5258,0.0104;-0.6498,2.1424,0.6504;1.5111,1.5466,-0.0041;2.1372,2.1804,0.624;1.5319,0.0168,-0.0125;2.175,-0.6067,0.6086;1.5173,0.025,-1.5424;2.1484,-0.5936,-2.1805;-0.0125,0.0041,-1.5279;-0.6405,-0.6297,-2.154;-0.0333,1.534,-1.5195;-0.6783,2.1574,-2.1387;1.4965,1.5548,-1.534;2.1106,2.1972,-2.1651)| +186: Best mapping +195: ........[12:25:18] non-ring atom 0 marked aromatic +195: [12:25:18] non-ring atom 0 marked aromatic +195: [12:25:18] +195: +195: **** +195: Range Error +195: idx +195: Violation occurred on line 209 in file ./Code/GraphMol/ROMol.cpp +195: Failed Expression: 12 < 6 +195: ---------- +195: Stacktrace: +195: 0# Invar::Invariant::toString[abi:cxx11]() const in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu//lib/libRDKitRDGeneral.so.1 +195: 1# Invar::operator<<(std::ostream&, Invar::Invariant const&) in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu//lib/libRDKitRDGeneral.so.1 +195: 2# RDKit::ROMol::getAtomWithIdx(unsigned int) in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu//lib/libRDKitGraphMol.so.1 +195: 3# RDKit::RWMol::removeAtom(unsigned int) in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu//lib/libRDKitGraphMol.so.1 +195: 4# 0x0000FFFF809855F0 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so +195: 5# boost::python::objects::function::call(_object*, _object*) const in /lib/aarch64-linux-gnu/libboost_python313.so.1.83.0 +195: 6# 0x0000FFFF82382680 in /lib/aarch64-linux-gnu/libboost_python313.so.1.83.0 +195: 7# boost::python::detail::exception_handler::operator()(boost::function0 const&) const in /lib/aarch64-linux-gnu/libboost_python313.so.1.83.0 +195: 8# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdSLNParse.so +195: 9# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdChemReactions.so +195: 10# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdChemReactions.so +195: 11# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdMolChemicalFeatures.so +195: 12# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdDepictor.so +195: 13# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdmolfiles.so +195: 14# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdmolfiles.so +195: 15# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdCIPLabeler.so +195: 16# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so +195: 17# 0x0000FFFF808BC320 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so +195: 18# 0x0000FFFF808BC2B8 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so +195: 19# 0x0000FFFF808BC248 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so +195: 20# 0x0000FFFF808BC1E0 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so +195: 21# 0x0000FFFF808BC178 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so +195: 22# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/rdBase.so +195: 23# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/rdBase.so +195: 24# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/rdBase.so +195: 25# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/rdBase.so +195: 26# boost::python::handle_exception_impl(boost::function0) in /lib/aarch64-linux-gnu/libboost_python313.so.1.83.0 +195: 27# 0x0000FFFF8237F25C in /lib/aarch64-linux-gnu/libboost_python313.so.1.83.0 +195: 28# _PyObject_MakeTpCall in /usr/bin/python3 +195: 29# _PyEval_EvalFrameDefault in /usr/bin/python3 +195: 30# 0x000000000053DD10 in /usr/bin/python3 +195: 31# _PyEval_EvalFrameDefault in /usr/bin/python3 +195: 32# 0x000000000061D100 in /usr/bin/python3 +195: 33# 0x00000000005A959C in /usr/bin/python3 +195: 34# _PyObject_MakeTpCall in /usr/bin/python3 +195: 35# _PyEval_EvalFrameDefault in /usr/bin/python3 +195: 36# 0x000000000053DD10 in /usr/bin/python3 +195: 37# _PyEval_EvalFrameDefault in /usr/bin/python3 +195: 38# 0x000000000061D100 in /usr/bin/python3 +195: 39# 0x00000000005A959C in /usr/bin/python3 +195: 40# _PyObject_MakeTpCall in /usr/bin/python3 +195: 41# _PyEval_EvalFrameDefault in /usr/bin/python3 +195: 42# 0x000000000053DD10 in /usr/bin/python3 +195: 43# _PyEval_EvalFrameDefault in /usr/bin/python3 +195: 44# 0x000000000061D100 in /usr/bin/python3 +195: 45# 0x00000000005A959C in /usr/bin/python3 +195: 46# _PyObject_MakeTpCall in /usr/bin/python3 +195: 47# _PyEval_EvalFrameDefault in /usr/bin/python3 +195: 48# 0x000000000050BA30 in /usr/bin/python3 +195: 49# _PyObject_MakeTpCall in /usr/bin/python3 +195: 50# _PyEval_EvalFrameDefault in /usr/bin/python3 +195: 51# PyEval_EvalCode in /usr/bin/python3 +195: 52# 0x0000000000640ABC in /usr/bin/python3 +195: 53# 0x000000000063C4B0 in /usr/bin/python3 +195: 54# 0x000000000065FFB0 in /usr/bin/python3 +195: 55# 0x000000000065F854 in /usr/bin/python3 +195: 56# 0x000000000065F5F0 in /usr/bin/python3 +195: 57# Py_RunMain in /usr/bin/python3 +195: 58# Py_BytesMain in /usr/bin/python3 +195: 59# 0x0000FFFF830C229C in /lib/aarch64-linux-gnu/libc.so.6 +195: 60# __libc_start_main in /lib/aarch64-linux-gnu/libc.so.6 +195: 61# _start in /usr/bin/python3 +195: ---------- +195: **** +195: +195: [12:25:18] non-ring atom 0 marked aromatic +195: [12:25:18] non-ring atom 0 marked aromatic +195: [12:25:18] +195: +195: **** +195: Range Error +195: idx +195: Violation occurred on line 209 in file ./Code/GraphMol/ROMol.cpp +195: Failed Expression: 12 < 6 +195: ---------- +195: Stacktrace: +195: 0# Invar::Invariant::toString[abi:cxx11]() const in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu//lib/libRDKitRDGeneral.so.1 +195: 1# Invar::operator<<(std::ostream&, Invar::Invariant const&) in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu//lib/libRDKitRDGeneral.so.1 +195: 2# RDKit::ROMol::getAtomWithIdx(unsigned int) in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu//lib/libRDKitGraphMol.so.1 +195: 3# RDKit::RWMol::removeAtom(unsigned int) in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu//lib/libRDKitGraphMol.so.1 +195: 4# 0x0000FFFF809855F0 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so +195: 5# boost::python::objects::function::call(_object*, _object*) const in /lib/aarch64-linux-gnu/libboost_python313.so.1.83.0 +195: 6# 0x0000FFFF82382680 in /lib/aarch64-linux-gnu/libboost_python313.so.1.83.0 +195: 7# boost::python::detail::exception_handler::operator()(boost::function0 const&) const in /lib/aarch64-linux-gnu/libboost_python313.so.1.83.0 +195: 8# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdSLNParse.so +195: 9# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdChemReactions.so +195: 10# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdChemReactions.so +195: 11# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdMolChemicalFeatures.so +195: 12# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdDepictor.so +195: 13# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdmolfiles.so +195: 14# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdmolfiles.so +195: 15# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdCIPLabeler.so +195: 16# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so +195: 17# 0x0000FFFF808BC320 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so +195: 18# 0x0000FFFF808BC2B8 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so +195: 19# 0x0000FFFF808BC248 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so +195: 20# 0x0000FFFF808BC1E0 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so +195: 21# 0x0000FFFF808BC178 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so +195: 22# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/rdBase.so +195: 23# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/rdBase.so +195: 24# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/rdBase.so +195: 25# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/rdBase.so +195: 26# boost::python::handle_exception_impl(boost::function0) in /lib/aarch64-linux-gnu/libboost_python313.so.1.83.0 +195: 27# 0x0000FFFF8237F25C in /lib/aarch64-linux-gnu/libboost_python313.so.1.83.0 +195: 28# _PyObject_MakeTpCall in /usr/bin/python3 +195: 29# _PyEval_EvalFrameDefault in /usr/bin/python3 +195: 30# 0x000000000053DD10 in /usr/bin/python3 +195: 31# _PyEval_EvalFrameDefault in /usr/bin/python3 +195: 32# 0x000000000061D100 in /usr/bin/python3 +195: 33# 0x00000000005A959C in /usr/bin/python3 +195: 34# _PyObject_MakeTpCall in /usr/bin/python3 +195: 35# _PyEval_EvalFrameDefault in /usr/bin/python3 +195: 36# 0x000000000053DD10 in /usr/bin/python3 +195: 37# _PyEval_EvalFrameDefault in /usr/bin/python3 +195: 38# 0x000000000061D100 in /usr/bin/python3 +195: 39# 0x00000000005A959C in /usr/bin/python3 +195: 40# _PyObject_MakeTpCall in /usr/bin/python3 +195: 41# _PyEval_EvalFrameDefault in /usr/bin/python3 +195: 42# 0x000000000053DD10 in /usr/bin/python3 +195: 43# _PyEval_EvalFrameDefault in /usr/bin/python3 +195: 44# 0x000000000061D100 in /usr/bin/python3 +195: 45# 0x00000000005A959C in /usr/bin/python3 +195: 46# _PyObject_MakeTpCall in /usr/bin/python3 +195: 47# _PyEval_EvalFrameDefault in /usr/bin/python3 +195: 48# 0x000000000050BA30 in /usr/bin/python3 +195: 49# _PyObject_MakeTpCall in /usr/bin/python3 +195: 50# _PyEval_EvalFrameDefault in /usr/bin/python3 +195: 51# PyEval_EvalCode in /usr/bin/python3 +195: 52# 0x0000000000640ABC in /usr/bin/python3 +195: 53# 0x000000000063C4B0 in /usr/bin/python3 +195: 54# 0x000000000065FFB0 in /usr/bin/python3 +195: 55# 0x000000000065F854 in /usr/bin/python3 +195: 56# 0x000000000065F5F0 in /usr/bin/python3 +195: 57# Py_RunMain in /usr/bin/python3 +195: 58# Py_BytesMain in /usr/bin/python3 +195: 59# 0x0000FFFF830C229C in /lib/aarch64-linux-gnu/libc.so.6 +195: 60# __libc_start_main in /lib/aarch64-linux-gnu/libc.so.6 +195: 61# _start in /usr/bin/python3 +195: ---------- +195: **** +195: +195: ...............[12:25:18] WARNING: the onlyHeavy argument to mol.GetNumAtoms() has been deprecated. Please use the onlyExplicit argument instead or mol.GetNumHeavyAtoms() if you want the heavy atom count. +195: [12:25:18] WARNING: the onlyHeavy argument to mol.GetNumAtoms() has been deprecated. Please use the onlyExplicit argument instead or mol.GetNumHeavyAtoms() if you want the heavy atom count. +195: ..............[12:25:18] Can't kekulize mol. Unkekulized atoms: 0 1 2 3 4 +195: [12:25:18] Explicit valence for atom # 1 C, 5, is greater than permitted +197: .[12:25:18] 197: 197: **** 197: Range Error @@ -32515,23 +32755,23 @@ 197: 3# RDKit::getSnapshot_wrap(RDKit::Trajectory*, unsigned int) in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdtrajectory.so 197: 4# boost::python::objects::caller_py_function_impl, boost::mpl::vector3 > >::operator()(_object*, _object*) in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdtrajectory.so 197: 5# boost::python::objects::function::call(_object*, _object*) const in /lib/aarch64-linux-gnu/libboost_python313.so.1.83.0 -197: 6# 0x0000FFFFABB42680 in /lib/aarch64-linux-gnu/libboost_python313.so.1.83.0 +197: 6# 0x0000FFFF809A2680 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/rdmolfiles.so 197: 9# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdmolfiles.so 197: 10# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdCIPLabeler.so 197: 11# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so -197: 12# 0x0000FFFFAA11C320 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so -197: 13# 0x0000FFFFAA11C2B8 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so -197: 14# 0x0000FFFFAA11C248 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so -197: 15# 0x0000FFFFAA11C1E0 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so -197: 16# 0x0000FFFFAA11C178 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so +197: 12# 0x0000FFFF7EF7C320 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so +197: 13# 0x0000FFFF7EF7C2B8 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so +197: 14# 0x0000FFFF7EF7C248 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so +197: 15# 0x0000FFFF7EF7C1E0 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so +197: 16# 0x0000FFFF7EF7C178 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so 197: 17# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/rdBase.so 197: 18# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/rdBase.so 197: 19# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/rdBase.so 197: 20# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/rdBase.so 197: 21# boost::python::handle_exception_impl(boost::function0) in /lib/aarch64-linux-gnu/libboost_python313.so.1.83.0 -197: 22# 0x0000FFFFABB3F25C in /lib/aarch64-linux-gnu/libboost_python313.so.1.83.0 +197: 22# 0x0000FFFF8099F25C in /lib/aarch64-linux-gnu/libboost_python313.so.1.83.0 197: 23# _PyObject_MakeTpCall in /usr/bin/python3 197: 24# _PyEval_EvalFrameDefault in /usr/bin/python3 197: 25# 0x000000000053DD10 in /usr/bin/python3 @@ -32563,13 +32803,13 @@ 197: 51# 0x000000000065F5F0 in /usr/bin/python3 197: 52# Py_RunMain in /usr/bin/python3 197: 53# Py_BytesMain in /usr/bin/python3 -197: 54# 0x0000FFFFAC32229C in /lib/aarch64-linux-gnu/libc.so.6 +197: 54# 0x0000FFFF8118229C in /lib/aarch64-linux-gnu/libc.so.6 197: 55# __libc_start_main in /lib/aarch64-linux-gnu/libc.so.6 197: 56# _start in /usr/bin/python3 197: ---------- 197: **** 197: -197: .[16:03:34] +197: .[12:25:18] 197: 197: **** 197: Pre-condition Violation @@ -32583,23 +32823,23 @@ 197: 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.1 197: 3# boost::python::objects::caller_py_function_impl, std::allocator > const&, RDKit::Trajectory&), boost::python::default_call_policies, boost::mpl::vector3, std::allocator > const&, RDKit::Trajectory&> > >::operator()(_object*, _object*) in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdtrajectory.so 197: 4# boost::python::objects::function::call(_object*, _object*) const in /lib/aarch64-linux-gnu/libboost_python313.so.1.83.0 -197: 5# 0x0000FFFFABB42680 in /lib/aarch64-linux-gnu/libboost_python313.so.1.83.0 +197: 5# 0x0000FFFF809A2680 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/rdmolfiles.so 197: 8# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdmolfiles.so 197: 9# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdCIPLabeler.so 197: 10# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so -197: 11# 0x0000FFFFAA11C320 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so -197: 12# 0x0000FFFFAA11C2B8 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so -197: 13# 0x0000FFFFAA11C248 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so -197: 14# 0x0000FFFFAA11C1E0 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so -197: 15# 0x0000FFFFAA11C178 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so +197: 11# 0x0000FFFF7EF7C320 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so +197: 12# 0x0000FFFF7EF7C2B8 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so +197: 13# 0x0000FFFF7EF7C248 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so +197: 14# 0x0000FFFF7EF7C1E0 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so +197: 15# 0x0000FFFF7EF7C178 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so 197: 16# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/rdBase.so 197: 17# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/rdBase.so 197: 18# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/rdBase.so 197: 19# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/rdBase.so 197: 20# boost::python::handle_exception_impl(boost::function0) in /lib/aarch64-linux-gnu/libboost_python313.so.1.83.0 -197: 21# 0x0000FFFFABB3F25C in /lib/aarch64-linux-gnu/libboost_python313.so.1.83.0 +197: 21# 0x0000FFFF8099F25C in /lib/aarch64-linux-gnu/libboost_python313.so.1.83.0 197: 22# _PyObject_MakeTpCall in /usr/bin/python3 197: 23# _PyEval_EvalFrameDefault in /usr/bin/python3 197: 24# 0x000000000053DD10 in /usr/bin/python3 @@ -32631,13 +32871,13 @@ 197: 50# 0x000000000065F5F0 in /usr/bin/python3 197: 51# Py_RunMain in /usr/bin/python3 197: 52# Py_BytesMain in /usr/bin/python3 -197: 53# 0x0000FFFFAC32229C in /lib/aarch64-linux-gnu/libc.so.6 +197: 53# 0x0000FFFF8118229C in /lib/aarch64-linux-gnu/libc.so.6 197: 54# __libc_start_main in /lib/aarch64-linux-gnu/libc.so.6 197: 55# _start in /usr/bin/python3 197: ---------- 197: **** 197: -197: ..[16:03:34] +197: ..[12:25:18] 197: 197: **** 197: Pre-condition Violation @@ -32651,23 +32891,23 @@ 197: 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.1 197: 3# boost::python::objects::caller_py_function_impl, std::allocator > const&, RDKit::Trajectory&), boost::python::default_call_policies, boost::mpl::vector3, std::allocator > const&, RDKit::Trajectory&> > >::operator()(_object*, _object*) in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdtrajectory.so 197: 4# boost::python::objects::function::call(_object*, _object*) const in /lib/aarch64-linux-gnu/libboost_python313.so.1.83.0 -197: 5# 0x0000FFFFABB42680 in /lib/aarch64-linux-gnu/libboost_python313.so.1.83.0 +197: 5# 0x0000FFFF809A2680 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/rdmolfiles.so 197: 8# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdmolfiles.so 197: 9# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdCIPLabeler.so 197: 10# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so -197: 11# 0x0000FFFFAA11C320 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so -197: 12# 0x0000FFFFAA11C2B8 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so -197: 13# 0x0000FFFFAA11C248 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so -197: 14# 0x0000FFFFAA11C1E0 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so -197: 15# 0x0000FFFFAA11C178 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so +197: 11# 0x0000FFFF7EF7C320 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so +197: 12# 0x0000FFFF7EF7C2B8 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so +197: 13# 0x0000FFFF7EF7C248 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so +197: 14# 0x0000FFFF7EF7C1E0 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so +197: 15# 0x0000FFFF7EF7C178 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so 197: 16# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/rdBase.so 197: 17# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/rdBase.so 197: 18# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/rdBase.so 197: 19# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/rdBase.so 197: 20# boost::python::handle_exception_impl(boost::function0) in /lib/aarch64-linux-gnu/libboost_python313.so.1.83.0 -197: 21# 0x0000FFFFABB3F25C in /lib/aarch64-linux-gnu/libboost_python313.so.1.83.0 +197: 21# 0x0000FFFF8099F25C in /lib/aarch64-linux-gnu/libboost_python313.so.1.83.0 197: 22# _PyObject_MakeTpCall in /usr/bin/python3 197: 23# _PyEval_EvalFrameDefault in /usr/bin/python3 197: 24# 0x000000000053DD10 in /usr/bin/python3 @@ -32699,13 +32939,13 @@ 197: 50# 0x000000000065F5F0 in /usr/bin/python3 197: 51# Py_RunMain in /usr/bin/python3 197: 52# Py_BytesMain in /usr/bin/python3 -197: 53# 0x0000FFFFAC32229C in /lib/aarch64-linux-gnu/libc.so.6 +197: 53# 0x0000FFFF8118229C in /lib/aarch64-linux-gnu/libc.so.6 197: 54# __libc_start_main in /lib/aarch64-linux-gnu/libc.so.6 197: 55# _start in /usr/bin/python3 197: ---------- 197: **** 197: -197: .[16:03:34] +197: .[12:25:18] 197: 197: **** 197: Pre-condition Violation @@ -32719,23 +32959,23 @@ 197: 2# RDKit::Snapshot::getPoint2D(unsigned int) const in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu//lib/libRDKitTrajectory.so.1 197: 3# boost::python::objects::caller_py_function_impl > >::operator()(_object*, _object*) in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdtrajectory.so 197: 4# boost::python::objects::function::call(_object*, _object*) const in /lib/aarch64-linux-gnu/libboost_python313.so.1.83.0 -197: 5# 0x0000FFFFABB42680 in /lib/aarch64-linux-gnu/libboost_python313.so.1.83.0 +197: 5# 0x0000FFFF809A2680 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/rdmolfiles.so 197: 8# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdmolfiles.so 197: 9# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdCIPLabeler.so 197: 10# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so -197: 11# 0x0000FFFFAA11C320 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so -197: 12# 0x0000FFFFAA11C2B8 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so -197: 13# 0x0000FFFFAA11C248 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so -197: 14# 0x0000FFFFAA11C1E0 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so -197: 15# 0x0000FFFFAA11C178 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so +197: 11# 0x0000FFFF7EF7C320 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so +197: 12# 0x0000FFFF7EF7C2B8 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so +197: 13# 0x0000FFFF7EF7C248 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so +197: 14# 0x0000FFFF7EF7C1E0 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so +197: 15# 0x0000FFFF7EF7C178 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so 197: 16# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/rdBase.so 197: 17# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/rdBase.so 197: 18# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/rdBase.so 197: 19# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/rdBase.so 197: 20# boost::python::handle_exception_impl(boost::function0) in /lib/aarch64-linux-gnu/libboost_python313.so.1.83.0 -197: 21# 0x0000FFFFABB3F25C in /lib/aarch64-linux-gnu/libboost_python313.so.1.83.0 +197: 21# 0x0000FFFF8099F25C in /lib/aarch64-linux-gnu/libboost_python313.so.1.83.0 197: 22# _PyObject_MakeTpCall in /usr/bin/python3 197: 23# _PyEval_EvalFrameDefault in /usr/bin/python3 197: 24# 0x000000000053DD10 in /usr/bin/python3 @@ -32767,13 +33007,13 @@ 197: 50# 0x000000000065F5F0 in /usr/bin/python3 197: 51# Py_RunMain in /usr/bin/python3 197: 52# Py_BytesMain in /usr/bin/python3 -197: 53# 0x0000FFFFAC32229C in /lib/aarch64-linux-gnu/libc.so.6 +197: 53# 0x0000FFFF8118229C in /lib/aarch64-linux-gnu/libc.so.6 197: 54# __libc_start_main in /lib/aarch64-linux-gnu/libc.so.6 197: 55# _start in /usr/bin/python3 197: ---------- 197: **** 197: -197: [16:03:34] +197: [12:25:18] 197: 197: **** 197: Pre-condition Violation @@ -32787,23 +33027,23 @@ 197: 2# RDKit::Snapshot::getPoint2D(unsigned int) const in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu//lib/libRDKitTrajectory.so.1 197: 3# boost::python::objects::caller_py_function_impl > >::operator()(_object*, _object*) in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdtrajectory.so 197: 4# boost::python::objects::function::call(_object*, _object*) const in /lib/aarch64-linux-gnu/libboost_python313.so.1.83.0 -197: 5# 0x0000FFFFABB42680 in /lib/aarch64-linux-gnu/libboost_python313.so.1.83.0 +197: 5# 0x0000FFFF809A2680 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/rdmolfiles.so 197: 8# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdmolfiles.so 197: 9# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdCIPLabeler.so 197: 10# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so -197: 11# 0x0000FFFFAA11C320 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so -197: 12# 0x0000FFFFAA11C2B8 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so -197: 13# 0x0000FFFFAA11C248 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so -197: 14# 0x0000FFFFAA11C1E0 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so -197: 15# 0x0000FFFFAA11C178 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so +197: 11# 0x0000FFFF7EF7C320 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so +197: 12# 0x0000FFFF7EF7C2B8 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so +197: 13# 0x0000FFFF7EF7C248 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so +197: 14# 0x0000FFFF7EF7C1E0 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so +197: 15# 0x0000FFFF7EF7C178 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so 197: 16# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/rdBase.so 197: 17# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/rdBase.so 197: 18# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/rdBase.so 197: 19# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/rdBase.so 197: 20# boost::python::handle_exception_impl(boost::function0) in /lib/aarch64-linux-gnu/libboost_python313.so.1.83.0 -197: 21# 0x0000FFFFABB3F25C in /lib/aarch64-linux-gnu/libboost_python313.so.1.83.0 +197: 21# 0x0000FFFF8099F25C in /lib/aarch64-linux-gnu/libboost_python313.so.1.83.0 197: 22# _PyObject_MakeTpCall in /usr/bin/python3 197: 23# _PyEval_EvalFrameDefault in /usr/bin/python3 197: 24# 0x000000000053DD10 in /usr/bin/python3 @@ -32835,13 +33075,13 @@ 197: 50# 0x000000000065F5F0 in /usr/bin/python3 197: 51# Py_RunMain in /usr/bin/python3 197: 52# Py_BytesMain in /usr/bin/python3 -197: 53# 0x0000FFFFAC32229C in /lib/aarch64-linux-gnu/libc.so.6 +197: 53# 0x0000FFFF8118229C in /lib/aarch64-linux-gnu/libc.so.6 197: 54# __libc_start_main in /lib/aarch64-linux-gnu/libc.so.6 197: 55# _start in /usr/bin/python3 197: ---------- 197: **** 197: -197: .[16:03:34] +197: .[12:25:18] 197: 197: **** 197: Range Error @@ -32856,23 +33096,23 @@ 197: 3# RDKit::getSnapshot_wrap(RDKit::Trajectory*, unsigned int) in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdtrajectory.so 197: 4# boost::python::objects::caller_py_function_impl, boost::mpl::vector3 > >::operator()(_object*, _object*) in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdtrajectory.so 197: 5# boost::python::objects::function::call(_object*, _object*) const in /lib/aarch64-linux-gnu/libboost_python313.so.1.83.0 -197: 6# 0x0000FFFFABB42680 in /lib/aarch64-linux-gnu/libboost_python313.so.1.83.0 +197: 6# 0x0000FFFF809A2680 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/rdmolfiles.so 197: 9# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdmolfiles.so 197: 10# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdCIPLabeler.so 197: 11# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so -197: 12# 0x0000FFFFAA11C320 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so -197: 13# 0x0000FFFFAA11C2B8 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so -197: 14# 0x0000FFFFAA11C248 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so -197: 15# 0x0000FFFFAA11C1E0 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so -197: 16# 0x0000FFFFAA11C178 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so +197: 12# 0x0000FFFF7EF7C320 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so +197: 13# 0x0000FFFF7EF7C2B8 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so +197: 14# 0x0000FFFF7EF7C248 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so +197: 15# 0x0000FFFF7EF7C1E0 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so +197: 16# 0x0000FFFF7EF7C178 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so 197: 17# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/rdBase.so 197: 18# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/rdBase.so 197: 19# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/rdBase.so 197: 20# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/rdBase.so 197: 21# boost::python::handle_exception_impl(boost::function0) in /lib/aarch64-linux-gnu/libboost_python313.so.1.83.0 -197: 22# 0x0000FFFFABB3F25C in /lib/aarch64-linux-gnu/libboost_python313.so.1.83.0 +197: 22# 0x0000FFFF8099F25C in /lib/aarch64-linux-gnu/libboost_python313.so.1.83.0 197: 23# _PyObject_MakeTpCall in /usr/bin/python3 197: 24# _PyEval_EvalFrameDefault in /usr/bin/python3 197: 25# 0x000000000053DD10 in /usr/bin/python3 @@ -32904,13 +33144,13 @@ 197: 51# 0x000000000065F5F0 in /usr/bin/python3 197: 52# Py_RunMain in /usr/bin/python3 197: 53# Py_BytesMain in /usr/bin/python3 -197: 54# 0x0000FFFFAC32229C in /lib/aarch64-linux-gnu/libc.so.6 +197: 54# 0x0000FFFF8118229C in /lib/aarch64-linux-gnu/libc.so.6 197: 55# __libc_start_main in /lib/aarch64-linux-gnu/libc.so.6 197: 56# _start in /usr/bin/python3 197: ---------- 197: **** 197: -197: [16:03:34] +197: [12:25:18] 197: 197: **** 197: Range Error @@ -32924,23 +33164,23 @@ 197: 2# RDKit::Snapshot::getPoint2D(unsigned int) const in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu//lib/libRDKitTrajectory.so.1 197: 3# boost::python::objects::caller_py_function_impl > >::operator()(_object*, _object*) in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdtrajectory.so 197: 4# boost::python::objects::function::call(_object*, _object*) const in /lib/aarch64-linux-gnu/libboost_python313.so.1.83.0 -197: 5# 0x0000FFFFABB42680 in /lib/aarch64-linux-gnu/libboost_python313.so.1.83.0 +197: 5# 0x0000FFFF809A2680 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/rdmolfiles.so 197: 8# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdmolfiles.so 197: 9# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdCIPLabeler.so 197: 10# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so -197: 11# 0x0000FFFFAA11C320 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so -197: 12# 0x0000FFFFAA11C2B8 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so -197: 13# 0x0000FFFFAA11C248 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so -197: 14# 0x0000FFFFAA11C1E0 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so -197: 15# 0x0000FFFFAA11C178 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so +197: 11# 0x0000FFFF7EF7C320 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so +197: 12# 0x0000FFFF7EF7C2B8 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so +197: 13# 0x0000FFFF7EF7C248 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so +197: 14# 0x0000FFFF7EF7C1E0 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so +197: 15# 0x0000FFFF7EF7C178 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so 197: 16# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/rdBase.so 197: 17# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/rdBase.so 197: 18# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/rdBase.so 197: 19# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/rdBase.so 197: 20# boost::python::handle_exception_impl(boost::function0) in /lib/aarch64-linux-gnu/libboost_python313.so.1.83.0 -197: 21# 0x0000FFFFABB3F25C in /lib/aarch64-linux-gnu/libboost_python313.so.1.83.0 +197: 21# 0x0000FFFF8099F25C in /lib/aarch64-linux-gnu/libboost_python313.so.1.83.0 197: 22# _PyObject_MakeTpCall in /usr/bin/python3 197: 23# _PyEval_EvalFrameDefault in /usr/bin/python3 197: 24# 0x000000000053DD10 in /usr/bin/python3 @@ -32972,13 +33212,13 @@ 197: 50# 0x000000000065F5F0 in /usr/bin/python3 197: 51# Py_RunMain in /usr/bin/python3 197: 52# Py_BytesMain in /usr/bin/python3 -197: 53# 0x0000FFFFAC32229C in /lib/aarch64-linux-gnu/libc.so.6 +197: 53# 0x0000FFFF8118229C in /lib/aarch64-linux-gnu/libc.so.6 197: 54# __libc_start_main in /lib/aarch64-linux-gnu/libc.so.6 197: 55# _start in /usr/bin/python3 197: ---------- 197: **** 197: -197: .[16:03:34] +197: .[12:25:18] 197: 197: **** 197: Range Error @@ -32993,23 +33233,23 @@ 197: 3# RDKit::getSnapshot_wrap(RDKit::Trajectory*, unsigned int) in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdtrajectory.so 197: 4# boost::python::objects::caller_py_function_impl, boost::mpl::vector3 > >::operator()(_object*, _object*) in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdtrajectory.so 197: 5# boost::python::objects::function::call(_object*, _object*) const in /lib/aarch64-linux-gnu/libboost_python313.so.1.83.0 -197: 6# 0x0000FFFFABB42680 in /lib/aarch64-linux-gnu/libboost_python313.so.1.83.0 +197: 6# 0x0000FFFF809A2680 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/rdmolfiles.so 197: 9# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdmolfiles.so 197: 10# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdCIPLabeler.so 197: 11# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so -197: 12# 0x0000FFFFAA11C320 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so -197: 13# 0x0000FFFFAA11C2B8 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so -197: 14# 0x0000FFFFAA11C248 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so -197: 15# 0x0000FFFFAA11C1E0 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so -197: 16# 0x0000FFFFAA11C178 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so +197: 12# 0x0000FFFF7EF7C320 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so +197: 13# 0x0000FFFF7EF7C2B8 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so +197: 14# 0x0000FFFF7EF7C248 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so +197: 15# 0x0000FFFF7EF7C1E0 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so +197: 16# 0x0000FFFF7EF7C178 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so 197: 17# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/rdBase.so 197: 18# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/rdBase.so 197: 19# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/rdBase.so 197: 20# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/rdBase.so 197: 21# boost::python::handle_exception_impl(boost::function0) in /lib/aarch64-linux-gnu/libboost_python313.so.1.83.0 -197: 22# 0x0000FFFFABB3F25C in /lib/aarch64-linux-gnu/libboost_python313.so.1.83.0 +197: 22# 0x0000FFFF8099F25C in /lib/aarch64-linux-gnu/libboost_python313.so.1.83.0 197: 23# _PyObject_MakeTpCall in /usr/bin/python3 197: 24# _PyEval_EvalFrameDefault in /usr/bin/python3 197: 25# 0x000000000053DD10 in /usr/bin/python3 @@ -33041,13 +33281,13 @@ 197: 51# 0x000000000065F5F0 in /usr/bin/python3 197: 52# Py_RunMain in /usr/bin/python3 197: 53# Py_BytesMain in /usr/bin/python3 -197: 54# 0x0000FFFFAC32229C in /lib/aarch64-linux-gnu/libc.so.6 +197: 54# 0x0000FFFF8118229C in /lib/aarch64-linux-gnu/libc.so.6 197: 55# __libc_start_main in /lib/aarch64-linux-gnu/libc.so.6 197: 56# _start in /usr/bin/python3 197: ---------- 197: **** 197: -197: [16:03:34] +197: [12:25:18] 197: 197: **** 197: Pre-condition Violation @@ -33061,23 +33301,23 @@ 197: 2# RDKit::Snapshot::getPoint2D(unsigned int) const in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu//lib/libRDKitTrajectory.so.1 197: 3# boost::python::objects::caller_py_function_impl > >::operator()(_object*, _object*) in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdtrajectory.so 197: 4# boost::python::objects::function::call(_object*, _object*) const in /lib/aarch64-linux-gnu/libboost_python313.so.1.83.0 -197: 5# 0x0000FFFFABB42680 in /lib/aarch64-linux-gnu/libboost_python313.so.1.83.0 +197: 5# 0x0000FFFF809A2680 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/rdmolfiles.so 197: 8# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdmolfiles.so 197: 9# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdCIPLabeler.so 197: 10# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so -197: 11# 0x0000FFFFAA11C320 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so -197: 12# 0x0000FFFFAA11C2B8 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so -197: 13# 0x0000FFFFAA11C248 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so -197: 14# 0x0000FFFFAA11C1E0 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so -197: 15# 0x0000FFFFAA11C178 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so +197: 11# 0x0000FFFF7EF7C320 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so +197: 12# 0x0000FFFF7EF7C2B8 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so +197: 13# 0x0000FFFF7EF7C248 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so +197: 14# 0x0000FFFF7EF7C1E0 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so +197: 15# 0x0000FFFF7EF7C178 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so 197: 16# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/rdBase.so 197: 17# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/rdBase.so 197: 18# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/rdBase.so 197: 19# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/rdBase.so 197: 20# boost::python::handle_exception_impl(boost::function0) in /lib/aarch64-linux-gnu/libboost_python313.so.1.83.0 -197: 21# 0x0000FFFFABB3F25C in /lib/aarch64-linux-gnu/libboost_python313.so.1.83.0 +197: 21# 0x0000FFFF8099F25C in /lib/aarch64-linux-gnu/libboost_python313.so.1.83.0 197: 22# _PyObject_MakeTpCall in /usr/bin/python3 197: 23# _PyEval_EvalFrameDefault in /usr/bin/python3 197: 24# 0x000000000053DD10 in /usr/bin/python3 @@ -33109,13 +33349,13 @@ 197: 50# 0x000000000065F5F0 in /usr/bin/python3 197: 51# Py_RunMain in /usr/bin/python3 197: 52# Py_BytesMain in /usr/bin/python3 -197: 53# 0x0000FFFFAC32229C in /lib/aarch64-linux-gnu/libc.so.6 +197: 53# 0x0000FFFF8118229C in /lib/aarch64-linux-gnu/libc.so.6 197: 54# __libc_start_main in /lib/aarch64-linux-gnu/libc.so.6 197: 55# _start in /usr/bin/python3 197: ---------- 197: **** 197: -197: [16:03:34] +197: [12:25:18] 197: 197: **** 197: Pre-condition Violation @@ -33129,23 +33369,23 @@ 197: 2# RDKit::Snapshot::getPoint2D(unsigned int) const in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu//lib/libRDKitTrajectory.so.1 197: 3# boost::python::objects::caller_py_function_impl > >::operator()(_object*, _object*) in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdtrajectory.so 197: 4# boost::python::objects::function::call(_object*, _object*) const in /lib/aarch64-linux-gnu/libboost_python313.so.1.83.0 -197: 5# 0x0000FFFFABB42680 in /lib/aarch64-linux-gnu/libboost_python313.so.1.83.0 +197: 5# 0x0000FFFF809A2680 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/rdmolfiles.so 197: 8# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdmolfiles.so 197: 9# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdCIPLabeler.so 197: 10# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so -197: 11# 0x0000FFFFAA11C320 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so -197: 12# 0x0000FFFFAA11C2B8 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so -197: 13# 0x0000FFFFAA11C248 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so -197: 14# 0x0000FFFFAA11C1E0 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so -197: 15# 0x0000FFFFAA11C178 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so +197: 11# 0x0000FFFF7EF7C320 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so +197: 12# 0x0000FFFF7EF7C2B8 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so +197: 13# 0x0000FFFF7EF7C248 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so +197: 14# 0x0000FFFF7EF7C1E0 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so +197: 15# 0x0000FFFF7EF7C178 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so 197: 16# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/rdBase.so 197: 17# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/rdBase.so 197: 18# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/rdBase.so 197: 19# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/rdBase.so 197: 20# boost::python::handle_exception_impl(boost::function0) in /lib/aarch64-linux-gnu/libboost_python313.so.1.83.0 -197: 21# 0x0000FFFFABB3F25C in /lib/aarch64-linux-gnu/libboost_python313.so.1.83.0 +197: 21# 0x0000FFFF8099F25C in /lib/aarch64-linux-gnu/libboost_python313.so.1.83.0 197: 22# _PyObject_MakeTpCall in /usr/bin/python3 197: 23# _PyEval_EvalFrameDefault in /usr/bin/python3 197: 24# 0x000000000053DD10 in /usr/bin/python3 @@ -33177,254 +33417,74 @@ 197: 50# 0x000000000065F5F0 in /usr/bin/python3 197: 51# Py_RunMain in /usr/bin/python3 197: 52# Py_BytesMain in /usr/bin/python3 -197: 53# 0x0000FFFFAC32229C in /lib/aarch64-linux-gnu/libc.so.6 +197: 53# 0x0000FFFF8118229C in /lib/aarch64-linux-gnu/libc.so.6 197: 54# __libc_start_main in /lib/aarch64-linux-gnu/libc.so.6 197: 55# _start in /usr/bin/python3 197: ---------- 197: **** 197: -197: . -197: ---------------------------------------------------------------------- -197: Ran 9 tests in 0.218s -197: -197: OK -197: Testing Trajectory wrapper -186/236 Test #197: pyTestTrajectory ....................... Passed 0.93 sec -test 198 - Start 198: pyTestSGroups - -198: Test command: /usr/bin/python3 "/build/reproducible-path/rdkit-202503.1/Code/GraphMol/Wrap/testSGroups.py" -198: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/Wrap -198: Test timeout computed to be: 1500 -195: ..............[16:03:34] SMARTS Parse Error: syntax error while parsing: fiib -195: [16:03:34] SMARTS Parse Error: Failed parsing SMARTS 'fiib' for input: 'fiib' -195: ....[16:03:34] ERROR: Problems encountered parsing data fields -195: [16:03:34] ERROR: moving to the beginning of the next molecule -195: [16:03:34] ERROR: Problems encountered parsing data fields -195: [16:03:34] ERROR: moving to the beginning of the next molecule -195: [16:03:34] Spurious data before the first property will be ignored -195: [16:03:34] Property will be truncated after the first blank line -195: [16:03:34] Property will be truncated after the first blank line -195: [16:03:34] Property will be truncated after the first blank line -195: [16:03:34] ERROR: Problems encountered parsing data fields -195: [16:03:34] ERROR: moving to the beginning of the next molecule -195: [16:03:34] ERROR: Problems encountered parsing data fields -195: [16:03:34] ERROR: moving to the beginning of the next molecule -195: [16:03:34] Spurious data before the first property will be ignored -195: [16:03:34] Property will be truncated after the first blank line -195: [16:03:34] Property will be truncated after the first blank line -195: [16:03:34] Property will be truncated after the first blank line -195: [16:03:34] ERROR: Problems encountered parsing data fields -195: [16:03:34] ERROR: moving to the beginning of the next molecule -195: [16:03:34] Property will be truncated after the first blank line -195: [16:03:34] ERROR: Problems encountered parsing data fields -195: [16:03:34] ERROR: moving to the beginning of the next molecule -195: [16:03:34] Property will be truncated after the first blank line -195: .[16:03:34] SMILES Parse Error: syntax error while parsing: fail -195: [16:03:34] SMILES Parse Error: check for mistakes around position 1: -195: [16:03:34] fail -195: [16:03:34] ^ -195: [16:03:34] SMILES Parse Error: Failed parsing SMILES 'fail' for input: 'fail' -195: [16:03:34] ERROR: Smiles parse error on line 2 -195: [16:03:34] ERROR: Cannot create molecule from : 'fail' -195: >>> This may result in an infinite loop. It should finish almost instantly -195: <<< OK, it finished. -195: ............[16:03:34] Explicit valence for atom # 1 C, 5, is greater than permitted -195: ......[16:03:34] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -195: [16:03:34] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -195: [16:03:34] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -195: [16:03:34] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -195: .inWedges: [H]C12C3([H])C4([H])C1([H])C1([H])C2([H])C3([H])C41[H] |(-0.612,-0.6446,0.635;0.0021,-0.0041,0.002;-0.0187,1.5258,0.0104;-0.6498,2.1424,0.6504;1.5111,1.5466,-0.0041;2.1372,2.1804,0.624;1.5319,0.0168,-0.0125;2.175,-0.6067,0.6086;1.5173,0.025,-1.5424;2.1484,-0.5936,-2.1805;-0.0125,0.0041,-1.5279;-0.6405,-0.6297,-2.154;-0.0333,1.534,-1.5195;-0.6783,2.1574,-2.1387;1.4965,1.5548,-1.534;2.1106,2.1972,-2.1651)| -195: ........[16:03:34] non-ring atom 0 marked aromatic -195: [16:03:34] non-ring atom 0 marked aromatic -195: [16:03:34] -195: -195: **** -195: Range Error -195: idx -195: Violation occurred on line 209 in file ./Code/GraphMol/ROMol.cpp -195: Failed Expression: 12 < 6 -195: ---------- -195: Stacktrace: -195: 0# Invar::Invariant::toString[abi:cxx11]() const in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu//lib/libRDKitRDGeneral.so.1 -195: 1# Invar::operator<<(std::ostream&, Invar::Invariant const&) in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu//lib/libRDKitRDGeneral.so.1 -195: 2# RDKit::ROMol::getAtomWithIdx(unsigned int) in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu//lib/libRDKitGraphMol.so.1 -195: 3# RDKit::RWMol::removeAtom(unsigned int) in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu//lib/libRDKitGraphMol.so.1 -195: 4# 0x0000FFFFB00B55F0 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so -195: 5# boost::python::objects::function::call(_object*, _object*) const in /lib/aarch64-linux-gnu/libboost_python313.so.1.83.0 -195: 6# 0x0000FFFFB1AB2680 in /lib/aarch64-linux-gnu/libboost_python313.so.1.83.0 -195: 7# boost::python::detail::exception_handler::operator()(boost::function0 const&) const in /lib/aarch64-linux-gnu/libboost_python313.so.1.83.0 -195: 8# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdSLNParse.so -195: 9# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdChemReactions.so -195: 10# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdChemReactions.so -195: 11# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdMolChemicalFeatures.so -195: 12# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdDepictor.so -195: 13# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdmolfiles.so -195: 14# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdmolfiles.so -195: 15# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdCIPLabeler.so -195: 16# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so -195: 17# 0x0000FFFFAFFEC320 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so -195: 18# 0x0000FFFFAFFEC2B8 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so -195: 19# 0x0000FFFFAFFEC248 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so -195: 20# 0x0000FFFFAFFEC1E0 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so -195: 21# 0x0000FFFFAFFEC178 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so -195: 22# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/rdBase.so -195: 23# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/rdBase.so -195: 24# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/rdBase.so -195: 25# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/rdBase.so -195: 26# boost::python::handle_exception_impl(boost::function0) in /lib/aarch64-linux-gnu/libboost_python313.so.1.83.0 -195: 27# 0x0000FFFFB1AAF25C in /lib/aarch64-linux-gnu/libboost_python313.so.1.83.0 -195: 28# _PyObject_MakeTpCall in /usr/bin/python3 -195: 29# _PyEval_EvalFrameDefault in /usr/bin/python3 -195: 30# 0x000000000053DD10 in /usr/bin/python3 -195: 31# _PyEval_EvalFrameDefault in /usr/bin/python3 -195: 32# 0x000000000061D100 in /usr/bin/python3 -195: 33# 0x00000000005A959C in /usr/bin/python3 -195: 34# _PyObject_MakeTpCall in /usr/bin/python3 -195: 35# _PyEval_EvalFrameDefault in /usr/bin/python3 -195: 36# 0x000000000053DD10 in /usr/bin/python3 -195: 37# _PyEval_EvalFrameDefault in /usr/bin/python3 -195: 38# 0x000000000061D100 in /usr/bin/python3 -195: 39# 0x00000000005A959C in /usr/bin/python3 -195: 40# _PyObject_MakeTpCall in /usr/bin/python3 -195: 41# _PyEval_EvalFrameDefault in /usr/bin/python3 -195: 42# 0x000000000053DD10 in /usr/bin/python3 -195: 43# _PyEval_EvalFrameDefault in /usr/bin/python3 -195: 44# 0x000000000061D100 in /usr/bin/python3 -195: 45# 0x00000000005A959C in /usr/bin/python3 -195: 46# _PyObject_MakeTpCall in /usr/bin/python3 -195: 47# _PyEval_EvalFrameDefault in /usr/bin/python3 -195: 48# 0x000000000050BA30 in /usr/bin/python3 -195: 49# _PyObject_MakeTpCall in /usr/bin/python3 -195: 50# _PyEval_EvalFrameDefault in /usr/bin/python3 -195: 51# PyEval_EvalCode in /usr/bin/python3 -195: 52# 0x0000000000640ABC in /usr/bin/python3 -195: 53# 0x000000000063C4B0 in /usr/bin/python3 -195: 54# 0x000000000065FFB0 in /usr/bin/python3 -195: 55# 0x000000000065F854 in /usr/bin/python3 -195: 56# 0x000000000065F5F0 in /usr/bin/python3 -195: 57# Py_RunMain in /usr/bin/python3 -195: 58# Py_BytesMain in /usr/bin/python3 -195: 59# 0x0000FFFFB27F229C in /lib/aarch64-linux-gnu/libc.so.6 -195: 60# __libc_start_main in /lib/aarch64-linux-gnu/libc.so.6 -195: 61# _start in /usr/bin/python3 -195: ---------- -195: **** -195: -195: [16:03:34] non-ring atom 0 marked aromatic -195: [16:03:34] non-ring atom 0 marked aromatic -195: [16:03:34] -195: -195: **** -195: Range Error -195: idx -195: Violation occurred on line 209 in file ./Code/GraphMol/ROMol.cpp -195: Failed Expression: 12 < 6 -195: ---------- -195: Stacktrace: -195: 0# Invar::Invariant::toString[abi:cxx11]() const in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu//lib/libRDKitRDGeneral.so.1 -195: 1# Invar::operator<<(std::ostream&, Invar::Invariant const&) in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu//lib/libRDKitRDGeneral.so.1 -195: 2# RDKit::ROMol::getAtomWithIdx(unsigned int) in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu//lib/libRDKitGraphMol.so.1 -195: 3# RDKit::RWMol::removeAtom(unsigned int) in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu//lib/libRDKitGraphMol.so.1 -195: 4# 0x0000FFFFB00B55F0 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so -195: 5# boost::python::objects::function::call(_object*, _object*) const in /lib/aarch64-linux-gnu/libboost_python313.so.1.83.0 -195: 6# 0x0000FFFFB1AB2680 in /lib/aarch64-linux-gnu/libboost_python313.so.1.83.0 -195: 7# boost::python::detail::exception_handler::operator()(boost::function0 const&) const in /lib/aarch64-linux-gnu/libboost_python313.so.1.83.0 -195: 8# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdSLNParse.so -195: 9# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdChemReactions.so -195: 10# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdChemReactions.so -195: 11# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdMolChemicalFeatures.so -195: 12# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdDepictor.so -195: 13# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdmolfiles.so -195: 14# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdmolfiles.so -195: 15# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdCIPLabeler.so -195: 16# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so -195: 17# 0x0000FFFFAFFEC320 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so -195: 18# 0x0000FFFFAFFEC2B8 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so -195: 19# 0x0000FFFFAFFEC248 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so -195: 20# 0x0000FFFFAFFEC1E0 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so -195: 21# 0x0000FFFFAFFEC178 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so -195: 22# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/rdBase.so -195: 23# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/rdBase.so -195: 24# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/rdBase.so -195: 25# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/rdBase.so -195: 26# boost::python::handle_exception_impl(boost::function0) in /lib/aarch64-linux-gnu/libboost_python313.so.1.83.0 -195: 27# 0x0000FFFFB1AAF25C in /lib/aarch64-linux-gnu/libboost_python313.so.1.83.0 -195: 28# _PyObject_MakeTpCall in /usr/bin/python3 -195: 29# _PyEval_EvalFrameDefault in /usr/bin/python3 -195: 30# 0x000000000053DD10 in /usr/bin/python3 -195: 31# _PyEval_EvalFrameDefault in /usr/bin/python3 -195: 32# 0x000000000061D100 in /usr/bin/python3 -195: 33# 0x00000000005A959C in /usr/bin/python3 -195: 34# _PyObject_MakeTpCall in /usr/bin/python3 -195: 35# _PyEval_EvalFrameDefault in /usr/bin/python3 -195: 36# 0x000000000053DD10 in /usr/bin/python3 -195: 37# _PyEval_EvalFrameDefault in /usr/bin/python3 -195: 38# 0x000000000061D100 in /usr/bin/python3 -195: 39# 0x00000000005A959C in /usr/bin/python3 -195: 40# _PyObject_MakeTpCall in /usr/bin/python3 -195: 41# _PyEval_EvalFrameDefault in /usr/bin/python3 -195: 42# 0x000000000053DD10 in /usr/bin/python3 -195: 43# _PyEval_EvalFrameDefault in /usr/bin/python3 -195: 44# 0x000000000061D100 in /usr/bin/python3 -195: 45# 0x00000000005A959C in /usr/bin/python3 -195: 46# _PyObject_MakeTpCall in /usr/bin/python3 -195: 47# _PyEval_EvalFrameDefault in /usr/bin/python3 -195: 48# 0x000000000050BA30 in /usr/bin/python3 -195: 49# _PyObject_MakeTpCall in /usr/bin/python3 -195: 50# _PyEval_EvalFrameDefault in /usr/bin/python3 -195: 51# PyEval_EvalCode in /usr/bin/python3 -195: 52# 0x0000000000640ABC in /usr/bin/python3 -195: 53# 0x000000000063C4B0 in /usr/bin/python3 -195: 54# 0x000000000065FFB0 in /usr/bin/python3 -195: 55# 0x000000000065F854 in /usr/bin/python3 -195: 56# 0x000000000065F5F0 in /usr/bin/python3 -195: 57# Py_RunMain in /usr/bin/python3 -195: 58# Py_BytesMain in /usr/bin/python3 -195: 59# 0x0000FFFFB27F229C in /lib/aarch64-linux-gnu/libc.so.6 -195: 60# __libc_start_main in /lib/aarch64-linux-gnu/libc.so.6 -195: 61# _start in /usr/bin/python3 -195: ---------- -195: **** -195: -195: ...............[16:03:34] WARNING: the onlyHeavy argument to mol.GetNumAtoms() has been deprecated. Please use the onlyExplicit argument instead or mol.GetNumHeavyAtoms() if you want the heavy atom count. -195: [16:03:34] 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. -196: ...... -196: ---------------------------------------------------------------------- -196: Ran 6 tests in 0.072s -196: -196: OK -187/236 Test #196: pyTestConformerWrap .................... Passed 1.89 sec +187/236 Test #186: testRGroupDecomp ....................... Passed 13.52 sec test 199 Start 199: pyTestThreads 199: Test command: /usr/bin/python3 "/build/reproducible-path/rdkit-202503.1/Code/GraphMol/Wrap/testThreads.py" 199: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/Wrap 199: Test timeout computed to be: 1500 -195: ..............[16:03:35] Can't kekulize mol. Unkekulized atoms: 0 1 2 3 4 -195: [16:03:35] Explicit valence for atom # 1 C, 5, is greater than permitted +197: . +197: ---------------------------------------------------------------------- +197: Ran 9 tests in 0.962s +197: +197: OK +197: Testing Trajectory wrapper 198: ............. 198: ---------------------------------------------------------------------- -198: Ran 13 tests in 0.173s +198: Ran 13 tests in 0.062s 198: 198: OK 198: Testing SubstanceGroups wrapper -186: [16:03:36] Relabelling existing label -188/236 Test #198: pyTestSGroups .......................... Passed 2.47 sec +188/236 Test #198: pyTestSGroups .......................... Passed 1.15 sec test 200 Start 200: pyTestMultithreadedMolSupplier 200: Test command: /usr/bin/python3 "/build/reproducible-path/rdkit-202503.1/Code/GraphMol/Wrap/testMultithreadedMolSupplier.py" 200: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/Wrap 200: Test timeout computed to be: 1500 -195: ............................[16:03:37] unable to set wavy bonds for double bonds: 3 +189/236 Test #197: pyTestTrajectory ....................... Passed 2.31 sec +test 201 + Start 201: pyTestPropertyLists + +201: Test command: /usr/bin/python3 "/build/reproducible-path/rdkit-202503.1/Code/GraphMol/Wrap/testPropertyLists.py" +201: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/Wrap +201: Test timeout computed to be: 1500 +201: [12:25:19] Value [?] for property atom.iprop.PartiallyMissingInt of atom 0 can not be parsed. Ignoring it. +201: [12:25:19] Value ? for property atom.iprop.PartiallyMissingInt of atom 3 can not be parsed. Ignoring it. +201: [12:25:19] Value $$$$ for property atom.iprop.PartiallyMissingInt of atom 4 can not be parsed. Ignoring it. +201: .[12:25:19] Value [?] for property atom.iprop.PartiallyMissingInt of atom 0 can not be parsed. Ignoring it. +201: [12:25:19] Value ? for property atom.iprop.PartiallyMissingInt of atom 3 can not be parsed. Ignoring it. +201: [12:25:19] Value $$$$ for property atom.iprop.PartiallyMissingInt of atom 4 can not be parsed. Ignoring it. +201: ...[12:25:19] Value [?] for property atom.iprop.PartiallyMissingInt of atom 0 can not be parsed. Ignoring it. +201: [12:25:19] Value ? for property atom.iprop.PartiallyMissingInt of atom 3 can not be parsed. Ignoring it. +201: [12:25:19] Value $$$$ for property atom.iprop.PartiallyMissingInt of atom 4 can not be parsed. Ignoring it. +201: . +201: ---------------------------------------------------------------------- +201: Ran 5 tests in 0.040s +201: +201: OK +190/236 Test #201: pyTestPropertyLists .................... Passed 0.91 sec +test 202 + Start 202: pyCDXMLTest + +202: Test command: /usr/bin/python3 "/build/reproducible-path/rdkit-202503.1/Code/GraphMol/Wrap/test_cdxml.py" +202: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/Wrap +202: Test timeout computed to be: 1500 200: .s. 200: ---------------------------------------------------------------------- -200: Ran 3 tests in 0.176s +200: Ran 3 tests in 0.226s 200: 200: OK (skipped=1) 200: Testing Smiles and SD MultithreadedMolSupplier -195: .............[16:03:37] +195: ............................[12:25:20] unable to set wavy bonds for double bonds: 3 +195: .............[12:25:20] 195: 195: **** 195: Range Error @@ -33439,7 +33499,7 @@ 195: 3# RDKit::RWMol::removeAtom(unsigned int) in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu//lib/libRDKitGraphMol.so.1 195: 4# boost::python::objects::caller_py_function_impl > >::operator()(_object*, _object*) in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so 195: 5# boost::python::objects::function::call(_object*, _object*) const in /lib/aarch64-linux-gnu/libboost_python313.so.1.83.0 -195: 6# 0x0000FFFFB1AB2680 in /lib/aarch64-linux-gnu/libboost_python313.so.1.83.0 +195: 6# 0x0000FFFF82382680 in /lib/aarch64-linux-gnu/libboost_python313.so.1.83.0 195: 7# boost::python::detail::exception_handler::operator()(boost::function0 const&) const in /lib/aarch64-linux-gnu/libboost_python313.so.1.83.0 195: 8# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdSLNParse.so 195: 9# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdChemReactions.so @@ -33450,17 +33510,17 @@ 195: 14# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdmolfiles.so 195: 15# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdCIPLabeler.so 195: 16# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so -195: 17# 0x0000FFFFAFFEC320 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so -195: 18# 0x0000FFFFAFFEC2B8 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so -195: 19# 0x0000FFFFAFFEC248 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so -195: 20# 0x0000FFFFAFFEC1E0 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so -195: 21# 0x0000FFFFAFFEC178 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so +195: 17# 0x0000FFFF808BC320 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so +195: 18# 0x0000FFFF808BC2B8 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so +195: 19# 0x0000FFFF808BC248 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so +195: 20# 0x0000FFFF808BC1E0 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so +195: 21# 0x0000FFFF808BC178 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so 195: 22# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/rdBase.so 195: 23# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/rdBase.so 195: 24# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/rdBase.so 195: 25# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/rdBase.so 195: 26# boost::python::handle_exception_impl(boost::function0) in /lib/aarch64-linux-gnu/libboost_python313.so.1.83.0 -195: 27# 0x0000FFFFB1AAF25C in /lib/aarch64-linux-gnu/libboost_python313.so.1.83.0 +195: 27# 0x0000FFFF8237F25C in /lib/aarch64-linux-gnu/libboost_python313.so.1.83.0 195: 28# _PyObject_MakeTpCall in /usr/bin/python3 195: 29# _PyEval_EvalFrameDefault in /usr/bin/python3 195: 30# 0x000000000053DD10 in /usr/bin/python3 @@ -33492,69 +33552,40 @@ 195: 56# 0x000000000065F5F0 in /usr/bin/python3 195: 57# Py_RunMain in /usr/bin/python3 195: 58# Py_BytesMain in /usr/bin/python3 -195: 59# 0x0000FFFFB27F229C in /lib/aarch64-linux-gnu/libc.so.6 +195: 59# 0x0000FFFF830C229C in /lib/aarch64-linux-gnu/libc.so.6 195: 60# __libc_start_main in /lib/aarch64-linux-gnu/libc.so.6 195: 61# _start in /usr/bin/python3 195: ---------- 195: **** 195: -189/236 Test #200: pyTestMultithreadedMolSupplier ......... Passed 0.75 sec -test 201 - Start 201: pyTestPropertyLists - -201: Test command: /usr/bin/python3 "/build/reproducible-path/rdkit-202503.1/Code/GraphMol/Wrap/testPropertyLists.py" -201: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/Wrap -201: Test timeout computed to be: 1500 -190/236 Test #199: pyTestThreads .......................... Passed 2.76 sec -test 202 - Start 202: pyCDXMLTest - -202: Test command: /usr/bin/python3 "/build/reproducible-path/rdkit-202503.1/Code/GraphMol/Wrap/test_cdxml.py" -202: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/Wrap -202: Test timeout computed to be: 1500 -202: . -202: ---------------------------------------------------------------------- -202: Ran 1 test in 0.022s -202: -202: OK -191/236 Test #202: pyCDXMLTest ............................ Passed 0.57 sec +191/236 Test #200: pyTestMultithreadedMolSupplier ......... Passed 1.21 sec test 203 Start 203: molStandardizeTest 203: Test command: /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/MolStandardize/molStandardizeTest 203: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/MolStandardize 203: Test timeout computed to be: 1500 -186: Best mapping -201: [16:03:39] Value [?] for property atom.iprop.PartiallyMissingInt of atom 0 can not be parsed. Ignoring it. -201: [16:03:39] Value ? for property atom.iprop.PartiallyMissingInt of atom 3 can not be parsed. Ignoring it. -201: [16:03:39] Value $$$$ for property atom.iprop.PartiallyMissingInt of atom 4 can not be parsed. Ignoring it. -201: .[16:03:39] Value [?] for property atom.iprop.PartiallyMissingInt of atom 0 can not be parsed. Ignoring it. -201: [16:03:39] Value ? for property atom.iprop.PartiallyMissingInt of atom 3 can not be parsed. Ignoring it. -201: [16:03:39] Value $$$$ for property atom.iprop.PartiallyMissingInt of atom 4 can not be parsed. Ignoring it. -201: ...[16:03:39] Value [?] for property atom.iprop.PartiallyMissingInt of atom 0 can not be parsed. Ignoring it. -201: [16:03:39] Value ? for property atom.iprop.PartiallyMissingInt of atom 3 can not be parsed. Ignoring it. -201: [16:03:39] Value $$$$ for property atom.iprop.PartiallyMissingInt of atom 4 can not be parsed. Ignoring it. -201: . -201: ---------------------------------------------------------------------- -201: Ran 5 tests in 0.055s -201: -201: OK -192/236 Test #201: pyTestPropertyLists .................... Passed 1.82 sec +202: . +202: ---------------------------------------------------------------------- +202: Ran 1 test in 0.030s +202: +202: OK +192/236 Test #202: pyCDXMLTest ............................ Passed 1.27 sec test 204 Start 204: molNormalizeTest 204: Test command: /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/MolStandardize/molNormalizeTest 204: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/MolStandardize 204: Test timeout computed to be: 1500 -204: [16:03:39] Can't kekulize mol. Unkekulized atoms: 3 7 8 9 -204: [16:03:39] Initializing Normalizer -204: [16:03:39] Running Normalizer -204: [16:03:39] Rule applied: BrokenazidetoN=N+=N- -204: [16:03:39] Initializing Normalizer -204: [16:03:39] Running Normalizer -204: [16:03:39] Initializing Normalizer -204: [16:03:39] Running Normalizer -193/236 Test #204: molNormalizeTest ....................... Passed 0.46 sec +204: [12:25:21] Can't kekulize mol. Unkekulized atoms: 3 7 8 9 +204: [12:25:21] Initializing Normalizer +204: [12:25:21] Running Normalizer +204: [12:25:21] Rule applied: BrokenazidetoN=N+=N- +204: [12:25:21] Initializing Normalizer +204: [12:25:21] Running Normalizer +204: [12:25:21] Initializing Normalizer +204: [12:25:21] Running Normalizer +193/236 Test #204: molNormalizeTest ....................... Passed 0.49 sec test 205 Start 205: molValidateTest @@ -33579,7 +33610,7 @@ 205: ERROR: [StereoValidation] Bond 3 has assigned stereo type, but unexpected bond order. 205: there 205: ERROR: [StereoValidation] Atom 0 has stereo bonds, but less than 3 explicit substituents. -194/236 Test #205: molValidateTest ........................ Passed 0.12 sec +194/236 Test #205: molValidateTest ........................ Passed 0.14 sec test 206 Start 206: molChargeTest @@ -33593,190 +33624,47 @@ 207: Test command: /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/MolStandardize/molTautomerTest 207: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/MolStandardize 207: Test timeout computed to be: 1500 -196/236 Test #186: testRGroupDecomp ....................... Passed 19.63 sec +195: ....................[12:25:23] Explicit valence for atom # 1 F, 2, is greater than permitted +195: [12:25:23] Explicit valence for atom # 6 F, 2, is greater than permitted +195: [12:25:23] Can't kekulize mol. Unkekulized atoms: 3 4 5 +196/236 Test #203: molStandardizeTest ..................... Passed 3.36 sec test 208 Start 208: molStandardizeSmallTest 208: Test command: /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/MolStandardize/molStandardizeSmallTest 208: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/MolStandardize 208: Test timeout computed to be: 1500 -197/236 Test #208: molStandardizeSmallTest ................ Passed 0.09 sec +207: [12:25:23] Tautomer enumeration stopped at 292 tautomers: max transforms reached +197/236 Test #208: molStandardizeSmallTest ................ Passed 0.13 sec test 209 Start 209: molFragmentTest 209: Test command: /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/MolStandardize/molFragmentTest 209: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/MolStandardize 209: Test timeout computed to be: 1500 -209: [16:03:40] SMARTS Parse Error: syntax error while parsing: [Cl -209: [16:03:40] SMARTS Parse Error: Failed parsing SMARTS '[Cl' for input: '[Cl' -198/236 Test #209: molFragmentTest ........................ Passed 0.10 sec +195: .................[12:25:23] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +209: [12:25:24] SMARTS Parse Error: syntax error while parsing: [Cl +209: [12:25:24] SMARTS Parse Error: Failed parsing SMARTS '[Cl' for input: '[Cl' +198/236 Test #209: molFragmentTest ........................ Passed 0.17 sec test 210 Start 210: molStandardizeCatchTest 210: Test command: /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/MolStandardize/molStandardizeCatchTest 210: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/MolStandardize 210: Test timeout computed to be: 1500 -210: Randomness seeded to: 3506973311 +210: Randomness seeded to: 1857823299 210: * - * - * - * m1 210: * - * - * - * m2 210: * - * - * - * m1 210: * - * - * - * m2 -210: [16:03:40] Can't kekulize mol. Unkekulized atoms: 3 7 -210: [16:03:40] Can't kekulize mol. Unkekulized atoms: 3 8 -210: [16:03:40] Can't kekulize mol. Unkekulized atoms: 2 3 4 -207: [16:03:41] Tautomer enumeration stopped at 292 tautomers: max transforms reached -199/236 Test #203: molStandardizeTest ..................... Passed 2.86 sec -test 211 - Start 211: molStandardizePipelineTest - -211: Test command: /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/MolStandardize/molStandardizePipelineTest -211: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/MolStandardize -211: Test timeout computed to be: 1500 -211: Randomness seeded to: 634326143 -211: 1 Counts line too short: '' on line4 -211: 1 Could not instantiate a valid molecule from input -211: 8 Molecule has no atoms -211: [16:03:41] Explicit valence for atom # 1 N, 4, is greater than permitted -211: [16:03:41] Explicit valence for atom # 1 N, 4, is greater than permitted -211: 8 Explicit valence for atom # 1 N, 4, is greater than permitted -211: 128 An error occurred while preparing the molecule for standardization. -211: 8 The molecule contains an unknown isotope: 3C -211: 4 Query atom 0 is not allowed -211: 4 Bond 0 of aromatic type is not allowed -211: 4 Bond 1 of aromatic type is not allowed -211: 4 Bond 2 of aromatic type is not allowed -211: 4 Bond 3 of aromatic type is not allowed -211: 4 Bond 5 of aromatic type is not allowed -211: 4 Bond 6 of aromatic type is not allowed -211: 4 Bond 2 of dative type is not allowed -211: 4 Bond 3 of dative type is not allowed -211: 4 Enhanced stereochemistry features are not allowed -211: 8 The radical at atom 0 is not allowed -211: [16:03:41] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -211: 16 The molecule includes non-null Z coordinates -211: 32 Atom 0 too close to bond 2 -211: 32 The length of bond 3 between atoms 0 and 3 exceeds a configured limit -211: 64 Atom 0 has 3 explicit substituents and multiple stereo bonds -211: 64 Atom 0 has adjacent stereo bonds with like orientation -211: [16:03:41] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -211: 16 The molecule includes non-null Z coordinates -211: 64 Atom 0 has adjacent stereo bonds with like orientation -211: 32 The length of bond 16 between atoms 16 and 1 exceeds a configured limit -211: 8388608 One or more metal atoms were disconnected. -211: 33554432 One or more disconnected fragments (e.g., counterions) were removed. -211: 67108864 The protonation state was adjusted. -211: 16777216 The representation of some functional groups was adjusted. -211: 67108864 The protonation state was adjusted. -211: 16777216 The representation of some functional groups was adjusted. -211: 67108864 The protonation state was adjusted. -211: 16777216 The representation of some functional groups was adjusted. -211: 16777216 The representation of some functional groups was adjusted. -211: 67108864 The protonation state was adjusted. -211: 16777216 The representation of some functional groups was adjusted. -211: 67108864 The protonation state was adjusted. -211: 16777216 The representation of some functional groups was adjusted. -211: 67108864 The protonation state was adjusted. -211: 16777216 The representation of some functional groups was adjusted. -211: 67108864 The protonation state was adjusted. -211: 8388608 One or more metal atoms were disconnected. -211: 33554432 One or more disconnected fragments (e.g., counterions) were removed. -211: 67108864 The protonation state was adjusted. -211: 8388608 One or more metal atoms were disconnected. -211: 33554432 One or more disconnected fragments (e.g., counterions) were removed. -211: 67108864 The protonation state was adjusted. -211: 8388608 One or more metal atoms were disconnected. -211: 33554432 One or more disconnected fragments (e.g., counterions) were removed. -211: 67108864 The protonation state was adjusted. -211: 8388608 One or more metal atoms were disconnected. -211: 33554432 One or more disconnected fragments (e.g., counterions) were removed. -211: 67108864 The protonation state was adjusted. -211: 8388608 One or more metal atoms were disconnected. -211: 33554432 One or more disconnected fragments (e.g., counterions) were removed. -211: 67108864 The protonation state was adjusted. -211: 16777216 The "wavy" style of bond 4 was removed -211: 16777216 Double bond 1 was assigned an undefined/unknown stereochemical configuration -211: 16777216 The "wavy" style of bond 2 was removed -211: 16777216 Double bond 2 was assigned an undefined/unknown stereochemical configuration -211: 16777216 The "wavy" style of bond 1 was removed -211: 16777216 Double bond 2 was assigned an undefined/unknown stereochemical configuration -211: 16777216 The "wavy" style of bond 1 was removed -211: 16777216 The "wavy" style of bond 4 was removed -211: 16777216 Double bond 2 was assigned an undefined/unknown stereochemical configuration -211: 16777216 The "wavy" style of bond 3 was removed -211: 16777216 The representation of some functional groups was adjusted. -211: [16:03:41] Can't kekulize mol. Unkekulized atoms: 2 3 5 -211: =============================================================================== -211: All tests passed (268 assertions in 5 test cases) -211: -200/236 Test #211: molStandardizePipelineTest ............. Passed 0.38 sec -test 212 - Start 212: pyMolStandardize - -212: Test command: /usr/bin/python3 "/build/reproducible-path/rdkit-202503.1/Code/GraphMol/MolStandardize/Wrap/testMolStandardize.py" -212: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/MolStandardize/Wrap -212: Test timeout computed to be: 1500 -207: [16:03:42] Tautomer enumeration stopped at 292 tautomers: max transforms reached -207: [16:03:42] Tautomer enumeration stopped at 50 tautomers: max tautomers reached -207: [16:03:43] Tautomer enumeration stopped at 7 tautomers: canceled +210: [12:25:24] Can't kekulize mol. Unkekulized atoms: 3 7 +210: [12:25:24] Can't kekulize mol. Unkekulized atoms: 3 8 +210: [12:25:24] Can't kekulize mol. Unkekulized atoms: 2 3 4 +207: [12:25:24] Tautomer enumeration stopped at 292 tautomers: max transforms reached +207: [12:25:25] Tautomer enumeration stopped at 50 tautomers: max tautomers reached +207: [12:25:25] Tautomer enumeration stopped at 34 tautomers: canceled 207: Enumeration was canceled due to timeout (50 ms) -212: .....[16:03:43] Tautomer enumeration stopped at 292 tautomers: max transforms reached -212: [16:03:43] Tautomer enumeration stopped at 50 tautomers: max tautomers reached -212: .[16:03:44] Tautomer enumeration stopped at 25 tautomers: canceled -212: Enumeration was canceled due to timeout (50 ms) -195: ....................[16:03:44] Explicit valence for atom # 1 F, 2, is greater than permitted -195: [16:03:44] Explicit valence for atom # 6 F, 2, is greater than permitted -195: [16:03:44] Can't kekulize mol. Unkekulized atoms: 3 4 5 -195: .................[16:03:44] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -207: 375 -207: Enumeration has completed -207: [16:03:46] Tautomer enumeration stopped at 22 tautomers: canceled -212: Enumeration has completed -212: [16:03:48] Tautomer enumeration stopped at 44 tautomers: canceled -207: CN=c1cc[nH]cn1 -207: CN=c1ccnc[nH]1 -207: CNc1ccncn1 -207: res: CNc1ccncn1 -207: CN=c1cccc[nH]1 -207: CNc1ccccn1 -207: res: CNc1ccccn1 -201/236 Test #207: molTautomerTest ........................ Passed 8.39 sec -test 213 - Start 213: testScaffoldNetwork - -213: Test command: /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/ScaffoldNetwork/testScaffoldNetwork -213: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/ScaffoldNetwork -213: Test timeout computed to be: 1500 -212: ..........[16:03:48] Explicit valence for atom # 1 N, 4, is greater than permitted -212: [16:03:48] Explicit valence for atom # 1 N, 4, is greater than permitted -212: [16:03:48] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -212: [16:03:48] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -213: Randomness seeded to: 3687467259 -213: =============================================================================== -213: All tests passed (273 assertions in 19 test cases) -213: -202/236 Test #213: testScaffoldNetwork .................... Passed 2.75 sec -test 214 - Start 214: pyScaffoldNetwork - -214: Test command: /usr/bin/python3 "/build/reproducible-path/rdkit-202503.1/Code/GraphMol/ScaffoldNetwork/Wrap/testScaffoldNetwork.py" -214: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/ScaffoldNetwork/Wrap -214: Test timeout computed to be: 1500 -212: ............[16:03:52] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -212: [16:03:52] Warning: ambiguous stereochemistry - opposing bonds have opposite wedging - at atom 1 ignored. -212: [16:03:52] Warning: ambiguous stereochemistry - opposing bonds have opposite wedging - at atom 1 ignored. -212: ........[16:03:52] Explicit valence for atom # 1 O, 3, is greater than permitted -212: .. -212: ---------------------------------------------------------------------- -212: Ran 38 tests in 10.193s -212: -212: OK -212: done -214: ....... -214: ---------------------------------------------------------------------- -214: Ran 7 tests in 0.144s -214: -214: OK -185: ......[16:03:52] +185: ......[12:25:25] 185: 185: **** 185: Pre-condition Violation @@ -33797,25 +33685,25 @@ 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# 0x0000FFFFA020F530 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so +185: 12# 0x0000FFFFA6F5F530 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# 0x0000FFFFA1C72680 in /lib/aarch64-linux-gnu/libboost_python313.so.1.83.0 +185: 14# 0x0000FFFFA89C2680 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# 0x0000FFFFA016C320 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so -185: 21# 0x0000FFFFA016C2B8 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so -185: 22# 0x0000FFFFA016C248 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so -185: 23# 0x0000FFFFA016C1E0 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so -185: 24# 0x0000FFFFA016C178 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so +185: 20# 0x0000FFFFA6EBC320 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so +185: 21# 0x0000FFFFA6EBC2B8 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so +185: 22# 0x0000FFFFA6EBC248 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so +185: 23# 0x0000FFFFA6EBC1E0 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so +185: 24# 0x0000FFFFA6EBC178 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# 0x0000FFFFA1C6F25C in /lib/aarch64-linux-gnu/libboost_python313.so.1.83.0 +185: 30# 0x0000FFFFA89BF25C 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# 0x000000000053DD10 in /usr/bin/python3 @@ -33847,13 +33735,13 @@ 185: 59# 0x000000000065F5F0 in /usr/bin/python3 185: 60# Py_RunMain in /usr/bin/python3 185: 61# Py_BytesMain in /usr/bin/python3 -185: 62# 0x0000FFFFA265229C in /lib/aarch64-linux-gnu/libc.so.6 +185: 62# 0x0000FFFFA93A229C 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: [16:03:52] +185: [12:25:25] 185: 185: **** 185: Pre-condition Violation @@ -33865,7 +33753,7 @@ 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# 0x0000FFFF9FCBFCE8 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu//lib/libRDKitGraphMol.so.1 +185: 3# 0x0000FFFFA6A0FCE8 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 @@ -33875,25 +33763,25 @@ 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# 0x0000FFFFA020F530 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so +185: 13# 0x0000FFFFA6F5F530 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# 0x0000FFFFA1C72680 in /lib/aarch64-linux-gnu/libboost_python313.so.1.83.0 +185: 15# 0x0000FFFFA89C2680 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# 0x0000FFFFA016C320 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so -185: 22# 0x0000FFFFA016C2B8 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so -185: 23# 0x0000FFFFA016C248 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so -185: 24# 0x0000FFFFA016C1E0 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so -185: 25# 0x0000FFFFA016C178 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so +185: 21# 0x0000FFFFA6EBC320 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so +185: 22# 0x0000FFFFA6EBC2B8 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so +185: 23# 0x0000FFFFA6EBC248 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so +185: 24# 0x0000FFFFA6EBC1E0 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so +185: 25# 0x0000FFFFA6EBC178 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# 0x0000FFFFA1C6F25C in /lib/aarch64-linux-gnu/libboost_python313.so.1.83.0 +185: 31# 0x0000FFFFA89BF25C 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# 0x000000000053DD10 in /usr/bin/python3 @@ -33925,148 +33813,128 @@ 185: 60# 0x000000000065F5F0 in /usr/bin/python3 185: 61# Py_RunMain in /usr/bin/python3 185: 62# Py_BytesMain in /usr/bin/python3 -185: 63# 0x0000FFFFA265229C in /lib/aarch64-linux-gnu/libc.so.6 +185: 63# 0x0000FFFFA93A229C 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: -203/236 Test #212: pyMolStandardize ....................... Passed 11.30 sec -test 215 - Start 215: pyScaffoldNetworkPickling - -215: Test command: /usr/bin/python3 "/build/reproducible-path/rdkit-202503.1/Code/GraphMol/ScaffoldNetwork/Wrap/testPickleScaffoldNetwork.py" -215: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/ScaffoldNetwork/Wrap -215: Test timeout computed to be: 1500 -204/236 Test #214: pyScaffoldNetwork ...................... Passed 1.86 sec -test 216 - Start 216: testMolEnumerator - -216: Test command: /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/MolEnumerator/testMolEnumerator -216: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/MolEnumerator -216: Test timeout computed to be: 1500 -216: Randomness seeded to: 3003558279 -216: [16:03:53] can only enumerate SRUs with CONNECT=HT or CONNECT=HH -216: =============================================================================== -216: All tests passed (321 assertions in 16 test cases) -216: -205/236 Test #216: testMolEnumerator ...................... Passed 0.19 sec -test 217 - Start 217: pyMolEnumerator - -217: Test command: /usr/bin/python3 "/build/reproducible-path/rdkit-202503.1/Code/GraphMol/MolEnumerator/Wrap/rough_test.py" -217: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/MolEnumerator/Wrap -217: Test timeout computed to be: 1500 -215: . -215: ---------------------------------------------------------------------- -215: Ran 1 test in 0.056s -215: -215: OK -217: ... -217: ---------------------------------------------------------------------- -217: Ran 3 tests in 0.016s -217: -217: OK -206/236 Test #215: pyScaffoldNetworkPickling .............. Passed 1.13 sec -test 218 - Start 218: testAbbreviations - -218: Test command: /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/Abbreviations/testAbbreviations -218: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/Abbreviations -218: Test timeout computed to be: 1500 -207/236 Test #217: pyMolEnumerator ........................ Passed 0.78 sec -test 219 - Start 219: pyAbbreviations - -219: Test command: /usr/bin/python3 "/build/reproducible-path/rdkit-202503.1/Code/GraphMol/Abbreviations/Wrap/testAbbreviations.py" -219: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/Abbreviations/Wrap -219: Test timeout computed to be: 1500 -218: Randomness seeded to: 2332913271 -218: [16:03:54] SMARTS Parse Error: syntax error while parsing: *fail -218: [16:03:54] SMARTS Parse Error: Failed parsing SMARTS '*fail' for input: '*fail' -218: [16:03:54] no suitable SubstanceGroups found -218: =============================================================================== -218: All tests passed (195 assertions in 12 test cases) -218: -208/236 Test #218: testAbbreviations ...................... Passed 0.45 sec -test 220 - Start 220: generalizedSubstructCatch - -220: Test command: /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/GeneralizedSubstruct/generalizedSubstructCatch -220: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/GeneralizedSubstruct -220: Test timeout computed to be: 1500 -220: Randomness seeded to: 1313860009 -220: =============================================================================== -220: All tests passed (486 assertions in 10 test cases) -220: -209/236 Test #220: generalizedSubstructCatch .............. Passed 0.57 sec -test 221 - Start 221: pyGeneralizedSubstruct +207: 375 +207: Enumeration has completed +207: [12:25:27] Tautomer enumeration stopped at 33 tautomers: canceled +207: CN=c1cc[nH]cn1 +207: CN=c1ccnc[nH]1 +207: CNc1ccncn1 +207: res: CNc1ccncn1 +207: CN=c1cccc[nH]1 +207: CNc1ccccn1 +207: res: CNc1ccccn1 +199/236 Test #207: molTautomerTest ........................ Passed 7.49 sec +test 211 + Start 211: molStandardizePipelineTest -221: Test command: /usr/bin/python3 "/build/reproducible-path/rdkit-202503.1/Code/GraphMol/GeneralizedSubstruct/Wrap/testGeneralizedSubstruct.py" -221: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/GeneralizedSubstruct/Wrap -221: Test timeout computed to be: 1500 -221: ....... -221: ---------------------------------------------------------------------- -221: Ran 7 tests in 0.185s -221: -221: OK -210/236 Test #221: pyGeneralizedSubstruct ................. Passed 0.60 sec -test 222 - Start 222: testMolProcessing +211: Test command: /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/MolStandardize/molStandardizePipelineTest +211: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/MolStandardize +211: Test timeout computed to be: 1500 +211: Randomness seeded to: 4138310918 +211: 1 Counts line too short: '' on line4 +211: 1 Could not instantiate a valid molecule from input +211: 8 Molecule has no atoms +211: [12:25:29] Explicit valence for atom # 1 N, 4, is greater than permitted +211: [12:25:29] Explicit valence for atom # 1 N, 4, is greater than permitted +211: 8 Explicit valence for atom # 1 N, 4, is greater than permitted +211: 128 An error occurred while preparing the molecule for standardization. +211: 8 The molecule contains an unknown isotope: 3C +211: 4 Query atom 0 is not allowed +211: 4 Bond 0 of aromatic type is not allowed +211: 4 Bond 1 of aromatic type is not allowed +211: 4 Bond 2 of aromatic type is not allowed +211: 4 Bond 3 of aromatic type is not allowed +211: 4 Bond 5 of aromatic type is not allowed +211: 4 Bond 6 of aromatic type is not allowed +211: 4 Bond 2 of dative type is not allowed +211: 4 Bond 3 of dative type is not allowed +211: 4 Enhanced stereochemistry features are not allowed +211: 8 The radical at atom 0 is not allowed +211: [12:25:29] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +211: 16 The molecule includes non-null Z coordinates +211: 32 Atom 0 too close to bond 2 +211: 32 The length of bond 3 between atoms 0 and 3 exceeds a configured limit +211: 64 Atom 0 has 3 explicit substituents and multiple stereo bonds +211: 64 Atom 0 has adjacent stereo bonds with like orientation +211: [12:25:29] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +211: 16 The molecule includes non-null Z coordinates +211: 64 Atom 0 has adjacent stereo bonds with like orientation +211: 32 The length of bond 16 between atoms 16 and 1 exceeds a configured limit +211: 8388608 One or more metal atoms were disconnected. +211: 33554432 One or more disconnected fragments (e.g., counterions) were removed. +211: 67108864 The protonation state was adjusted. +211: 16777216 The representation of some functional groups was adjusted. +211: 67108864 The protonation state was adjusted. +211: 16777216 The representation of some functional groups was adjusted. +211: 67108864 The protonation state was adjusted. +211: 16777216 The representation of some functional groups was adjusted. +211: 16777216 The representation of some functional groups was adjusted. +211: 67108864 The protonation state was adjusted. +211: 16777216 The representation of some functional groups was adjusted. +211: 67108864 The protonation state was adjusted. +211: 16777216 The representation of some functional groups was adjusted. +211: 67108864 The protonation state was adjusted. +211: 16777216 The representation of some functional groups was adjusted. +211: 67108864 The protonation state was adjusted. +211: 8388608 One or more metal atoms were disconnected. +211: 33554432 One or more disconnected fragments (e.g., counterions) were removed. +211: 67108864 The protonation state was adjusted. +211: 8388608 One or more metal atoms were disconnected. +211: 33554432 One or more disconnected fragments (e.g., counterions) were removed. +211: 67108864 The protonation state was adjusted. +211: 8388608 One or more metal atoms were disconnected. +211: 33554432 One or more disconnected fragments (e.g., counterions) were removed. +211: 67108864 The protonation state was adjusted. +211: 8388608 One or more metal atoms were disconnected. +211: 33554432 One or more disconnected fragments (e.g., counterions) were removed. +211: 67108864 The protonation state was adjusted. +211: 8388608 One or more metal atoms were disconnected. +211: 33554432 One or more disconnected fragments (e.g., counterions) were removed. +211: 67108864 The protonation state was adjusted. +211: 16777216 The "wavy" style of bond 4 was removed +211: 16777216 Double bond 1 was assigned an undefined/unknown stereochemical configuration +211: 16777216 The "wavy" style of bond 2 was removed +211: 16777216 Double bond 2 was assigned an undefined/unknown stereochemical configuration +211: 16777216 The "wavy" style of bond 1 was removed +211: 16777216 Double bond 2 was assigned an undefined/unknown stereochemical configuration +211: 16777216 The "wavy" style of bond 1 was removed +211: 16777216 The "wavy" style of bond 4 was removed +211: 16777216 Double bond 2 was assigned an undefined/unknown stereochemical configuration +211: 16777216 The "wavy" style of bond 3 was removed +211: 16777216 The representation of some functional groups was adjusted. +211: [12:25:30] Can't kekulize mol. Unkekulized atoms: 2 3 5 +211: =============================================================================== +211: All tests passed (268 assertions in 5 test cases) +211: +200/236 Test #211: molStandardizePipelineTest ............. Passed 0.54 sec +test 212 + Start 212: pyMolStandardize -222: Test command: /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/MolProcessing/testMolProcessing -222: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/MolProcessing -222: Test timeout computed to be: 1500 +212: Test command: /usr/bin/python3 "/build/reproducible-path/rdkit-202503.1/Code/GraphMol/MolStandardize/Wrap/testMolStandardize.py" +212: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/MolStandardize/Wrap +212: Test timeout computed to be: 1500 150: --------------------------------- 150: test getO3AForProbeConfs 150: 150: *********************************************************** -211/236 Test #150: testO3AAlign ........................... Passed 64.73 sec -test 223 - Start 223: pyMolProcessing - -223: Test command: /usr/bin/python3 "/build/reproducible-path/rdkit-202503.1/Code/GraphMol/MolProcessing/Wrap/testMolProcessing.py" -223: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/MolProcessing/Wrap -223: Test timeout computed to be: 1500 -219: ....... -219: ---------------------------------------------------------------------- -219: Ran 7 tests in 0.175s -219: -219: OK -212/236 Test #219: pyAbbreviations ........................ Passed 2.39 sec -test 224 - Start 224: testMIF - -224: Test command: /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/MolInteractionFields/testMIF -224: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/MolInteractionFields -224: Test timeout computed to be: 1500 -223: .. -223: ---------------------------------------------------------------------- -223: Ran 2 tests in 0.548s -223: -223: OK -224: Randomness seeded to: 2409188246 -224: =============================================================================== -224: All tests passed (27926 assertions in 8 test cases) -224: -213/236 Test #224: testMIF ................................ Passed 0.88 sec -test 225 - Start 225: pyMIF - -225: Test command: /usr/bin/python3 "/build/reproducible-path/rdkit-202503.1/Code/GraphMol/MolInteractionFields/Wrap/testMIF.py" -225: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/MolInteractionFields/Wrap -225: Test timeout computed to be: 1500 -214/236 Test #223: pyMolProcessing ........................ Passed 1.51 sec -test 226 - Start 226: testQuery +201/236 Test #150: testO3AAlign ........................... Passed 73.00 sec +test 213 + Start 213: testScaffoldNetwork -226: Test command: /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/Query/testQuery -226: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/Query -226: Test timeout computed to be: 1500 -226: Query -226: Query2 -195: ..[16:03:57] +213: Test command: /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/ScaffoldNetwork/testScaffoldNetwork +213: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/ScaffoldNetwork +213: Test timeout computed to be: 1500 +212: .....[12:25:32] Tautomer enumeration stopped at 292 tautomers: max transforms reached +212: [12:25:32] Tautomer enumeration stopped at 50 tautomers: max tautomers reached +212: .[12:25:33] Tautomer enumeration stopped at 25 tautomers: canceled +212: Enumeration was canceled due to timeout (50 ms) +195: ..[12:25:34] 195: 195: **** 195: Pre-condition Violation @@ -34080,7 +33948,7 @@ 195: 2# RDKit::Atom::getOwningMol() const in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so 195: 3# boost::python::objects::caller_py_function_impl, boost::mpl::vector2 > >::operator()(_object*, _object*) in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so 195: 4# boost::python::objects::function::call(_object*, _object*) const in /lib/aarch64-linux-gnu/libboost_python313.so.1.83.0 -195: 5# 0x0000FFFFB1AB2680 in /lib/aarch64-linux-gnu/libboost_python313.so.1.83.0 +195: 5# 0x0000FFFF82382680 in /lib/aarch64-linux-gnu/libboost_python313.so.1.83.0 195: 6# boost::python::detail::exception_handler::operator()(boost::function0 const&) const in /lib/aarch64-linux-gnu/libboost_python313.so.1.83.0 195: 7# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdSLNParse.so 195: 8# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdChemReactions.so @@ -34091,17 +33959,17 @@ 195: 13# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdmolfiles.so 195: 14# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdCIPLabeler.so 195: 15# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so -195: 16# 0x0000FFFFAFFEC320 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so -195: 17# 0x0000FFFFAFFEC2B8 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so -195: 18# 0x0000FFFFAFFEC248 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so -195: 19# 0x0000FFFFAFFEC1E0 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so -195: 20# 0x0000FFFFAFFEC178 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so +195: 16# 0x0000FFFF808BC320 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so +195: 17# 0x0000FFFF808BC2B8 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so +195: 18# 0x0000FFFF808BC248 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so +195: 19# 0x0000FFFF808BC1E0 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so +195: 20# 0x0000FFFF808BC178 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so 195: 21# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/rdBase.so 195: 22# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/rdBase.so 195: 23# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/rdBase.so 195: 24# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/rdBase.so 195: 25# boost::python::handle_exception_impl(boost::function0) in /lib/aarch64-linux-gnu/libboost_python313.so.1.83.0 -195: 26# 0x0000FFFFB1AAF25C in /lib/aarch64-linux-gnu/libboost_python313.so.1.83.0 +195: 26# 0x0000FFFF8237F25C in /lib/aarch64-linux-gnu/libboost_python313.so.1.83.0 195: 27# _PyObject_MakeTpCall in /usr/bin/python3 195: 28# _PyEval_EvalFrameDefault in /usr/bin/python3 195: 29# 0x000000000053DD10 in /usr/bin/python3 @@ -34133,13 +34001,13 @@ 195: 55# 0x000000000065F5F0 in /usr/bin/python3 195: 56# Py_RunMain in /usr/bin/python3 195: 57# Py_BytesMain in /usr/bin/python3 -195: 58# 0x0000FFFFB27F229C in /lib/aarch64-linux-gnu/libc.so.6 +195: 58# 0x0000FFFF830C229C in /lib/aarch64-linux-gnu/libc.so.6 195: 59# __libc_start_main in /lib/aarch64-linux-gnu/libc.so.6 195: 60# _start in /usr/bin/python3 195: ---------- 195: **** 195: -195: [16:03:57] +195: [12:25:34] 195: 195: **** 195: Pre-condition Violation @@ -34153,7 +34021,7 @@ 195: 2# RDKit::AtomGetNeighbors(RDKit::Atom*) in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so 195: 3# boost::python::objects::caller_py_function_impl > >::operator()(_object*, _object*) in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so 195: 4# boost::python::objects::function::call(_object*, _object*) const in /lib/aarch64-linux-gnu/libboost_python313.so.1.83.0 -195: 5# 0x0000FFFFB1AB2680 in /lib/aarch64-linux-gnu/libboost_python313.so.1.83.0 +195: 5# 0x0000FFFF82382680 in /lib/aarch64-linux-gnu/libboost_python313.so.1.83.0 195: 6# boost::python::detail::exception_handler::operator()(boost::function0 const&) const in /lib/aarch64-linux-gnu/libboost_python313.so.1.83.0 195: 7# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdSLNParse.so 195: 8# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdChemReactions.so @@ -34164,17 +34032,17 @@ 195: 13# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdmolfiles.so 195: 14# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdCIPLabeler.so 195: 15# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so -195: 16# 0x0000FFFFAFFEC320 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so -195: 17# 0x0000FFFFAFFEC2B8 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so -195: 18# 0x0000FFFFAFFEC248 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so -195: 19# 0x0000FFFFAFFEC1E0 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so -195: 20# 0x0000FFFFAFFEC178 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so +195: 16# 0x0000FFFF808BC320 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so +195: 17# 0x0000FFFF808BC2B8 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so +195: 18# 0x0000FFFF808BC248 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so +195: 19# 0x0000FFFF808BC1E0 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so +195: 20# 0x0000FFFF808BC178 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so 195: 21# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/rdBase.so 195: 22# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/rdBase.so 195: 23# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/rdBase.so 195: 24# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/rdBase.so 195: 25# boost::python::handle_exception_impl(boost::function0) in /lib/aarch64-linux-gnu/libboost_python313.so.1.83.0 -195: 26# 0x0000FFFFB1AAF25C in /lib/aarch64-linux-gnu/libboost_python313.so.1.83.0 +195: 26# 0x0000FFFF8237F25C in /lib/aarch64-linux-gnu/libboost_python313.so.1.83.0 195: 27# _PyObject_MakeTpCall in /usr/bin/python3 195: 28# _PyEval_EvalFrameDefault in /usr/bin/python3 195: 29# 0x000000000053DD10 in /usr/bin/python3 @@ -34206,22 +34074,15 @@ 195: 55# 0x000000000065F5F0 in /usr/bin/python3 195: 56# Py_RunMain in /usr/bin/python3 195: 57# Py_BytesMain in /usr/bin/python3 -195: 58# 0x0000FFFFB27F229C in /lib/aarch64-linux-gnu/libc.so.6 +195: 58# 0x0000FFFF830C229C in /lib/aarch64-linux-gnu/libc.so.6 195: 59# __libc_start_main in /lib/aarch64-linux-gnu/libc.so.6 195: 60# _start in /usr/bin/python3 195: ---------- 195: **** 195: -195: [16:03:57] +195: [12:25:34] 195: 195: **** -226: Equality -226: Greater -226: GreaterEqual -226: Less -226: LessEqual -226: Open Range -226: Closed Range 195: Pre-condition Violation 195: no owner 195: Violation occurred on line 153 in file ./Code/GraphMol/Atom.h @@ -34233,7 +34094,7 @@ 195: 2# RDKit::AtomGetBonds(RDKit::Atom*) in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so 195: 3# boost::python::objects::caller_py_function_impl > >::operator()(_object*, _object*) in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so 195: 4# boost::python::objects::function::call(_object*, _object*) const in /lib/aarch64-linux-gnu/libboost_python313.so.1.83.0 -195: 5# 0x0000FFFFB1AB2680 in /lib/aarch64-linux-gnu/libboost_python313.so.1.83.0 +195: 5# 0x0000FFFF82382680 in /lib/aarch64-linux-gnu/libboost_python313.so.1.83.0 195: 6# boost::python::detail::exception_handler::operator()(boost::function0 const&) const in /lib/aarch64-linux-gnu/libboost_python313.so.1.83.0 195: 7# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdSLNParse.so 195: 8# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdChemReactions.so @@ -34244,17 +34105,17 @@ 195: 13# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdmolfiles.so 195: 14# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdCIPLabeler.so 195: 15# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so -195: 16# 0x0000FFFFAFFEC320 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so -195: 17# 0x0000FFFFAFFEC2B8 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so -195: 18# 0x0000FFFFAFFEC248 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so -195: 19# 0x0000FFFFAFFEC1E0 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so -195: 20# 0x0000FFFFAFFEC178 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so +195: 16# 0x0000FFFF808BC320 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so +195: 17# 0x0000FFFF808BC2B8 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so +195: 18# 0x0000FFFF808BC248 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so +195: 19# 0x0000FFFF808BC1E0 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so +195: 20# 0x0000FFFF808BC178 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so 195: 21# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/rdBase.so 195: 22# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/rdBase.so 195: 23# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/rdBase.so 195: 24# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/rdBase.so 195: 25# boost::python::handle_exception_impl(boost::function0) in /lib/aarch64-linux-gnu/libboost_python313.so.1.83.0 -195: 26# 0x0000FFFFB1AAF25C in /lib/aarch64-linux-gnu/libboost_python313.so.1.83.0 +195: 26# 0x0000FFFF8237F25C in /lib/aarch64-linux-gnu/libboost_python313.so.1.83.0 195: 27# _PyObject_MakeTpCall in /usr/bin/python3 195: 28# _PyEval_EvalFrameDefault in /usr/bin/python3 195: 29# 0x000000000053DD10 in /usr/bin/python3 @@ -34286,13 +34147,13 @@ 195: 55# 0x000000000065F5F0 in /usr/bin/python3 195: 56# Py_RunMain in /usr/bin/python3 195: 57# Py_BytesMain in /usr/bin/python3 -195: 58# 0x0000FFFFB27F229C in /lib/aarch64-linux-gnu/libc.so.6 +195: 58# 0x0000FFFF830C229C in /lib/aarch64-linux-gnu/libc.so.6 195: 59# __libc_start_main in /lib/aarch64-linux-gnu/libc.so.6 195: 60# _start in /usr/bin/python3 195: ---------- 195: **** 195: -195: [16:03:57] +195: [12:25:34] 195: 195: **** 195: Pre-condition Violation @@ -34306,7 +34167,7 @@ 195: 2# RDKit::AtomIsInRing(RDKit::Atom const*) in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so 195: 3# boost::python::objects::caller_py_function_impl > >::operator()(_object*, _object*) in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so 195: 4# boost::python::objects::function::call(_object*, _object*) const in /lib/aarch64-linux-gnu/libboost_python313.so.1.83.0 -195: 5# 0x0000FFFFB1AB2680 in /lib/aarch64-linux-gnu/libboost_python313.so.1.83.0 +195: 5# 0x0000FFFF82382680 in /lib/aarch64-linux-gnu/libboost_python313.so.1.83.0 195: 6# boost::python::detail::exception_handler::operator()(boost::function0 const&) const in /lib/aarch64-linux-gnu/libboost_python313.so.1.83.0 195: 7# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdSLNParse.so 195: 8# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdChemReactions.so @@ -34317,17 +34178,17 @@ 195: 13# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdmolfiles.so 195: 14# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdCIPLabeler.so 195: 15# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so -195: 16# 0x0000FFFFAFFEC320 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so -195: 17# 0x0000FFFFAFFEC2B8 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so -195: 18# 0x0000FFFFAFFEC248 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so -195: 19# 0x0000FFFFAFFEC1E0 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so -195: 20# 0x0000FFFFAFFEC178 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so +195: 16# 0x0000FFFF808BC320 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so +195: 17# 0x0000FFFF808BC2B8 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so +195: 18# 0x0000FFFF808BC248 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so +195: 19# 0x0000FFFF808BC1E0 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so +195: 20# 0x0000FFFF808BC178 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so 195: 21# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/rdBase.so 195: 22# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/rdBase.so 195: 23# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/rdBase.so 195: 24# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/rdBase.so 195: 25# boost::python::handle_exception_impl(boost::function0) in /lib/aarch64-linux-gnu/libboost_python313.so.1.83.0 -195: 26# 0x0000FFFFB1AAF25C in /lib/aarch64-linux-gnu/libboost_python313.so.1.83.0 +195: 26# 0x0000FFFF8237F25C in /lib/aarch64-linux-gnu/libboost_python313.so.1.83.0 195: 27# _PyObject_MakeTpCall in /usr/bin/python3 195: 28# _PyEval_EvalFrameDefault in /usr/bin/python3 195: 29# 0x000000000053DD10 in /usr/bin/python3 @@ -34359,19 +34220,15 @@ 195: 55# 0x000000000065F5F0 in /usr/bin/python3 195: 56# Py_RunMain in /usr/bin/python3 195: 57# Py_BytesMain in /usr/bin/python3 -195: 58# 0x0000FFFFB27F229C in /lib/aarch64-linux-gnu/libc.so.6 +195: 58# 0x0000FFFF830C229C in /lib/aarch64-linux-gnu/libc.so.6 195: 59# __libc_start_main in /lib/aarch64-linux-gnu/libc.so.6 195: 60# _start in /usr/bin/python3 195: ---------- 195: **** 195: -195: [16:03:57] +195: [12:25:34] 195: 195: **** -226: Float -226: With Tolerance -226: Set -226: And 195: Pre-condition Violation 195: no owner 195: Violation occurred on line 153 in file ./Code/GraphMol/Atom.h @@ -34383,7 +34240,7 @@ 195: 2# RDKit::AtomIsInRingSize(RDKit::Atom const*, int) in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so 195: 3# boost::python::objects::caller_py_function_impl > >::operator()(_object*, _object*) in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so 195: 4# boost::python::objects::function::call(_object*, _object*) const in /lib/aarch64-linux-gnu/libboost_python313.so.1.83.0 -195: 5# 0x0000FFFFB1AB2680 in /lib/aarch64-linux-gnu/libboost_python313.so.1.83.0 +195: 5# 0x0000FFFF82382680 in /lib/aarch64-linux-gnu/libboost_python313.so.1.83.0 195: 6# boost::python::detail::exception_handler::operator()(boost::function0 const&) const in /lib/aarch64-linux-gnu/libboost_python313.so.1.83.0 195: 7# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdSLNParse.so 195: 8# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdChemReactions.so @@ -34394,17 +34251,17 @@ 195: 13# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdmolfiles.so 195: 14# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdCIPLabeler.so 195: 15# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so -195: 16# 0x0000FFFFAFFEC320 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so -195: 17# 0x0000FFFFAFFEC2B8 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so -195: 18# 0x0000FFFFAFFEC248 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so -195: 19# 0x0000FFFFAFFEC1E0 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so -195: 20# 0x0000FFFFAFFEC178 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so +195: 16# 0x0000FFFF808BC320 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so +195: 17# 0x0000FFFF808BC2B8 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so +195: 18# 0x0000FFFF808BC248 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so +195: 19# 0x0000FFFF808BC1E0 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so +195: 20# 0x0000FFFF808BC178 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so 195: 21# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/rdBase.so 195: 22# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/rdBase.so 195: 23# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/rdBase.so 195: 24# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/rdBase.so 195: 25# boost::python::handle_exception_impl(boost::function0) in /lib/aarch64-linux-gnu/libboost_python313.so.1.83.0 -195: 26# 0x0000FFFFB1AAF25C in /lib/aarch64-linux-gnu/libboost_python313.so.1.83.0 +195: 26# 0x0000FFFF8237F25C in /lib/aarch64-linux-gnu/libboost_python313.so.1.83.0 195: 27# _PyObject_MakeTpCall in /usr/bin/python3 195: 28# _PyEval_EvalFrameDefault in /usr/bin/python3 195: 29# 0x000000000053DD10 in /usr/bin/python3 @@ -34436,26 +34293,15 @@ 195: 55# 0x000000000065F5F0 in /usr/bin/python3 195: 56# Py_RunMain in /usr/bin/python3 195: 57# Py_BytesMain in /usr/bin/python3 -195: 58# 0x0000FFFFB27F229C in /lib/aarch64-linux-gnu/libc.so.6 +195: 58# 0x0000FFFF830C229C in /lib/aarch64-linux-gnu/libc.so.6 195: 59# __libc_start_main in /lib/aarch64-linux-gnu/libc.so.6 195: 60# _start in /usr/bin/python3 195: ---------- 195: **** 195: -195: .....[16:03:57] +195: .....[12:25:34] 195: 195: **** -226: Or -226: XOr -226: pointer and copy foo -226: Set2 -215/236 Test #226: testQuery .............................. Passed 0.15 sec -test 227 - Start 227: testBaseFeatures - -227: Test command: /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/Features/testBaseFeatures -227: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/Features -227: Test timeout computed to be: 1500 195: Range Error 195: atomIdx1 195: Violation occurred on line 498 in file ./Code/GraphMol/RWMol.cpp @@ -34467,7 +34313,7 @@ 195: 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.1 195: 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 195: 4# boost::python::objects::function::call(_object*, _object*) const in /lib/aarch64-linux-gnu/libboost_python313.so.1.83.0 -195: 5# 0x0000FFFFB1AB2680 in /lib/aarch64-linux-gnu/libboost_python313.so.1.83.0 +195: 5# 0x0000FFFF82382680 in /lib/aarch64-linux-gnu/libboost_python313.so.1.83.0 195: 6# boost::python::detail::exception_handler::operator()(boost::function0 const&) const in /lib/aarch64-linux-gnu/libboost_python313.so.1.83.0 195: 7# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdSLNParse.so 195: 8# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdChemReactions.so @@ -34478,17 +34324,17 @@ 195: 13# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdmolfiles.so 195: 14# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdCIPLabeler.so 195: 15# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so -195: 16# 0x0000FFFFAFFEC320 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so -195: 17# 0x0000FFFFAFFEC2B8 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so -195: 18# 0x0000FFFFAFFEC248 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so -195: 19# 0x0000FFFFAFFEC1E0 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so -195: 20# 0x0000FFFFAFFEC178 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so +195: 16# 0x0000FFFF808BC320 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so +195: 17# 0x0000FFFF808BC2B8 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so +195: 18# 0x0000FFFF808BC248 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so +195: 19# 0x0000FFFF808BC1E0 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so +195: 20# 0x0000FFFF808BC178 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so 195: 21# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/rdBase.so 195: 22# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/rdBase.so 195: 23# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/rdBase.so 195: 24# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/rdBase.so 195: 25# boost::python::handle_exception_impl(boost::function0) in /lib/aarch64-linux-gnu/libboost_python313.so.1.83.0 -195: 26# 0x0000FFFFB1AAF25C in /lib/aarch64-linux-gnu/libboost_python313.so.1.83.0 +195: 26# 0x0000FFFF8237F25C in /lib/aarch64-linux-gnu/libboost_python313.so.1.83.0 195: 27# _PyObject_MakeTpCall in /usr/bin/python3 195: 28# _PyEval_EvalFrameDefault in /usr/bin/python3 195: 29# 0x000000000053DD10 in /usr/bin/python3 @@ -34520,49 +34366,49 @@ 195: 55# 0x000000000065F5F0 in /usr/bin/python3 195: 56# Py_RunMain in /usr/bin/python3 195: 57# Py_BytesMain in /usr/bin/python3 -195: 58# 0x0000FFFFB27F229C in /lib/aarch64-linux-gnu/libc.so.6 +195: 58# 0x0000FFFF830C229C in /lib/aarch64-linux-gnu/libc.so.6 195: 59# __libc_start_main in /lib/aarch64-linux-gnu/libc.so.6 195: 60# _start in /usr/bin/python3 195: ---------- 195: **** 195: -195: ......[16:03:57] SMILES Parse Error: unclosed ring for input: 'c1ccccc' -195: [16:03:57] ERROR: Smiles parse error on line 0 -195: [16:03:57] ERROR: Cannot create molecule from : 'c1ccccc' -195: [16:03:57] SMILES Parse Error: extra open parentheses while parsing: C(C -195: [16:03:57] SMILES Parse Error: check for mistakes around position 2: -195: [16:03:57] C(C -195: [16:03:57] ~^ -195: [16:03:57] SMILES Parse Error: Failed parsing SMILES 'C(C' for input: 'C(C' -195: [16:03:57] ERROR: Smiles parse error on line 3 -195: [16:03:57] ERROR: Cannot create molecule from : 'C(C' -195: [16:03:57] Explicit valence for atom # 1 C, 5, is greater than permitted -195: [16:03:57] ERROR: Could not sanitize molecule on line 6 -195: [16:03:57] ERROR: Explicit valence for atom # 1 C, 5, is greater than permitted -195: [16:03:57] SMILES Parse Error: unclosed ring for input: 'c1ccccc' -195: [16:03:57] ERROR: Smiles parse error on line 0 -195: [16:03:57] ERROR: Cannot create molecule from : 'c1ccccc' -195: [16:03:57] SMILES Parse Error: extra open parentheses while parsing: C(C -195: [16:03:57] SMILES Parse Error: check for mistakes around position 2: -195: [16:03:57] C(C -195: [16:03:57] ~^ -195: [16:03:57] SMILES Parse Error: Failed parsing SMILES 'C(C' for input: 'C(C' -195: [16:03:57] ERROR: Smiles parse error on line 3 -195: [16:03:57] ERROR: Cannot create molecule from : 'C(C' -195: [16:03:57] SMILES Parse Error: unclosed ring for input: 'C1C(Cl)CCCC' -195: [16:03:57] ERROR: Smiles parse error on line 6 -195: [16:03:57] ERROR: Cannot create molecule from : 'C1C(Cl)CCCC' -195: [16:03:57] Explicit valence for atom # 1 F, 2, is greater than permitted -195: [16:03:57] ERROR: Could not sanitize molecule ending on line 21 -195: [16:03:57] ERROR: Explicit valence for atom # 1 F, 2, is greater than permitted -195: [16:03:57] ERROR: EOF hit while reading atoms -195: [16:03:57] ERROR: moving to the beginning of the next molecule -195: [16:03:57] Explicit valence for atom # 1 F, 2, is greater than permitted -195: [16:03:57] ERROR: Could not sanitize molecule ending on line 21 -195: [16:03:57] ERROR: Explicit valence for atom # 1 F, 2, is greater than permitted -195: [16:03:57] ERROR: EOF hit while reading atoms -195: [16:03:57] ERROR: moving to the beginning of the next molecule -195: ....[16:03:57] +195: ......[12:25:34] SMILES Parse Error: unclosed ring for input: 'c1ccccc' +195: [12:25:34] ERROR: Smiles parse error on line 0 +195: [12:25:34] ERROR: Cannot create molecule from : 'c1ccccc' +195: [12:25:34] SMILES Parse Error: extra open parentheses while parsing: C(C +195: [12:25:34] SMILES Parse Error: check for mistakes around position 2: +195: [12:25:34] C(C +195: [12:25:34] ~^ +195: [12:25:34] SMILES Parse Error: Failed parsing SMILES 'C(C' for input: 'C(C' +195: [12:25:34] ERROR: Smiles parse error on line 3 +195: [12:25:34] ERROR: Cannot create molecule from : 'C(C' +195: [12:25:34] Explicit valence for atom # 1 C, 5, is greater than permitted +195: [12:25:34] ERROR: Could not sanitize molecule on line 6 +195: [12:25:34] ERROR: Explicit valence for atom # 1 C, 5, is greater than permitted +195: [12:25:34] SMILES Parse Error: unclosed ring for input: 'c1ccccc' +195: [12:25:34] ERROR: Smiles parse error on line 0 +195: [12:25:34] ERROR: Cannot create molecule from : 'c1ccccc' +195: [12:25:34] SMILES Parse Error: extra open parentheses while parsing: C(C +195: [12:25:34] SMILES Parse Error: check for mistakes around position 2: +195: [12:25:34] C(C +195: [12:25:34] ~^ +195: [12:25:34] SMILES Parse Error: Failed parsing SMILES 'C(C' for input: 'C(C' +195: [12:25:34] ERROR: Smiles parse error on line 3 +195: [12:25:34] ERROR: Cannot create molecule from : 'C(C' +195: [12:25:34] SMILES Parse Error: unclosed ring for input: 'C1C(Cl)CCCC' +195: [12:25:34] ERROR: Smiles parse error on line 6 +195: [12:25:34] ERROR: Cannot create molecule from : 'C1C(Cl)CCCC' +195: [12:25:34] Explicit valence for atom # 1 F, 2, is greater than permitted +195: [12:25:34] ERROR: Could not sanitize molecule ending on line 21 +195: [12:25:34] ERROR: Explicit valence for atom # 1 F, 2, is greater than permitted +195: [12:25:34] ERROR: EOF hit while reading atoms +195: [12:25:34] ERROR: moving to the beginning of the next molecule +195: [12:25:34] Explicit valence for atom # 1 F, 2, is greater than permitted +195: [12:25:34] ERROR: Could not sanitize molecule ending on line 21 +195: [12:25:34] ERROR: Explicit valence for atom # 1 F, 2, is greater than permitted +195: [12:25:34] ERROR: EOF hit while reading atoms +195: [12:25:34] ERROR: moving to the beginning of the next molecule +195: ....[12:25:34] 195: 195: **** 195: Pre-condition Violation @@ -34576,7 +34422,7 @@ 195: 2# RDKit::RingInfo::numRings() const in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu//lib/libRDKitGraphMol.so.1 195: 3# boost::python::objects::caller_py_function_impl > >::operator()(_object*, _object*) in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so 195: 4# boost::python::objects::function::call(_object*, _object*) const in /lib/aarch64-linux-gnu/libboost_python313.so.1.83.0 -195: 5# 0x0000FFFFB1AB2680 in /lib/aarch64-linux-gnu/libboost_python313.so.1.83.0 +195: 5# 0x0000FFFF82382680 in /lib/aarch64-linux-gnu/libboost_python313.so.1.83.0 195: 6# boost::python::detail::exception_handler::operator()(boost::function0 const&) const in /lib/aarch64-linux-gnu/libboost_python313.so.1.83.0 195: 7# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdSLNParse.so 195: 8# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdChemReactions.so @@ -34587,17 +34433,17 @@ 195: 13# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdmolfiles.so 195: 14# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdCIPLabeler.so 195: 15# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so -195: 16# 0x0000FFFFAFFEC320 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so -195: 17# 0x0000FFFFAFFEC2B8 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so -195: 18# 0x0000FFFFAFFEC248 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so -195: 19# 0x0000FFFFAFFEC1E0 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so -195: 20# 0x0000FFFFAFFEC178 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so +195: 16# 0x0000FFFF808BC320 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so +195: 17# 0x0000FFFF808BC2B8 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so +195: 18# 0x0000FFFF808BC248 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so +195: 19# 0x0000FFFF808BC1E0 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so +195: 20# 0x0000FFFF808BC178 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so 195: 21# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/rdBase.so 195: 22# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/rdBase.so 195: 23# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/rdBase.so 195: 24# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/rdBase.so 195: 25# boost::python::handle_exception_impl(boost::function0) in /lib/aarch64-linux-gnu/libboost_python313.so.1.83.0 -195: 26# 0x0000FFFFB1AAF25C in /lib/aarch64-linux-gnu/libboost_python313.so.1.83.0 +195: 26# 0x0000FFFF8237F25C in /lib/aarch64-linux-gnu/libboost_python313.so.1.83.0 195: 27# _PyObject_MakeTpCall in /usr/bin/python3 195: 28# _PyEval_EvalFrameDefault in /usr/bin/python3 195: 29# 0x000000000053DD10 in /usr/bin/python3 @@ -34629,16 +34475,13 @@ 195: 55# 0x000000000065F5F0 in /usr/bin/python3 195: 56# Py_RunMain in /usr/bin/python3 195: 57# Py_BytesMain in /usr/bin/python3 -195: 58# 0x0000FFFFB27F229C in /lib/aarch64-linux-gnu/libc.so.6 +195: 58# 0x0000FFFF830C229C in /lib/aarch64-linux-gnu/libc.so.6 195: 59# __libc_start_main in /lib/aarch64-linux-gnu/libc.so.6 195: 60# _start in /usr/bin/python3 195: ---------- 195: **** 195: -227: ------------------------------------- -227: Basics for ExplicitFeatures. -227: done -195: .............[16:03:57] +195: .............[12:25:34] 195: 195: **** 195: Range Error @@ -34652,7 +34495,7 @@ 195: 2# RDKit::ROMol::getAtomWithIdx(unsigned int) in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu//lib/libRDKitGraphMol.so.1 195: 3# boost::python::objects::caller_py_function_impl >, boost::mpl::vector3 > >::operator()(_object*, _object*) in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so 195: 4# boost::python::objects::function::call(_object*, _object*) const in /lib/aarch64-linux-gnu/libboost_python313.so.1.83.0 -195: 5# 0x0000FFFFB1AB2680 in /lib/aarch64-linux-gnu/libboost_python313.so.1.83.0 +195: 5# 0x0000FFFF82382680 in /lib/aarch64-linux-gnu/libboost_python313.so.1.83.0 195: 6# boost::python::detail::exception_handler::operator()(boost::function0 const&) const in /lib/aarch64-linux-gnu/libboost_python313.so.1.83.0 195: 7# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdSLNParse.so 195: 8# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdChemReactions.so @@ -34663,17 +34506,17 @@ 195: 13# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdmolfiles.so 195: 14# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdCIPLabeler.so 195: 15# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so -195: 16# 0x0000FFFFAFFEC320 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so -195: 17# 0x0000FFFFAFFEC2B8 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so -195: 18# 0x0000FFFFAFFEC248 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so -195: 19# 0x0000FFFFAFFEC1E0 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so -195: 20# 0x0000FFFFAFFEC178 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so +195: 16# 0x0000FFFF808BC320 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so +195: 17# 0x0000FFFF808BC2B8 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so +195: 18# 0x0000FFFF808BC248 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so +195: 19# 0x0000FFFF808BC1E0 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so +195: 20# 0x0000FFFF808BC178 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so 195: 21# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/rdBase.so 195: 22# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/rdBase.so 195: 23# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/rdBase.so 195: 24# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/rdBase.so 195: 25# boost::python::handle_exception_impl(boost::function0) in /lib/aarch64-linux-gnu/libboost_python313.so.1.83.0 -195: 26# 0x0000FFFFB1AAF25C in /lib/aarch64-linux-gnu/libboost_python313.so.1.83.0 +195: 26# 0x0000FFFF8237F25C in /lib/aarch64-linux-gnu/libboost_python313.so.1.83.0 195: 27# _PyObject_MakeTpCall in /usr/bin/python3 195: 28# _PyEval_EvalFrameDefault in /usr/bin/python3 195: 29# 0x000000000053DD10 in /usr/bin/python3 @@ -34705,20 +34548,266 @@ 195: 55# 0x000000000065F5F0 in /usr/bin/python3 195: 56# Py_RunMain in /usr/bin/python3 195: 57# Py_BytesMain in /usr/bin/python3 -195: 58# 0x0000FFFFB27F229C in /lib/aarch64-linux-gnu/libc.so.6 +195: 58# 0x0000FFFF830C229C in /lib/aarch64-linux-gnu/libc.so.6 195: 59# __libc_start_main in /lib/aarch64-linux-gnu/libc.so.6 195: 60# _start in /usr/bin/python3 195: ---------- 195: **** 195: +195: ...[12:25:34] Can't kekulize mol. Unkekulized atoms: 0 1 2 3 4 +195: ............................[12:25:34] SMILES Parse Error: unclosed ring for input: 'C1CC' +195: ......smi: CC1=C(n2cccc2[C@H](C)Cl)C(C)CCC1 |(2.679,0.4142,;1.3509,1.181,;0.0229,0.4141,;0.0229,-1.1195,;1.2645,-2.0302,;0.7901,-3.4813,;-0.7446,-3.4813,;-1.219,-2.0302,;-2.679,-1.5609,;-3.0039,-0.0556,;-3.8202,-2.595,;-1.3054,1.1809,;-2.6335,0.4141,;-1.3054,2.7145,;0.0229,3.4813,;1.3509,2.7146,),wD:8.9,2.11,a:2,&1:8| +195: 1 +195: ..[12:25:34] WARNING: not removing hydrogen atom without neighbors +195: [12:25:34] WARNING: not removing hydrogen atom with dummy atom neighbors +195: [12:25:34] WARNING: not removing hydrogen atom with wedged bond +195: [12:25:34] WARNING: not removing hydrogen atom without neighbors +195: [12:25:34] WARNING: not removing hydrogen atom with dummy atom neighbors +213: Randomness seeded to: 889931290 +213: =============================================================================== +213: All tests passed (273 assertions in 19 test cases) +213: +202/236 Test #213: testScaffoldNetwork .................... Passed 3.52 sec +test 214 + Start 214: pyScaffoldNetwork + +214: Test command: /usr/bin/python3 "/build/reproducible-path/rdkit-202503.1/Code/GraphMol/ScaffoldNetwork/Wrap/testScaffoldNetwork.py" +214: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/ScaffoldNetwork/Wrap +214: Test timeout computed to be: 1500 +195: ......[12:25:35] Explicit valence for atom # 1 F, 2, is greater than permitted +195: [12:25:35] Can't kekulize mol. Unkekulized atoms: 0 1 2 +195: .[12:25:35] Explicit valence for atom # 1 F, 2, is greater than permitted +195: [12:25:35] Explicit valence for atom # 1 F, 2, is greater than permitted +195: [12:25:35] Explicit valence for atom # 1 F, 2, is greater than permitted +195: [12:25:35] Explicit valence for atom # 1 F, 2, is greater than permitted +195: [12:25:35] Can't kekulize mol. Unkekulized atoms: 0 1 2 +195: [12:25:35] Can't kekulize mol. Unkekulized atoms: 0 1 2 +195: [12:25:35] Can't kekulize mol. Unkekulized atoms: 0 1 2 +195: ..........[12:25:35] SMARTS Parse Error: syntax error while parsing: CCC |$foo;;bar$| ourname +195: [12:25:35] SMARTS Parse Error: Failed parsing SMARTS 'CCC |$foo;;bar$| ourname' for input: 'CCC |$foo;;bar$| ourname' +195: .[12:25:35] SMILES Parse Error: syntax error while parsing: CCC |$foo;;bar$| ourname +195: [12:25:35] SMILES Parse Error: check for mistakes around position 4: +195: [12:25:35] CCC |$foo;;bar$| ourname +195: [12:25:35] ~~~^ +195: [12:25:35] SMILES Parse Error: Failed parsing SMILES 'CCC |$foo;;bar$| ourname' for input: 'CCC |$foo;;bar$| ourname' +195: ..[12:25:35] SMILES Parse Error: syntax error while parsing: error +195: [12:25:35] SMILES Parse Error: check for mistakes around position 1: +195: [12:25:35] error +195: [12:25:35] ^ +195: [12:25:35] SMILES Parse Error: Failed parsing SMILES 'error' for input: 'error' +195: [12:25:35] SMILES Parse Error: Failed parsing SMILES 'd' for input: 'd' +195: [12:25:35] SMARTS Parse Error: Failed parsing SMARTS 'error' for input: 'error' +195: [12:25:35] SMARTS Parse Error: Failed parsing SMARTS 'd' for input: 'd' +195: .........................[12:25:35] SMILES Parse Error: syntax error while parsing: garbage_0 +195: [12:25:35] SMILES Parse Error: check for mistakes around position 1: +195: [12:25:35] garbage_0 +195: [12:25:35] ^ +195: [12:25:35] SMILES Parse Error: Failed parsing SMILES 'garbage_0' for input: 'garbage_0' +195: [12:25:35] SMILES Parse Error: syntax error while parsing: garbage_2 +195: [12:25:35] SMILES Parse Error: check for mistakes around position 1: +195: [12:25:35] garbage_2 +195: [12:25:35] ^ +195: [12:25:35] SMILES Parse Error: Failed parsing SMILES 'garbage_2' for input: 'garbage_2' +195: [12:25:35] SMILES Parse Error: syntax error while parsing: garbage_4 +195: [12:25:35] SMILES Parse Error: check for mistakes around position 1: +195: [12:25:35] garbage_4 +195: [12:25:35] ^ +195: [12:25:35] SMILES Parse Error: Failed parsing SMILES 'garbage_4' for input: 'garbage_4' +195: ............ +195: ---------------------------------------------------------------------- +195: Ran 279 tests in 17.784s +195: +195: OK +195: supplier: +195: supplier: +195: supplier: +214: ....... +214: ---------------------------------------------------------------------- +214: Ran 7 tests in 0.189s +214: +214: OK +203/236 Test #214: pyScaffoldNetwork ...................... Passed 1.18 sec +test 215 + Start 215: pyScaffoldNetworkPickling + +215: Test command: /usr/bin/python3 "/build/reproducible-path/rdkit-202503.1/Code/GraphMol/ScaffoldNetwork/Wrap/testPickleScaffoldNetwork.py" +215: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/ScaffoldNetwork/Wrap +215: Test timeout computed to be: 1500 +204/236 Test #195: pyGraphMolWrap ......................... Passed 19.57 sec +test 216 + Start 216: testMolEnumerator + +216: Test command: /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/MolEnumerator/testMolEnumerator +216: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/MolEnumerator +216: Test timeout computed to be: 1500 +212: Enumeration has completed +212: [12:25:36] Tautomer enumeration stopped at 21 tautomers: canceled +216: Randomness seeded to: 785311550 +216: [12:25:37] can only enumerate SRUs with CONNECT=HT or CONNECT=HH +215: . +215: ---------------------------------------------------------------------- +215: Ran 1 test in 0.048s +215: +215: OK +216: =============================================================================== +216: All tests passed (321 assertions in 16 test cases) +216: +205/236 Test #216: testMolEnumerator ...................... Passed 0.89 sec +test 217 + Start 217: pyMolEnumerator + +217: Test command: /usr/bin/python3 "/build/reproducible-path/rdkit-202503.1/Code/GraphMol/MolEnumerator/Wrap/rough_test.py" +217: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/MolEnumerator/Wrap +217: Test timeout computed to be: 1500 +212: ..........[12:25:37] Explicit valence for atom # 1 N, 4, is greater than permitted +212: [12:25:37] Explicit valence for atom # 1 N, 4, is greater than permitted +212: [12:25:37] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +212: [12:25:37] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +206/236 Test #215: pyScaffoldNetworkPickling .............. Passed 0.99 sec +test 218 + Start 218: testAbbreviations + +218: Test command: /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/Abbreviations/testAbbreviations +218: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/Abbreviations +218: Test timeout computed to be: 1500 +218: Randomness seeded to: 3456947860 +218: [12:25:37] SMARTS Parse Error: syntax error while parsing: *fail +218: [12:25:37] SMARTS Parse Error: Failed parsing SMARTS '*fail' for input: '*fail' +147: [12:25:37] UFFTYPER: Unrecognized atom type: S_6+6 (0) +147: [12:25:37] UFFTYPER: Warning: hybridization set to SP3 for atom 0 +147: [12:25:37] UFFTYPER: Unrecognized charge state for atom: 0 +218: [12:25:37] no suitable SubstanceGroups found +218: =============================================================================== +218: All tests passed (195 assertions in 12 test cases) +218: +207/236 Test #218: testAbbreviations ...................... Passed 0.58 sec +test 219 + Start 219: pyAbbreviations + +219: Test command: /usr/bin/python3 "/build/reproducible-path/rdkit-202503.1/Code/GraphMol/Abbreviations/Wrap/testAbbreviations.py" +219: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/Abbreviations/Wrap +219: Test timeout computed to be: 1500 +217: ... +217: ---------------------------------------------------------------------- +217: Ran 3 tests in 0.060s +217: +217: OK +208/236 Test #217: pyMolEnumerator ........................ Passed 1.08 sec +test 220 + Start 220: generalizedSubstructCatch + +220: Test command: /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/GeneralizedSubstruct/generalizedSubstructCatch +220: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/GeneralizedSubstruct +220: Test timeout computed to be: 1500 +209/236 Test #199: pyTestThreads .......................... Passed 19.46 sec +test 221 + Start 221: pyGeneralizedSubstruct + +221: Test command: /usr/bin/python3 "/build/reproducible-path/rdkit-202503.1/Code/GraphMol/GeneralizedSubstruct/Wrap/testGeneralizedSubstruct.py" +221: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/GeneralizedSubstruct/Wrap +221: Test timeout computed to be: 1500 +219: ....... +219: ---------------------------------------------------------------------- +219: Ran 7 tests in 0.066s +219: +219: OK +210/236 Test #219: pyAbbreviations ........................ Passed 0.85 sec +test 222 + Start 222: testMolProcessing + +222: Test command: /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/MolProcessing/testMolProcessing +222: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/MolProcessing +222: Test timeout computed to be: 1500 +220: Randomness seeded to: 301334022 +220: =============================================================================== +220: All tests passed (486 assertions in 10 test cases) +220: +211/236 Test #220: generalizedSubstructCatch .............. Passed 0.79 sec +test 223 + Start 223: pyMolProcessing + +223: Test command: /usr/bin/python3 "/build/reproducible-path/rdkit-202503.1/Code/GraphMol/MolProcessing/Wrap/testMolProcessing.py" +223: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/MolProcessing/Wrap +223: Test timeout computed to be: 1500 +212: ............[12:25:39] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +212: [12:25:39] Warning: ambiguous stereochemistry - opposing bonds have opposite wedging - at atom 1 ignored. +212: [12:25:39] Warning: ambiguous stereochemistry - opposing bonds have opposite wedging - at atom 1 ignored. +221: ....... +221: ---------------------------------------------------------------------- +221: Ran 7 tests in 0.499s +221: +221: OK +212/236 Test #221: pyGeneralizedSubstruct ................. Passed 1.59 sec +test 224 + Start 224: testMIF + +224: Test command: /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/MolInteractionFields/testMIF +224: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/MolInteractionFields +224: Test timeout computed to be: 1500 +212: ........[12:25:40] Explicit valence for atom # 1 O, 3, is greater than permitted +224: Randomness seeded to: 2839571424 +224: =============================================================================== +224: All tests passed (27926 assertions in 8 test cases) +224: +213/236 Test #224: testMIF ................................ Passed 0.48 sec +test 225 + Start 225: pyMIF + +225: Test command: /usr/bin/python3 "/build/reproducible-path/rdkit-202503.1/Code/GraphMol/MolInteractionFields/Wrap/testMIF.py" +225: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/MolInteractionFields/Wrap +225: Test timeout computed to be: 1500 +223: .. +223: ---------------------------------------------------------------------- +223: Ran 2 tests in 0.588s +223: +223: OK +214/236 Test #223: pyMolProcessing ........................ Passed 1.72 sec +test 226 + Start 226: testQuery + +226: Test command: /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/Query/testQuery +226: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/Query +226: Test timeout computed to be: 1500 +212: .. +212: ---------------------------------------------------------------------- +212: Ran 38 tests in 9.565s +212: +212: OK +212: done +226: Query +226: Query2 +226: Equality +226: Greater +226: GreaterEqual +226: Less +226: LessEqual +226: Open Range +226: Closed Range +226: Float +226: With Tolerance +226: Set +226: And +226: Or +226: XOr +226: pointer and copy foo +226: Set2 +215/236 Test #226: testQuery .............................. Passed 0.06 sec +test 227 + Start 227: testBaseFeatures + +227: Test command: /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/Features/testBaseFeatures +227: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/Features +227: Test timeout computed to be: 1500 +227: ------------------------------------- +227: Basics for ExplicitFeatures. +227: done 227: ------------------------------------- 227: Basics for ImplicitFeatures. -195: ...[16:03:57] Can't kekulize mol. Unkekulized atoms: 0 1 2 3 4 227: done 227: ------------------------------------- 227: ExplicitFeatures 2D, string type. 227: done -216/236 Test #227: testBaseFeatures ....................... Passed 0.16 sec +216/236 Test #227: testBaseFeatures ....................... Passed 0.03 sec test 228 Start 228: testMatCalc @@ -34770,114 +34859,58 @@ 228: 9.49496e+07 228: 2.25618e+08 228: 1.30219e+08 -217/236 Test #228: testMatCalc ............................ Passed 0.07 sec +217/236 Test #228: testMatCalc ............................ Passed 0.02 sec test 229 Start 229: pyMatCalc 229: Test command: /usr/bin/python3 "/build/reproducible-path/rdkit-202503.1/Code/DataManip/MetricMatrixCalc/Wrap/testMatricCalc.py" 229: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/DataManip/MetricMatrixCalc/Wrap 229: Test timeout computed to be: 1500 -195: ............................[16:03:58] SMILES Parse Error: unclosed ring for input: 'C1CC' -195: ......smi: CC1=C(n2cccc2[C@H](C)Cl)C(C)CCC1 |(2.679,0.4142,;1.3509,1.181,;0.0229,0.4141,;0.0229,-1.1195,;1.2645,-2.0302,;0.7901,-3.4813,;-0.7446,-3.4813,;-1.219,-2.0302,;-2.679,-1.5609,;-3.0039,-0.0556,;-3.8202,-2.595,;-1.3054,1.1809,;-2.6335,0.4141,;-1.3054,2.7145,;0.0229,3.4813,;1.3509,2.7146,),wD:8.9,2.11,a:2,&1:8| -195: 1 -195: ..[16:03:58] WARNING: not removing hydrogen atom without neighbors -195: [16:03:58] WARNING: not removing hydrogen atom with dummy atom neighbors -195: [16:03:58] WARNING: not removing hydrogen atom with wedged bond -195: [16:03:58] WARNING: not removing hydrogen atom without neighbors -195: [16:03:58] WARNING: not removing hydrogen atom with dummy atom neighbors -225: ....... -225: ---------------------------------------------------------------------- -225: Ran 7 tests in 0.245s -225: -225: OK -225: Testing MIF wrapper -218/236 Test #225: pyMIF .................................. Passed 1.63 sec +218/236 Test #212: pyMolStandardize ....................... Passed 10.80 sec test 230 Start 230: testSimDivPickers 230: Test command: /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/SimDivPickers/testSimDivPickers 230: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/SimDivPickers 230: Test timeout computed to be: 1500 -230: [16:03:59] ------------------------------------- -230: [16:03:59] Testing github issue 1421: MaxMinPicker picking non-existent element. -230: [16:03:59] Done -230: [16:03:59] ------------------------------------- -230: [16:03:59] Testing github issue 2245: MinMax Diversity picker seeding shows deterministic / non-random behaviour. -230: [16:03:59] Done -219/236 Test #230: testSimDivPickers ...................... Passed 0.10 sec +230: [12:25:41] ------------------------------------- +230: [12:25:41] Testing github issue 1421: MaxMinPicker picking non-existent element. +230: [12:25:41] Done +230: [12:25:41] ------------------------------------- +230: [12:25:41] Testing github issue 2245: MinMax Diversity picker seeding shows deterministic / non-random behaviour. +230: [12:25:41] Done +219/236 Test #230: testSimDivPickers ...................... Passed 0.06 sec test 231 Start 231: pickersTestsCatch 231: Test command: /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/SimDivPickers/pickersTestsCatch 231: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/SimDivPickers 231: Test timeout computed to be: 1500 -231: Randomness seeded to: 2938208917 +231: Randomness seeded to: 4189835597 231: =============================================================================== 231: All tests passed (21267 assertions in 1 test case) 231: -220/236 Test #231: pickersTestsCatch ...................... Passed 0.70 sec +220/236 Test #231: pickersTestsCatch ...................... Passed 0.84 sec test 232 Start 232: pySimDivPickers 232: Test command: /usr/bin/python3 "/build/reproducible-path/rdkit-202503.1/Code/SimDivPickers/Wrap/testPickers.py" 232: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/SimDivPickers/Wrap 232: Test timeout computed to be: 1500 -195: ......[16:04:00] Explicit valence for atom # 1 F, 2, is greater than permitted -195: [16:04:00] Can't kekulize mol. Unkekulized atoms: 0 1 2 -195: .[16:04:00] Explicit valence for atom # 1 F, 2, is greater than permitted -195: [16:04:00] Explicit valence for atom # 1 F, 2, is greater than permitted -195: [16:04:00] Explicit valence for atom # 1 F, 2, is greater than permitted -195: [16:04:00] Explicit valence for atom # 1 F, 2, is greater than permitted -195: [16:04:00] Can't kekulize mol. Unkekulized atoms: 0 1 2 -195: [16:04:00] Can't kekulize mol. Unkekulized atoms: 0 1 2 -195: [16:04:00] Can't kekulize mol. Unkekulized atoms: 0 1 2 -195: ..........[16:04:00] SMARTS Parse Error: syntax error while parsing: CCC |$foo;;bar$| ourname -195: [16:04:00] SMARTS Parse Error: Failed parsing SMARTS 'CCC |$foo;;bar$| ourname' for input: 'CCC |$foo;;bar$| ourname' -195: .[16:04:00] SMILES Parse Error: syntax error while parsing: CCC |$foo;;bar$| ourname -195: [16:04:00] SMILES Parse Error: check for mistakes around position 4: -195: [16:04:00] CCC |$foo;;bar$| ourname -195: [16:04:00] ~~~^ -195: [16:04:00] SMILES Parse Error: Failed parsing SMILES 'CCC |$foo;;bar$| ourname' for input: 'CCC |$foo;;bar$| ourname' -195: ..[16:04:00] SMILES Parse Error: syntax error while parsing: error -195: [16:04:00] SMILES Parse Error: check for mistakes around position 1: -195: [16:04:00] error -195: [16:04:00] ^ -195: [16:04:00] SMILES Parse Error: Failed parsing SMILES 'error' for input: 'error' -195: [16:04:00] SMILES Parse Error: Failed parsing SMILES 'd' for input: 'd' -195: [16:04:00] SMARTS Parse Error: Failed parsing SMARTS 'error' for input: 'error' -195: [16:04:00] SMARTS Parse Error: Failed parsing SMARTS 'd' for input: 'd' -195: .........................[16:04:00] SMILES Parse Error: syntax error while parsing: garbage_0 -195: [16:04:00] SMILES Parse Error: check for mistakes around position 1: -195: [16:04:00] garbage_0 -195: [16:04:00] ^ -195: [16:04:00] SMILES Parse Error: Failed parsing SMILES 'garbage_0' for input: 'garbage_0' -195: [16:04:00] SMILES Parse Error: syntax error while parsing: garbage_2 -195: [16:04:00] SMILES Parse Error: check for mistakes around position 1: -195: [16:04:00] garbage_2 -195: [16:04:00] ^ -195: [16:04:00] SMILES Parse Error: Failed parsing SMILES 'garbage_2' for input: 'garbage_2' -195: [16:04:00] SMILES Parse Error: syntax error while parsing: garbage_4 -195: [16:04:00] SMILES Parse Error: check for mistakes around position 1: -195: [16:04:00] garbage_4 -195: [16:04:00] ^ -195: [16:04:00] SMILES Parse Error: Failed parsing SMILES 'garbage_4' for input: 'garbage_4' -195: ............ -195: ---------------------------------------------------------------------- -195: Ran 279 tests in 26.128s -195: -195: OK -195: supplier: -195: supplier: -195: supplier: -221/236 Test #195: pyGraphMolWrap ......................... Passed 28.38 sec +225: ....... +225: ---------------------------------------------------------------------- +225: Ran 7 tests in 0.245s +225: +225: OK +225: Testing MIF wrapper +221/236 Test #225: pyMIF .................................. Passed 1.80 sec test 233 Start 233: pyRanker 233: Test command: /usr/bin/python3 "/build/reproducible-path/rdkit-202503.1/Code/ML/InfoTheory/Wrap/testRanker.py" 233: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/ML/InfoTheory/Wrap 233: Test timeout computed to be: 1500 -232: [16:04:01] the useCache argument is deprecated and ignored -233: ..[16:04:01] +233: ..[12:25:42] 233: 233: **** 233: Invariant Violation @@ -34892,14 +34925,14 @@ 233: 3# RDInfoTheory::getTopNbits(RDInfoTheory::InfoBitRanker*, int) in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/ML/InfoTheory/rdInfoTheory.so 233: 4# boost::python::objects::caller_py_function_impl > >::operator()(_object*, _object*) in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/ML/InfoTheory/rdInfoTheory.so 233: 5# boost::python::objects::function::call(_object*, _object*) const in /lib/aarch64-linux-gnu/libboost_python313.so.1.83.0 -233: 6# 0x0000FFFF98E62680 in /lib/aarch64-linux-gnu/libboost_python313.so.1.83.0 +233: 6# 0x0000FFFF86932680 in /lib/aarch64-linux-gnu/libboost_python313.so.1.83.0 233: 7# boost::python::detail::exception_handler::operator()(boost::function0 const&) const in /lib/aarch64-linux-gnu/libboost_python313.so.1.83.0 233: 8# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/rdBase.so 233: 9# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/rdBase.so 233: 10# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/rdBase.so 233: 11# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/rdBase.so 233: 12# boost::python::handle_exception_impl(boost::function0) in /lib/aarch64-linux-gnu/libboost_python313.so.1.83.0 -233: 13# 0x0000FFFF98E5F25C in /lib/aarch64-linux-gnu/libboost_python313.so.1.83.0 +233: 13# 0x0000FFFF8692F25C in /lib/aarch64-linux-gnu/libboost_python313.so.1.83.0 233: 14# _PyObject_MakeTpCall in /usr/bin/python3 233: 15# _PyEval_EvalFrameDefault in /usr/bin/python3 233: 16# 0x000000000053DD10 in /usr/bin/python3 @@ -34931,7 +34964,7 @@ 233: 42# 0x000000000065F5F0 in /usr/bin/python3 233: 43# Py_RunMain in /usr/bin/python3 233: 44# Py_BytesMain in /usr/bin/python3 -233: 45# 0x0000FFFF9A78229C in /lib/aarch64-linux-gnu/libc.so.6 +233: 45# 0x0000FFFF8825229C in /lib/aarch64-linux-gnu/libc.so.6 233: 46# __libc_start_main in /lib/aarch64-linux-gnu/libc.so.6 233: 47# _start in /usr/bin/python3 233: ---------- @@ -34939,10 +34972,11 @@ 233: 233: ... 233: ---------------------------------------------------------------------- -233: Ran 5 tests in 0.058s +233: Ran 5 tests in 0.078s 233: 233: OK -222/236 Test #233: pyRanker ............................... Passed 0.62 sec +232: [12:25:43] the useCache argument is deprecated and ignored +222/236 Test #233: pyRanker ............................... Passed 0.78 sec test 234 Start 234: testChemicalFeatures @@ -34952,87 +34986,84 @@ 234: ----------------------------------------- 234: Test1 234: Done -223/236 Test #234: testChemicalFeatures ................... Passed 0.09 sec +223/236 Test #234: testChemicalFeatures ................... Passed 0.05 sec test 235 Start 235: pyFeatures 235: Test command: /usr/bin/python3 "/build/reproducible-path/rdkit-202503.1/Code/ChemicalFeatures/Wrap/testFeatures.py" 235: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/ChemicalFeatures/Wrap 235: Test timeout computed to be: 1500 -232: ...[16:04:01] the useCache argument is deprecated and ignored -232: [16:04:01] the useCache argument is deprecated and ignored -232: .[16:04:01] the useCache argument is deprecated and ignored -235: .. -235: ---------------------------------------------------------------------- -235: Ran 2 tests in 0.036s -235: -235: OK -235: Testing ChemicalFeatures Wrapper code: -222: Randomness seeded to: 3187570088 +229: ..... +229: ---------------------------------------------------------------------- +229: Ran 5 tests in 1.521s +229: +229: OK +222: Randomness seeded to: 653924488 222: =============================================================================== 222: All tests passed (203 assertions in 1 test case) 222: -224/236 Test #222: testMolProcessing ...................... Passed 7.36 sec +224/236 Test #222: testMolProcessing ...................... Passed 4.59 sec test 236 Start 236: pythonProjectTests 236: Test command: /usr/bin/python3 "-m" "pytest" 236: Working Directory: /build/reproducible-path/rdkit-202503.1/Projects 236: Test timeout computed to be: 1500 -225/236 Test #235: pyFeatures ............................. Passed 1.40 sec -229: ..... -229: ---------------------------------------------------------------------- -229: Ran 5 tests in 3.489s -229: -229: OK -226/236 Test #229: pyMatCalc .............................. Passed 5.30 sec -147: [16:04:04] UFFTYPER: Unrecognized atom type: S_6+6 (0) -147: [16:04:04] UFFTYPER: Warning: hybridization set to SP3 for atom 0 -147: [16:04:04] UFFTYPER: Unrecognized charge state for atom: 0 +225/236 Test #229: pyMatCalc .............................. Passed 2.46 sec +232: ...[12:25:43] the useCache argument is deprecated and ignored +232: [12:25:43] the useCache argument is deprecated and ignored +232: .[12:25:43] the useCache argument is deprecated and ignored +235: .. +235: ---------------------------------------------------------------------- +235: Ran 2 tests in 0.011s +235: +235: OK +235: Testing ChemicalFeatures Wrapper code: +226/236 Test #235: pyFeatures ............................. Passed 0.93 sec +185: ............. +185: ---------------------------------------------------------------------- +185: Ran 19 tests in 42.342s +185: +185: OK +185: Testing atom rings +185: testing bond rings +185: searching atom rings +185: searching bond rings +185: done +227/236 Test #185: pySubstructLibrary ..................... Passed 43.44 sec 232: ....... 232: ---------------------------------------------------------------------- -232: Ran 11 tests in 5.315s +232: Ran 11 tests in 3.580s 232: 232: OK -227/236 Test #232: pySimDivPickers ........................ Passed 6.63 sec +228/236 Test #232: pySimDivPickers ........................ Passed 4.61 sec 236: ============================= test session starts ============================== 236: platform linux -- Python 3.13.5, pytest-8.3.5, pluggy-1.5.0 236: rootdir: /build/reproducible-path/rdkit-202503.1/Projects 236: configfile: pytest.ini 236: collected 12 items 236: -185: ............. -185: ---------------------------------------------------------------------- -185: Ran 19 tests in 59.011s -185: -185: OK -185: Testing atom rings -185: testing bond rings -185: searching atom rings -185: searching bond rings -185: done -228/236 Test #185: pySubstructLibrary ..................... Passed 59.54 sec -170: [16:04:23] Timed out after 71 seconds. -146: [16:04:23] done -210: [16:04:26] Explicit valence for atom # 0 Br, 1, is greater than permitted +170: [12:25:51] Timed out after 71 seconds. +146: [12:26:05] done +210: [12:26:11] Explicit valence for atom # 0 Br, 1, is greater than permitted 210: =============================================================================== 210: All tests passed (38344 assertions in 51 test cases) 210: -229/236 Test #210: molStandardizeCatchTest ................ Passed 46.06 sec -146: [16:04:23] --------------------------------- -146: [16:04:23] test github issue 256: handling of zero-atom molecules +229/236 Test #210: molStandardizeCatchTest ................ Passed 47.16 sec +146: [12:26:05] --------------------------------- +146: [12:26:05] test github issue 256: handling of zero-atom molecules 146: -146: [16:04:23] --------------------------------- -146: [16:04:23] test embedder callback function -146: [16:04:23] --------------------------------- -146: [16:04:23] test multi-threaded multi-conf embedding +146: [12:26:05] --------------------------------- +146: [12:26:05] test embedder callback function +146: [12:26:05] --------------------------------- +146: [12:26:05] test multi-threaded multi-conf embedding 146: -146: [16:04:30] --------------------------------- -146: [16:04:30] test github issue 563: Incorrect ring stereochemistry after embedding +146: [12:26:14] --------------------------------- +146: [12:26:14] test github issue 563: Incorrect ring stereochemistry after embedding 146: 146: CNC[C@H]1CC[C@H](C[NH3+])CC1 -146: [16:04:33] --------------------------------- -146: [16:04:33] test github issue 568: Incorrect stereochemistry after embedding +146: [12:26:17] --------------------------------- +146: [12:26:17] 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 @@ -35051,16 +35082,16 @@ 146: O=C(O)[C@@H]1C[C@H]2C[C@@H](CCc3nn[nH]n3)CC[C@H]2CN1 146: COc1ccc2c(c1)OC[C@@H](N1CCC(O)(c3ccc(F)cc3)CC1)[C@H]2O 146: Oc1ccc2c(c1)OC[C@@H](N1CCC(Cc3ccccc3)CC1)[C@H]2O -236: DbCLI/UnitTestDbCLI.py ............ [100%] -236: -236: =============================== warnings summary =============================== -236: ../obj-aarch64-linux-gnu/rdkit/Chem/MolDb/Loader_sa.py:20 -236: /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) -236: decBase = declarative_base() -236: -236: -- Docs: https://docs.pytest.org/en/stable/how-to/capture-warnings.html -236: ======================== 12 passed, 1 warning in 39.76s ======================== -147: [16:04:44] Interrupted, cancelling conformer generation +146: Oc1ccc2c(c1)OC[C@H](N1CCC(O)(c3ccccc3)CC1)[C@@H]2O +171: =============================================================================== +171: All tests passed (93 assertions in 5 test cases) +171: +230/236 Test #171: testRascalCluster ...................... Passed 117.74 sec +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 +147: [12:26:34] 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] @@ -35093,76 +35124,76 @@ 147: 13 7->5 order: 1 147: 14 8->12 order: a conj?: 1 aromatic?: 1 147: 15 11->2 order: 1 stereo: CCW bonds: (9 4 5) conj?: 1 -146: Oc1ccc2c(c1)OC[C@H](N1CCC(O)(c3ccccc3)CC1)[C@@H]2O -230/236 Test #236: pythonProjectTests ..................... Passed 41.87 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 147: =============================================================================== 147: All tests passed (12742 assertions in 21 test cases) 147: -231/236 Test #147: distGeomHelpersCatch ................... Passed 115.41 sec -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 +231/236 Test #147: distGeomHelpersCatch ................... Passed 137.74 sec 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 +236: DbCLI/UnitTestDbCLI.py ............ [100%] +236: +236: =============================== warnings summary =============================== +236: ../obj-aarch64-linux-gnu/rdkit/Chem/MolDb/Loader_sa.py:20 +236: /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) +236: decBase = declarative_base() +236: +236: -- Docs: https://docs.pytest.org/en/stable/how-to/capture-warnings.html +236: ======================== 12 passed, 1 warning in 52.64s ======================== +232/236 Test #236: pythonProjectTests ..................... Passed 54.58 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-] -171: =============================================================================== -171: All tests passed (93 assertions in 5 test cases) -171: -232/236 Test #171: testRascalCluster ...................... Passed 109.88 sec -146: [16:04:58] Molecule does not have explicit Hs. Consider calling AddHs() -146: [16:04:52] --------------------------------- -146: [16:04:52] test github issue 696: Bad 1-4 bounds matrix elements in highly constrained system -146: [16:04:52] --------------------------------- -146: [16:04:52] More ChEMBL molecules failing bounds smoothing. -146: [16:04:52] --------------------------------- -146: [16:04:52] ugly conformations can be generated for highly constrained ring systems. -146: [16:04:52] --------------------------------- -146: [16:04:52] test embed parameters structure. -146: [16:04:52] --------------------------------- -146: [16:04:52] test github 1227: Hs being used in RMSD filtering. -146: [16:04:52] --------------------------------- -146: [16:04:52] Failure to embed larger aromatic rings. -146: [16:04:55] --------------------------------- -146: [16:04:55] Deterministic with large random seeds -146: [16:04:57] --------------------------------- -146: [16:04:57] Github #1990: seg fault after RemoveHs -146: [16:04:57] --------------------------------- -146: [16:04:57] Github #2246: Use coordMap when starting embedding from random coords -146: [16:04:58] --------------------------------- -146: [16:04:58] Providing a distance bounds matrix. -146: [16:04:58] --------------------------------- -146: [16:04:58] Disabling fragmentation. -146: [16:04:58] --------------------------------- -146: [16:04:58] Using symmetry in conformation pruning. -146: [16:04:58] --------------------------------- -146: [16:04:58] Force trans amides. -146: [16:04:58] --------------------------------- -146: [16:04:58] test missing Hs warning. -146: [16:04:58] --------------------------------- -146: [16:04:58] basic H bond support. -146: [16:04:58] ******************************************************* -233/236 Test #146: testDistGeomHelpers .................... Passed 129.13 sec +146: [12:26:50] Molecule does not have explicit Hs. Consider calling AddHs() +146: [12:26:38] --------------------------------- +146: [12:26:38] test github issue 696: Bad 1-4 bounds matrix elements in highly constrained system +146: [12:26:38] --------------------------------- +146: [12:26:38] More ChEMBL molecules failing bounds smoothing. +146: [12:26:38] --------------------------------- +146: [12:26:38] ugly conformations can be generated for highly constrained ring systems. +146: [12:26:38] --------------------------------- +146: [12:26:38] test embed parameters structure. +146: [12:26:39] --------------------------------- +146: [12:26:39] test github 1227: Hs being used in RMSD filtering. +146: [12:26:39] --------------------------------- +146: [12:26:39] Failure to embed larger aromatic rings. +146: [12:26:41] --------------------------------- +146: [12:26:41] Deterministic with large random seeds +146: [12:26:47] --------------------------------- +146: [12:26:47] Github #1990: seg fault after RemoveHs +146: [12:26:47] --------------------------------- +146: [12:26:47] Github #2246: Use coordMap when starting embedding from random coords +146: [12:26:50] --------------------------------- +146: [12:26:50] Providing a distance bounds matrix. +146: [12:26:50] --------------------------------- +146: [12:26:50] Disabling fragmentation. +146: [12:26:50] --------------------------------- +146: [12:26:50] Using symmetry in conformation pruning. +146: [12:26:50] --------------------------------- +146: [12:26:50] Force trans amides. +146: [12:26:50] --------------------------------- +146: [12:26:50] test missing Hs warning. +146: [12:26:50] --------------------------------- +146: [12:26:50] basic H bond support. +146: [12:26:50] ******************************************************* +233/236 Test #146: testDistGeomHelpers .................... Passed 153.72 sec 170: =============================================================================== 170: All tests passed (3590 assertions in 35 test cases) 170: -234/236 Test #170: testRascalMCES ......................... Passed 120.67 sec -174: Randomness seeded to: 286458229 +234/236 Test #170: testRascalMCES ......................... Passed 150.77 sec +174: Randomness seeded to: 1751505648 174: =============================================================================== 174: All tests passed (28 assertions in 2 test cases) 174: -235/236 Test #174: testSynthonSpaceRascalSearch ........... Passed 140.63 sec -5: [16:11:19] Finished: testMultipleTimes() -5: [16:11:19] +235/236 Test #174: testSynthonSpaceRascalSearch ........... Passed 202.88 sec +5: [12:45:42] Finished: testMultipleTimes() +5: [12:45:42] 5: ----------------------------------------- -236/236 Test #5: testConcurrentQueue .................... Passed 526.68 sec +236/236 Test #5: testConcurrentQueue .................... Passed 1311.95 sec 100% tests passed, 0 tests failed out of 236 -Total Test time (real) = 526.78 sec +Total Test time (real) = 1312.68 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 @@ -37817,37 +37848,37 @@ 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 DefineCustomRealVariable: 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 errfinish: it's probably a plugin dpkg-shlibdeps: warning: 24 other similar warnings have been skipped (use -v to see them all) -dpkg-shlibdeps: warning: symbol PyExc_ValueError 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_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_KeyError used by debian/librdkit1t64/usr/lib/libRDKitRDBoost.so.1.2025.03.1 found in none of the libraries +dpkg-shlibdeps: warning: symbol PyExc_RuntimeError used by debian/librdkit1t64/usr/lib/libRDKitRDBoost.so.1.2025.03.1 found in none of the libraries dpkg-shlibdeps: warning: symbol PyObject_IsTrue used by debian/librdkit1t64/usr/lib/libRDKitRDBoost.so.1.2025.03.1 found in none of the libraries -dpkg-shlibdeps: warning: symbol PyLong_FromUnsignedLong 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 PyErr_SetString 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 PyErr_SetObject used by debian/librdkit1t64/usr/lib/libRDKitRDBoost.so.1.2025.03.1 found in none of the libraries +dpkg-shlibdeps: warning: symbol PyExc_IndexError used by debian/librdkit1t64/usr/lib/libRDKitRDBoost.so.1.2025.03.1 found in none of the libraries dpkg-shlibdeps: warning: symbol PyLong_FromLong 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_KeyError used by debian/librdkit1t64/usr/lib/libRDKitRDBoost.so.1.2025.03.1 found in none of the libraries +dpkg-shlibdeps: warning: symbol PyLong_FromUnsignedLong used by debian/librdkit1t64/usr/lib/libRDKitRDBoost.so.1.2025.03.1 found in none of the libraries dpkg-shlibdeps: warning: 2 other similar warnings have been skipped (use -v to see them all) 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: Depends field of package rdkit-data: substitution variable ${shlibs:Depends} used, but is not defined dpkg-gencontrol: warning: Provides field of package python3-rdkit: substitution variable ${python3:Provides} used, but is not defined -dpkg-gencontrol: warning: Depends field of package librdkit-dev: substitution variable ${shlibs:Depends} used, but is not defined dpkg-gencontrol: warning: Provides field of package python3-rdkit: substitution variable ${python3:Provides} used, but is not defined dh_md5sums -O--buildsystem=cmake dh_builddeb -O--buildsystem=cmake -dpkg-deb: building package 'rdkit-data' in '../rdkit-data_202503.1-4_all.deb'. -dpkg-deb: building package 'python3-rdkit-dbgsym' in '../python3-rdkit-dbgsym_202503.1-4_arm64.deb'. -dpkg-deb: building package 'postgresql-17-rdkit' in '../postgresql-17-rdkit_202503.1-4_arm64.deb'. dpkg-deb: building package 'librdkit1t64-dbgsym' in '../librdkit1t64-dbgsym_202503.1-4_arm64.deb'. -dpkg-deb: building package 'librdkit-dev' in '../librdkit-dev_202503.1-4_arm64.deb'. -dpkg-deb: building package 'python3-rdkit' in '../python3-rdkit_202503.1-4_arm64.deb'. -dpkg-deb: building package 'librdkit1t64' in '../librdkit1t64_202503.1-4_arm64.deb'. dpkg-deb: building package 'postgresql-17-rdkit-dbgsym' in '../postgresql-17-rdkit-dbgsym_202503.1-4_arm64.deb'. +dpkg-deb: building package 'python3-rdkit-dbgsym' in '../python3-rdkit-dbgsym_202503.1-4_arm64.deb'. +dpkg-deb: building package 'librdkit-dev' in '../librdkit-dev_202503.1-4_arm64.deb'. dpkg-deb: building package 'rdkit-doc' in '../rdkit-doc_202503.1-4_all.deb'. +dpkg-deb: building package 'rdkit-data' in '../rdkit-data_202503.1-4_all.deb'. +dpkg-deb: building package 'librdkit1t64' in '../librdkit1t64_202503.1-4_arm64.deb'. +dpkg-deb: building package 'postgresql-17-rdkit' in '../postgresql-17-rdkit_202503.1-4_arm64.deb'. +dpkg-deb: building package 'python3-rdkit' in '../python3-rdkit_202503.1-4_arm64.deb'. dpkg-genbuildinfo --build=binary -O../rdkit_202503.1-4_arm64.buildinfo dpkg-genchanges --build=binary -O../rdkit_202503.1-4_arm64.changes dpkg-genchanges: info: binary-only upload (no source code included) @@ -37855,12 +37886,14 @@ 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/1849633/tmp/hooks/B01_cleanup starting +I: user script /srv/workspace/pbuilder/1849633/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/4014508 and its subdirectories -I: Current time: Tue Aug 25 16:14:10 -12 2026 -I: pbuilder-time-stamp: 1787717650 +I: removing directory /srv/workspace/pbuilder/1849633 and its subdirectories +I: Current time: Thu Jul 24 13:02:11 +14 2025 +I: pbuilder-time-stamp: 1753311731