Diff of the two buildlogs: -- --- b1/build.log 2025-08-19 14:24:00.113022277 +0000 +++ b2/build.log 2025-08-19 14:47:55.442775170 +0000 @@ -1,6 +1,6 @@ I: pbuilder: network access will be disabled during build -I: Current time: Tue Aug 19 01:59:40 -12 2025 -I: pbuilder-time-stamp: 1755611980 +I: Current time: Tue Sep 22 10:47:17 +14 2026 +I: pbuilder-time-stamp: 1790023637 I: Building the build Environment I: extracting base tarball [/var/cache/pbuilder/forky-reproducible-base.tgz] I: copying local configuration @@ -36,53 +36,85 @@ dpkg-source: info: applying better_enums.patch I: Not using root during the build. I: Installing the build-deps -I: user script /srv/workspace/pbuilder/1886249/tmp/hooks/D02_print_environment starting +I: user script /srv/workspace/pbuilder/2894544/tmp/hooks/D01_modify_environment starting +debug: Running on codethink03-arm64. +I: Changing host+domainname to test build reproducibility +I: Adding a custom variable just for the fun of it... +I: Changing /bin/sh to bash +'/bin/sh' -> '/bin/bash' +lrwxrwxrwx 1 root root 9 Sep 21 20:47 /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/2894544/tmp/hooks/D01_modify_environment finished +I: user script /srv/workspace/pbuilder/2894544/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='forky' - HOME='/root' - HOST_ARCH='arm64' + DIRSTACK=() + DISTRIBUTION=forky + EUID=0 + FUNCNAME=([0]="Echo" [1]="main") + GROUPS=() + HOME=/root + HOSTNAME=i-capture-the-hostname + HOSTTYPE=aarch64 + HOST_ARCH=arm64 IFS=' ' - INVOCATION_ID='798e669ba7824b6cb223fb9d0398b029' - 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='1886249' - PS1='# ' - PS2='> ' + INVOCATION_ID=129e7b0852484f7a8366a4e0d7ca811e + 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=2894544 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.g24aSAKS/pbuilderrc_bZYl --distribution forky --hookdir /etc/pbuilder/first-build-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/forky-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/r-b-build.g24aSAKS/b1 --logfile b1/build.log rdkit_202503.1-5.dsc' - SUDO_GID='109' - SUDO_HOME='/var/lib/jenkins' - SUDO_UID='104' - SUDO_USER='jenkins' - TERM='unknown' - TZ='/usr/share/zoneinfo/Etc/GMT+12' - USER='root' - _='/usr/bin/systemd-run' - http_proxy='http://192.168.101.4:3128' + PWD=/ + SHELL=/bin/bash + SHELLOPTS=braceexpand:errexit:hashall:interactive-comments:posix + SHLVL=3 + SUDO_COMMAND='/usr/bin/timeout -k 24.1h 24h /usr/bin/ionice -c 3 /usr/bin/nice -n 11 /usr/bin/unshare --uts -- /usr/sbin/pbuilder --build --configfile /srv/reproducible-results/rbuild-debian/r-b-build.g24aSAKS/pbuilderrc_vKs0 --distribution forky --hookdir /etc/pbuilder/rebuild-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/forky-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/r-b-build.g24aSAKS/b2 --logfile b2/build.log rdkit_202503.1-5.dsc' + SUDO_GID=109 + SUDO_HOME=/var/lib/jenkins + SUDO_UID=104 + SUDO_USER=jenkins + TERM=unknown + TZ=/usr/share/zoneinfo/Etc/GMT-14 + UID=0 + USER=root + _='I: set' + http_proxy=http://192.168.101.4:3128 I: uname -a - Linux codethink04-arm64 6.12.41+deb13-cloud-arm64 #1 SMP Debian 6.12.41-1 (2025-08-12) aarch64 GNU/Linux + Linux i-capture-the-hostname 6.12.41+deb13-cloud-arm64 #1 SMP Debian 6.12.41-1 (2025-08-12) aarch64 GNU/Linux I: ls -l /bin - lrwxrwxrwx 1 root root 7 Aug 10 12:30 /bin -> usr/bin -I: user script /srv/workspace/pbuilder/1886249/tmp/hooks/D02_print_environment finished + lrwxrwxrwx 1 root root 7 Aug 10 2025 /bin -> usr/bin +I: user script /srv/workspace/pbuilder/2894544/tmp/hooks/D02_print_environment finished -> Attempting to satisfy build-dependencies -> Creating pbuilder-satisfydepends-dummy package Package: pbuilder-satisfydepends-dummy @@ -576,7 +608,7 @@ Get: 369 http://deb.debian.org/debian forky/main arm64 texlive-latex-recommended all 2024.20250309-1 [8745 kB] Get: 370 http://deb.debian.org/debian forky/main arm64 texlive-pictures all 2024.20250309-1 [17.0 MB] Get: 371 http://deb.debian.org/debian forky/main arm64 texlive-latex-extra all 2024.20250309-2 [25.2 MB] -Fetched 399 MB in 2s (242 MB/s) +Fetched 399 MB in 3s (143 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 ... 20004 files and directories currently installed.) @@ -1768,8 +1800,8 @@ Setting up tzdata (2025b-5) ... Current default time zone: 'Etc/UTC' -Local time is now: Tue Aug 19 14:00:39 UTC 2025. -Universal Time is now: Tue Aug 19 14:00:39 UTC 2025. +Local time is now: Mon Sep 21 20:48:25 UTC 2026. +Universal Time is now: Mon Sep 21 20:48:25 UTC 2026. Run 'dpkg-reconfigure tzdata' if you wish to change it. Setting up libboost-atomic1.83.0:arm64 (1.83.0-4.2) ... @@ -1935,11 +1967,6 @@ Setting up pandoc (3.1.11.1+ds-3) ... Setting up libfreetype6:arm64 (2.13.3+dfsg-1) ... Setting up ssl-cert (1.1.3) ... -hostname: Name or service not known -make-ssl-cert: Could not get FQDN, using 'codethink04-arm64'. -make-ssl-cert: You may want to fix your /etc/hosts and/or DNS setup and run -make-ssl-cert: 'make-ssl-cert generate-default-snakeoil --force-overwrite' -make-ssl-cert: again. Setting up libboost-date-time1.83-dev:arm64 (1.83.0-4.2) ... Setting up shared-mime-info (2.4-5+b3) ... Setting up libp11-kit0:arm64 (0.25.5-3) ... @@ -2160,7 +2187,11 @@ Building tag database... -> Finished parsing the build-deps I: Building the package -I: Running cd /build/reproducible-path/rdkit-202503.1/ && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games" HOME="/nonexistent/first-build" dpkg-buildpackage -us -uc -b && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games" HOME="/nonexistent/first-build" dpkg-genchanges -S > ../rdkit_202503.1-5_source.changes +I: user script /srv/workspace/pbuilder/2894544/tmp/hooks/A99_set_merged_usr starting +Not re-configuring usrmerge for forky +I: user script /srv/workspace/pbuilder/2894544/tmp/hooks/A99_set_merged_usr finished +hostname: Name or service not known +I: Running cd /build/reproducible-path/rdkit-202503.1/ && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/i/capture/the/path" HOME="/nonexistent/second-build" dpkg-buildpackage -us -uc -b && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/i/capture/the/path" HOME="/nonexistent/second-build" dpkg-genchanges -S > ../rdkit_202503.1-5_source.changes dpkg-buildpackage: info: source package rdkit dpkg-buildpackage: info: source version 202503.1-5 dpkg-buildpackage: info: source distribution unstable @@ -2285,7 +2316,7 @@ This warning is for project developers. Use -Wno-dev to suppress it. -- Configuring done (3.3s) --- Generating done (0.9s) +-- Generating done (1.0s) CMake Warning: Manually-specified variables were not used by the project: @@ -2367,15 +2398,15 @@ 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 Code/RDGeneral/CMakeFiles/rdkitCatch.dir/build.make Code/RDGeneral/CMakeFiles/rdkitCatch.dir/depend -make -f Code/RDStreams/CMakeFiles/RDStreams.dir/build.make Code/RDStreams/CMakeFiles/RDStreams.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/coordgen_support.dir/DependInfo.cmake "--color=" +make -f Code/RDStreams/CMakeFiles/RDStreams.dir/build.make Code/RDStreams/CMakeFiles/RDStreams.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/RDGeneral.dir/DependInfo.cmake "--color=" -cd /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202503.1 /build/reproducible-path/rdkit-202503.1/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/coordgen_support.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/External/RingFamilies /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/External/RingFamilies /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/External/RingFamilies/CMakeFiles/ringdecomposerlib_support.dir/DependInfo.cmake "--color=" -make -f Code/ML/Cluster/Murtagh/CMakeFiles/hc.dir/build.make Code/ML/Cluster/Murtagh/CMakeFiles/hc.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu' +make -f Code/ML/Cluster/Murtagh/CMakeFiles/hc.dir/build.make Code/ML/Cluster/Murtagh/CMakeFiles/hc.dir/depend cd /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202503.1 /build/reproducible-path/rdkit-202503.1/External/GA /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/External/GA /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/External/GA/CMakeFiles/ga.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/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/rdkitCatch.dir/DependInfo.cmake "--color=" @@ -2384,27 +2415,24 @@ 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/ML/Cluster/Murtagh /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/ML/Cluster/Murtagh /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/ML/Cluster/Murtagh/CMakeFiles/hc.dir/DependInfo.cmake "--color=" make[4]: Leaving 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/build -make[4]: Leaving 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[4]: Leaving directory '/build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu' make[4]: 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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 -f Code/RDGeneral/CMakeFiles/RDGeneral.dir/build.make Code/RDGeneral/CMakeFiles/RDGeneral.dir/build make -f External/RingFamilies/CMakeFiles/ringdecomposerlib_support.dir/build.make External/RingFamilies/CMakeFiles/ringdecomposerlib_support.dir/build make -f External/GA/CMakeFiles/ga.dir/build.make External/GA/CMakeFiles/ga.dir/build -make -f Code/RDStreams/CMakeFiles/RDStreams.dir/build.make Code/RDStreams/CMakeFiles/RDStreams.dir/build -make[4]: Entering directory '/build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu' -make -f Code/ML/Cluster/Murtagh/CMakeFiles/hc.dir/build.make Code/ML/Cluster/Murtagh/CMakeFiles/hc.dir/build make[4]: Entering directory '/build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu' make[4]: Nothing to be done for 'External/CoordGen/CMakeFiles/coordgen_support.dir/build'. make[4]: Leaving directory '/build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu' +make -f Code/RDGeneral/CMakeFiles/rdkitCatch.dir/build.make Code/RDGeneral/CMakeFiles/rdkitCatch.dir/build +make[4]: Leaving directory '/build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu' +make[4]: Entering directory '/build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu' +cd /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/External/INCHI-API && /usr/bin/cmake -E copy /build/reproducible-path/rdkit-202503.1/External/INCHI-API/python/inchi.py /build/reproducible-path/rdkit-202503.1/rdkit/Chem/inchi.py +make -f Code/RDStreams/CMakeFiles/RDStreams.dir/build.make Code/RDStreams/CMakeFiles/RDStreams.dir/build make[4]: Entering directory '/build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu' make[4]: Nothing to be done for 'External/RingFamilies/CMakeFiles/ringdecomposerlib_support.dir/build'. make[4]: Leaving directory 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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 -DRDKIT_DYN_LINK -DRDKIT_RDSTREAMS_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_BUILD_XYZ2MOL_SUPPORT -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DRDStreams_EXPORTS -I/build/reproducible-path/rdkit-202503.1/External -I/build/reproducible-path/rdkit-202503.1/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT 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-fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -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/RDLog.cpp.o -MF CMakeFiles/RDGeneral.dir/RDLog.cpp.o.d -o CMakeFiles/RDGeneral.dir/RDLog.cpp.o -c /build/reproducible-path/rdkit-202503.1/Code/RDGeneral/RDLog.cpp -[ 1%] 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 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-I/build/reproducible-path/rdkit-202503.1/External -I/build/reproducible-path/rdkit-202503.1/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/DataStructs/CMakeFiles/DataStructs.dir/BitVect.cpp.o -MF CMakeFiles/DataStructs.dir/BitVect.cpp.o.d -o CMakeFiles/DataStructs.dir/BitVect.cpp.o -c /build/reproducible-path/rdkit-202503.1/Code/DataStructs/BitVect.cpp [ 3%] Building CXX object Code/Query/CMakeFiles/testQuery.dir/test.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 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-I/build/reproducible-path/rdkit-202503.1/External -I/build/reproducible-path/rdkit-202503.1/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/DataStructs/CMakeFiles/DataStructs.dir/SparseBitVect.cpp.o -MF CMakeFiles/DataStructs.dir/SparseBitVect.cpp.o.d -o CMakeFiles/DataStructs.dir/SparseBitVect.cpp.o -c /build/reproducible-path/rdkit-202503.1/Code/DataStructs/SparseBitVect.cpp +[ 4%] Linking CXX executable testConcurrentQueue +cd /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/RDGeneral && /usr/bin/cmake -E cmake_link_script CMakeFiles/testConcurrentQueue.dir/link.txt --verbose=1 make -f 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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/testConcurrentQueue.dir/link.d CMakeFiles/testConcurrentQueue.dir/testConcurrentQueue.cpp.o -o testConcurrentQueue ../../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' [ 4%] Built target testConcurrentQueue -[ 5%] Building CXX object Code/DataStructs/CMakeFiles/DataStructs.dir/ExplicitBitVect.cpp.o -cd /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/DataStructs && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK 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Code/DataStructs/CMakeFiles/DataStructs.dir/ExplicitBitVect.cpp.o -MF CMakeFiles/DataStructs.dir/ExplicitBitVect.cpp.o.d -o CMakeFiles/DataStructs.dir/ExplicitBitVect.cpp.o -c /build/reproducible-path/rdkit-202503.1/Code/DataStructs/ExplicitBitVect.cpp -[ 5%] Building CXX object Code/Catalogs/CMakeFiles/Catalogs.dir/CatalogParams.cpp.o +[ 4%] Building CXX object Code/Catalogs/CMakeFiles/Catalogs.dir/CatalogParams.cpp.o cd /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/Catalogs && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DCatalogs_EXPORTS -DRDKIT_CATALOGS_BUILD -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_BUILD_XYZ2MOL_SUPPORT -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202503.1/External -I/build/reproducible-path/rdkit-202503.1/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/Catalogs/CMakeFiles/Catalogs.dir/CatalogParams.cpp.o -MF CMakeFiles/Catalogs.dir/CatalogParams.cpp.o.d -o CMakeFiles/Catalogs.dir/CatalogParams.cpp.o -c /build/reproducible-path/rdkit-202503.1/Code/Catalogs/CatalogParams.cpp -[ 5%] Linking CXX shared library ../../../lib/libRDKitEigenSolvers.so +[ 4%] Linking CXX shared library ../../../lib/libRDKitEigenSolvers.so cd /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/Numerics/EigenSolvers && /usr/bin/cmake -E cmake_link_script CMakeFiles/EigenSolvers.dir/link.txt --verbose=1 +[ 5%] Building CXX object Code/DataStructs/CMakeFiles/DataStructs.dir/ExplicitBitVect.cpp.o +cd /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/DataStructs && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DDataStructs_EXPORTS -DRDKIT_DATASTRUCTS_BUILD -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_BUILD_XYZ2MOL_SUPPORT -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202503.1/External -I/build/reproducible-path/rdkit-202503.1/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong 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../../../lib/libRDKitEigenSolvers.so.1.2025.03.1 CMakeFiles/EigenSolvers.dir/PowerEigenSolver.cpp.o ../../../lib/libRDKitRDGeneral.so.1.2025.03.1 /usr/lib/aarch64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl cd /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/Numerics/EigenSolvers && /usr/bin/cmake -E cmake_symlink_library ../../../lib/libRDKitEigenSolvers.so.1.2025.03.1 ../../../lib/libRDKitEigenSolvers.so.1 ../../../lib/libRDKitEigenSolvers.so make[4]: Leaving directory '/build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu' [ 5%] Built target EigenSolvers +[ 5%] Building CXX object Code/SimDivPickers/CMakeFiles/SimDivPickers.dir/MaxMinPicker.cpp.o +cd /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/SimDivPickers && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK 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CMakeFiles/SimDivPickers.dir/MaxMinPicker.cpp.o.d -o CMakeFiles/SimDivPickers.dir/MaxMinPicker.cpp.o -c /build/reproducible-path/rdkit-202503.1/Code/SimDivPickers/MaxMinPicker.cpp +[ 5%] Linking CXX executable logTestsCatch +cd /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/RDGeneral && /usr/bin/cmake -E cmake_link_script CMakeFiles/logTestsCatch.dir/link.txt --verbose=1 +/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/logTestsCatch.dir/link.d CMakeFiles/logTestsCatch.dir/catch_logs.cpp.o -o logTestsCatch librdkitCatch.a ../../lib/libRDKitRDGeneral.so.1.2025.03.1 /usr/lib/libCatch2.a /usr/lib/aarch64-linux-gnu/libboost_system.so.1.83.0 /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' +[ 5%] Built target logTestsCatch [ 6%] Building CXX object Code/Catalogs/CMakeFiles/Catalogs.dir/CatalogEntry.cpp.o cd /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/Catalogs && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DCatalogs_EXPORTS -DRDKIT_CATALOGS_BUILD -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_BUILD_XYZ2MOL_SUPPORT -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202503.1/External -I/build/reproducible-path/rdkit-202503.1/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/Catalogs/CMakeFiles/Catalogs.dir/CatalogEntry.cpp.o -MF CMakeFiles/Catalogs.dir/CatalogEntry.cpp.o.d -o CMakeFiles/Catalogs.dir/CatalogEntry.cpp.o -c /build/reproducible-path/rdkit-202503.1/Code/Catalogs/CatalogEntry.cpp +[ 6%] Building CXX object Code/SimDivPickers/CMakeFiles/SimDivPickers.dir/HierarchicalClusterPicker.cpp.o +cd /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/SimDivPickers && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK 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CMakeFiles/SimDivPickers.dir/HierarchicalClusterPicker.cpp.o.d -o CMakeFiles/SimDivPickers.dir/HierarchicalClusterPicker.cpp.o -c /build/reproducible-path/rdkit-202503.1/Code/SimDivPickers/HierarchicalClusterPicker.cpp [ 6%] Building CXX object Code/DataStructs/CMakeFiles/DataStructs.dir/Utils.cpp.o cd /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/DataStructs && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DDataStructs_EXPORTS -DRDKIT_DATASTRUCTS_BUILD -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_BUILD_XYZ2MOL_SUPPORT -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202503.1/External -I/build/reproducible-path/rdkit-202503.1/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/DataStructs/CMakeFiles/DataStructs.dir/Utils.cpp.o -MF CMakeFiles/DataStructs.dir/Utils.cpp.o.d -o CMakeFiles/DataStructs.dir/Utils.cpp.o -c /build/reproducible-path/rdkit-202503.1/Code/DataStructs/Utils.cpp [ 6%] Linking CXX shared library ../../lib/libRDKitCatalogs.so @@ -2617,40 +2657,31 @@ cd /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/Catalogs && /usr/bin/cmake -E cmake_symlink_library ../../lib/libRDKitCatalogs.so.1.2025.03.1 ../../lib/libRDKitCatalogs.so.1 ../../lib/libRDKitCatalogs.so make[4]: Leaving directory 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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/DataStructs/CMakeFiles/DataStructs.dir/base64.cpp.o -MF CMakeFiles/DataStructs.dir/base64.cpp.o.d -o CMakeFiles/DataStructs.dir/base64.cpp.o -c /build/reproducible-path/rdkit-202503.1/Code/DataStructs/base64.cpp [ 6%] Building CXX object Code/DataStructs/CMakeFiles/DataStructs.dir/BitOps.cpp.o cd /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/DataStructs && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DDataStructs_EXPORTS -DRDKIT_DATASTRUCTS_BUILD -DRDKIT_DYN_LINK 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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/DataStructs/CMakeFiles/DataStructs.dir/MultiFPBReader.cpp.o -MF CMakeFiles/DataStructs.dir/MultiFPBReader.cpp.o.d -o CMakeFiles/DataStructs.dir/MultiFPBReader.cpp.o -c /build/reproducible-path/rdkit-202503.1/Code/DataStructs/MultiFPBReader.cpp +[ 6%] Building CXX object Code/DataStructs/CMakeFiles/DataStructs.dir/RealValueVect.cpp.o +cd /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/DataStructs && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK 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CMakeFiles/DataStructs.dir/RealValueVect.cpp.o -c /build/reproducible-path/rdkit-202503.1/Code/DataStructs/RealValueVect.cpp [ 6%] Linking CXX shared library ../../lib/libRDKitRDBoost.so cd /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/RDBoost && /usr/bin/cmake -E cmake_link_script CMakeFiles/RDBoost.dir/link.txt --verbose=1 /usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,--dependency-file=CMakeFiles/RDBoost.dir/link.d -Wl,-z,relro -Wl,-z,now -shared -Wl,-soname,libRDKitRDBoost.so.1 -o ../../lib/libRDKitRDBoost.so.1.2025.03.1 CMakeFiles/RDBoost.dir/Wrap.cpp.o ../../lib/libRDKitRDGeneral.so.1.2025.03.1 /usr/lib/aarch64-linux-gnu/libboost_system.so.1.83.0 /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/libboost_numpy313.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_python313.so.1.83.0 cd /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/RDBoost && /usr/bin/cmake -E cmake_symlink_library ../../lib/libRDKitRDBoost.so.1.2025.03.1 ../../lib/libRDKitRDBoost.so.1 ../../lib/libRDKitRDBoost.so make[4]: Leaving directory '/build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu' [ 6%] Built target RDBoost -[ 6%] Building CXX object Code/DataStructs/CMakeFiles/DataStructs.dir/MultiFPBReader.cpp.o -cd /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/DataStructs && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DDataStructs_EXPORTS -DRDKIT_DATASTRUCTS_BUILD -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_BUILD_XYZ2MOL_SUPPORT -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202503.1/External -I/build/reproducible-path/rdkit-202503.1/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/DataStructs/CMakeFiles/DataStructs.dir/MultiFPBReader.cpp.o -MF CMakeFiles/DataStructs.dir/MultiFPBReader.cpp.o.d -o CMakeFiles/DataStructs.dir/MultiFPBReader.cpp.o -c 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make[4]: Entering directory '/build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu' [ 6%] Building CXX object Code/RDBoost/Wrap/CMakeFiles/rdBase.dir/RDBase.cpp.o cd /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/RDBoost/Wrap && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_NUMPY_DYN_LINK -DBOOST_NUMPY_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_BUILD_XYZ2MOL_SUPPORT -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DrdBase_EXPORTS -I/build/reproducible-path/rdkit-202503.1/External -I/build/reproducible-path/rdkit-202503.1/Code -I/usr/lib/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/RDBoost/Wrap/CMakeFiles/rdBase.dir/RDBase.cpp.o -MF CMakeFiles/rdBase.dir/RDBase.cpp.o.d -o CMakeFiles/rdBase.dir/RDBase.cpp.o -c /build/reproducible-path/rdkit-202503.1/Code/RDBoost/Wrap/RDBase.cpp +[ 6%] Linking CXX executable dictTestsCatch +cd /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/RDGeneral && /usr/bin/cmake -E cmake_link_script CMakeFiles/dictTestsCatch.dir/link.txt --verbose=1 [ 6%] Linking CXX executable testQuery cd 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/build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/DataStructs && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DDataStructs_EXPORTS -DRDKIT_DATASTRUCTS_BUILD -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_BUILD_XYZ2MOL_SUPPORT -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202503.1/External -I/build/reproducible-path/rdkit-202503.1/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/DataStructs/CMakeFiles/DataStructs.dir/RealValueVect.cpp.o -MF CMakeFiles/DataStructs.dir/RealValueVect.cpp.o.d -o CMakeFiles/DataStructs.dir/RealValueVect.cpp.o -c /build/reproducible-path/rdkit-202503.1/Code/DataStructs/RealValueVect.cpp 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/testQuery.dir/link.d CMakeFiles/testQuery.dir/test.cpp.o -o testQuery ../../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 [ 6%] Built target dictTestsCatch -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/testQuery.dir/link.d CMakeFiles/testQuery.dir/test.cpp.o -o testQuery ../../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/ML/Cluster/Murtagh/CMakeFiles/Clustering.dir/build.make 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make[4]: Entering directory '/build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu' +[ 6%] Built target testQuery [ 6%] Building CXX object Code/ML/Cluster/Murtagh/CMakeFiles/Clustering.dir/Clustering.cpp.o cd /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/ML/Cluster/Murtagh && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_NUMPY_DYN_LINK -DBOOST_NUMPY_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DClustering_EXPORTS -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_BUILD_XYZ2MOL_SUPPORT -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202503.1/External -I/build/reproducible-path/rdkit-202503.1/Code -I/usr/lib/aarch64-linux-gnu/python3-numpy/numpy/_core/include -isystem /usr/include/python3.13 -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/ML/Cluster/Murtagh/CMakeFiles/Clustering.dir/Clustering.cpp.o -MF CMakeFiles/Clustering.dir/Clustering.cpp.o.d -o CMakeFiles/Clustering.dir/Clustering.cpp.o -c /build/reproducible-path/rdkit-202503.1/Code/ML/Cluster/Murtagh/Clustering.cpp [ 6%] Linking CXX shared library ../../lib/libRDKitSimDivPickers.so @@ -2701,21 +2732,18 @@ /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 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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/DataStructs && /usr/bin/cmake -E cmake_symlink_library ../../lib/libRDKitDataStructs.so.1.2025.03.1 ../../lib/libRDKitDataStructs.so.1 ../../lib/libRDKitDataStructs.so make[4]: Leaving directory '/build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu' [ 7%] Built target DataStructs +[ 7%] Linking CXX shared module ../../../../rdkit/ML/Cluster/Clustering.so make -f Code/Geometry/CMakeFiles/RDGeometryLib.dir/build.make Code/Geometry/CMakeFiles/RDGeometryLib.dir/depend make -f Code/DataStructs/CMakeFiles/testDataStructs.dir/build.make Code/DataStructs/CMakeFiles/testDataStructs.dir/depend make -f Code/DataStructs/CMakeFiles/testFPB.dir/build.make Code/DataStructs/CMakeFiles/testFPB.dir/depend make -f Code/DataStructs/CMakeFiles/testMultiFPB.dir/build.make Code/DataStructs/CMakeFiles/testMultiFPB.dir/depend +cd /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/ML/Cluster/Murtagh && /usr/bin/cmake -E cmake_link_script CMakeFiles/Clustering.dir/link.txt --verbose=1 make -f Code/DataStructs/CMakeFiles/catchDataStructs.dir/build.make Code/DataStructs/CMakeFiles/catchDataStructs.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu' cd /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202503.1 /build/reproducible-path/rdkit-202503.1/Code/Geometry /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/Geometry /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/Geometry/CMakeFiles/RDGeometryLib.dir/DependInfo.cmake "--color=" @@ -2724,104 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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/SparseIntVect.cpp.o -MF CMakeFiles/cDataStructs.dir/SparseIntVect.cpp.o.d -o CMakeFiles/cDataStructs.dir/SparseIntVect.cpp.o -c /build/reproducible-path/rdkit-202503.1/Code/DataStructs/Wrap/SparseIntVect.cpp +[ 8%] Linking CXX executable testMultiFPB +cd /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/DataStructs && /usr/bin/cmake -E cmake_link_script CMakeFiles/testMultiFPB.dir/link.txt --verbose=1 +[ 8%] Linking CXX shared 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/DataStructs/Wrap/CMakeFiles/cDataStructs.dir/DiscreteValueVect.cpp.o -MF CMakeFiles/cDataStructs.dir/DiscreteValueVect.cpp.o.d -o CMakeFiles/cDataStructs.dir/DiscreteValueVect.cpp.o -c /build/reproducible-path/rdkit-202503.1/Code/DataStructs/Wrap/DiscreteValueVect.cpp [ 8%] Linking CXX shared module ../../../../rdkit/DataManip/Metric/rdMetricMatrixCalc.so cd /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/DataManip/MetricMatrixCalc/Wrap && 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../../../../lib/libRDKitRDBoost.so.1.2025.03.1 /usr/lib/aarch64-linux-gnu/libboost_numpy313.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_python313.so.1.83.0 ../../../../lib/libRDKitRDGeneral.so.1.2025.03.1 /usr/lib/aarch64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl make[4]: Leaving directory '/build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu' [ 8%] Built target rdMetricMatrixCalc -[ 8%] Building CXX object Code/SimDivPickers/Wrap/CMakeFiles/rdSimDivPickers.dir/HierarchicalClusterPicker.cpp.o -cd /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/SimDivPickers/Wrap && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_NUMPY_DYN_LINK -DBOOST_NUMPY_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK 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-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 -[ 8%] Building CXX object Code/ML/InfoTheory/Wrap/CMakeFiles/rdInfoTheory.dir/rdInfoTheory.cpp.o -cd /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/ML/InfoTheory/Wrap && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_NUMPY_DYN_LINK -DBOOST_NUMPY_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_BUILD_XYZ2MOL_SUPPORT -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DrdInfoTheory_EXPORTS -I/build/reproducible-path/rdkit-202503.1/External -I/build/reproducible-path/rdkit-202503.1/Code -I/usr/lib/aarch64-linux-gnu/python3-numpy/numpy/_core/include -isystem /usr/include/python3.13 -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/ML/InfoTheory/Wrap/CMakeFiles/rdInfoTheory.dir/rdInfoTheory.cpp.o -MF CMakeFiles/rdInfoTheory.dir/rdInfoTheory.cpp.o.d -o CMakeFiles/rdInfoTheory.dir/rdInfoTheory.cpp.o -c /build/reproducible-path/rdkit-202503.1/Code/ML/InfoTheory/Wrap/rdInfoTheory.cpp -[ 8%] Building CXX object Code/DataStructs/Wrap/CMakeFiles/cDataStructs.dir/RealValueVect.cpp.o -cd /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/DataStructs/Wrap && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_NUMPY_DYN_LINK -DBOOST_NUMPY_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_BUILD_XYZ2MOL_SUPPORT -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DcDataStructs_EXPORTS -I/build/reproducible-path/rdkit-202503.1/External -I/build/reproducible-path/rdkit-202503.1/Code -I/usr/lib/aarch64-linux-gnu/python3-numpy/numpy/_core/include -isystem /usr/include/python3.13 -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -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/RealValueVect.cpp.o -MF CMakeFiles/cDataStructs.dir/RealValueVect.cpp.o.d -o CMakeFiles/cDataStructs.dir/RealValueVect.cpp.o -c /build/reproducible-path/rdkit-202503.1/Code/DataStructs/Wrap/RealValueVect.cpp +[ 8%] Built target rdSimDivPickers +[ 8%] Building CXX object Code/DataStructs/Wrap/CMakeFiles/cDataStructs.dir/wrap_BitOps.cpp.o +cd /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/DataStructs/Wrap && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_NUMPY_DYN_LINK -DBOOST_NUMPY_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB 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CMakeFiles/cDataStructs.dir/wrap_BitOps.cpp.o.d -o CMakeFiles/cDataStructs.dir/wrap_BitOps.cpp.o -c /build/reproducible-path/rdkit-202503.1/Code/DataStructs/Wrap/wrap_BitOps.cpp [ 8%] Linking CXX shared library ../../lib/libRDKitRDGeometryLib.so cd /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/Geometry && /usr/bin/cmake -E cmake_link_script CMakeFiles/RDGeometryLib.dir/link.txt --verbose=1 /usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,--dependency-file=CMakeFiles/RDGeometryLib.dir/link.d -Wl,-z,relro -Wl,-z,now -shared -Wl,-soname,libRDKitRDGeometryLib.so.1 -o ../../lib/libRDKitRDGeometryLib.so.1.2025.03.1 CMakeFiles/RDGeometryLib.dir/point.cpp.o CMakeFiles/RDGeometryLib.dir/Transform2D.cpp.o CMakeFiles/RDGeometryLib.dir/Transform3D.cpp.o CMakeFiles/RDGeometryLib.dir/UniformGrid3D.cpp.o CMakeFiles/RDGeometryLib.dir/UniformRealValueGrid3D.cpp.o CMakeFiles/RDGeometryLib.dir/GridUtils.cpp.o ../../lib/libRDKitDataStructs.so.1.2025.03.1 ../../lib/libRDKitRDGeneral.so.1.2025.03.1 /usr/lib/aarch64-linux-gnu/libboost_system.so.1.83.0 /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/Geometry && /usr/bin/cmake -E cmake_symlink_library ../../lib/libRDKitRDGeometryLib.so.1.2025.03.1 ../../lib/libRDKitRDGeometryLib.so.1 ../../lib/libRDKitRDGeometryLib.so make[4]: Leaving directory '/build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu' [ 8%] Built target RDGeometryLib -[ 8%] Building CXX object Code/DataStructs/Wrap/CMakeFiles/cDataStructs.dir/wrap_SparseBV.cpp.o -cd 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-fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/DataStructs/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 -[ 8%] Building CXX object Code/DataStructs/Wrap/CMakeFiles/cDataStructs.dir/wrap_ExplicitBV.cpp.o -cd /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/DataStructs/Wrap && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_NUMPY_DYN_LINK -DBOOST_NUMPY_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_BUILD_XYZ2MOL_SUPPORT -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DcDataStructs_EXPORTS -I/build/reproducible-path/rdkit-202503.1/External -I/build/reproducible-path/rdkit-202503.1/Code -I/usr/lib/aarch64-linux-gnu/python3-numpy/numpy/_core/include -isystem /usr/include/python3.13 -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -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 -[ 8%] Linking CXX shared module ../../../rdkit/SimDivFilters/rdSimDivPickers.so -cd /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/SimDivPickers/Wrap && /usr/bin/cmake -E cmake_link_script CMakeFiles/rdSimDivPickers.dir/link.txt --verbose=1 -/usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -g -fwrapv -O2 -Wl,--dependency-file=CMakeFiles/rdSimDivPickers.dir/link.d -Wl,-z,relro -Wl,-z,now -shared -o ../../../rdkit/SimDivFilters/rdSimDivPickers.so CMakeFiles/rdSimDivPickers.dir/MaxMinPicker.cpp.o CMakeFiles/rdSimDivPickers.dir/LeaderPicker.cpp.o CMakeFiles/rdSimDivPickers.dir/HierarchicalClusterPicker.cpp.o CMakeFiles/rdSimDivPickers.dir/rdSimDivPickers.cpp.o ../../../lib/libRDKitSimDivPickers.so.1.2025.03.1 ../../../lib/libRDKitDataStructs.so.1.2025.03.1 ../../../lib/libRDKitRDBoost.so.1.2025.03.1 ../../../lib/libRDKithc.so.1.2025.03.1 /usr/lib/aarch64-linux-gnu/libboost_numpy313.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_python313.so.1.83.0 ../../../lib/libRDKitRDGeneral.so.1.2025.03.1 /usr/lib/aarch64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl -make[4]: Leaving directory '/build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu' -[ 8%] Built target rdSimDivPickers make -f Code/GraphMol/CMakeFiles/GraphMol.dir/build.make Code/GraphMol/CMakeFiles/GraphMol.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/GraphMol.dir/DependInfo.cmake "--color=" @@ -2893,10 +2926,6 @@ make[4]: Entering directory '/build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu' [ 9%] Building CXX object Code/GraphMol/CMakeFiles/GraphMol.dir/Atom.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 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../../../lib/libRDKitAlignment.so.1.2025.03.1 ../../../lib/libRDKitAlignment.so.1 ../../../lib/libRDKitAlignment.so make[4]: Leaving directory '/build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu' -[ 11%] Built target testDataStructs +[ 11%] Built target Alignment make -f Code/Geometry/CMakeFiles/testTransforms.dir/build.make Code/Geometry/CMakeFiles/testTransforms.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu' cd /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202503.1 /build/reproducible-path/rdkit-202503.1/Code/Geometry /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/Geometry /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/Geometry/CMakeFiles/testTransforms.dir/DependInfo.cmake "--color=" @@ -2934,16 +2966,6 @@ make[4]: Entering directory '/build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu' [ 11%] Building CXX object Code/Geometry/CMakeFiles/testTransforms.dir/testTransforms.cpp.o cd /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/Geometry && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_BUILD_XYZ2MOL_SUPPORT -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202503.1/External -I/build/reproducible-path/rdkit-202503.1/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/Geometry/CMakeFiles/testTransforms.dir/testTransforms.cpp.o -MF CMakeFiles/testTransforms.dir/testTransforms.cpp.o.d -o CMakeFiles/testTransforms.dir/testTransforms.cpp.o -c /build/reproducible-path/rdkit-202503.1/Code/Geometry/testTransforms.cpp -[ 11%] Linking CXX shared library ../../../lib/libRDKitAlignment.so -cd /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/Numerics/Alignment && /usr/bin/cmake -E cmake_link_script CMakeFiles/Alignment.dir/link.txt --verbose=1 -/usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,--dependency-file=CMakeFiles/Alignment.dir/link.d -Wl,-z,relro -Wl,-z,now -shared -Wl,-soname,libRDKitAlignment.so.1 -o ../../../lib/libRDKitAlignment.so.1.2025.03.1 CMakeFiles/Alignment.dir/AlignPoints.cpp.o ../../../lib/libRDKitRDGeometryLib.so.1.2025.03.1 ../../../lib/libRDKitDataStructs.so.1.2025.03.1 ../../../lib/libRDKitRDGeneral.so.1.2025.03.1 /usr/lib/aarch64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl -cd /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/Numerics/Alignment && /usr/bin/cmake -E cmake_symlink_library ../../../lib/libRDKitAlignment.so.1.2025.03.1 ../../../lib/libRDKitAlignment.so.1 ../../../lib/libRDKitAlignment.so -make[4]: Leaving directory '/build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu' -[ 11%] Built target Alignment -[ 11%] Building CXX object Code/GraphMol/CMakeFiles/GraphMol.dir/Bond.cpp.o -cd /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DGraphMol_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_GRAPHMOL_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_BUILD_XYZ2MOL_SUPPORT -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202503.1/External -I/build/reproducible-path/rdkit-202503.1/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/CMakeFiles/GraphMol.dir/Bond.cpp.o -MF CMakeFiles/GraphMol.dir/Bond.cpp.o.d -o CMakeFiles/GraphMol.dir/Bond.cpp.o -c /build/reproducible-path/rdkit-202503.1/Code/GraphMol/Bond.cpp -[ 11%] Building CXX object Code/GraphMol/CMakeFiles/GraphMol.dir/MolOps.cpp.o -cd /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DGraphMol_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_GRAPHMOL_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_BUILD_XYZ2MOL_SUPPORT -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202503.1/External -I/build/reproducible-path/rdkit-202503.1/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/CMakeFiles/GraphMol.dir/MolOps.cpp.o -MF CMakeFiles/GraphMol.dir/MolOps.cpp.o.d -o CMakeFiles/GraphMol.dir/MolOps.cpp.o -c /build/reproducible-path/rdkit-202503.1/Code/GraphMol/MolOps.cpp make -f Code/Geometry/CMakeFiles/testGrid.dir/build.make Code/Geometry/CMakeFiles/testGrid.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu' cd /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202503.1 /build/reproducible-path/rdkit-202503.1/Code/Geometry /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/Geometry /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/Geometry/CMakeFiles/testGrid.dir/DependInfo.cmake "--color=" @@ -2952,13 +2974,15 @@ make[4]: Entering directory '/build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu' [ 11%] Building CXX object Code/Geometry/CMakeFiles/testGrid.dir/testGrid.cpp.o cd /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/Geometry && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_BUILD_XYZ2MOL_SUPPORT -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202503.1/External -I/build/reproducible-path/rdkit-202503.1/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/Geometry/CMakeFiles/testGrid.dir/testGrid.cpp.o -MF CMakeFiles/testGrid.dir/testGrid.cpp.o.d -o CMakeFiles/testGrid.dir/testGrid.cpp.o -c /build/reproducible-path/rdkit-202503.1/Code/Geometry/testGrid.cpp -[ 11%] Linking CXX executable testTransforms -cd /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/Geometry && /usr/bin/cmake -E cmake_link_script CMakeFiles/testTransforms.dir/link.txt --verbose=1 -/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/testTransforms.dir/link.d CMakeFiles/testTransforms.dir/testTransforms.cpp.o -o testTransforms ../../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 +[ 11%] Building CXX object Code/GraphMol/CMakeFiles/GraphMol.dir/Bond.cpp.o +cd /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DGraphMol_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_GRAPHMOL_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_BUILD_XYZ2MOL_SUPPORT -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202503.1/External -I/build/reproducible-path/rdkit-202503.1/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/CMakeFiles/GraphMol.dir/Bond.cpp.o -MF CMakeFiles/GraphMol.dir/Bond.cpp.o.d -o CMakeFiles/GraphMol.dir/Bond.cpp.o -c /build/reproducible-path/rdkit-202503.1/Code/GraphMol/Bond.cpp +[ 11%] Linking CXX executable testDataStructs +cd /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/DataStructs && /usr/bin/cmake -E cmake_link_script CMakeFiles/testDataStructs.dir/link.txt --verbose=1 +/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/testDataStructs.dir/link.d CMakeFiles/testDataStructs.dir/testDatastructs.cpp.o -o testDataStructs ../../lib/libRDKitDataStructs.so.1.2025.03.1 ../../lib/libRDKitRDGeneral.so.1.2025.03.1 /usr/lib/aarch64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl make[4]: Leaving directory '/build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu' -[ 11%] Built target testTransforms -[ 11%] Building CXX object Code/GraphMol/CMakeFiles/GraphMol.dir/FindRings.cpp.o -cd /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DGraphMol_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_GRAPHMOL_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_BUILD_XYZ2MOL_SUPPORT -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202503.1/External -I/build/reproducible-path/rdkit-202503.1/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/CMakeFiles/GraphMol.dir/FindRings.cpp.o -MF CMakeFiles/GraphMol.dir/FindRings.cpp.o.d -o CMakeFiles/GraphMol.dir/FindRings.cpp.o -c /build/reproducible-path/rdkit-202503.1/Code/GraphMol/FindRings.cpp +[ 11%] Built target testDataStructs +[ 11%] Building CXX object Code/GraphMol/CMakeFiles/GraphMol.dir/MolOps.cpp.o +cd /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DGraphMol_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_GRAPHMOL_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_BUILD_XYZ2MOL_SUPPORT -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202503.1/External -I/build/reproducible-path/rdkit-202503.1/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/CMakeFiles/GraphMol.dir/MolOps.cpp.o -MF CMakeFiles/GraphMol.dir/MolOps.cpp.o.d -o CMakeFiles/GraphMol.dir/MolOps.cpp.o -c /build/reproducible-path/rdkit-202503.1/Code/GraphMol/MolOps.cpp make -f Code/Geometry/CMakeFiles/testRealValueGrid.dir/build.make Code/Geometry/CMakeFiles/testRealValueGrid.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu' cd /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202503.1 /build/reproducible-path/rdkit-202503.1/Code/Geometry /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/Geometry /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/Geometry/CMakeFiles/testRealValueGrid.dir/DependInfo.cmake "--color=" @@ -2975,10 +2999,6 @@ make[4]: Entering directory '/build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu' [ 12%] Building CXX object Code/Geometry/CMakeFiles/geometryTestsCatch.dir/catch_tests.cpp.o cd /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/Geometry && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_BUILD_XYZ2MOL_SUPPORT -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202503.1/External -I/build/reproducible-path/rdkit-202503.1/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security 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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/Geometry/Wrap/CMakeFiles/rdGeometry.dir/Point.cpp.o -MF CMakeFiles/rdGeometry.dir/Point.cpp.o.d -o CMakeFiles/rdGeometry.dir/Point.cpp.o -c /build/reproducible-path/rdkit-202503.1/Code/Geometry/Wrap/Point.cpp -/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) { - | ~~~~~~~~~~~~~^~~ +[ 12%] Linking CXX executable testTransforms +cd /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/Geometry && /usr/bin/cmake -E cmake_link_script CMakeFiles/testTransforms.dir/link.txt --verbose=1 [ 12%] Linking CXX executable testGrid cd /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/Geometry && /usr/bin/cmake -E cmake_link_script CMakeFiles/testGrid.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/testGrid.dir/link.d CMakeFiles/testGrid.dir/testGrid.cpp.o -o testGrid ../../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 -[ 12%] Building CXX object Code/Geometry/Wrap/CMakeFiles/rdGeometry.dir/UniformGrid3D.cpp.o 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/Geometry/Wrap && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_NUMPY_DYN_LINK -DBOOST_NUMPY_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_BUILD_XYZ2MOL_SUPPORT -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION 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-/build/reproducible-path/rdkit-202503.1/Code/GraphMol/PeriodicTable.cpp:96:57: required from here - 96 | adata.d_isotopeInfoMap[isotope] = std::make_pair(mass, abundance); - | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~ -/usr/include/c++/14/bits/stl_pair.h:1132:5: note: parameter passing for argument of type 'std::pair' when C++17 is enabled changed to match C++14 in GCC 10.1 - 1132 | make_pair(_T1&& __x, _T2&& __y) - | ^~~~~~~~~ -[ 12%] Building CXX object 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_BUILD_XYZ2MOL_SUPPORT -DRDK_HAS_EIGEN3 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-DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202503.1/External -I/build/reproducible-path/rdkit-202503.1/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-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 +In file included from /usr/include/c++/14/bits/stl_algobase.h:64, + from /usr/include/c++/14/bits/stl_tree.h:63, + from /usr/include/c++/14/map:62, + from /build/reproducible-path/rdkit-202503.1/Code/GraphMol/PeriodicTable.h:14, + from /build/reproducible-path/rdkit-202503.1/Code/GraphMol/PeriodicTable.cpp:11: +/usr/include/c++/14/bits/stl_pair.h: In instantiation of 'constexpr std::pair::type>::__type, typename std::__strip_reference_wrapper::type>::__type> std::make_pair(_T1&&, _T2&&) [with _T1 = double&; _T2 = double&; typename __strip_reference_wrapper::type>::__type = double; typename decay<_Tp>::type = double; typename __strip_reference_wrapper::type>::__type = double; typename decay<_Tp2>::type = double]': +/build/reproducible-path/rdkit-202503.1/Code/GraphMol/PeriodicTable.cpp:96:57: required from here + 96 | adata.d_isotopeInfoMap[isotope] = std::make_pair(mass, abundance); + | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~ +/usr/include/c++/14/bits/stl_pair.h:1132:5: note: parameter passing for argument of type 'std::pair' when C++17 is enabled changed to match C++14 in GCC 10.1 + 1132 | make_pair(_T1&& __x, _T2&& __y) + | ^~~~~~~~~ +[ 14%] 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-DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202503.1/External -I/build/reproducible-path/rdkit-202503.1/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/CMakeFiles/GraphMol.dir/RingInfo.cpp.o -MF CMakeFiles/GraphMol.dir/RingInfo.cpp.o.d -o CMakeFiles/GraphMol.dir/RingInfo.cpp.o -c /build/reproducible-path/rdkit-202503.1/Code/GraphMol/RingInfo.cpp [ 16%] Building CXX object Code/GraphMol/CMakeFiles/GraphMol.dir/Conformer.cpp.o @@ -3151,11 +3187,6 @@ cd /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DGraphMol_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_GRAPHMOL_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_BUILD_XYZ2MOL_SUPPORT -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202503.1/External -I/build/reproducible-path/rdkit-202503.1/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/CMakeFiles/GraphMol.dir/Renumber.cpp.o -MF CMakeFiles/GraphMol.dir/Renumber.cpp.o.d -o CMakeFiles/GraphMol.dir/Renumber.cpp.o -c /build/reproducible-path/rdkit-202503.1/Code/GraphMol/Renumber.cpp [ 16%] Building CXX object Code/GraphMol/CMakeFiles/GraphMol.dir/AdjustQuery.cpp.o cd /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DGraphMol_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_GRAPHMOL_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_BUILD_XYZ2MOL_SUPPORT -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202503.1/External -I/build/reproducible-path/rdkit-202503.1/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/CMakeFiles/GraphMol.dir/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 -[ 16%] Linking CXX executable testChemicalFeatures -cd /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/ChemicalFeatures && /usr/bin/cmake -E cmake_link_script CMakeFiles/testChemicalFeatures.dir/link.txt --verbose=1 -/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/testChemicalFeatures.dir/link.d CMakeFiles/testChemicalFeatures.dir/testChemicalFeatures.cpp.o -o testChemicalFeatures ../../lib/libRDKitChemicalFeatures.so.1.2025.03.1 ../../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' -[ 16%] Built target testChemicalFeatures [ 16%] Building CXX object 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_BUILD_XYZ2MOL_SUPPORT -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202503.1/External -I/build/reproducible-path/rdkit-202503.1/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/CMakeFiles/GraphMol.dir/Resonance.cpp.o -MF CMakeFiles/GraphMol.dir/Resonance.cpp.o.d -o CMakeFiles/GraphMol.dir/Resonance.cpp.o -c /build/reproducible-path/rdkit-202503.1/Code/GraphMol/Resonance.cpp [ 16%] Building CXX object Code/GraphMol/CMakeFiles/GraphMol.dir/StereoGroup.cpp.o @@ -3189,9 +3220,9 @@ make[4]: Entering directory '/build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu' cd /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202503.1 /build/reproducible-path/rdkit-202503.1/Code/GraphMol/MolTransforms /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/MolTransforms /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/MolTransforms/CMakeFiles/MolTransforms.dir/DependInfo.cmake "--color=" make -f Code/GraphMol/CIPLabeler/CMakeFiles/CIPLabeler.dir/build.make Code/GraphMol/CIPLabeler/CMakeFiles/CIPLabeler.dir/depend +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' cd /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202503.1 /build/reproducible-path/rdkit-202503.1/Code/GraphMol/SmilesParse /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/SmilesParse /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/SmilesParse/CMakeFiles/SmilesParse.dir/DependInfo.cmake "--color=" -make -f Code/GraphMol/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' 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/GenericGroups /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/GenericGroups /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/GenericGroups/CMakeFiles/GenericGroups.dir/DependInfo.cmake "--color=" make -f Code/GraphMol/Subgraphs/CMakeFiles/Subgraphs.dir/build.make Code/GraphMol/Subgraphs/CMakeFiles/Subgraphs.dir/depend @@ -3201,17 +3232,17 @@ 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 /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/CMakeFiles/tableTestsCatch.dir/DependInfo.cmake "--color=" -make[4]: Entering directory '/build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu' -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/Subgraphs /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/Subgraphs /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/Subgraphs/CMakeFiles/Subgraphs.dir/DependInfo.cmake "--color=" make -f Code/GraphMol/MolInterchange/CMakeFiles/MolInterchange.dir/build.make Code/GraphMol/MolInterchange/CMakeFiles/MolInterchange.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/CIPLabeler /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/CIPLabeler /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/CIPLabeler/CMakeFiles/CIPLabeler.dir/DependInfo.cmake "--color=" +make[4]: Entering directory '/build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu' make -f Code/GraphMol/SLNParse/CMakeFiles/SLNParse.dir/build.make Code/GraphMol/SLNParse/CMakeFiles/SLNParse.dir/depend +cd /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202503.1 /build/reproducible-path/rdkit-202503.1/Code/GraphMol/Subgraphs /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/Subgraphs /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/Subgraphs/CMakeFiles/Subgraphs.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/PartialCharges /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/PartialCharges /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/PartialCharges/CMakeFiles/PartialCharges.dir/DependInfo.cmake "--color=" -make -f Code/GraphMol/Wrap/CMakeFiles/rdqueries.dir/build.make Code/GraphMol/Wrap/CMakeFiles/rdqueries.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-202503.1/obj-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=" +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/MolInterchange /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/MolInterchange /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/MolInterchange/CMakeFiles/MolInterchange.dir/DependInfo.cmake "--color=" make[4]: Entering directory '/build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu' @@ -3219,78 +3250,80 @@ 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=" make[4]: Leaving directory '/build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu' -make -f Code/GraphMol/Trajectory/CMakeFiles/Trajectory.dir/build.make Code/GraphMol/Trajectory/CMakeFiles/Trajectory.dir/build -make[4]: Entering directory '/build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu' +make -f Code/GraphMol/SmilesParse/CMakeFiles/SmilesParse.dir/build.make Code/GraphMol/SmilesParse/CMakeFiles/SmilesParse.dir/build make[4]: Leaving directory '/build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu' +make -f 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+make[4]: Entering directory '/build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu' +make[4]: Entering directory '/build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu' make[4]: Entering directory '/build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu' -make -f Code/GraphMol/Subgraphs/CMakeFiles/Subgraphs.dir/build.make Code/GraphMol/Subgraphs/CMakeFiles/Subgraphs.dir/build -make[4]: Leaving directory '/build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu' -make -f Code/GraphMol/MolInterchange/CMakeFiles/MolInterchange.dir/build.make Code/GraphMol/MolInterchange/CMakeFiles/MolInterchange.dir/build make[4]: Leaving directory '/build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu' make[4]: Leaving 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[4]: Entering directory '/build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu' -make -f Code/GraphMol/MolTransforms/CMakeFiles/MolTransforms.dir/build.make Code/GraphMol/MolTransforms/CMakeFiles/MolTransforms.dir/build -make -f Code/GraphMol/CIPLabeler/CMakeFiles/CIPLabeler.dir/build.make Code/GraphMol/CIPLabeler/CMakeFiles/CIPLabeler.dir/build make[4]: Leaving directory '/build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu' -make[4]: Entering directory '/build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu' -make -f Code/GraphMol/PartialCharges/CMakeFiles/PartialCharges.dir/build.make Code/GraphMol/PartialCharges/CMakeFiles/PartialCharges.dir/build -make -f Code/GraphMol/MolCatalog/CMakeFiles/MolCatalog.dir/build.make Code/GraphMol/MolCatalog/CMakeFiles/MolCatalog.dir/build +make -f Code/GraphMol/Subgraphs/CMakeFiles/Subgraphs.dir/build.make Code/GraphMol/Subgraphs/CMakeFiles/Subgraphs.dir/build +make -f Code/GraphMol/MolInterchange/CMakeFiles/MolInterchange.dir/build.make 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-Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/Trajectory/CMakeFiles/Trajectory.dir/Trajectory.cpp.o -MF CMakeFiles/Trajectory.dir/Trajectory.cpp.o.d -o CMakeFiles/Trajectory.dir/Trajectory.cpp.o -c /build/reproducible-path/rdkit-202503.1/Code/GraphMol/Trajectory/Trajectory.cpp 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/MolTransforms/CMakeFiles/MolTransforms.dir/build.make Code/GraphMol/MolTransforms/CMakeFiles/MolTransforms.dir/build +make[4]: Leaving directory '/build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu' +make -f Code/GraphMol/MolCatalog/CMakeFiles/MolCatalog.dir/build.make Code/GraphMol/MolCatalog/CMakeFiles/MolCatalog.dir/build make[4]: Leaving directory '/build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu' -make -f 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19%] Building CXX object Code/GraphMol/Wrap/CMakeFiles/rdqueries.dir/Queries.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_BUILD_XYZ2MOL_SUPPORT -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -Drdqueries_EXPORTS -I/build/reproducible-path/rdkit-202503.1/External -I/build/reproducible-path/rdkit-202503.1/Code -I/usr/lib/aarch64-linux-gnu/python3-numpy/numpy/_core/include -isystem /usr/include/python3.13 -isystem /usr/include/eigen3 -g -O2 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directory '/build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu' [ 19%] Built target tableTestsCatch -[ 19%] Building CXX object Code/GraphMol/Wrap/CMakeFiles/rdqueries.dir/Queries.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_BUILD_XYZ2MOL_SUPPORT -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -Drdqueries_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/rdqueries.dir/Queries.cpp.o -MF CMakeFiles/rdqueries.dir/Queries.cpp.o.d -o CMakeFiles/rdqueries.dir/Queries.cpp.o -c /build/reproducible-path/rdkit-202503.1/Code/GraphMol/Wrap/Queries.cpp +[ 19%] Building CXX object Code/GraphMol/Subgraphs/CMakeFiles/Subgraphs.dir/SubgraphUtils.cpp.o +cd /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/Subgraphs && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK 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Code/GraphMol/Subgraphs/CMakeFiles/Subgraphs.dir/SubgraphUtils.cpp.o -MF CMakeFiles/Subgraphs.dir/SubgraphUtils.cpp.o.d -o CMakeFiles/Subgraphs.dir/SubgraphUtils.cpp.o -c /build/reproducible-path/rdkit-202503.1/Code/GraphMol/Subgraphs/SubgraphUtils.cpp +[ 19%] 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_BUILD_XYZ2MOL_SUPPORT -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202503.1/External -I/build/reproducible-path/rdkit-202503.1/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/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 [ 19%] Building CXX object Code/GraphMol/MolInterchange/CMakeFiles/MolInterchange.dir/Writer.cpp.o cd /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/MolInterchange && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK 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-Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/MolInterchange/CMakeFiles/MolInterchange.dir/Writer.cpp.o -MF CMakeFiles/MolInterchange.dir/Writer.cpp.o.d -o CMakeFiles/MolInterchange.dir/Writer.cpp.o -c /build/reproducible-path/rdkit-202503.1/Code/GraphMol/MolInterchange/Writer.cpp [ 19%] Linking CXX shared library ../../../lib/libRDKitTrajectory.so @@ -3303,74 +3336,58 @@ cd /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/SmilesParse && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDKIT_SMILESPARSE_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_BUILD_XYZ2MOL_SUPPORT -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DSmilesParse_EXPORTS -I/build/reproducible-path/rdkit-202503.1/External -I/build/reproducible-path/rdkit-202503.1/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/SmilesParse/CMakeFiles/SmilesParse.dir/SmilesParseOps.cpp.o -MF CMakeFiles/SmilesParse.dir/SmilesParseOps.cpp.o.d -o CMakeFiles/SmilesParse.dir/SmilesParseOps.cpp.o -c /build/reproducible-path/rdkit-202503.1/Code/GraphMol/SmilesParse/SmilesParseOps.cpp [ 19%] Linking CXX shared library ../../../lib/libRDKitMolCatalog.so cd /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/MolCatalog && /usr/bin/cmake -E cmake_link_script CMakeFiles/MolCatalog.dir/link.txt --verbose=1 -[ 19%] Building CXX object Code/GraphMol/Subgraphs/CMakeFiles/Subgraphs.dir/SubgraphUtils.cpp.o -cd /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/Subgraphs && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDKIT_SUBGRAPHS_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_BUILD_XYZ2MOL_SUPPORT -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DSubgraphs_EXPORTS -I/build/reproducible-path/rdkit-202503.1/External -I/build/reproducible-path/rdkit-202503.1/External/boost-numeric-bindings -I/build/reproducible-path/rdkit-202503.1/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/Subgraphs/CMakeFiles/Subgraphs.dir/SubgraphUtils.cpp.o -MF CMakeFiles/Subgraphs.dir/SubgraphUtils.cpp.o.d -o CMakeFiles/Subgraphs.dir/SubgraphUtils.cpp.o -c /build/reproducible-path/rdkit-202503.1/Code/GraphMol/Subgraphs/SubgraphUtils.cpp /usr/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/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 make[4]: Leaving directory '/build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu' [ 19%] Built target MolCatalog +make -f 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+make[4]: Entering directory '/build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu' +[ 19%] Building CXX object Code/ChemicalFeatures/Wrap/CMakeFiles/rdChemicalFeatures.dir/rdChemicalFeatures.cpp.o +cd /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/ChemicalFeatures/Wrap && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_NUMPY_DYN_LINK -DBOOST_NUMPY_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_BUILD_XYZ2MOL_SUPPORT -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -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 [ 19%] Building CXX object Code/GraphMol/SLNParse/CMakeFiles/SLNParse.dir/SLNAttribs.cpp.o cd /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/SLNParse && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK 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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/SmilesWrite.cpp.o -MF CMakeFiles/SmilesParse.dir/SmilesWrite.cpp.o.d -o CMakeFiles/SmilesParse.dir/SmilesWrite.cpp.o -c /build/reproducible-path/rdkit-202503.1/Code/GraphMol/SmilesParse/SmilesWrite.cpp -[ 20%] Linking CXX shared library ../../../lib/libRDKitPartialCharges.so +[ 19%] 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 make[4]: Leaving directory '/build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu' -[ 20%] Built target PartialCharges -[ 20%] Building CXX object Code/GraphMol/CIPLabeler/CMakeFiles/CIPLabeler.dir/Mancude.cpp.o +[ 19%] Built target PartialCharges +[ 19%] 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 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-Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/CIPLabeler/CMakeFiles/CIPLabeler.dir/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 make[4]: Leaving directory '/build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu' -[ 20%] Built target GenericGroups -[ 20%] 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 -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDKIT_SLNPARSE_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_BUILD_XYZ2MOL_SUPPORT -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DSLNParse_EXPORTS -I/build/reproducible-path/rdkit-202503.1/External -I/build/reproducible-path/rdkit-202503.1/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/SLNParse/CMakeFiles/SLNParse.dir/sln.tab.cpp.o -MF CMakeFiles/SLNParse.dir/sln.tab.cpp.o.d -o CMakeFiles/SLNParse.dir/sln.tab.cpp.o -c /build/reproducible-path/rdkit-202503.1/Code/GraphMol/SLNParse/sln.tab.cpp -[ 20%] Linking CXX shared library ../../../lib/libRDKitMolTransforms.so -cd 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-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/FreeChemicalFeature.cpp.o -MF CMakeFiles/rdChemicalFeatures.dir/FreeChemicalFeature.cpp.o.d -o CMakeFiles/rdChemicalFeatures.dir/FreeChemicalFeature.cpp.o -c /build/reproducible-path/rdkit-202503.1/Code/ChemicalFeatures/Wrap/FreeChemicalFeature.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/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 ../../../lib/libRDKitMolTransforms.so.1.2025.03.1 ../../../lib/libRDKitMolTransforms.so.1 ../../../lib/libRDKitMolTransforms.so make[4]: Leaving directory '/build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu' -[ 20%] Built target MolTransforms -[ 20%] 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_BUILD_XYZ2MOL_SUPPORT -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DSmilesParse_EXPORTS -I/build/reproducible-path/rdkit-202503.1/External -I/build/reproducible-path/rdkit-202503.1/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/SmilesParse/CMakeFiles/SmilesParse.dir/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 -[ 20%] Building CXX object Code/GraphMol/CIPLabeler/CMakeFiles/CIPLabeler.dir/Digraph.cpp.o -cd /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/CIPLabeler && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK 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-Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/CIPLabeler/CMakeFiles/CIPLabeler.dir/Edge.cpp.o -MF CMakeFiles/CIPLabeler.dir/Edge.cpp.o.d -o CMakeFiles/CIPLabeler.dir/Edge.cpp.o -c /build/reproducible-path/rdkit-202503.1/Code/GraphMol/CIPLabeler/Edge.cpp make -f Code/Numerics/Optimizer/CMakeFiles/Optimizer.dir/build.make Code/Numerics/Optimizer/CMakeFiles/Optimizer.dir/depend @@ -3381,16 +3398,14 @@ make[4]: Entering directory '/build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu' [ 21%] Building CXX object Code/Numerics/Optimizer/CMakeFiles/Optimizer.dir/BFGSOpt.cpp.o cd /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/Numerics/Optimizer && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DOptimizer_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_OPTIMIZER_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_BUILD_XYZ2MOL_SUPPORT -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202503.1/External -I/build/reproducible-path/rdkit-202503.1/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/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 -[ 21%] Linking CXX shared library ../../../lib/libRDKitMolInterchange.so -cd /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/MolInterchange && /usr/bin/cmake -E cmake_link_script CMakeFiles/MolInterchange.dir/link.txt --verbose=1 -/usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,--dependency-file=CMakeFiles/MolInterchange.dir/link.d -Wl,-z,relro -Wl,-z,now -shared -Wl,-soname,libRDKitMolInterchange.so.1 -o ../../../lib/libRDKitMolInterchange.so.1.2025.03.1 CMakeFiles/MolInterchange.dir/Parser.cpp.o CMakeFiles/MolInterchange.dir/Writer.cpp.o ../../../lib/libRDKitGraphMol.so.1.2025.03.1 ../../../lib/libRDKitRDGeometryLib.so.1.2025.03.1 ../../../lib/libRDKitDataStructs.so.1.2025.03.1 ../../../lib/libRDKitRDGeneral.so.1.2025.03.1 /usr/lib/aarch64-linux-gnu/libboost_system.so.1.83.0 /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/MolInterchange && /usr/bin/cmake -E cmake_symlink_library ../../../lib/libRDKitMolInterchange.so.1.2025.03.1 ../../../lib/libRDKitMolInterchange.so.1 ../../../lib/libRDKitMolInterchange.so -make[4]: Leaving directory '/build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu' -[ 21%] Built target MolInterchange -[ 21%] 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 -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDKIT_SUBSTRUCTMATCH_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_BUILD_XYZ2MOL_SUPPORT -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DSubstructMatch_EXPORTS -I/build/reproducible-path/rdkit-202503.1/External -I/build/reproducible-path/rdkit-202503.1/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/Substruct/CMakeFiles/SubstructMatch.dir/SubstructUtils.cpp.o -MF CMakeFiles/SubstructMatch.dir/SubstructUtils.cpp.o.d -o CMakeFiles/SubstructMatch.dir/SubstructUtils.cpp.o -c /build/reproducible-path/rdkit-202503.1/Code/GraphMol/Substruct/SubstructUtils.cpp +[ 21%] 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_BUILD_XYZ2MOL_SUPPORT -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DSmilesParse_EXPORTS -I/build/reproducible-path/rdkit-202503.1/External -I/build/reproducible-path/rdkit-202503.1/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/SmilesParse/CMakeFiles/SmilesParse.dir/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 [ 21%] Building CXX object Code/GraphMol/CIPLabeler/CMakeFiles/CIPLabeler.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 -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DCIPLabeler_EXPORTS -DRDKIT_CIPLABELER_BUILD 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/build/reproducible-path/rdkit-202503.1/Code/GraphMol/CIPLabeler/Sort.cpp +[ 21%] Building CXX object Code/GraphMol/CIPLabeler/CMakeFiles/CIPLabeler.dir/configs/Configuration.cpp.o +cd /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/CIPLabeler && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DCIPLabeler_EXPORTS -DRDKIT_CIPLABELER_BUILD -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_BUILD_XYZ2MOL_SUPPORT -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202503.1/External -I/build/reproducible-path/rdkit-202503.1/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/CIPLabeler/CMakeFiles/CIPLabeler.dir/configs/Configuration.cpp.o -MF CMakeFiles/CIPLabeler.dir/configs/Configuration.cpp.o.d -o CMakeFiles/CIPLabeler.dir/configs/Configuration.cpp.o -c /build/reproducible-path/rdkit-202503.1/Code/GraphMol/CIPLabeler/configs/Configuration.cpp +[ 21%] Building CXX object Code/Numerics/Optimizer/CMakeFiles/Optimizer.dir/LinearSearch.cpp.o +cd /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/Numerics/Optimizer && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DOptimizer_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_OPTIMIZER_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_BUILD_XYZ2MOL_SUPPORT -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202503.1/External -I/build/reproducible-path/rdkit-202503.1/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/Numerics/Optimizer/CMakeFiles/Optimizer.dir/LinearSearch.cpp.o -MF CMakeFiles/Optimizer.dir/LinearSearch.cpp.o.d -o CMakeFiles/Optimizer.dir/LinearSearch.cpp.o -c /build/reproducible-path/rdkit-202503.1/Code/Numerics/Optimizer/LinearSearch.cpp make -f Code/GraphMol/PartialCharges/Wrap/CMakeFiles/rdPartialCharges.dir/build.make Code/GraphMol/PartialCharges/Wrap/CMakeFiles/rdPartialCharges.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/PartialCharges/Wrap /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/PartialCharges/Wrap /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/PartialCharges/Wrap/CMakeFiles/rdPartialCharges.dir/DependInfo.cmake "--color=" @@ -3399,20 +3414,10 @@ make[4]: Entering directory '/build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu' [ 21%] 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-isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/PartialCharges/Wrap/CMakeFiles/rdPartialCharges.dir/rdPartialCharges.cpp.o -MF CMakeFiles/rdPartialCharges.dir/rdPartialCharges.cpp.o.d -o CMakeFiles/rdPartialCharges.dir/rdPartialCharges.cpp.o -c /build/reproducible-path/rdkit-202503.1/Code/GraphMol/PartialCharges/Wrap/rdPartialCharges.cpp -[ 21%] 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_BUILD_XYZ2MOL_SUPPORT -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DSmilesParse_EXPORTS -I/build/reproducible-path/rdkit-202503.1/External -I/build/reproducible-path/rdkit-202503.1/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/SmilesParse/CMakeFiles/SmilesParse.dir/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 -[ 21%] Building CXX object Code/Numerics/Optimizer/CMakeFiles/Optimizer.dir/LinearSearch.cpp.o -cd /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/Numerics/Optimizer && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DOptimizer_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_OPTIMIZER_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_BUILD_XYZ2MOL_SUPPORT -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202503.1/External -I/build/reproducible-path/rdkit-202503.1/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/Numerics/Optimizer/CMakeFiles/Optimizer.dir/LinearSearch.cpp.o -MF CMakeFiles/Optimizer.dir/LinearSearch.cpp.o.d -o CMakeFiles/Optimizer.dir/LinearSearch.cpp.o -c /build/reproducible-path/rdkit-202503.1/Code/Numerics/Optimizer/LinearSearch.cpp -[ 21%] Building CXX object Code/GraphMol/CIPLabeler/CMakeFiles/CIPLabeler.dir/configs/Configuration.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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CMakeFiles/CIPLabeler.dir/configs/Configuration.cpp.o.d -o CMakeFiles/CIPLabeler.dir/configs/Configuration.cpp.o -c /build/reproducible-path/rdkit-202503.1/Code/GraphMol/CIPLabeler/configs/Configuration.cpp -[ 21%] Linking CXX shared library ../../../lib/libRDKitSLNParse.so -cd /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/SLNParse && /usr/bin/cmake -E cmake_link_script CMakeFiles/SLNParse.dir/link.txt --verbose=1 -/usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,--dependency-file=CMakeFiles/SLNParse.dir/link.d -Wl,-z,relro -Wl,-z,now -shared -Wl,-soname,libRDKitSLNParse.so.1 -o ../../../lib/libRDKitSLNParse.so.1.2025.03.1 CMakeFiles/SLNParse.dir/SLNParse.cpp.o CMakeFiles/SLNParse.dir/SLNAttribs.cpp.o CMakeFiles/SLNParse.dir/sln.tab.cpp.o CMakeFiles/SLNParse.dir/lex.yysln.cpp.o ../../../lib/libRDKitGraphMol.so.1.2025.03.1 ../../../lib/libRDKitRDGeometryLib.so.1.2025.03.1 ../../../lib/libRDKitDataStructs.so.1.2025.03.1 ../../../lib/libRDKitRDGeneral.so.1.2025.03.1 /usr/lib/aarch64-linux-gnu/libboost_system.so.1.83.0 /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/SLNParse && /usr/bin/cmake -E cmake_symlink_library ../../../lib/libRDKitSLNParse.so.1.2025.03.1 ../../../lib/libRDKitSLNParse.so.1 ../../../lib/libRDKitSLNParse.so -make[4]: Leaving directory '/build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu' -[ 21%] Built target SLNParse -[ 21%] Building CXX object Code/GraphMol/SmilesParse/CMakeFiles/SmilesParse.dir/smarts.tab.cpp.o -cd 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../../../rdkit/Chem/rdqueries.so -cd /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/Wrap && /usr/bin/cmake -E cmake_link_script CMakeFiles/rdqueries.dir/link.txt --verbose=1 -/usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=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/rdqueries.dir/link.d -Wl,-z,relro -Wl,-z,now -shared -o ../../../rdkit/Chem/rdqueries.so CMakeFiles/rdqueries.dir/rdqueries.cpp.o CMakeFiles/rdqueries.dir/Queries.cpp.o ../../../lib/libRDKitGraphMol.so.1.2025.03.1 ../../../lib/libRDKitRDBoost.so.1.2025.03.1 ../../../lib/libRDKitRDGeometryLib.so.1.2025.03.1 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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 -Wl,--dependency-file=CMakeFiles/Optimizer.dir/link.d -Wl,-z,relro -Wl,-z,now -shared -Wl,-soname,libRDKitOptimizer.so.1 -o ../../../lib/libRDKitOptimizer.so.1.2025.03.1 CMakeFiles/Optimizer.dir/BFGSOpt.cpp.o CMakeFiles/Optimizer.dir/LinearSearch.cpp.o ../../../lib/libRDKitTrajectory.so.1.2025.03.1 ../../../lib/libRDKitGraphMol.so.1.2025.03.1 ../../../lib/libRDKitRDGeometryLib.so.1.2025.03.1 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Code/GraphMol/CIPLabeler/CMakeFiles/CIPLabeler.dir/configs/AtropisomerBond.cpp.o -MF CMakeFiles/CIPLabeler.dir/configs/AtropisomerBond.cpp.o.d -o CMakeFiles/CIPLabeler.dir/configs/AtropisomerBond.cpp.o -c /build/reproducible-path/rdkit-202503.1/Code/GraphMol/CIPLabeler/configs/AtropisomerBond.cpp -[ 22%] Building CXX object Code/GraphMol/ShapeHelpers/CMakeFiles/ShapeHelpers.dir/ShapeUtils.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_BUILD_XYZ2MOL_SUPPORT -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/ShapeUtils.cpp.o -MF CMakeFiles/ShapeHelpers.dir/ShapeUtils.cpp.o.d -o CMakeFiles/ShapeHelpers.dir/ShapeUtils.cpp.o -c /build/reproducible-path/rdkit-202503.1/Code/GraphMol/ShapeHelpers/ShapeUtils.cpp +make -f Code/GraphMol/ShapeHelpers/CMakeFiles/ShapeHelpers.dir/build.make Code/GraphMol/ShapeHelpers/CMakeFiles/ShapeHelpers.dir/build +make[4]: Entering directory '/build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu' make -f 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"--color=" +[ 22%] Built target MolInterchange +[ 22%] Building CXX object Code/GraphMol/CIPLabeler/CMakeFiles/CIPLabeler.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 -DCIPLabeler_EXPORTS -DRDKIT_CIPLABELER_BUILD -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_BUILD_XYZ2MOL_SUPPORT -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202503.1/External -I/build/reproducible-path/rdkit-202503.1/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/CIPLabeler/CMakeFiles/CIPLabeler.dir/configs/Tetrahedral.cpp.o -MF CMakeFiles/CIPLabeler.dir/configs/Tetrahedral.cpp.o.d -o CMakeFiles/CIPLabeler.dir/configs/Tetrahedral.cpp.o -c /build/reproducible-path/rdkit-202503.1/Code/GraphMol/CIPLabeler/configs/Tetrahedral.cpp +[ 22%] Linking CXX shared library ../../../lib/libRDKitSLNParse.so +cd /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/SLNParse && /usr/bin/cmake -E cmake_link_script CMakeFiles/SLNParse.dir/link.txt --verbose=1 +/usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time 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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_BUILD_XYZ2MOL_SUPPORT -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 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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/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 +[ 23%] 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 -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDKIT_SMILESPARSE_BUILD -DRDK_64BIT_BUILD 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-DRDK_BUILD_THREADSAFE_SSS -DRDK_BUILD_XYZ2MOL_SUPPORT -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202503.1/External -I/build/reproducible-path/rdkit-202503.1/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/CIPLabeler/CMakeFiles/CIPLabeler.dir/configs/AtropisomerBond.cpp.o -MF CMakeFiles/CIPLabeler.dir/configs/AtropisomerBond.cpp.o.d -o CMakeFiles/CIPLabeler.dir/configs/AtropisomerBond.cpp.o -c /build/reproducible-path/rdkit-202503.1/Code/GraphMol/CIPLabeler/configs/AtropisomerBond.cpp make -f 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+[ 24%] 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 -Wl,--dependency-file=CMakeFiles/rdtrajectory.dir/link.d -Wl,-z,relro -Wl,-z,now -shared -o ../../../rdkit/Chem/rdtrajectory.so CMakeFiles/rdtrajectory.dir/Trajectory.cpp.o CMakeFiles/rdtrajectory.dir/rdTrajectory.cpp.o ../../../lib/libRDKitTrajectory.so.1.2025.03.1 ../../../lib/libRDKitGraphMol.so.1.2025.03.1 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+[ 26%] Building CXX object Code/ForceField/CMakeFiles/ForceField.dir/PositionConstraint.cpp.o +cd /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/ForceField && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DForceField_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_FORCEFIELD_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_BUILD_XYZ2MOL_SUPPORT -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202503.1/External -I/build/reproducible-path/rdkit-202503.1/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/ForceField/CMakeFiles/ForceField.dir/PositionConstraint.cpp.o -MF CMakeFiles/ForceField.dir/PositionConstraint.cpp.o.d -o CMakeFiles/ForceField.dir/PositionConstraint.cpp.o -c /build/reproducible-path/rdkit-202503.1/Code/ForceField/PositionConstraint.cpp +[ 26%] Building CXX object Code/GraphMol/CIPLabeler/CMakeFiles/CIPLabeler.dir/rules/Rule5.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 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Code/ForceField/CMakeFiles/ForceField.dir/TorsionConstraint.cpp.o +cd /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/ForceField && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DForceField_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_FORCEFIELD_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_BUILD_XYZ2MOL_SUPPORT -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202503.1/External -I/build/reproducible-path/rdkit-202503.1/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/ForceField/CMakeFiles/ForceField.dir/TorsionConstraint.cpp.o -MF CMakeFiles/ForceField.dir/TorsionConstraint.cpp.o.d -o CMakeFiles/ForceField.dir/TorsionConstraint.cpp.o -c /build/reproducible-path/rdkit-202503.1/Code/ForceField/TorsionConstraint.cpp +[ 26%] Building CXX object Code/GraphMol/CIPLabeler/CMakeFiles/CIPLabeler.dir/rules/Rule5New.cpp.o +cd /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/CIPLabeler && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DCIPLabeler_EXPORTS -DRDKIT_CIPLABELER_BUILD -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_BUILD_XYZ2MOL_SUPPORT -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202503.1/External -I/build/reproducible-path/rdkit-202503.1/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/CIPLabeler/CMakeFiles/CIPLabeler.dir/rules/Rule5New.cpp.o -MF CMakeFiles/CIPLabeler.dir/rules/Rule5New.cpp.o.d -o CMakeFiles/CIPLabeler.dir/rules/Rule5New.cpp.o -c /build/reproducible-path/rdkit-202503.1/Code/GraphMol/CIPLabeler/rules/Rule5New.cpp +[ 26%] Linking CXX shared library ../../../lib/libRDKitSubstructMatch.so +cd 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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/Substruct && /usr/bin/cmake -E cmake_symlink_library ../../../lib/libRDKitSubstructMatch.so.1.2025.03.1 ../../../lib/libRDKitSubstructMatch.so.1 ../../../lib/libRDKitSubstructMatch.so +make[4]: Leaving directory '/build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu' +[ 26%] Built target SubstructMatch +[ 26%] Building CXX object Code/GraphMol/CIPLabeler/CMakeFiles/CIPLabeler.dir/rules/Rule6.cpp.o +cd /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/CIPLabeler && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DCIPLabeler_EXPORTS 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-Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/CIPLabeler/CMakeFiles/CIPLabeler.dir/rules/SequenceRule.cpp.o -MF CMakeFiles/CIPLabeler.dir/rules/SequenceRule.cpp.o.d -o CMakeFiles/CIPLabeler.dir/rules/SequenceRule.cpp.o -c /build/reproducible-path/rdkit-202503.1/Code/GraphMol/CIPLabeler/rules/SequenceRule.cpp +[ 26%] Building CXX object Code/ForceField/CMakeFiles/ForceField.dir/UFF/Nonbonded.cpp.o +cd /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/ForceField && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DForceField_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_FORCEFIELD_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS 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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/UFF/Inversions.cpp.o -MF CMakeFiles/ForceField.dir/UFF/Inversions.cpp.o.d -o CMakeFiles/ForceField.dir/UFF/Inversions.cpp.o -c /build/reproducible-path/rdkit-202503.1/Code/ForceField/UFF/Inversions.cpp +[ 26%] Linking CXX shared module ../../../../rdkit/Chem/rdMolInterchange.so +cd /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/MolInterchange/Wrap && /usr/bin/cmake -E cmake_link_script 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../../../../rdkit/Chem/rdMolInterchange.so CMakeFiles/rdMolInterchange.dir/rdMolInterchange.cpp.o ../../../../lib/libRDKitMolInterchange.so.1.2025.03.1 ../../../../lib/libRDKitRDBoost.so.1.2025.03.1 ../../../../lib/libRDKitGraphMol.so.1.2025.03.1 ../../../../lib/libRDKitRDGeometryLib.so.1.2025.03.1 ../../../../lib/libRDKitDataStructs.so.1.2025.03.1 /usr/lib/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' +[ 26%] Built target rdMolInterchange +[ 26%] Building CXX object Code/ForceField/CMakeFiles/ForceField.dir/UFF/Params.cpp.o +cd /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/ForceField && /usr/bin/c++ 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'/build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu' -[ 25%] Built target SmilesParse -[ 26%] Building CXX object Code/ForceField/CMakeFiles/ForceField.dir/DistanceConstraints.cpp.o -cd /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/ForceField && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DForceField_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_FORCEFIELD_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_BUILD_XYZ2MOL_SUPPORT -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202503.1/External -I/build/reproducible-path/rdkit-202503.1/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/ForceField/CMakeFiles/ForceField.dir/DistanceConstraints.cpp.o -MF CMakeFiles/ForceField.dir/DistanceConstraints.cpp.o.d -o CMakeFiles/ForceField.dir/DistanceConstraints.cpp.o -c /build/reproducible-path/rdkit-202503.1/Code/ForceField/DistanceConstraints.cpp +[ 28%] Built target SmilesParse +[ 28%] Building CXX object Code/ForceField/CMakeFiles/ForceField.dir/MMFF/TorsionAngle.cpp.o +cd /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/ForceField && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DForceField_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_FORCEFIELD_BUILD 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-fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/ForceField/CMakeFiles/ForceField.dir/MMFF/Nonbonded.cpp.o -MF CMakeFiles/ForceField.dir/MMFF/Nonbonded.cpp.o.d -o CMakeFiles/ForceField.dir/MMFF/Nonbonded.cpp.o -c /build/reproducible-path/rdkit-202503.1/Code/ForceField/MMFF/Nonbonded.cpp +[ 28%] Linking CXX shared module ../../../../rdkit/Chem/rdShapeHelpers.so +cd /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/ShapeHelpers/Wrap && /usr/bin/cmake -E cmake_link_script CMakeFiles/rdShapeHelpers.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/rdShapeHelpers.dir/link.d -Wl,-z,relro -Wl,-z,now -shared -o ../../../../rdkit/Chem/rdShapeHelpers.so CMakeFiles/rdShapeHelpers.dir/rdShapeHelpers.cpp.o ../../../../lib/libRDKitShapeHelpers.so.1.2025.03.1 ../../../../lib/libRDKitRDBoost.so.1.2025.03.1 ../../../../lib/libRDKitMolTransforms.so.1.2025.03.1 ../../../../lib/libRDKitEigenSolvers.so.1.2025.03.1 ../../../../lib/libRDKitGraphMol.so.1.2025.03.1 ../../../../lib/libRDKitRDGeometryLib.so.1.2025.03.1 ../../../../lib/libRDKitDataStructs.so.1.2025.03.1 /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' +[ 28%] Built target rdShapeHelpers make -f Code/GraphMol/MolAlign/CMakeFiles/MolAlign.dir/build.make Code/GraphMol/MolAlign/CMakeFiles/MolAlign.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/MolAlign.dir/DependInfo.cmake "--color=" +[ 28%] Building CXX object Code/ForceField/CMakeFiles/ForceField.dir/MMFF/Params.cpp.o +cd 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-Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/ForceField/CMakeFiles/ForceField.dir/MMFF/Params.cpp.o -MF CMakeFiles/ForceField.dir/MMFF/Params.cpp.o.d -o CMakeFiles/ForceField.dir/MMFF/Params.cpp.o -c /build/reproducible-path/rdkit-202503.1/Code/ForceField/MMFF/Params.cpp make[4]: Leaving directory '/build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu' make -f Code/GraphMol/MolAlign/CMakeFiles/MolAlign.dir/build.make Code/GraphMol/MolAlign/CMakeFiles/MolAlign.dir/build make[4]: Entering directory '/build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu' -[ 26%] Building CXX object Code/GraphMol/MolAlign/CMakeFiles/MolAlign.dir/AlignMolecules.cpp.o +[ 28%] Building CXX object Code/GraphMol/MolAlign/CMakeFiles/MolAlign.dir/AlignMolecules.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 -DMolAlign_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_MOLALIGN_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_BUILD_XYZ2MOL_SUPPORT -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202503.1/External -I/build/reproducible-path/rdkit-202503.1/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/MolAlign/CMakeFiles/MolAlign.dir/AlignMolecules.cpp.o -MF CMakeFiles/MolAlign.dir/AlignMolecules.cpp.o.d -o CMakeFiles/MolAlign.dir/AlignMolecules.cpp.o -c /build/reproducible-path/rdkit-202503.1/Code/GraphMol/MolAlign/AlignMolecules.cpp -[ 27%] Linking CXX shared module ../../../../rdkit/Chem/rdSLNParse.so -cd /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/SLNParse/Wrap && /usr/bin/cmake -E cmake_link_script CMakeFiles/rdSLNParse.dir/link.txt --verbose=1 -[ 27%] Building CXX object Code/GraphMol/CIPLabeler/CMakeFiles/CIPLabeler.dir/rules/Rule5.cpp.o -cd /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/CIPLabeler && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DCIPLabeler_EXPORTS -DRDKIT_CIPLABELER_BUILD -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_BUILD_XYZ2MOL_SUPPORT -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202503.1/External -I/build/reproducible-path/rdkit-202503.1/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/CIPLabeler/CMakeFiles/CIPLabeler.dir/rules/Rule5.cpp.o -MF CMakeFiles/CIPLabeler.dir/rules/Rule5.cpp.o.d -o CMakeFiles/CIPLabeler.dir/rules/Rule5.cpp.o -c /build/reproducible-path/rdkit-202503.1/Code/GraphMol/CIPLabeler/rules/Rule5.cpp -/usr/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/rdSLNParse.dir/link.d -Wl,-z,relro -Wl,-z,now -shared -o ../../../../rdkit/Chem/rdSLNParse.so CMakeFiles/rdSLNParse.dir/rdSLNParse.cpp.o ../../../../lib/libRDKitSLNParse.so.1.2025.03.1 ../../../../lib/libRDKitRDBoost.so.1.2025.03.1 ../../../../lib/libRDKitGraphMol.so.1.2025.03.1 ../../../../lib/libRDKitRDGeometryLib.so.1.2025.03.1 ../../../../lib/libRDKitDataStructs.so.1.2025.03.1 /usr/lib/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' -[ 27%] Built target rdSLNParse -[ 27%] Building CXX object Code/ForceField/CMakeFiles/ForceField.dir/PositionConstraint.cpp.o -cd /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/ForceField && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DForceField_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_FORCEFIELD_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_BUILD_XYZ2MOL_SUPPORT -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202503.1/External -I/build/reproducible-path/rdkit-202503.1/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/ForceField/CMakeFiles/ForceField.dir/PositionConstraint.cpp.o -MF CMakeFiles/ForceField.dir/PositionConstraint.cpp.o.d -o CMakeFiles/ForceField.dir/PositionConstraint.cpp.o -c /build/reproducible-path/rdkit-202503.1/Code/ForceField/PositionConstraint.cpp +[ 28%] Linking CXX shared library ../../../lib/libRDKitCIPLabeler.so +cd /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/CIPLabeler && /usr/bin/cmake -E cmake_link_script CMakeFiles/CIPLabeler.dir/link.txt --verbose=1 +/usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong 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Code/GraphMol/CMakeFiles/graphmolMemTest1.dir/memtest1.cpp.o cd /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_BUILD_XYZ2MOL_SUPPORT -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202503.1/External -I/build/reproducible-path/rdkit-202503.1/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 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-DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_BUILD_XYZ2MOL_SUPPORT -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202503.1/External -I/build/reproducible-path/rdkit-202503.1/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/ForceField/CMakeFiles/ForceField.dir/UFF/BondStretch.cpp.o -MF CMakeFiles/ForceField.dir/UFF/BondStretch.cpp.o.d -o CMakeFiles/ForceField.dir/UFF/BondStretch.cpp.o -c /build/reproducible-path/rdkit-202503.1/Code/ForceField/UFF/BondStretch.cpp make 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'/build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu' -[ 27%] Building CXX object Code/GraphMol/CMakeFiles/molbundleTestsCatch.dir/catch_molbundle.cpp.o +[ 28%] Building CXX object Code/GraphMol/CMakeFiles/molbundleTestsCatch.dir/catch_molbundle.cpp.o cd /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_BUILD_XYZ2MOL_SUPPORT -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202503.1/External -I/build/reproducible-path/rdkit-202503.1/Code -isystem /usr/include/eigen3 -g -O2 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moliteratorTestsCatch -cd /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol && /usr/bin/cmake -E cmake_link_script CMakeFiles/moliteratorTestsCatch.dir/link.txt --verbose=1 -/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/moliteratorTestsCatch.dir/link.d CMakeFiles/moliteratorTestsCatch.dir/catch_moliterators.cpp.o -o moliteratorTestsCatch ../RDGeneral/librdkitCatch.a ../../lib/libRDKitSubstructMatch.so.1.2025.03.1 ../../lib/libRDKitSmilesParse.so.1.2025.03.1 /usr/lib/libCatch2.a ../../lib/libRDKitGenericGroups.so.1.2025.03.1 ../../lib/libRDKitGraphMol.so.1.2025.03.1 ../../lib/libRDKitRDGeometryLib.so.1.2025.03.1 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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 +[ 28%] Building CXX object Code/GraphMol/FilterCatalog/CMakeFiles/FilterCatalog.dir/FilterCatalogRunner.cpp.o +cd /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FilterCatalog && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DFilterCatalog_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_FILTERCATALOG_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_BUILD_XYZ2MOL_SUPPORT -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS 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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/ForceField/CMakeFiles/ForceField.dir/MMFF/OopBend.cpp.o -MF CMakeFiles/ForceField.dir/MMFF/OopBend.cpp.o.d -o CMakeFiles/ForceField.dir/MMFF/OopBend.cpp.o -c /build/reproducible-path/rdkit-202503.1/Code/ForceField/MMFF/OopBend.cpp -[ 31%] 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 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/build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/Subgraphs && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_BUILD_XYZ2MOL_SUPPORT -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202503.1/External -I/build/reproducible-path/rdkit-202503.1/Code -I/build/reproducible-path/rdkit-202503.1/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/GraphMol/Subgraphs/CMakeFiles/testSubgraphs2.dir/test2.cpp.o -MF CMakeFiles/testSubgraphs2.dir/test2.cpp.o.d -o CMakeFiles/testSubgraphs2.dir/test2.cpp.o -c /build/reproducible-path/rdkit-202503.1/Code/GraphMol/Subgraphs/test2.cpp make -f Code/GraphMol/Subgraphs/CMakeFiles/subgraphsCatch.dir/build.make Code/GraphMol/Subgraphs/CMakeFiles/subgraphsCatch.dir/depend -[ 31%] Building CXX object Code/GraphMol/Subgraphs/CMakeFiles/testSubgraphs2.dir/test2.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/Subgraphs /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu 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/usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/GraphMol/Subgraphs/CMakeFiles/testSubgraphs2.dir/test2.cpp.o -MF CMakeFiles/testSubgraphs2.dir/test2.cpp.o.d -o CMakeFiles/testSubgraphs2.dir/test2.cpp.o -c /build/reproducible-path/rdkit-202503.1/Code/GraphMol/Subgraphs/test2.cpp make[4]: Leaving directory '/build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu' make -f Code/GraphMol/Subgraphs/CMakeFiles/subgraphsCatch.dir/build.make Code/GraphMol/Subgraphs/CMakeFiles/subgraphsCatch.dir/build make[4]: Entering directory '/build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu' -[ 31%] Building CXX object Code/GraphMol/Subgraphs/CMakeFiles/subgraphsCatch.dir/catch_tests.cpp.o +[ 28%] Building CXX object Code/GraphMol/Subgraphs/CMakeFiles/subgraphsCatch.dir/catch_tests.cpp.o cd /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/Subgraphs && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_BUILD_XYZ2MOL_SUPPORT -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202503.1/External -I/build/reproducible-path/rdkit-202503.1/Code -I/build/reproducible-path/rdkit-202503.1/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/GraphMol/Subgraphs/CMakeFiles/subgraphsCatch.dir/catch_tests.cpp.o -MF CMakeFiles/subgraphsCatch.dir/catch_tests.cpp.o.d -o CMakeFiles/subgraphsCatch.dir/catch_tests.cpp.o -c /build/reproducible-path/rdkit-202503.1/Code/GraphMol/Subgraphs/catch_tests.cpp -[ 31%] 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_BUILD_XYZ2MOL_SUPPORT -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202503.1/External -I/build/reproducible-path/rdkit-202503.1/Code -I/build/reproducible-path/rdkit-202503.1/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/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 -[ 31%] Linking CXX shared library ../../../lib/libRDKitFilterCatalog.so -cd /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FilterCatalog && /usr/bin/cmake -E cmake_link_script CMakeFiles/FilterCatalog.dir/link.txt --verbose=1 -/usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,--dependency-file=CMakeFiles/FilterCatalog.dir/link.d -Wl,-z,relro -Wl,-z,now -shared -Wl,-soname,libRDKitFilterCatalog.so.1 -o ../../../lib/libRDKitFilterCatalog.so.1.2025.03.1 CMakeFiles/FilterCatalog.dir/Filters.cpp.o CMakeFiles/FilterCatalog.dir/FilterCatalog.cpp.o CMakeFiles/FilterCatalog.dir/FilterCatalogEntry.cpp.o CMakeFiles/FilterCatalog.dir/FilterCatalogRunner.cpp.o CMakeFiles/FilterCatalog.dir/FilterMatchers.cpp.o CMakeFiles/FilterCatalog.dir/FunctionalGroupHierarchy.cpp.o ../../../lib/libRDKitSubgraphs.so.1.2025.03.1 ../../../lib/libRDKitSubstructMatch.so.1.2025.03.1 ../../../lib/libRDKitSmilesParse.so.1.2025.03.1 ../../../lib/libRDKitCatalogs.so.1.2025.03.1 ../../../lib/libRDKitGenericGroups.so.1.2025.03.1 ../../../lib/libRDKitGraphMol.so.1.2025.03.1 ../../../lib/libRDKitRDGeometryLib.so.1.2025.03.1 ../../../lib/libRDKitDataStructs.so.1.2025.03.1 ../../../lib/libRDKitRDGeneral.so.1.2025.03.1 /usr/lib/aarch64-linux-gnu/libboost_system.so.1.83.0 /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/FilterCatalog && /usr/bin/cmake -E cmake_symlink_library ../../../lib/libRDKitFilterCatalog.so.1.2025.03.1 ../../../lib/libRDKitFilterCatalog.so.1 ../../../lib/libRDKitFilterCatalog.so +[ 29%] Building CXX object Code/GraphMol/FilterCatalog/CMakeFiles/FilterCatalog.dir/FilterMatchers.cpp.o +cd /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FilterCatalog && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DFilterCatalog_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_FILTERCATALOG_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_BUILD_XYZ2MOL_SUPPORT -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202503.1/External -I/build/reproducible-path/rdkit-202503.1/Code -I/build/reproducible-path/rdkit-202503.1/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/FilterCatalog/CMakeFiles/FilterCatalog.dir/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 +[ 30%] Linking CXX executable v2smiTestCatch +cd /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/SmilesParse && /usr/bin/cmake -E cmake_link_script CMakeFiles/v2smiTestCatch.dir/link.txt --verbose=1 +/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/v2smiTestCatch.dir/link.d CMakeFiles/v2smiTestCatch.dir/v2catch_tests.cpp.o -o v2smiTestCatch ../../RDGeneral/librdkitCatch.a ../../../lib/libRDKitSmilesParse.so.1.2025.03.1 /usr/lib/libCatch2.a ../../../lib/libRDKitGraphMol.so.1.2025.03.1 ../../../lib/libRDKitRDGeometryLib.so.1.2025.03.1 ../../../lib/libRDKitDataStructs.so.1.2025.03.1 ../../../lib/libRDKitRDGeneral.so.1.2025.03.1 /usr/lib/aarch64-linux-gnu/libboost_system.so.1.83.0 /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' -[ 31%] Built target FilterCatalog -[ 31%] 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_BUILD_XYZ2MOL_SUPPORT -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202503.1/External -I/build/reproducible-path/rdkit-202503.1/Code -I/build/reproducible-path/rdkit-202503.1/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/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 -[ 31%] Building CXX object Code/GraphMol/Fingerprints/CMakeFiles/Fingerprints.dir/TopologicalTorsionGenerator.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_BUILD_XYZ2MOL_SUPPORT -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202503.1/External -I/build/reproducible-path/rdkit-202503.1/Code -I/build/reproducible-path/rdkit-202503.1/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function 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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/ForceField/CMakeFiles/ForceField.dir/MMFF/Nonbonded.cpp.o -MF CMakeFiles/ForceField.dir/MMFF/Nonbonded.cpp.o.d -o CMakeFiles/ForceField.dir/MMFF/Nonbonded.cpp.o -c /build/reproducible-path/rdkit-202503.1/Code/ForceField/MMFF/Nonbonded.cpp +[ 30%] Built target v2smiTestCatch make -f Code/GraphMol/FragCatalog/CMakeFiles/FragCatalog.dir/build.make 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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/FragCatalog/CMakeFiles/FragCatalog.dir/FragFPGenerator.cpp.o -MF CMakeFiles/FragCatalog.dir/FragFPGenerator.cpp.o.d -o CMakeFiles/FragCatalog.dir/FragFPGenerator.cpp.o -c /build/reproducible-path/rdkit-202503.1/Code/GraphMol/FragCatalog/FragFPGenerator.cpp make -f Code/GraphMol/SLNParse/CMakeFiles/testSLNParse.dir/build.make Code/GraphMol/SLNParse/CMakeFiles/testSLNParse.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-202503.1/obj-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/testSLNParse.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu' make -f Code/GraphMol/SLNParse/CMakeFiles/testSLNParse.dir/build.make Code/GraphMol/SLNParse/CMakeFiles/testSLNParse.dir/build make[4]: Entering directory '/build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu' -[ 34%] Building CXX object Code/GraphMol/SLNParse/CMakeFiles/testSLNParse.dir/test.cpp.o +[ 32%] Building CXX object Code/GraphMol/SLNParse/CMakeFiles/testSLNParse.dir/test.cpp.o cd /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/SLNParse && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_BUILD_XYZ2MOL_SUPPORT -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202503.1/External -I/build/reproducible-path/rdkit-202503.1/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/GraphMol/SLNParse/CMakeFiles/testSLNParse.dir/test.cpp.o -MF CMakeFiles/testSLNParse.dir/test.cpp.o.d -o CMakeFiles/testSLNParse.dir/test.cpp.o -c /build/reproducible-path/rdkit-202503.1/Code/GraphMol/SLNParse/test.cpp +[ 32%] Building CXX object Code/GraphMol/MolChemicalFeatures/CMakeFiles/MolChemicalFeatures.dir/FeatureParser.cpp.o +cd /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/MolChemicalFeatures && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DMolChemicalFeatures_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_MOLCHEMICALFEATURES_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_BUILD_XYZ2MOL_SUPPORT -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202503.1/External -I/build/reproducible-path/rdkit-202503.1/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/MolChemicalFeatures/CMakeFiles/MolChemicalFeatures.dir/FeatureParser.cpp.o -MF CMakeFiles/MolChemicalFeatures.dir/FeatureParser.cpp.o.d -o CMakeFiles/MolChemicalFeatures.dir/FeatureParser.cpp.o -c /build/reproducible-path/rdkit-202503.1/Code/GraphMol/MolChemicalFeatures/FeatureParser.cpp +[ 33%] 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 -DRDK_BUILD_THREADSAFE_SSS -DRDK_BUILD_XYZ2MOL_SUPPORT -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202503.1/External -I/build/reproducible-path/rdkit-202503.1/Code -I/build/reproducible-path/rdkit-202503.1/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/Fingerprints/CMakeFiles/Fingerprints.dir/AtomPairGenerator.cpp.o -MF CMakeFiles/Fingerprints.dir/AtomPairGenerator.cpp.o.d -o CMakeFiles/Fingerprints.dir/AtomPairGenerator.cpp.o -c /build/reproducible-path/rdkit-202503.1/Code/GraphMol/Fingerprints/AtomPairGenerator.cpp +[ 33%] Linking CXX shared module ../../../../rdkit/Chem/rdCIPLabeler.so +cd /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/CIPLabeler/Wrap && /usr/bin/cmake -E cmake_link_script CMakeFiles/rdCIPLabeler.dir/link.txt --verbose=1 +/usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -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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target rdCIPLabeler +[ 33%] 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_BUILD_XYZ2MOL_SUPPORT -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202503.1/External -I/build/reproducible-path/rdkit-202503.1/Code -I/build/reproducible-path/rdkit-202503.1/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 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Code/GraphMol/Abbreviations/CMakeFiles/Abbreviations.dir/Abbreviations.cpp.o cd /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/Abbreviations && /usr/bin/c++ -DAbbreviations_EXPORTS -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_ABBREVIATIONS_BUILD -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_BUILD_XYZ2MOL_SUPPORT -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202503.1/External -I/build/reproducible-path/rdkit-202503.1/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security 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Code/GraphMol/FilterCatalog/Wrap/CMakeFiles/rdfiltercatalog.dir/FilterCatalog.cpp.o -cd /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FilterCatalog/Wrap && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_NUMPY_DYN_LINK -DBOOST_NUMPY_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_BUILD_XYZ2MOL_SUPPORT -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -Drdfiltercatalog_EXPORTS -I/build/reproducible-path/rdkit-202503.1/External -I/build/reproducible-path/rdkit-202503.1/Code -I/build/reproducible-path/rdkit-202503.1/External/boost-numeric-bindings -I/usr/lib/aarch64-linux-gnu/python3-numpy/numpy/_core/include -isystem /usr/include/python3.13 -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/FilterCatalog/Wrap/CMakeFiles/rdfiltercatalog.dir/FilterCatalog.cpp.o -MF CMakeFiles/rdfiltercatalog.dir/FilterCatalog.cpp.o.d -o CMakeFiles/rdfiltercatalog.dir/FilterCatalog.cpp.o -c /build/reproducible-path/rdkit-202503.1/Code/GraphMol/FilterCatalog/Wrap/FilterCatalog.cpp [ 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 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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/Depictor/CMakeFiles/Depictor.dir/Templates.cpp.o -MF CMakeFiles/Depictor.dir/Templates.cpp.o.d -o CMakeFiles/Depictor.dir/Templates.cpp.o -c /build/reproducible-path/rdkit-202503.1/Code/GraphMol/Depictor/Templates.cpp +[ 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++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 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&& /usr/bin/cmake -E cmake_symlink_library ../../../lib/libRDKitAbbreviations.so.1.2025.03.1 ../../../lib/libRDKitAbbreviations.so.1 ../../../lib/libRDKitAbbreviations.so make[4]: Leaving directory '/build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu' -[ 35%] Built target Abbreviations -make -f Code/GraphMol/ForceFieldHelpers/CMakeFiles/ForceFieldHelpers.dir/build.make Code/GraphMol/ForceFieldHelpers/CMakeFiles/ForceFieldHelpers.dir/depend +[ 36%] Built target Abbreviations +make -f Code/GraphMol/FilterCatalog/Wrap/CMakeFiles/rdfiltercatalog.dir/build.make Code/GraphMol/FilterCatalog/Wrap/CMakeFiles/rdfiltercatalog.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-202503.1/obj-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 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Code/GraphMol/MolChemicalFeatures/Wrap/CMakeFiles/rdMolChemicalFeatures.dir/MolChemicalFeatureFactory.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_BUILD_XYZ2MOL_SUPPORT -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 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+/build/reproducible-path/rdkit-202503.1/Code/GraphMol/ForceFieldHelpers/MMFF/Builder.cpp:428:68: note: parameter passing for argument of type 'std::pair' when C++17 is enabled changed to match C++14 in GCC 10.1 + 428 | MMFF::Utils::calcStbnForceConstants(&mmffStbnParams); + | ^ +[ 36%] Building CXX object Code/GraphMol/ForceFieldHelpers/CMakeFiles/ForceFieldHelpers.dir/CrystalFF/TorsionAngleContribs.cpp.o +cd /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/ForceFieldHelpers && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DForceFieldHelpers_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_FORCEFIELDHELPERS_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_BUILD_XYZ2MOL_SUPPORT -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS 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"--color=" @@ -4141,21 +4166,10 @@ make[4]: Entering directory '/build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu' [ 38%] 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 -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_BUILD_XYZ2MOL_SUPPORT -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202503.1/External -I/build/reproducible-path/rdkit-202503.1/Code -isystem /usr/include/eigen3 -g -O2 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/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' -[ 38%] Built target testSLNParse [ 38%] Building CXX object Code/GraphMol/ChemTransforms/CMakeFiles/ChemTransforms.dir/MolFragmenter.cpp.o cd /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/ChemTransforms && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DChemTransforms_EXPORTS -DRDKIT_CHEMTRANSFORMS_BUILD -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_BUILD_XYZ2MOL_SUPPORT -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202503.1/External 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-I/build/reproducible-path/rdkit-202503.1/External -I/build/reproducible-path/rdkit-202503.1/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-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/MolFragmenterJSONParser.cpp.o -MF CMakeFiles/ChemTransforms.dir/MolFragmenterJSONParser.cpp.o.d -o CMakeFiles/ChemTransforms.dir/MolFragmenterJSONParser.cpp.o -c /build/reproducible-path/rdkit-202503.1/Code/GraphMol/ChemTransforms/MolFragmenterJSONParser.cpp -make -f Code/GraphMol/MolHash/CMakeFiles/MolHash.dir/build.make Code/GraphMol/MolHash/CMakeFiles/MolHash.dir/depend +make -f Code/GraphMol/Fingerprints/Wrap/CMakeFiles/rdFingerprintGenerator.dir/build.make 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CMakeFiles/MolHash.dir/hashfunctions.cpp.o.d -o CMakeFiles/MolHash.dir/hashfunctions.cpp.o -c /build/reproducible-path/rdkit-202503.1/Code/GraphMol/MolHash/hashfunctions.cpp -[ 38%] 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 -[ 38%] 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 -/usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated 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/usr/lib/aarch64-linux-gnu/libboost_system.so.1.83.0 /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' -/usr/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/rdMHFPFingerprint.dir/link.d -Wl,-z,relro -Wl,-z,now -shared -o ../../../../rdkit/Chem/rdMHFPFingerprint.so CMakeFiles/rdMHFPFingerprint.dir/MHFPWrapper.cpp.o ../../../../lib/libRDKitFingerprints.so.1.2025.03.1 ../../../../lib/libRDKitRDBoost.so.1.2025.03.1 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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/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 [ 38%] Linking CXX shared library ../../../lib/libRDKitForceFieldHelpers.so cd /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/ForceFieldHelpers && /usr/bin/cmake -E cmake_link_script CMakeFiles/ForceFieldHelpers.dir/link.txt --verbose=1 /usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,--dependency-file=CMakeFiles/ForceFieldHelpers.dir/link.d -Wl,-z,relro -Wl,-z,now -shared -Wl,-soname,libRDKitForceFieldHelpers.so.1 -o ../../../lib/libRDKitForceFieldHelpers.so.1.2025.03.1 CMakeFiles/ForceFieldHelpers.dir/UFF/AtomTyper.cpp.o CMakeFiles/ForceFieldHelpers.dir/UFF/Builder.cpp.o CMakeFiles/ForceFieldHelpers.dir/MMFF/AtomTyper.cpp.o CMakeFiles/ForceFieldHelpers.dir/MMFF/Builder.cpp.o 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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 -f Code/ForceField/Wrap/CMakeFiles/rdForceField.dir/build.make Code/ForceField/Wrap/CMakeFiles/rdForceField.dir/build +make -f Code/GraphMol/Fingerprints/Wrap/CMakeFiles/rdMHFPFingerprint.dir/build.make Code/GraphMol/Fingerprints/Wrap/CMakeFiles/rdMHFPFingerprint.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu' -[ 38%] Building CXX object Code/ForceField/CMakeFiles/ForceFieldsCatch.dir/catch_tests.cpp.o +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 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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/ChiralViolationContribs.cpp.o -MF CMakeFiles/DistGeometry.dir/ChiralViolationContribs.cpp.o.d -o CMakeFiles/DistGeometry.dir/ChiralViolationContribs.cpp.o -c /build/reproducible-path/rdkit-202503.1/Code/DistGeom/ChiralViolationContribs.cpp +[ 38%] Built target rdReducedGraphs make -f Code/GraphMol/ForceFieldHelpers/Wrap/CMakeFiles/rdForceFieldHelpers.dir/build.make Code/GraphMol/ForceFieldHelpers/Wrap/CMakeFiles/rdForceFieldHelpers.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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/usr/lib/aarch64-linux-gnu/libboost_numpy313.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_python313.so.1.83.0 ../../../../lib/libRDKitRDGeneral.so.1.2025.03.1 /usr/lib/aarch64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl +make[4]: Leaving directory '/build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu' +[ 39%] Built target rdAbbreviations +[ 39%] Building CXX object Code/DistGeom/CMakeFiles/DistGeometry.dir/TriangleSmooth.cpp.o +cd /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/DistGeom && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DDistGeometry_EXPORTS -DRDKIT_DISTGEOMETRY_BUILD -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_BUILD_XYZ2MOL_SUPPORT -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202503.1/External -I/build/reproducible-path/rdkit-202503.1/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -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 [ 39%] Linking CXX shared library ../../../lib/libRDKitMolHash.so cd 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../../../lib/libRDKitSmilesParse.so.1.2025.03.1 ../../../lib/libRDKitMolTransforms.so.1.2025.03.1 ../../../lib/libRDKitGraphMol.so.1.2025.03.1 ../../../lib/libRDKitEigenSolvers.so.1.2025.03.1 ../../../lib/libRDKitAlignment.so.1.2025.03.1 ../../../lib/libRDKitRDGeometryLib.so.1.2025.03.1 ../../../lib/libRDKitDataStructs.so.1.2025.03.1 ../../../lib/libRDKitRDGeneral.so.1.2025.03.1 /usr/lib/aarch64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl cd /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/MolHash && /usr/bin/cmake -E cmake_symlink_library ../../../lib/libRDKitMolHash.so.1.2025.03.1 ../../../lib/libRDKitMolHash.so.1 ../../../lib/libRDKitMolHash.so make[4]: Leaving directory '/build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu' [ 39%] Built target MolHash +make -f Code/ForceField/Wrap/CMakeFiles/rdForceField.dir/build.make 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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 -DBOOST_PYTHON_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_BUILD_XYZ2MOL_SUPPORT -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DrdForceField_EXPORTS -I/build/reproducible-path/rdkit-202503.1/External -I/build/reproducible-path/rdkit-202503.1/Code -I/usr/lib/aarch64-linux-gnu/python3-numpy/numpy/_core/include -isystem /usr/include/python3.13 -isystem /usr/include/eigen3 -g -O2 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/build/reproducible-path/rdkit-202503.1/Code/GraphMol/MolHash/Wrap/rdMolHash.cpp +[ 39%] Building CXX object Code/DistGeom/CMakeFiles/DistGeometry.dir/DistViolationContribs.cpp.o +cd /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/DistGeom && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DDistGeometry_EXPORTS -DRDKIT_DISTGEOMETRY_BUILD -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_BUILD_XYZ2MOL_SUPPORT -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202503.1/External -I/build/reproducible-path/rdkit-202503.1/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -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 +[ 39%] Linking CXX shared module ../../../../rdkit/Chem/rdForceFieldHelpers.so +cd /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/ForceFieldHelpers/Wrap && /usr/bin/cmake -E cmake_link_script CMakeFiles/rdForceFieldHelpers.dir/link.txt --verbose=1 +/usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat 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-DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_BUILD_XYZ2MOL_SUPPORT -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202503.1/External -I/build/reproducible-path/rdkit-202503.1/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/DistGeom/CMakeFiles/DistGeometry.dir/ChiralViolationContribs.cpp.o -MF CMakeFiles/DistGeometry.dir/ChiralViolationContribs.cpp.o.d -o CMakeFiles/DistGeometry.dir/ChiralViolationContribs.cpp.o -c /build/reproducible-path/rdkit-202503.1/Code/DistGeom/ChiralViolationContribs.cpp +[ 39%] 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 [ 39%] Linking CXX executable ForceFieldsCatch cd /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/ForceField && /usr/bin/cmake -E cmake_link_script CMakeFiles/ForceFieldsCatch.dir/link.txt --verbose=1 +[ 39%] Linking CXX shared module ../../../../rdkit/Chem/rdDepictor.so +cd /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/Depictor/Wrap && /usr/bin/cmake -E cmake_link_script CMakeFiles/rdDepictor.dir/link.txt --verbose=1 +/usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 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-DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202503.1/External -I/build/reproducible-path/rdkit-202503.1/Code -I/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 -[ 39%] Linking CXX shared module ../../../../rdkit/Chem/rdDepictor.so -cd /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/Depictor/Wrap && 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../../../../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 +[ 39%] Linking CXX shared library ../../../lib/libRDKitMolInteractionFields.so +cd /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/MolInteractionFields && /usr/bin/cmake -E cmake_link_script CMakeFiles/MolInteractionFields.dir/link.txt --verbose=1 +/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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-DRDK_USE_STRICT_ROTOR_DEFINITION -DrdMIF_EXPORTS -I/build/reproducible-path/rdkit-202503.1/External -I/build/reproducible-path/rdkit-202503.1/Code -I/usr/lib/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/MolInteractionFields/Wrap/CMakeFiles/rdMIF.dir/rdMIF.cpp.o -MF CMakeFiles/rdMIF.dir/rdMIF.cpp.o.d -o CMakeFiles/rdMIF.dir/rdMIF.cpp.o -c /build/reproducible-path/rdkit-202503.1/Code/GraphMol/MolInteractionFields/Wrap/rdMIF.cpp +[ 39%] Linking CXX shared module ../../../../rdkit/Chem/rdMolHash.so +cd 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CMakeFiles/FileParsers.dir/ForwardSDMolSupplier.cpp.o.d -o CMakeFiles/FileParsers.dir/ForwardSDMolSupplier.cpp.o -c /build/reproducible-path/rdkit-202503.1/Code/GraphMol/FileParsers/ForwardSDMolSupplier.cpp +[ 40%] Building CXX object Code/GraphMol/DistGeomHelpers/CMakeFiles/DistGeomHelpers.dir/EmbedderUtils.cpp.o +cd /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/DistGeomHelpers && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DDistGeomHelpers_EXPORTS -DRDKIT_DISTGEOMHELPERS_BUILD -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_BUILD_XYZ2MOL_SUPPORT -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_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/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 +[ 40%] 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 +[ 40%] Linking CXX shared module 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/build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DFileParsers_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_FILEPARSERS_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_BUILD_XYZ2MOL_SUPPORT -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202503.1/External -I/build/reproducible-path/rdkit-202503.1/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/FileParsers/CMakeFiles/FileParsers.dir/ForwardSDMolSupplier.cpp.o -MF CMakeFiles/FileParsers.dir/ForwardSDMolSupplier.cpp.o.d -o CMakeFiles/FileParsers.dir/ForwardSDMolSupplier.cpp.o -c /build/reproducible-path/rdkit-202503.1/Code/GraphMol/FileParsers/ForwardSDMolSupplier.cpp -[ 40%] 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 [ 40%] 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 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/usr/lib/aarch64-linux-gnu/libboost_numpy313.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_python313.so.1.83.0 ../../../../lib/libRDKitRDGeneral.so.1.2025.03.1 /usr/lib/aarch64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl make[4]: Leaving directory '/build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu' -make -f Code/GraphMol/MolInteractionFields/Wrap/CMakeFiles/rdMIF.dir/build.make Code/GraphMol/MolInteractionFields/Wrap/CMakeFiles/rdMIF.dir/build -make[4]: Entering directory '/build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu' -[ 40%] Building CXX object Code/GraphMol/MolInteractionFields/Wrap/CMakeFiles/rdMIF.dir/rdMIF.cpp.o -cd /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/MolInteractionFields/Wrap && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_NUMPY_DYN_LINK -DBOOST_NUMPY_NO_LIB 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-Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/MolInteractionFields/Wrap/CMakeFiles/rdMIF.dir/rdMIF.cpp.o -MF CMakeFiles/rdMIF.dir/rdMIF.cpp.o.d -o CMakeFiles/rdMIF.dir/rdMIF.cpp.o -c /build/reproducible-path/rdkit-202503.1/Code/GraphMol/MolInteractionFields/Wrap/rdMIF.cpp +[ 40%] Built target rdfiltercatalog [ 40%] 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 -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DFileParsers_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_FILEPARSERS_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_BUILD_XYZ2MOL_SUPPORT -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202503.1/External -I/build/reproducible-path/rdkit-202503.1/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/FileParsers/CMakeFiles/FileParsers.dir/SDWriter.cpp.o -MF CMakeFiles/FileParsers.dir/SDWriter.cpp.o.d -o CMakeFiles/FileParsers.dir/SDWriter.cpp.o -c /build/reproducible-path/rdkit-202503.1/Code/GraphMol/FileParsers/SDWriter.cpp -[ 40%] Linking CXX shared 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 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../../../lib/libRDKitSubstructMatch.so.1.2025.03.1 ../../../lib/libRDKitGenericGroups.so.1.2025.03.1 ../../../lib/libRDKitSmilesParse.so.1.2025.03.1 ../../../lib/libRDKitForceField.so.1.2025.03.1 ../../../lib/libRDKitOptimizer.so.1.2025.03.1 ../../../lib/libRDKitTrajectory.so.1.2025.03.1 ../../../lib/libRDKitGraphMol.so.1.2025.03.1 ../../../lib/libRDKitRDGeometryLib.so.1.2025.03.1 ../../../lib/libRDKitDataStructs.so.1.2025.03.1 ../../../lib/libRDKitEigenSolvers.so.1.2025.03.1 ../../../lib/libRDKitRDGeneral.so.1.2025.03.1 /usr/lib/aarch64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl -cd /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/DistGeomHelpers && /usr/bin/cmake -E cmake_symlink_library ../../../lib/libRDKitDistGeomHelpers.so.1.2025.03.1 ../../../lib/libRDKitDistGeomHelpers.so.1 ../../../lib/libRDKitDistGeomHelpers.so -make[4]: Leaving directory '/build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu' -[ 40%] Built target DistGeomHelpers [ 40%] Building CXX object Code/GraphMol/FileParsers/CMakeFiles/FileParsers.dir/SmilesMolSupplier.cpp.o cd /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DFileParsers_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_FILEPARSERS_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_BUILD_XYZ2MOL_SUPPORT -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202503.1/External -I/build/reproducible-path/rdkit-202503.1/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/FileParsers/CMakeFiles/FileParsers.dir/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 [ 40%] Building CXX object 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 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CMakeFiles/FileParsers.dir/SmilesWriter.cpp.o -c /build/reproducible-path/rdkit-202503.1/Code/GraphMol/FileParsers/SmilesWriter.cpp [ 40%] Building CXX object Code/GraphMol/FileParsers/CMakeFiles/FileParsers.dir/TDTMolSupplier.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_BUILD_XYZ2MOL_SUPPORT -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202503.1/External -I/build/reproducible-path/rdkit-202503.1/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/FileParsers/CMakeFiles/FileParsers.dir/TDTMolSupplier.cpp.o -MF CMakeFiles/FileParsers.dir/TDTMolSupplier.cpp.o.d -o CMakeFiles/FileParsers.dir/TDTMolSupplier.cpp.o -c /build/reproducible-path/rdkit-202503.1/Code/GraphMol/FileParsers/TDTMolSupplier.cpp +[ 40%] Linking CXX shared module ../../../rdkit/DistanceGeometry/DistGeom.so +cd /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/DistGeom/Wrap && /usr/bin/cmake -E cmake_link_script CMakeFiles/DistGeom.dir/link.txt --verbose=1 +/usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat 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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' +[ 40%] Built target DistGeom [ 40%] Building CXX object Code/GraphMol/FileParsers/CMakeFiles/FileParsers.dir/TDTWriter.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_BUILD_XYZ2MOL_SUPPORT -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202503.1/External -I/build/reproducible-path/rdkit-202503.1/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/FileParsers/CMakeFiles/FileParsers.dir/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 [ 40%] 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_BUILD_XYZ2MOL_SUPPORT -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202503.1/External -I/build/reproducible-path/rdkit-202503.1/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/FileParsers/CMakeFiles/FileParsers.dir/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 +[ 40%] 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' +[ 40%] Built target rdMIF [ 40%] 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_BUILD_XYZ2MOL_SUPPORT -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202503.1/External -I/build/reproducible-path/rdkit-202503.1/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/FileParsers/CMakeFiles/FileParsers.dir/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 [ 41%] Building CXX object Code/GraphMol/FileParsers/CMakeFiles/FileParsers.dir/PDBParser.cpp.o @@ -4431,6 +4461,12 @@ cd /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DFileParsers_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_FILEPARSERS_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_BUILD_XYZ2MOL_SUPPORT -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202503.1/External -I/build/reproducible-path/rdkit-202503.1/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/FileParsers/CMakeFiles/FileParsers.dir/XYZFileWriter.cpp.o -MF CMakeFiles/FileParsers.dir/XYZFileWriter.cpp.o.d -o CMakeFiles/FileParsers.dir/XYZFileWriter.cpp.o -c /build/reproducible-path/rdkit-202503.1/Code/GraphMol/FileParsers/XYZFileWriter.cpp [ 41%] Building CXX object Code/GraphMol/FileParsers/CMakeFiles/FileParsers.dir/XYZFileParser.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_BUILD_XYZ2MOL_SUPPORT -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202503.1/External -I/build/reproducible-path/rdkit-202503.1/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/FileParsers/CMakeFiles/FileParsers.dir/XYZFileParser.cpp.o -MF CMakeFiles/FileParsers.dir/XYZFileParser.cpp.o.d -o CMakeFiles/FileParsers.dir/XYZFileParser.cpp.o -c /build/reproducible-path/rdkit-202503.1/Code/GraphMol/FileParsers/XYZFileParser.cpp +[ 41%] 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 -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,--dependency-file=CMakeFiles/DistGeomHelpers.dir/link.d -Wl,-z,relro -Wl,-z,now -shared -Wl,-soname,libRDKitDistGeomHelpers.so.1 -o ../../../lib/libRDKitDistGeomHelpers.so.1.2025.03.1 CMakeFiles/DistGeomHelpers.dir/BoundsMatrixBuilder.cpp.o CMakeFiles/DistGeomHelpers.dir/Embedder.cpp.o CMakeFiles/DistGeomHelpers.dir/EmbedderUtils.cpp.o ../../../lib/libRDKitMolAlign.so.1.2025.03.1 ../../../lib/libRDKitDistGeometry.so.1.2025.03.1 ../../../lib/libRDKitAlignment.so.1.2025.03.1 ../../../lib/libRDKitMolTransforms.so.1.2025.03.1 ../../../lib/libRDKitForceFieldHelpers.so.1.2025.03.1 ../../../lib/libRDKitSubstructMatch.so.1.2025.03.1 ../../../lib/libRDKitGenericGroups.so.1.2025.03.1 ../../../lib/libRDKitSmilesParse.so.1.2025.03.1 ../../../lib/libRDKitForceField.so.1.2025.03.1 ../../../lib/libRDKitOptimizer.so.1.2025.03.1 ../../../lib/libRDKitTrajectory.so.1.2025.03.1 ../../../lib/libRDKitGraphMol.so.1.2025.03.1 ../../../lib/libRDKitRDGeometryLib.so.1.2025.03.1 ../../../lib/libRDKitDataStructs.so.1.2025.03.1 ../../../lib/libRDKitEigenSolvers.so.1.2025.03.1 ../../../lib/libRDKitRDGeneral.so.1.2025.03.1 /usr/lib/aarch64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl +cd /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/DistGeomHelpers && /usr/bin/cmake -E cmake_symlink_library ../../../lib/libRDKitDistGeomHelpers.so.1.2025.03.1 ../../../lib/libRDKitDistGeomHelpers.so.1 ../../../lib/libRDKitDistGeomHelpers.so +make[4]: Leaving directory '/build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu' +[ 41%] Built target DistGeomHelpers [ 41%] Building CXX object Code/GraphMol/FileParsers/CMakeFiles/FileParsers.dir/MaeMolSupplier.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_BUILD_XYZ2MOL_SUPPORT -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202503.1/External -I/build/reproducible-path/rdkit-202503.1/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/FileParsers/CMakeFiles/FileParsers.dir/MaeMolSupplier.cpp.o -MF CMakeFiles/FileParsers.dir/MaeMolSupplier.cpp.o.d -o CMakeFiles/FileParsers.dir/MaeMolSupplier.cpp.o -c /build/reproducible-path/rdkit-202503.1/Code/GraphMol/FileParsers/MaeMolSupplier.cpp [ 41%] Building CXX object Code/GraphMol/FileParsers/CMakeFiles/FileParsers.dir/MaeWriter.cpp.o @@ -4441,11 +4477,6 @@ 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_BUILD_XYZ2MOL_SUPPORT -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202503.1/External -I/build/reproducible-path/rdkit-202503.1/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/FileParsers/CMakeFiles/FileParsers.dir/SequenceParsers.cpp.o -MF CMakeFiles/FileParsers.dir/SequenceParsers.cpp.o.d -o CMakeFiles/FileParsers.dir/SequenceParsers.cpp.o -c /build/reproducible-path/rdkit-202503.1/Code/GraphMol/FileParsers/SequenceParsers.cpp [ 41%] Building CXX object Code/GraphMol/FileParsers/CMakeFiles/FileParsers.dir/SequenceWriters.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_BUILD_XYZ2MOL_SUPPORT -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202503.1/External -I/build/reproducible-path/rdkit-202503.1/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/FileParsers/CMakeFiles/FileParsers.dir/SequenceWriters.cpp.o -MF CMakeFiles/FileParsers.dir/SequenceWriters.cpp.o.d -o CMakeFiles/FileParsers.dir/SequenceWriters.cpp.o -c /build/reproducible-path/rdkit-202503.1/Code/GraphMol/FileParsers/SequenceWriters.cpp -[ 41%] 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' -[ 41%] Built target rdMIF [ 42%] Building CXX object Code/GraphMol/FileParsers/CMakeFiles/FileParsers.dir/SVGParser.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_BUILD_XYZ2MOL_SUPPORT -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202503.1/External -I/build/reproducible-path/rdkit-202503.1/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/FileParsers/CMakeFiles/FileParsers.dir/SVGParser.cpp.o -MF CMakeFiles/FileParsers.dir/SVGParser.cpp.o.d -o CMakeFiles/FileParsers.dir/SVGParser.cpp.o -c /build/reproducible-path/rdkit-202503.1/Code/GraphMol/FileParsers/SVGParser.cpp [ 42%] Building CXX object Code/GraphMol/FileParsers/CMakeFiles/FileParsers.dir/PNGParser.cpp.o @@ -4467,97 +4498,97 @@ make -f Code/ForceField/MMFF/CMakeFiles/testMMFFForceField.dir/build.make Code/ForceField/MMFF/CMakeFiles/testMMFFForceField.dir/depend make -f Code/GraphMol/CMakeFiles/graphmolMolOpsTest.dir/build.make Code/GraphMol/CMakeFiles/graphmolMolOpsTest.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-202503.1/obj-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[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/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/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 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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=" +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 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../../lib/libRDKitSubstructMatch.so.1.2025.03.1 ../../lib/libRDKitGenericGroups.so.1.2025.03.1 ../../lib/libRDKitGraphMol.so.1.2025.03.1 ../../lib/libRDKitRDGeometryLib.so.1.2025.03.1 ../../lib/libRDKitDataStructs.so.1.2025.03.1 ../../lib/libRDKitRDGeneral.so.1.2025.03.1 /usr/lib/aarch64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl /usr/lib/aarch64-linux-gnu/libmaeparser.so @@ -4662,24 +4693,24 @@ make[4]: Entering directory '/build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu' [ 45%] Building CXX object Code/GraphMol/CMakeFiles/molopsTestsCatch.dir/catch_molops.cpp.o cd /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD 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../../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' -[ 46%] Built target graphmolSGroupCatch +[ 46%] Built target testSGroup make -f Code/GraphMol/ChemReactions/CMakeFiles/ChemReactions.dir/build.make Code/GraphMol/ChemReactions/CMakeFiles/ChemReactions.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu' cd /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202503.1 /build/reproducible-path/rdkit-202503.1/Code/GraphMol/ChemReactions /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu 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-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 [ 46%] Linking CXX executable graphmolAdjustQueryCatch cd /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol && /usr/bin/cmake -E cmake_link_script CMakeFiles/graphmolAdjustQueryCatch.dir/link.txt --verbose=1 +[ 47%] 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 /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 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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/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 -[ 47%] Linking CXX executable graphmoltestPickler -cd /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol && /usr/bin/cmake -E cmake_link_script CMakeFiles/graphmoltestPickler.dir/link.txt --verbose=1 -/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/graphmoltestPickler.dir/link.d CMakeFiles/graphmoltestPickler.dir/testPickler.cpp.o -o graphmoltestPickler ../../lib/libRDKitFileParsers.so.1.2025.03.1 ../../lib/libRDKitChemTransforms.so.1.2025.03.1 ../../lib/libRDKitDepictor.so.1.2025.03.1 /usr/lib/aarch64-linux-gnu/libcoordgen.so ../../lib/libRDKitMolAlign.so.1.2025.03.1 ../../lib/libRDKitSmilesParse.so.1.2025.03.1 ../../lib/libRDKitSubstructMatch.so.1.2025.03.1 ../../lib/libRDKitGenericGroups.so.1.2025.03.1 ../../lib/libRDKitMolTransforms.so.1.2025.03.1 ../../lib/libRDKitGraphMol.so.1.2025.03.1 ../../lib/libRDKitEigenSolvers.so.1.2025.03.1 ../../lib/libRDKitAlignment.so.1.2025.03.1 ../../lib/libRDKitRDGeometryLib.so.1.2025.03.1 ../../lib/libRDKitDataStructs.so.1.2025.03.1 ../../lib/libRDKitRDGeneral.so.1.2025.03.1 /usr/lib/aarch64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl /usr/lib/aarch64-linux-gnu/libmaeparser.so +[ 47%] Linking CXX executable canonTestsCatch +cd /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol && /usr/bin/cmake -E cmake_link_script 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/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' -[ 47%] Built target graphmoltestPickler +[ 47%] Built target canonTestsCatch 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=" @@ -4734,11 +4765,11 @@ make[4]: Entering directory '/build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu' [ 47%] Building CXX object Code/GraphMol/Depictor/CMakeFiles/testDepictor.dir/testDepictor.cpp.o cd /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/Depictor && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DIN_COORDGEN -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_BUILD_XYZ2MOL_SUPPORT -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202503.1/External -I/build/reproducible-path/rdkit-202503.1/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/GraphMol/Depictor/CMakeFiles/testDepictor.dir/testDepictor.cpp.o -MF CMakeFiles/testDepictor.dir/testDepictor.cpp.o.d -o CMakeFiles/testDepictor.dir/testDepictor.cpp.o -c /build/reproducible-path/rdkit-202503.1/Code/GraphMol/Depictor/testDepictor.cpp -[ 47%] Linking CXX executable 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/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 +[ 47%] Linking CXX executable molopsTestsCatch +cd /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol && /usr/bin/cmake -E cmake_link_script CMakeFiles/molopsTestsCatch.dir/link.txt --verbose=1 +/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/molopsTestsCatch.dir/link.d CMakeFiles/molopsTestsCatch.dir/catch_molops.cpp.o -o molopsTestsCatch ../RDGeneral/librdkitCatch.a ../../lib/libRDKitFileParsers.so.1.2025.03.1 /usr/lib/libCatch2.a ../../lib/libRDKitChemTransforms.so.1.2025.03.1 ../../lib/libRDKitDepictor.so.1.2025.03.1 /usr/lib/aarch64-linux-gnu/libcoordgen.so ../../lib/libRDKitMolAlign.so.1.2025.03.1 ../../lib/libRDKitSmilesParse.so.1.2025.03.1 ../../lib/libRDKitMolTransforms.so.1.2025.03.1 ../../lib/libRDKitEigenSolvers.so.1.2025.03.1 ../../lib/libRDKitAlignment.so.1.2025.03.1 ../../lib/libRDKitSubstructMatch.so.1.2025.03.1 ../../lib/libRDKitGenericGroups.so.1.2025.03.1 ../../lib/libRDKitGraphMol.so.1.2025.03.1 ../../lib/libRDKitRDGeometryLib.so.1.2025.03.1 ../../lib/libRDKitDataStructs.so.1.2025.03.1 ../../lib/libRDKitRDGeneral.so.1.2025.03.1 /usr/lib/aarch64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl /usr/lib/aarch64-linux-gnu/libmaeparser.so make[4]: Leaving directory '/build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu' -[ 47%] Built target canonTestsCatch +[ 47%] Built target molopsTestsCatch 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=" @@ -4747,11 +4778,11 @@ make[4]: Entering directory '/build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu' [ 47%] Building CXX object Code/GraphMol/Depictor/CMakeFiles/depictorCatch.dir/catch_tests.cpp.o cd /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/Depictor && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DIN_COORDGEN -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_BUILD_XYZ2MOL_SUPPORT -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202503.1/External -I/build/reproducible-path/rdkit-202503.1/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/GraphMol/Depictor/CMakeFiles/depictorCatch.dir/catch_tests.cpp.o -MF CMakeFiles/depictorCatch.dir/catch_tests.cpp.o.d -o CMakeFiles/depictorCatch.dir/catch_tests.cpp.o -c /build/reproducible-path/rdkit-202503.1/Code/GraphMol/Depictor/catch_tests.cpp -[ 47%] Linking CXX executable molopsTestsCatch -cd /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol && /usr/bin/cmake -E cmake_link_script CMakeFiles/molopsTestsCatch.dir/link.txt --verbose=1 -/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/molopsTestsCatch.dir/link.d CMakeFiles/molopsTestsCatch.dir/catch_molops.cpp.o -o molopsTestsCatch ../RDGeneral/librdkitCatch.a ../../lib/libRDKitFileParsers.so.1.2025.03.1 /usr/lib/libCatch2.a ../../lib/libRDKitChemTransforms.so.1.2025.03.1 ../../lib/libRDKitDepictor.so.1.2025.03.1 /usr/lib/aarch64-linux-gnu/libcoordgen.so ../../lib/libRDKitMolAlign.so.1.2025.03.1 ../../lib/libRDKitSmilesParse.so.1.2025.03.1 ../../lib/libRDKitMolTransforms.so.1.2025.03.1 ../../lib/libRDKitEigenSolvers.so.1.2025.03.1 ../../lib/libRDKitAlignment.so.1.2025.03.1 ../../lib/libRDKitSubstructMatch.so.1.2025.03.1 ../../lib/libRDKitGenericGroups.so.1.2025.03.1 ../../lib/libRDKitGraphMol.so.1.2025.03.1 ../../lib/libRDKitRDGeometryLib.so.1.2025.03.1 ../../lib/libRDKitDataStructs.so.1.2025.03.1 ../../lib/libRDKitRDGeneral.so.1.2025.03.1 /usr/lib/aarch64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl /usr/lib/aarch64-linux-gnu/libmaeparser.so +[ 47%] Linking CXX executable graphmoltestPickler +cd /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol && /usr/bin/cmake -E cmake_link_script CMakeFiles/graphmoltestPickler.dir/link.txt --verbose=1 +/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/graphmoltestPickler.dir/link.d CMakeFiles/graphmoltestPickler.dir/testPickler.cpp.o -o graphmoltestPickler ../../lib/libRDKitFileParsers.so.1.2025.03.1 ../../lib/libRDKitChemTransforms.so.1.2025.03.1 ../../lib/libRDKitDepictor.so.1.2025.03.1 /usr/lib/aarch64-linux-gnu/libcoordgen.so ../../lib/libRDKitMolAlign.so.1.2025.03.1 ../../lib/libRDKitSmilesParse.so.1.2025.03.1 ../../lib/libRDKitSubstructMatch.so.1.2025.03.1 ../../lib/libRDKitGenericGroups.so.1.2025.03.1 ../../lib/libRDKitMolTransforms.so.1.2025.03.1 ../../lib/libRDKitGraphMol.so.1.2025.03.1 ../../lib/libRDKitEigenSolvers.so.1.2025.03.1 ../../lib/libRDKitAlignment.so.1.2025.03.1 ../../lib/libRDKitRDGeometryLib.so.1.2025.03.1 ../../lib/libRDKitDataStructs.so.1.2025.03.1 ../../lib/libRDKitRDGeneral.so.1.2025.03.1 /usr/lib/aarch64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl /usr/lib/aarch64-linux-gnu/libmaeparser.so make[4]: Leaving directory '/build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu' -[ 47%] Built target molopsTestsCatch +[ 47%] Built target graphmoltestPickler make -f Code/GraphMol/FileParsers/CMakeFiles/fileParsersTest1.dir/build.make Code/GraphMol/FileParsers/CMakeFiles/fileParsersTest1.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu' cd /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202503.1 /build/reproducible-path/rdkit-202503.1/Code/GraphMol/FileParsers /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/CMakeFiles/fileParsersTest1.dir/DependInfo.cmake "--color=" @@ -4760,11 +4791,6 @@ make[4]: Entering directory '/build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu' [ 47%] Building CXX object Code/GraphMol/FileParsers/CMakeFiles/fileParsersTest1.dir/test1.cpp.o cd /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_BUILD_XYZ2MOL_SUPPORT -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202503.1/External -I/build/reproducible-path/rdkit-202503.1/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/GraphMol/FileParsers/CMakeFiles/fileParsersTest1.dir/test1.cpp.o -MF CMakeFiles/fileParsersTest1.dir/test1.cpp.o.d -o CMakeFiles/fileParsersTest1.dir/test1.cpp.o -c /build/reproducible-path/rdkit-202503.1/Code/GraphMol/FileParsers/test1.cpp -[ 47%] Linking CXX executable graphmoltestChirality -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' -[ 47%] Built target graphmoltestChirality make -f Code/GraphMol/FileParsers/CMakeFiles/testAtropisomers.dir/build.make Code/GraphMol/FileParsers/CMakeFiles/testAtropisomers.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu' cd /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202503.1 /build/reproducible-path/rdkit-202503.1/Code/GraphMol/FileParsers /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/CMakeFiles/testAtropisomers.dir/DependInfo.cmake "--color=" @@ -4773,12 +4799,17 @@ make[4]: Entering directory '/build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu' [ 47%] Building CXX object Code/GraphMol/FileParsers/CMakeFiles/testAtropisomers.dir/testAtropisomers.cpp.o cd /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_BUILD_XYZ2MOL_SUPPORT -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202503.1/External -I/build/reproducible-path/rdkit-202503.1/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/GraphMol/FileParsers/CMakeFiles/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 +[ 47%] Linking CXX executable graphmoltestChirality +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' +[ 47%] Built target graphmoltestChirality [ 47%] Building CXX object Code/GraphMol/ChemReactions/CMakeFiles/ChemReactions.dir/DaylightParser.cpp.o cd /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/ChemReactions && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DChemReactions_EXPORTS -DRDKIT_CHEMREACTIONS_BUILD -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_BUILD_XYZ2MOL_SUPPORT -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202503.1/External 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-DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DChemReactions_EXPORTS -DRDKIT_CHEMREACTIONS_BUILD -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_BUILD_XYZ2MOL_SUPPORT -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202503.1/External -I/build/reproducible-path/rdkit-202503.1/Code -I/build/reproducible-path/rdkit-202503.1/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/ChemReactions/CMakeFiles/ChemReactions.dir/ReactionPickler.cpp.o -MF CMakeFiles/ChemReactions.dir/ReactionPickler.cpp.o.d -o CMakeFiles/ChemReactions.dir/ReactionPickler.cpp.o -c /build/reproducible-path/rdkit-202503.1/Code/GraphMol/ChemReactions/ReactionPickler.cpp [ 48%] 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 +[ 48%] Building CXX object Code/GraphMol/ChemReactions/CMakeFiles/ChemReactions.dir/ReactionPickler.cpp.o +cd /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/ChemReactions && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DChemReactions_EXPORTS -DRDKIT_CHEMREACTIONS_BUILD -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_BUILD_XYZ2MOL_SUPPORT -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202503.1/External -I/build/reproducible-path/rdkit-202503.1/Code -I/build/reproducible-path/rdkit-202503.1/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/ChemReactions/CMakeFiles/ChemReactions.dir/ReactionPickler.cpp.o -MF CMakeFiles/ChemReactions.dir/ReactionPickler.cpp.o.d -o CMakeFiles/ChemReactions.dir/ReactionPickler.cpp.o -c /build/reproducible-path/rdkit-202503.1/Code/GraphMol/ChemReactions/ReactionPickler.cpp /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' [ 48%] Built target nontetrahedralCatch @@ -4805,30 +4836,26 @@ make[4]: Entering directory '/build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu' [ 48%] Building CXX object Code/GraphMol/FileParsers/CMakeFiles/testMolSupplier.dir/testMolSupplier.cpp.o cd /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_BUILD_XYZ2MOL_SUPPORT -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202503.1/External -I/build/reproducible-path/rdkit-202503.1/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/GraphMol/FileParsers/CMakeFiles/testMolSupplier.dir/testMolSupplier.cpp.o -MF CMakeFiles/testMolSupplier.dir/testMolSupplier.cpp.o.d -o CMakeFiles/testMolSupplier.dir/testMolSupplier.cpp.o -c /build/reproducible-path/rdkit-202503.1/Code/GraphMol/FileParsers/testMolSupplier.cpp -[ 49%] Linking CXX executable testDepictor -cd /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/Depictor && /usr/bin/cmake -E cmake_link_script CMakeFiles/testDepictor.dir/link.txt --verbose=1 -/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/testDepictor.dir/link.d CMakeFiles/testDepictor.dir/testDepictor.cpp.o -o testDepictor ../../../lib/libRDKitFileParsers.so.1.2025.03.1 ../../../lib/libRDKitChemTransforms.so.1.2025.03.1 ../../../lib/libRDKitDepictor.so.1.2025.03.1 ../../../lib/libRDKitMolAlign.so.1.2025.03.1 ../../../lib/libRDKitAlignment.so.1.2025.03.1 /usr/lib/aarch64-linux-gnu/libcoordgen.so ../../../lib/libRDKitMolTransforms.so.1.2025.03.1 ../../../lib/libRDKitEigenSolvers.so.1.2025.03.1 ../../../lib/libRDKitSubstructMatch.so.1.2025.03.1 ../../../lib/libRDKitSmilesParse.so.1.2025.03.1 ../../../lib/libRDKitGenericGroups.so.1.2025.03.1 ../../../lib/libRDKitGraphMol.so.1.2025.03.1 ../../../lib/libRDKitRDGeometryLib.so.1.2025.03.1 ../../../lib/libRDKitDataStructs.so.1.2025.03.1 ../../../lib/libRDKitRDGeneral.so.1.2025.03.1 /usr/lib/aarch64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl /usr/lib/aarch64-linux-gnu/libmaeparser.so -make[4]: Leaving directory '/build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu' -[ 49%] Built target testDepictor -[ 49%] 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_BUILD_XYZ2MOL_SUPPORT -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202503.1/External -I/build/reproducible-path/rdkit-202503.1/Code -I/build/reproducible-path/rdkit-202503.1/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/ChemReactions/CMakeFiles/ChemReactions.dir/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 -[ 49%] Building CXX object Code/GraphMol/ChemReactions/CMakeFiles/ChemReactions.dir/ReactionFingerprints.cpp.o -cd 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-ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/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 -/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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/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' -[ 51%] Built target testMultithreadedMolSupplier +[ 50%] Built target testGeneralFileReader +/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 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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_BUILD_XYZ2MOL_SUPPORT -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202503.1/External -I/build/reproducible-path/rdkit-202503.1/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time 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-I/build/reproducible-path/rdkit-202503.1/Code -I/build/reproducible-path/rdkit-202503.1/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/ChemReactions/CMakeFiles/ChemReactions.dir/ReactionRunner.cpp.o -MF CMakeFiles/ChemReactions.dir/ReactionRunner.cpp.o.d -o CMakeFiles/ChemReactions.dir/ReactionRunner.cpp.o -c /build/reproducible-path/rdkit-202503.1/Code/GraphMol/ChemReactions/ReactionRunner.cpp +[ 51%] Linking CXX executable testMol2ToMol +cd /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers && /usr/bin/cmake -E cmake_link_script CMakeFiles/testMol2ToMol.dir/link.txt --verbose=1 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depictorCatch +[ 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 +[ 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 +[ 52%] 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 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/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=" make[4]: Leaving directory '/build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu' make -f Code/GraphMol/FileParsers/CMakeFiles/testExtendedStereoParsing.dir/build.make Code/GraphMol/FileParsers/CMakeFiles/testExtendedStereoParsing.dir/build make[4]: Entering directory '/build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu' -[ 51%] Building CXX object Code/GraphMol/FileParsers/CMakeFiles/testExtendedStereoParsing.dir/testExtendedStereoParsing.cpp.o +[ 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_BUILD_XYZ2MOL_SUPPORT -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202503.1/External -I/build/reproducible-path/rdkit-202503.1/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/GraphMol/FileParsers/CMakeFiles/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 -[ 51%] Linking CXX executable smiTest1 -cd /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/SmilesParse && /usr/bin/cmake -E cmake_link_script CMakeFiles/smiTest1.dir/link.txt --verbose=1 -/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated 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Code/GraphMol/FileParsers/CMakeFiles/fileParsersCatchTest.dir/file_parsers_catch.cpp.o +[ 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_BUILD_XYZ2MOL_SUPPORT -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202503.1/External -I/build/reproducible-path/rdkit-202503.1/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong 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../../../lib/libRDKitRDGeneral.so.1.2025.03.1 /usr/lib/aarch64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl /usr/lib/aarch64-linux-gnu/libmaeparser.so +make[4]: Leaving directory '/build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu' +[ 52%] Built target smiTest1 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 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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=" @@ -4951,9 +4992,13 @@ make[4]: Entering directory '/build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu' [ 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_BUILD_XYZ2MOL_SUPPORT -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202503.1/External -I/build/reproducible-path/rdkit-202503.1/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time 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../../../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%] Building CXX object Code/GraphMol/ChemReactions/CMakeFiles/ChemReactions.dir/CDXMLParser.cpp.o +cd /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/ChemReactions && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DChemReactions_EXPORTS -DRDKIT_CHEMREACTIONS_BUILD -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_BUILD_XYZ2MOL_SUPPORT -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202503.1/External -I/build/reproducible-path/rdkit-202503.1/Code -I/build/reproducible-path/rdkit-202503.1/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong 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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 /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 testExtendedStereoParsing make -f Code/GraphMol/FileParsers/CMakeFiles/cdxmlParserCatchTest.dir/build.make Code/GraphMol/FileParsers/CMakeFiles/cdxmlParserCatchTest.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu' cd /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202503.1 /build/reproducible-path/rdkit-202503.1/Code/GraphMol/FileParsers /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu 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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 -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 -[ 52%] 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/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 +[ 52%] 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 +[ 52%] 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/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' -[ 52%] Built target smiTestCatch +[ 52%] Built target testMolWriter make -f Code/GraphMol/FileParsers/CMakeFiles/molfileStereoCatchTest.dir/build.make Code/GraphMol/FileParsers/CMakeFiles/molfileStereoCatchTest.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu' cd /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202503.1 /build/reproducible-path/rdkit-202503.1/Code/GraphMol/FileParsers /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/CMakeFiles/molfileStereoCatchTest.dir/DependInfo.cmake "--color=" @@ -4975,11 +5022,13 @@ make[4]: Entering directory '/build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu' [ 52%] 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_BUILD_XYZ2MOL_SUPPORT -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202503.1/External -I/build/reproducible-path/rdkit-202503.1/Code -I/build/reproducible-path/rdkit-202503.1/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/GraphMol/FileParsers/CMakeFiles/molfileStereoCatchTest.dir/molfile_stereo_catch.cpp.o -MF CMakeFiles/molfileStereoCatchTest.dir/molfile_stereo_catch.cpp.o.d -o CMakeFiles/molfileStereoCatchTest.dir/molfile_stereo_catch.cpp.o -c /build/reproducible-path/rdkit-202503.1/Code/GraphMol/FileParsers/molfile_stereo_catch.cpp -[ 52%] 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 -/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 +/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' -[ 52%] Built target testExtendedStereoParsing +[ 52%] Built target testMolSupplier +[ 52%] Building CXX object Code/GraphMol/ChemReactions/CMakeFiles/ChemReactions.dir/Enumerate/Enumerate.cpp.o +cd /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/ChemReactions && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DChemReactions_EXPORTS -DRDKIT_CHEMREACTIONS_BUILD -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_BUILD_XYZ2MOL_SUPPORT -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202503.1/External -I/build/reproducible-path/rdkit-202503.1/Code -I/build/reproducible-path/rdkit-202503.1/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -fpermissive -MD -MT Code/GraphMol/ChemReactions/CMakeFiles/ChemReactions.dir/Enumerate/Enumerate.cpp.o -MF CMakeFiles/ChemReactions.dir/Enumerate/Enumerate.cpp.o.d -o CMakeFiles/ChemReactions.dir/Enumerate/Enumerate.cpp.o -c /build/reproducible-path/rdkit-202503.1/Code/GraphMol/ChemReactions/Enumerate/Enumerate.cpp +[ 52%] Building CXX object Code/GraphMol/ChemReactions/CMakeFiles/ChemReactions.dir/Enumerate/EnumerationPickler.cpp.o +cd /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/ChemReactions && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DChemReactions_EXPORTS -DRDKIT_CHEMREACTIONS_BUILD -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_BUILD_XYZ2MOL_SUPPORT -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202503.1/External -I/build/reproducible-path/rdkit-202503.1/Code -I/build/reproducible-path/rdkit-202503.1/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/ChemReactions/CMakeFiles/ChemReactions.dir/Enumerate/EnumerationPickler.cpp.o -MF CMakeFiles/ChemReactions.dir/Enumerate/EnumerationPickler.cpp.o.d -o CMakeFiles/ChemReactions.dir/Enumerate/EnumerationPickler.cpp.o -c /build/reproducible-path/rdkit-202503.1/Code/GraphMol/ChemReactions/Enumerate/EnumerationPickler.cpp 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=" @@ -4988,21 +5037,19 @@ make[4]: Entering directory '/build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu' [ 52%] Building CXX object Code/GraphMol/FileParsers/CMakeFiles/connectTheDotsTest.dir/connectTheDots_catch.cpp.o cd /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_BUILD_XYZ2MOL_SUPPORT -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202503.1/External -I/build/reproducible-path/rdkit-202503.1/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/GraphMol/FileParsers/CMakeFiles/connectTheDotsTest.dir/connectTheDots_catch.cpp.o -MF CMakeFiles/connectTheDotsTest.dir/connectTheDots_catch.cpp.o.d -o CMakeFiles/connectTheDotsTest.dir/connectTheDots_catch.cpp.o -c /build/reproducible-path/rdkit-202503.1/Code/GraphMol/FileParsers/connectTheDots_catch.cpp -[ 52%] 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 -[ 52%] Building CXX object Code/GraphMol/ChemReactions/CMakeFiles/ChemReactions.dir/PNGParser.cpp.o -cd /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/ChemReactions && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DChemReactions_EXPORTS -DRDKIT_CHEMREACTIONS_BUILD -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_BUILD_XYZ2MOL_SUPPORT -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202503.1/External -I/build/reproducible-path/rdkit-202503.1/Code -I/build/reproducible-path/rdkit-202503.1/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/ChemReactions/CMakeFiles/ChemReactions.dir/PNGParser.cpp.o -MF CMakeFiles/ChemReactions.dir/PNGParser.cpp.o.d -o CMakeFiles/ChemReactions.dir/PNGParser.cpp.o -c /build/reproducible-path/rdkit-202503.1/Code/GraphMol/ChemReactions/PNGParser.cpp -/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 +[ 52%] Linking CXX executable graphmolMolOpsTest +cd /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol && /usr/bin/cmake -E cmake_link_script CMakeFiles/graphmolMolOpsTest.dir/link.txt --verbose=1 +/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/graphmolMolOpsTest.dir/link.d CMakeFiles/graphmolMolOpsTest.dir/molopstest.cpp.o -o graphmolMolOpsTest ../../lib/libRDKitFileParsers.so.1.2025.03.1 ../../lib/libRDKitChemTransforms.so.1.2025.03.1 ../../lib/libRDKitDepictor.so.1.2025.03.1 /usr/lib/aarch64-linux-gnu/libcoordgen.so ../../lib/libRDKitMolAlign.so.1.2025.03.1 ../../lib/libRDKitSubstructMatch.so.1.2025.03.1 ../../lib/libRDKitGenericGroups.so.1.2025.03.1 ../../lib/libRDKitSmilesParse.so.1.2025.03.1 ../../lib/libRDKitMolTransforms.so.1.2025.03.1 ../../lib/libRDKitGraphMol.so.1.2025.03.1 ../../lib/libRDKitEigenSolvers.so.1.2025.03.1 ../../lib/libRDKitAlignment.so.1.2025.03.1 ../../lib/libRDKitRDGeometryLib.so.1.2025.03.1 ../../lib/libRDKitDataStructs.so.1.2025.03.1 ../../lib/libRDKitRDGeneral.so.1.2025.03.1 /usr/lib/aarch64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl /usr/lib/aarch64-linux-gnu/libmaeparser.so make[4]: Leaving directory '/build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu' -[ 52%] Built target testMolSupplier +[ 52%] Built target graphmolMolOpsTest +[ 52%] Building CXX object Code/GraphMol/ChemReactions/CMakeFiles/ChemReactions.dir/Enumerate/EvenSamplePairs.cpp.o +cd /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/ChemReactions && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DChemReactions_EXPORTS -DRDKIT_CHEMREACTIONS_BUILD -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_BUILD_XYZ2MOL_SUPPORT -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202503.1/External -I/build/reproducible-path/rdkit-202503.1/Code -I/build/reproducible-path/rdkit-202503.1/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/ChemReactions/CMakeFiles/ChemReactions.dir/Enumerate/EvenSamplePairs.cpp.o -MF CMakeFiles/ChemReactions.dir/Enumerate/EvenSamplePairs.cpp.o.d -o CMakeFiles/ChemReactions.dir/Enumerate/EvenSamplePairs.cpp.o -c /build/reproducible-path/rdkit-202503.1/Code/GraphMol/ChemReactions/Enumerate/EvenSamplePairs.cpp 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=" make[4]: Leaving directory '/build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu' make -f Code/GraphMol/FileParsers/CMakeFiles/v2MolSuppliers.dir/build.make Code/GraphMol/FileParsers/CMakeFiles/v2MolSuppliers.dir/build make[4]: Entering directory '/build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu' -[ 52%] Building CXX object Code/GraphMol/ChemReactions/CMakeFiles/ChemReactions.dir/CDXMLParser.cpp.o -cd /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/ChemReactions && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DChemReactions_EXPORTS -DRDKIT_CHEMREACTIONS_BUILD -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_BUILD_XYZ2MOL_SUPPORT -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202503.1/External -I/build/reproducible-path/rdkit-202503.1/Code -I/build/reproducible-path/rdkit-202503.1/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/ChemReactions/CMakeFiles/ChemReactions.dir/CDXMLParser.cpp.o -MF CMakeFiles/ChemReactions.dir/CDXMLParser.cpp.o.d -o CMakeFiles/ChemReactions.dir/CDXMLParser.cpp.o -c /build/reproducible-path/rdkit-202503.1/Code/GraphMol/ChemReactions/CDXMLParser.cpp [ 52%] 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_BUILD_XYZ2MOL_SUPPORT -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202503.1/External -I/build/reproducible-path/rdkit-202503.1/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/GraphMol/FileParsers/CMakeFiles/v2MolSuppliers.dir/v2_suppliers_catch.cpp.o -MF CMakeFiles/v2MolSuppliers.dir/v2_suppliers_catch.cpp.o.d -o CMakeFiles/v2MolSuppliers.dir/v2_suppliers_catch.cpp.o -c /build/reproducible-path/rdkit-202503.1/Code/GraphMol/FileParsers/v2_suppliers_catch.cpp [ 52%] Linking CXX executable XYZFileParserCatchTest @@ -5018,11 +5065,6 @@ make[4]: Entering directory '/build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu' [ 52%] 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_BUILD_XYZ2MOL_SUPPORT -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202503.1/External -I/build/reproducible-path/rdkit-202503.1/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/GraphMol/FileParsers/CMakeFiles/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 -[ 52%] 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' -[ 52%] Built target testMolWriter 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=" @@ -5031,24 +5073,19 @@ make[4]: Entering directory '/build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu' [ 52%] Building CXX object Code/GraphMol/FileParsers/CMakeFiles/atropisomersCatch.dir/atropisomers_catch.cpp.o cd /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_BUILD_XYZ2MOL_SUPPORT -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202503.1/External -I/build/reproducible-path/rdkit-202503.1/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/GraphMol/FileParsers/CMakeFiles/atropisomersCatch.dir/atropisomers_catch.cpp.o -MF CMakeFiles/atropisomersCatch.dir/atropisomers_catch.cpp.o.d -o CMakeFiles/atropisomersCatch.dir/atropisomers_catch.cpp.o -c /build/reproducible-path/rdkit-202503.1/Code/GraphMol/FileParsers/atropisomers_catch.cpp -[ 52%] Linking CXX executable graphmolMolOpsTest -cd /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol && /usr/bin/cmake -E cmake_link_script CMakeFiles/graphmolMolOpsTest.dir/link.txt --verbose=1 [ 52%] Linking CXX executable 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/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 +/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/connectTheDotsTest.dir/link.d CMakeFiles/connectTheDotsTest.dir/connectTheDots_catch.cpp.o -o connectTheDotsTest ../../RDGeneral/librdkitCatch.a ../../../lib/libRDKitFileParsers.so.1.2025.03.1 /usr/lib/libCatch2.a ../../../lib/libRDKitChemTransforms.so.1.2025.03.1 ../../../lib/libRDKitDepictor.so.1.2025.03.1 /usr/lib/aarch64-linux-gnu/libcoordgen.so ../../../lib/libRDKitMolAlign.so.1.2025.03.1 ../../../lib/libRDKitMolTransforms.so.1.2025.03.1 ../../../lib/libRDKitEigenSolvers.so.1.2025.03.1 ../../../lib/libRDKitAlignment.so.1.2025.03.1 ../../../lib/libRDKitSmilesParse.so.1.2025.03.1 ../../../lib/libRDKitSubstructMatch.so.1.2025.03.1 ../../../lib/libRDKitGenericGroups.so.1.2025.03.1 ../../../lib/libRDKitGraphMol.so.1.2025.03.1 ../../../lib/libRDKitRDGeometryLib.so.1.2025.03.1 ../../../lib/libRDKitDataStructs.so.1.2025.03.1 ../../../lib/libRDKitRDGeneral.so.1.2025.03.1 /usr/lib/aarch64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl /usr/lib/aarch64-linux-gnu/libmaeparser.so make[4]: Leaving directory '/build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu' -[ 52%] Built target graphmolMolOpsTest +[ 52%] Built target connectTheDotsTest make -f Code/GraphMol/FileParsers/CMakeFiles/multithreadedSupplierCatchTest.dir/build.make Code/GraphMol/FileParsers/CMakeFiles/multithreadedSupplierCatchTest.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu' cd /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202503.1 /build/reproducible-path/rdkit-202503.1/Code/GraphMol/FileParsers /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/CMakeFiles/multithreadedSupplierCatchTest.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu' make -f Code/GraphMol/FileParsers/CMakeFiles/multithreadedSupplierCatchTest.dir/build.make Code/GraphMol/FileParsers/CMakeFiles/multithreadedSupplierCatchTest.dir/build make[4]: Entering directory '/build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu' -/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/connectTheDotsTest.dir/link.d CMakeFiles/connectTheDotsTest.dir/connectTheDots_catch.cpp.o -o connectTheDotsTest ../../RDGeneral/librdkitCatch.a ../../../lib/libRDKitFileParsers.so.1.2025.03.1 /usr/lib/libCatch2.a ../../../lib/libRDKitChemTransforms.so.1.2025.03.1 ../../../lib/libRDKitDepictor.so.1.2025.03.1 /usr/lib/aarch64-linux-gnu/libcoordgen.so ../../../lib/libRDKitMolAlign.so.1.2025.03.1 ../../../lib/libRDKitMolTransforms.so.1.2025.03.1 ../../../lib/libRDKitEigenSolvers.so.1.2025.03.1 ../../../lib/libRDKitAlignment.so.1.2025.03.1 ../../../lib/libRDKitSmilesParse.so.1.2025.03.1 ../../../lib/libRDKitSubstructMatch.so.1.2025.03.1 ../../../lib/libRDKitGenericGroups.so.1.2025.03.1 ../../../lib/libRDKitGraphMol.so.1.2025.03.1 ../../../lib/libRDKitRDGeometryLib.so.1.2025.03.1 ../../../lib/libRDKitDataStructs.so.1.2025.03.1 ../../../lib/libRDKitRDGeneral.so.1.2025.03.1 /usr/lib/aarch64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl /usr/lib/aarch64-linux-gnu/libmaeparser.so -make[4]: Leaving directory '/build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu' [ 52%] Building CXX object Code/GraphMol/FileParsers/CMakeFiles/multithreadedSupplierCatchTest.dir/multithreaded_supplier_catch.cpp.o cd /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_BUILD_XYZ2MOL_SUPPORT -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202503.1/External -I/build/reproducible-path/rdkit-202503.1/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/GraphMol/FileParsers/CMakeFiles/multithreadedSupplierCatchTest.dir/multithreaded_supplier_catch.cpp.o -MF CMakeFiles/multithreadedSupplierCatchTest.dir/multithreaded_supplier_catch.cpp.o.d -o CMakeFiles/multithreadedSupplierCatchTest.dir/multithreaded_supplier_catch.cpp.o -c /build/reproducible-path/rdkit-202503.1/Code/GraphMol/FileParsers/multithreaded_supplier_catch.cpp -[ 52%] 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=" @@ -5057,15 +5094,11 @@ make[4]: Entering directory '/build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu' [ 52%] Building CXX object Code/GraphMol/Substruct/CMakeFiles/testSubstructMatch.dir/test1.cpp.o cd /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/Substruct && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_BUILD_XYZ2MOL_SUPPORT -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202503.1/External -I/build/reproducible-path/rdkit-202503.1/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/GraphMol/Substruct/CMakeFiles/testSubstructMatch.dir/test1.cpp.o -MF CMakeFiles/testSubstructMatch.dir/test1.cpp.o.d -o CMakeFiles/testSubstructMatch.dir/test1.cpp.o -c /build/reproducible-path/rdkit-202503.1/Code/GraphMol/Substruct/test1.cpp -[ 52%] Building CXX object Code/GraphMol/ChemReactions/CMakeFiles/ChemReactions.dir/Enumerate/Enumerate.cpp.o -cd /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/ChemReactions && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DChemReactions_EXPORTS -DRDKIT_CHEMREACTIONS_BUILD -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_BUILD_XYZ2MOL_SUPPORT -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202503.1/External -I/build/reproducible-path/rdkit-202503.1/Code -I/build/reproducible-path/rdkit-202503.1/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -fpermissive -MD -MT Code/GraphMol/ChemReactions/CMakeFiles/ChemReactions.dir/Enumerate/Enumerate.cpp.o -MF CMakeFiles/ChemReactions.dir/Enumerate/Enumerate.cpp.o.d -o CMakeFiles/ChemReactions.dir/Enumerate/Enumerate.cpp.o -c /build/reproducible-path/rdkit-202503.1/Code/GraphMol/ChemReactions/Enumerate/Enumerate.cpp -[ 52%] Building CXX object Code/GraphMol/ChemReactions/CMakeFiles/ChemReactions.dir/Enumerate/EnumerationPickler.cpp.o -cd /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/ChemReactions && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DChemReactions_EXPORTS -DRDKIT_CHEMREACTIONS_BUILD -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_BUILD_XYZ2MOL_SUPPORT -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202503.1/External -I/build/reproducible-path/rdkit-202503.1/Code -I/build/reproducible-path/rdkit-202503.1/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/ChemReactions/CMakeFiles/ChemReactions.dir/Enumerate/EnumerationPickler.cpp.o -MF CMakeFiles/ChemReactions.dir/Enumerate/EnumerationPickler.cpp.o.d -o CMakeFiles/ChemReactions.dir/Enumerate/EnumerationPickler.cpp.o -c /build/reproducible-path/rdkit-202503.1/Code/GraphMol/ChemReactions/Enumerate/EnumerationPickler.cpp -[ 52%] Linking CXX executable 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 +[ 52%] Linking CXX executable molfileStereoCatchTest +cd /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers && /usr/bin/cmake -E cmake_link_script CMakeFiles/molfileStereoCatchTest.dir/link.txt --verbose=1 +/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/molfileStereoCatchTest.dir/link.d CMakeFiles/molfileStereoCatchTest.dir/molfile_stereo_catch.cpp.o -o molfileStereoCatchTest ../../RDGeneral/librdkitCatch.a ../../../lib/libRDKitFileParsers.so.1.2025.03.1 ../../../lib/libRDKitCIPLabeler.so.1.2025.03.1 ../../../lib/libRDKitSubgraphs.so.1.2025.03.1 /usr/lib/libCatch2.a ../../../lib/libRDKitChemTransforms.so.1.2025.03.1 ../../../lib/libRDKitDepictor.so.1.2025.03.1 /usr/lib/aarch64-linux-gnu/libcoordgen.so ../../../lib/libRDKitMolAlign.so.1.2025.03.1 ../../../lib/libRDKitMolTransforms.so.1.2025.03.1 ../../../lib/libRDKitEigenSolvers.so.1.2025.03.1 ../../../lib/libRDKitAlignment.so.1.2025.03.1 ../../../lib/libRDKitSmilesParse.so.1.2025.03.1 ../../../lib/libRDKitSubstructMatch.so.1.2025.03.1 ../../../lib/libRDKitGenericGroups.so.1.2025.03.1 /usr/lib/aarch64-linux-gnu/libmaeparser.so ../../../lib/libRDKitGraphMol.so.1.2025.03.1 ../../../lib/libRDKitRDGeometryLib.so.1.2025.03.1 ../../../lib/libRDKitDataStructs.so.1.2025.03.1 ../../../lib/libRDKitRDGeneral.so.1.2025.03.1 /usr/lib/aarch64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl make[4]: Leaving directory '/build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu' -[ 52%] Built target cdxmlParserCatchTest +[ 52%] Built target molfileStereoCatchTest 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=" @@ -5074,11 +5107,11 @@ make[4]: Entering directory '/build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu' [ 52%] Building CXX object Code/GraphMol/Substruct/CMakeFiles/substructTestCatch.dir/catch_tests.cpp.o cd /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/Substruct && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_BUILD_XYZ2MOL_SUPPORT -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202503.1/External -I/build/reproducible-path/rdkit-202503.1/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/GraphMol/Substruct/CMakeFiles/substructTestCatch.dir/catch_tests.cpp.o -MF CMakeFiles/substructTestCatch.dir/catch_tests.cpp.o.d -o CMakeFiles/substructTestCatch.dir/catch_tests.cpp.o -c /build/reproducible-path/rdkit-202503.1/Code/GraphMol/Substruct/catch_tests.cpp -[ 52%] Linking CXX executable v2MolSuppliers -cd /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers && /usr/bin/cmake -E cmake_link_script CMakeFiles/v2MolSuppliers.dir/link.txt --verbose=1 -/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/v2MolSuppliers.dir/link.d CMakeFiles/v2MolSuppliers.dir/v2_suppliers_catch.cpp.o -o v2MolSuppliers ../../RDGeneral/librdkitCatch.a ../../../lib/libRDKitFileParsers.so.1.2025.03.1 /usr/lib/libCatch2.a ../../../lib/libRDKitChemTransforms.so.1.2025.03.1 ../../../lib/libRDKitDepictor.so.1.2025.03.1 /usr/lib/aarch64-linux-gnu/libcoordgen.so ../../../lib/libRDKitMolAlign.so.1.2025.03.1 ../../../lib/libRDKitMolTransforms.so.1.2025.03.1 ../../../lib/libRDKitEigenSolvers.so.1.2025.03.1 ../../../lib/libRDKitAlignment.so.1.2025.03.1 ../../../lib/libRDKitSmilesParse.so.1.2025.03.1 ../../../lib/libRDKitSubstructMatch.so.1.2025.03.1 ../../../lib/libRDKitGenericGroups.so.1.2025.03.1 ../../../lib/libRDKitGraphMol.so.1.2025.03.1 ../../../lib/libRDKitRDGeometryLib.so.1.2025.03.1 ../../../lib/libRDKitDataStructs.so.1.2025.03.1 ../../../lib/libRDKitRDGeneral.so.1.2025.03.1 /usr/lib/aarch64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl /usr/lib/aarch64-linux-gnu/libmaeparser.so +[ 52%] Linking CXX executable v2FileParsersCatchTest +cd /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers && /usr/bin/cmake -E cmake_link_script CMakeFiles/v2FileParsersCatchTest.dir/link.txt --verbose=1 +/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/v2FileParsersCatchTest.dir/link.d CMakeFiles/v2FileParsersCatchTest.dir/v2_file_parsers_catch.cpp.o -o v2FileParsersCatchTest ../../RDGeneral/librdkitCatch.a ../../../lib/libRDKitFileParsers.so.1.2025.03.1 /usr/lib/libCatch2.a ../../../lib/libRDKitChemTransforms.so.1.2025.03.1 ../../../lib/libRDKitDepictor.so.1.2025.03.1 /usr/lib/aarch64-linux-gnu/libcoordgen.so ../../../lib/libRDKitMolAlign.so.1.2025.03.1 ../../../lib/libRDKitMolTransforms.so.1.2025.03.1 ../../../lib/libRDKitEigenSolvers.so.1.2025.03.1 ../../../lib/libRDKitAlignment.so.1.2025.03.1 ../../../lib/libRDKitSmilesParse.so.1.2025.03.1 ../../../lib/libRDKitSubstructMatch.so.1.2025.03.1 ../../../lib/libRDKitGenericGroups.so.1.2025.03.1 ../../../lib/libRDKitGraphMol.so.1.2025.03.1 ../../../lib/libRDKitRDGeometryLib.so.1.2025.03.1 ../../../lib/libRDKitDataStructs.so.1.2025.03.1 ../../../lib/libRDKitRDGeneral.so.1.2025.03.1 /usr/lib/aarch64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl /usr/lib/aarch64-linux-gnu/libmaeparser.so make[4]: Leaving directory '/build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu' -[ 52%] Built target v2MolSuppliers +[ 52%] 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=" @@ -5087,44 +5120,34 @@ make[4]: Entering directory '/build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu' [ 52%] Building CXX object Code/GraphMol/ChemTransforms/CMakeFiles/testChemTransforms.dir/testChemTransforms.cpp.o cd /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/ChemTransforms && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_BUILD_XYZ2MOL_SUPPORT -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202503.1/External -I/build/reproducible-path/rdkit-202503.1/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/GraphMol/ChemTransforms/CMakeFiles/testChemTransforms.dir/testChemTransforms.cpp.o -MF CMakeFiles/testChemTransforms.dir/testChemTransforms.cpp.o.d -o CMakeFiles/testChemTransforms.dir/testChemTransforms.cpp.o -c /build/reproducible-path/rdkit-202503.1/Code/GraphMol/ChemTransforms/testChemTransforms.cpp -[ 52%] Linking CXX executable molfileStereoCatchTest -cd /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers && /usr/bin/cmake -E cmake_link_script CMakeFiles/molfileStereoCatchTest.dir/link.txt --verbose=1 -/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/molfileStereoCatchTest.dir/link.d CMakeFiles/molfileStereoCatchTest.dir/molfile_stereo_catch.cpp.o -o molfileStereoCatchTest ../../RDGeneral/librdkitCatch.a ../../../lib/libRDKitFileParsers.so.1.2025.03.1 ../../../lib/libRDKitCIPLabeler.so.1.2025.03.1 ../../../lib/libRDKitSubgraphs.so.1.2025.03.1 /usr/lib/libCatch2.a ../../../lib/libRDKitChemTransforms.so.1.2025.03.1 ../../../lib/libRDKitDepictor.so.1.2025.03.1 /usr/lib/aarch64-linux-gnu/libcoordgen.so ../../../lib/libRDKitMolAlign.so.1.2025.03.1 ../../../lib/libRDKitMolTransforms.so.1.2025.03.1 ../../../lib/libRDKitEigenSolvers.so.1.2025.03.1 ../../../lib/libRDKitAlignment.so.1.2025.03.1 ../../../lib/libRDKitSmilesParse.so.1.2025.03.1 ../../../lib/libRDKitSubstructMatch.so.1.2025.03.1 ../../../lib/libRDKitGenericGroups.so.1.2025.03.1 /usr/lib/aarch64-linux-gnu/libmaeparser.so ../../../lib/libRDKitGraphMol.so.1.2025.03.1 ../../../lib/libRDKitRDGeometryLib.so.1.2025.03.1 ../../../lib/libRDKitDataStructs.so.1.2025.03.1 ../../../lib/libRDKitRDGeneral.so.1.2025.03.1 /usr/lib/aarch64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl +[ 52%] Linking CXX executable cdxmlParserCatchTest +cd /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers && /usr/bin/cmake -E cmake_link_script CMakeFiles/cdxmlParserCatchTest.dir/link.txt --verbose=1 +[ 52%] Linking CXX executable atropisomersCatch +cd /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers && /usr/bin/cmake -E cmake_link_script CMakeFiles/atropisomersCatch.dir/link.txt --verbose=1 +/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/cdxmlParserCatchTest.dir/link.d CMakeFiles/cdxmlParserCatchTest.dir/cdxml_parser_catch.cpp.o -o cdxmlParserCatchTest ../../RDGeneral/librdkitCatch.a ../../../lib/libRDKitFileParsers.so.1.2025.03.1 /usr/lib/libCatch2.a ../../../lib/libRDKitChemTransforms.so.1.2025.03.1 ../../../lib/libRDKitDepictor.so.1.2025.03.1 /usr/lib/aarch64-linux-gnu/libcoordgen.so ../../../lib/libRDKitMolAlign.so.1.2025.03.1 ../../../lib/libRDKitMolTransforms.so.1.2025.03.1 ../../../lib/libRDKitEigenSolvers.so.1.2025.03.1 ../../../lib/libRDKitAlignment.so.1.2025.03.1 ../../../lib/libRDKitSmilesParse.so.1.2025.03.1 ../../../lib/libRDKitSubstructMatch.so.1.2025.03.1 ../../../lib/libRDKitGenericGroups.so.1.2025.03.1 ../../../lib/libRDKitGraphMol.so.1.2025.03.1 ../../../lib/libRDKitRDGeometryLib.so.1.2025.03.1 ../../../lib/libRDKitDataStructs.so.1.2025.03.1 ../../../lib/libRDKitRDGeneral.so.1.2025.03.1 /usr/lib/aarch64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl /usr/lib/aarch64-linux-gnu/libmaeparser.so make[4]: Leaving directory '/build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu' -[ 52%] Built target molfileStereoCatchTest -[ 52%] Building CXX object Code/GraphMol/ChemReactions/CMakeFiles/ChemReactions.dir/Enumerate/EvenSamplePairs.cpp.o -cd /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/ChemReactions && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DChemReactions_EXPORTS -DRDKIT_CHEMREACTIONS_BUILD -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_BUILD_XYZ2MOL_SUPPORT -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202503.1/External -I/build/reproducible-path/rdkit-202503.1/Code -I/build/reproducible-path/rdkit-202503.1/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/ChemReactions/CMakeFiles/ChemReactions.dir/Enumerate/EvenSamplePairs.cpp.o -MF CMakeFiles/ChemReactions.dir/Enumerate/EvenSamplePairs.cpp.o.d -o CMakeFiles/ChemReactions.dir/Enumerate/EvenSamplePairs.cpp.o -c /build/reproducible-path/rdkit-202503.1/Code/GraphMol/ChemReactions/Enumerate/EvenSamplePairs.cpp -[ 52%] Linking CXX executable v2FileParsersCatchTest -cd /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers && /usr/bin/cmake -E cmake_link_script CMakeFiles/v2FileParsersCatchTest.dir/link.txt --verbose=1 -/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/v2FileParsersCatchTest.dir/link.d CMakeFiles/v2FileParsersCatchTest.dir/v2_file_parsers_catch.cpp.o -o v2FileParsersCatchTest ../../RDGeneral/librdkitCatch.a ../../../lib/libRDKitFileParsers.so.1.2025.03.1 /usr/lib/libCatch2.a ../../../lib/libRDKitChemTransforms.so.1.2025.03.1 ../../../lib/libRDKitDepictor.so.1.2025.03.1 /usr/lib/aarch64-linux-gnu/libcoordgen.so ../../../lib/libRDKitMolAlign.so.1.2025.03.1 ../../../lib/libRDKitMolTransforms.so.1.2025.03.1 ../../../lib/libRDKitEigenSolvers.so.1.2025.03.1 ../../../lib/libRDKitAlignment.so.1.2025.03.1 ../../../lib/libRDKitSmilesParse.so.1.2025.03.1 ../../../lib/libRDKitSubstructMatch.so.1.2025.03.1 ../../../lib/libRDKitGenericGroups.so.1.2025.03.1 ../../../lib/libRDKitGraphMol.so.1.2025.03.1 ../../../lib/libRDKitRDGeometryLib.so.1.2025.03.1 ../../../lib/libRDKitDataStructs.so.1.2025.03.1 ../../../lib/libRDKitRDGeneral.so.1.2025.03.1 /usr/lib/aarch64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl /usr/lib/aarch64-linux-gnu/libmaeparser.so +/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 make[4]: Leaving directory '/build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu' -[ 52%] Built target v2FileParsersCatchTest +[ 52%] Built target cdxmlParserCatchTest make -f Code/GraphMol/ChemTransforms/CMakeFiles/chemTransformsTestCatch.dir/build.make Code/GraphMol/ChemTransforms/CMakeFiles/chemTransformsTestCatch.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu' cd /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202503.1 /build/reproducible-path/rdkit-202503.1/Code/GraphMol/ChemTransforms /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/ChemTransforms /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/ChemTransforms/CMakeFiles/chemTransformsTestCatch.dir/DependInfo.cmake "--color=" -make[4]: Leaving directory '/build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu' -make -f Code/GraphMol/ChemTransforms/CMakeFiles/chemTransformsTestCatch.dir/build.make Code/GraphMol/ChemTransforms/CMakeFiles/chemTransformsTestCatch.dir/build -make[4]: Entering directory '/build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu' -[ 52%] Building CXX object Code/GraphMol/ChemTransforms/CMakeFiles/chemTransformsTestCatch.dir/catch_tests.cpp.o -cd /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/ChemTransforms && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_BUILD_XYZ2MOL_SUPPORT -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202503.1/External -I/build/reproducible-path/rdkit-202503.1/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/GraphMol/ChemTransforms/CMakeFiles/chemTransformsTestCatch.dir/catch_tests.cpp.o -MF CMakeFiles/chemTransformsTestCatch.dir/catch_tests.cpp.o.d -o CMakeFiles/chemTransformsTestCatch.dir/catch_tests.cpp.o -c /build/reproducible-path/rdkit-202503.1/Code/GraphMol/ChemTransforms/catch_tests.cpp -[ 52%] 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 -[ 52%] Linking CXX executable testPropertyLists -cd /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers && /usr/bin/cmake -E cmake_link_script CMakeFiles/testPropertyLists.dir/link.txt --verbose=1 -/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/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 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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' -[ 52%] Built target multithreadedSupplierCatchTest +[ 52%] Built target testPropertyLists make -f Code/GraphMol/FragCatalog/Wrap/CMakeFiles/rdfragcatalog.dir/build.make Code/GraphMol/FragCatalog/Wrap/CMakeFiles/rdfragcatalog.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/Wrap /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FragCatalog/Wrap 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../../../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' +[ 52%] Built target ChemReactions +[ 52%] Building CXX object Code/GraphMol/FragCatalog/Wrap/CMakeFiles/rdfragcatalog.dir/FragCatParams.cpp.o +cd /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FragCatalog/Wrap && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_NUMPY_DYN_LINK -DBOOST_NUMPY_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_BUILD_XYZ2MOL_SUPPORT -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -Drdfragcatalog_EXPORTS -I/build/reproducible-path/rdkit-202503.1/External -I/build/reproducible-path/rdkit-202503.1/Code -I/build/reproducible-path/rdkit-202503.1/External/boost-numeric-bindings 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../../../lib/libRDKitSmilesParse.so.1.2025.03.1 ../../../lib/libRDKitSubstructMatch.so.1.2025.03.1 ../../../lib/libRDKitGenericGroups.so.1.2025.03.1 ../../../lib/libRDKitGraphMol.so.1.2025.03.1 ../../../lib/libRDKitRDGeometryLib.so.1.2025.03.1 ../../../lib/libRDKitDataStructs.so.1.2025.03.1 ../../../lib/libRDKitRDGeneral.so.1.2025.03.1 /usr/lib/aarch64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl /usr/lib/aarch64-linux-gnu/libmaeparser.so +make[4]: Leaving directory '/build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu' +[ 52%] Built target multithreadedSupplierCatchTest +[ 52%] 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_BUILD_XYZ2MOL_SUPPORT -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -Drdfragcatalog_EXPORTS -I/build/reproducible-path/rdkit-202503.1/External -I/build/reproducible-path/rdkit-202503.1/Code -I/build/reproducible-path/rdkit-202503.1/External/boost-numeric-bindings -I/usr/lib/aarch64-linux-gnu/python3-numpy/numpy/_core/include -isystem /usr/include/python3.13 -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/FragCatalog/Wrap/CMakeFiles/rdfragcatalog.dir/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 make -f Code/GraphMol/Descriptors/CMakeFiles/Descriptors.dir/build.make Code/GraphMol/Descriptors/CMakeFiles/Descriptors.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/Descriptors /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/Descriptors /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/Descriptors/CMakeFiles/Descriptors.dir/DependInfo.cmake "--color=" @@ -5158,8 +5199,6 @@ cd /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/Descriptors && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DDescriptors_EXPORTS -DRDKIT_DESCRIPTORS_BUILD -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_BUILD_XYZ2MOL_SUPPORT -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202503.1/External -I/build/reproducible-path/rdkit-202503.1/Code -I/build/reproducible-path/rdkit-202503.1/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/Descriptors/CMakeFiles/Descriptors.dir/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 [ 53%] Linking CXX executable fileParsersTest1 cd /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers && /usr/bin/cmake -E cmake_link_script CMakeFiles/fileParsersTest1.dir/link.txt --verbose=1 -[ 53%] Building CXX object Code/GraphMol/FragCatalog/Wrap/CMakeFiles/rdfragcatalog.dir/FragCatParams.cpp.o -cd /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FragCatalog/Wrap && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_NUMPY_DYN_LINK -DBOOST_NUMPY_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_BUILD_XYZ2MOL_SUPPORT -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -Drdfragcatalog_EXPORTS -I/build/reproducible-path/rdkit-202503.1/External -I/build/reproducible-path/rdkit-202503.1/Code -I/build/reproducible-path/rdkit-202503.1/External/boost-numeric-bindings -I/usr/lib/aarch64-linux-gnu/python3-numpy/numpy/_core/include -isystem /usr/include/python3.13 -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/FragCatalog/Wrap/CMakeFiles/rdfragcatalog.dir/FragCatParams.cpp.o -MF CMakeFiles/rdfragcatalog.dir/FragCatParams.cpp.o.d -o CMakeFiles/rdfragcatalog.dir/FragCatParams.cpp.o -c /build/reproducible-path/rdkit-202503.1/Code/GraphMol/FragCatalog/Wrap/FragCatParams.cpp /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/fileParsersTest1.dir/link.d CMakeFiles/fileParsersTest1.dir/test1.cpp.o -o fileParsersTest1 ../../../lib/libRDKitFileParsers.so.1.2025.03.1 ../../../lib/libRDKitChemTransforms.so.1.2025.03.1 ../../../lib/libRDKitDepictor.so.1.2025.03.1 /usr/lib/aarch64-linux-gnu/libcoordgen.so ../../../lib/libRDKitMolAlign.so.1.2025.03.1 ../../../lib/libRDKitSubstructMatch.so.1.2025.03.1 ../../../lib/libRDKitGenericGroups.so.1.2025.03.1 ../../../lib/libRDKitMolTransforms.so.1.2025.03.1 ../../../lib/libRDKitEigenSolvers.so.1.2025.03.1 ../../../lib/libRDKitAlignment.so.1.2025.03.1 ../../../lib/libRDKitSmilesParse.so.1.2025.03.1 ../../../lib/libRDKitGraphMol.so.1.2025.03.1 ../../../lib/libRDKitRDGeometryLib.so.1.2025.03.1 ../../../lib/libRDKitDataStructs.so.1.2025.03.1 ../../../lib/libRDKitRDGeneral.so.1.2025.03.1 /usr/lib/aarch64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl /usr/lib/aarch64-linux-gnu/libmaeparser.so make[4]: Leaving directory '/build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu' [ 53%] Built target fileParsersTest1 @@ -5171,11 +5210,20 @@ make[4]: Entering directory '/build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu' [ 53%] Building CXX object Code/GraphMol/Fingerprints/CMakeFiles/testFingerprints.dir/test1.cpp.o cd /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/Fingerprints && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_BUILD_XYZ2MOL_SUPPORT -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202503.1/External -I/build/reproducible-path/rdkit-202503.1/Code -I/build/reproducible-path/rdkit-202503.1/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/GraphMol/Fingerprints/CMakeFiles/testFingerprints.dir/test1.cpp.o -MF CMakeFiles/testFingerprints.dir/test1.cpp.o.d -o CMakeFiles/testFingerprints.dir/test1.cpp.o -c /build/reproducible-path/rdkit-202503.1/Code/GraphMol/Fingerprints/test1.cpp +[ 53%] Linking CXX executable filterCatalogTest +cd /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FilterCatalog && /usr/bin/cmake -E cmake_link_script CMakeFiles/filterCatalogTest.dir/link.txt --verbose=1 +/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/filterCatalogTest.dir/link.d CMakeFiles/filterCatalogTest.dir/filtercatalogtest.cpp.o -o filterCatalogTest ../../../lib/libRDKitFilterCatalog.so.1.2025.03.1 ../../../lib/libRDKitFileParsers.so.1.2025.03.1 ../../../lib/libRDKitSubgraphs.so.1.2025.03.1 ../../../lib/libRDKitCatalogs.so.1.2025.03.1 ../../../lib/libRDKitChemTransforms.so.1.2025.03.1 ../../../lib/libRDKitDepictor.so.1.2025.03.1 /usr/lib/aarch64-linux-gnu/libcoordgen.so ../../../lib/libRDKitMolAlign.so.1.2025.03.1 ../../../lib/libRDKitSmilesParse.so.1.2025.03.1 ../../../lib/libRDKitSubstructMatch.so.1.2025.03.1 ../../../lib/libRDKitGenericGroups.so.1.2025.03.1 ../../../lib/libRDKitMolTransforms.so.1.2025.03.1 ../../../lib/libRDKitGraphMol.so.1.2025.03.1 ../../../lib/libRDKitEigenSolvers.so.1.2025.03.1 ../../../lib/libRDKitAlignment.so.1.2025.03.1 ../../../lib/libRDKitRDGeometryLib.so.1.2025.03.1 ../../../lib/libRDKitDataStructs.so.1.2025.03.1 ../../../lib/libRDKitRDGeneral.so.1.2025.03.1 /usr/lib/aarch64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl /usr/lib/aarch64-linux-gnu/libmaeparser.so +make[4]: Leaving directory '/build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu' +[ 53%] Built target filterCatalogTest +[ 53%] Building CXX object Code/GraphMol/Descriptors/CMakeFiles/Descriptors.dir/BCUT.cpp.o +cd /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/Descriptors && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DDescriptors_EXPORTS -DRDKIT_DESCRIPTORS_BUILD -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_BUILD_XYZ2MOL_SUPPORT -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202503.1/External -I/build/reproducible-path/rdkit-202503.1/Code -I/build/reproducible-path/rdkit-202503.1/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/Descriptors/CMakeFiles/Descriptors.dir/BCUT.cpp.o -MF CMakeFiles/Descriptors.dir/BCUT.cpp.o.d -o CMakeFiles/Descriptors.dir/BCUT.cpp.o -c /build/reproducible-path/rdkit-202503.1/Code/GraphMol/Descriptors/BCUT.cpp [ 53%] Linking CXX executable testFragCatalog cd /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FragCatalog && /usr/bin/cmake -E cmake_link_script CMakeFiles/testFragCatalog.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated 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make[4]: Entering directory '/build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu' [ 53%] Building CXX object Code/GraphMol/Fingerprints/CMakeFiles/testMHFPFingerprint.dir/testMHFPFingerprint.cpp.o cd /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/Fingerprints && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_BUILD_XYZ2MOL_SUPPORT -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202503.1/External -I/build/reproducible-path/rdkit-202503.1/Code -I/build/reproducible-path/rdkit-202503.1/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/GraphMol/Fingerprints/CMakeFiles/testMHFPFingerprint.dir/testMHFPFingerprint.cpp.o -MF CMakeFiles/testMHFPFingerprint.dir/testMHFPFingerprint.cpp.o.d -o CMakeFiles/testMHFPFingerprint.dir/testMHFPFingerprint.cpp.o -c /build/reproducible-path/rdkit-202503.1/Code/GraphMol/Fingerprints/testMHFPFingerprint.cpp -[ 53%] Linking CXX shared library ../../../lib/libRDKitChemReactions.so -cd /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/ChemReactions && /usr/bin/cmake -E cmake_link_script CMakeFiles/ChemReactions.dir/link.txt --verbose=1 -/usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. 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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 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/build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/Descriptors && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DDescriptors_EXPORTS -DRDKIT_DESCRIPTORS_BUILD -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_BUILD_XYZ2MOL_SUPPORT -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202503.1/External -I/build/reproducible-path/rdkit-202503.1/Code -I/build/reproducible-path/rdkit-202503.1/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/Descriptors/CMakeFiles/Descriptors.dir/BCUT.cpp.o -MF CMakeFiles/Descriptors.dir/BCUT.cpp.o.d -o CMakeFiles/Descriptors.dir/BCUT.cpp.o -c /build/reproducible-path/rdkit-202503.1/Code/GraphMol/Descriptors/BCUT.cpp -[ 53%] Linking CXX executable filterCatalogTest -cd /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FilterCatalog && /usr/bin/cmake -E cmake_link_script CMakeFiles/filterCatalogTest.dir/link.txt --verbose=1 -/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/filterCatalogTest.dir/link.d CMakeFiles/filterCatalogTest.dir/filtercatalogtest.cpp.o -o filterCatalogTest ../../../lib/libRDKitFilterCatalog.so.1.2025.03.1 ../../../lib/libRDKitFileParsers.so.1.2025.03.1 ../../../lib/libRDKitSubgraphs.so.1.2025.03.1 ../../../lib/libRDKitCatalogs.so.1.2025.03.1 ../../../lib/libRDKitChemTransforms.so.1.2025.03.1 ../../../lib/libRDKitDepictor.so.1.2025.03.1 /usr/lib/aarch64-linux-gnu/libcoordgen.so ../../../lib/libRDKitMolAlign.so.1.2025.03.1 ../../../lib/libRDKitSmilesParse.so.1.2025.03.1 ../../../lib/libRDKitSubstructMatch.so.1.2025.03.1 ../../../lib/libRDKitGenericGroups.so.1.2025.03.1 ../../../lib/libRDKitMolTransforms.so.1.2025.03.1 ../../../lib/libRDKitGraphMol.so.1.2025.03.1 ../../../lib/libRDKitEigenSolvers.so.1.2025.03.1 ../../../lib/libRDKitAlignment.so.1.2025.03.1 ../../../lib/libRDKitRDGeometryLib.so.1.2025.03.1 ../../../lib/libRDKitDataStructs.so.1.2025.03.1 ../../../lib/libRDKitRDGeneral.so.1.2025.03.1 /usr/lib/aarch64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl /usr/lib/aarch64-linux-gnu/libmaeparser.so -make[4]: Leaving directory '/build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu' -[ 53%] Built target filterCatalogTest -[ 53%] 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_BUILD_XYZ2MOL_SUPPORT 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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' +[ 54%] Built target testSubstructMatch make -f Code/GraphMol/Fingerprints/CMakeFiles/fpTestCatch.dir/build.make Code/GraphMol/Fingerprints/CMakeFiles/fpTestCatch.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu' cd /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202503.1 /build/reproducible-path/rdkit-202503.1/Code/GraphMol/Fingerprints /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/Fingerprints 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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/Fingerprints/CMakeFiles/fpTestCatch.dir/catch_tests.cpp.o -MF CMakeFiles/fpTestCatch.dir/catch_tests.cpp.o.d -o CMakeFiles/fpTestCatch.dir/catch_tests.cpp.o -c /build/reproducible-path/rdkit-202503.1/Code/GraphMol/Fingerprints/catch_tests.cpp -[ 54%] Building CXX object Code/GraphMol/Descriptors/CMakeFiles/Descriptors.dir/Lipinski.cpp.o -cd /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/Descriptors && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK 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-Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/Descriptors/CMakeFiles/Descriptors.dir/Lipinski.cpp.o -MF CMakeFiles/Descriptors.dir/Lipinski.cpp.o.d -o CMakeFiles/Descriptors.dir/Lipinski.cpp.o -c /build/reproducible-path/rdkit-202503.1/Code/GraphMol/Descriptors/Lipinski.cpp +[ 54%] 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 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/testMHFPFingerprint.dir/link.d 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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' +[ 54%] Built target testMHFPFingerprint make -f Code/GraphMol/Fingerprints/CMakeFiles/fpGenTestCatch.dir/build.make Code/GraphMol/Fingerprints/CMakeFiles/fpGenTestCatch.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu' cd /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202503.1 /build/reproducible-path/rdkit-202503.1/Code/GraphMol/Fingerprints /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/Fingerprints /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/Fingerprints/CMakeFiles/fpGenTestCatch.dir/DependInfo.cmake "--color=" @@ -5250,11 +5274,6 @@ make[4]: Entering directory '/build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu' [ 54%] Building CXX object Code/GraphMol/Fingerprints/CMakeFiles/fpGenTestCatch.dir/fpgen_catch_tests.cpp.o cd /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/Fingerprints && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_BUILD_XYZ2MOL_SUPPORT -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202503.1/External -I/build/reproducible-path/rdkit-202503.1/Code -I/build/reproducible-path/rdkit-202503.1/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/GraphMol/Fingerprints/CMakeFiles/fpGenTestCatch.dir/fpgen_catch_tests.cpp.o -MF CMakeFiles/fpGenTestCatch.dir/fpgen_catch_tests.cpp.o.d -o CMakeFiles/fpGenTestCatch.dir/fpgen_catch_tests.cpp.o -c /build/reproducible-path/rdkit-202503.1/Code/GraphMol/Fingerprints/fpgen_catch_tests.cpp -[ 54%] Linking CXX executable chemTransformsTestCatch -cd /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/ChemTransforms && /usr/bin/cmake -E cmake_link_script CMakeFiles/chemTransformsTestCatch.dir/link.txt --verbose=1 -/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/chemTransformsTestCatch.dir/link.d CMakeFiles/chemTransformsTestCatch.dir/catch_tests.cpp.o -o chemTransformsTestCatch ../../RDGeneral/librdkitCatch.a ../../../lib/libRDKitFileParsers.so.1.2025.03.1 /usr/lib/libCatch2.a ../../../lib/libRDKitChemTransforms.so.1.2025.03.1 ../../../lib/libRDKitDepictor.so.1.2025.03.1 /usr/lib/aarch64-linux-gnu/libcoordgen.so ../../../lib/libRDKitMolAlign.so.1.2025.03.1 ../../../lib/libRDKitSubstructMatch.so.1.2025.03.1 ../../../lib/libRDKitSmilesParse.so.1.2025.03.1 ../../../lib/libRDKitMolTransforms.so.1.2025.03.1 ../../../lib/libRDKitEigenSolvers.so.1.2025.03.1 ../../../lib/libRDKitAlignment.so.1.2025.03.1 ../../../lib/libRDKitGenericGroups.so.1.2025.03.1 ../../../lib/libRDKitGraphMol.so.1.2025.03.1 ../../../lib/libRDKitRDGeometryLib.so.1.2025.03.1 ../../../lib/libRDKitDataStructs.so.1.2025.03.1 ../../../lib/libRDKitRDGeneral.so.1.2025.03.1 /usr/lib/aarch64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl /usr/lib/aarch64-linux-gnu/libmaeparser.so -make[4]: Leaving directory '/build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu' -[ 54%] Built target chemTransformsTestCatch make -f Code/GraphMol/MolTransforms/CMakeFiles/testMolTransforms.dir/build.make Code/GraphMol/MolTransforms/CMakeFiles/testMolTransforms.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu' cd /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202503.1 /build/reproducible-path/rdkit-202503.1/Code/GraphMol/MolTransforms /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/MolTransforms /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/MolTransforms/CMakeFiles/testMolTransforms.dir/DependInfo.cmake "--color=" @@ -5263,26 +5282,46 @@ make[4]: Entering directory '/build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu' [ 54%] Building CXX object Code/GraphMol/MolTransforms/CMakeFiles/testMolTransforms.dir/test1.cpp.o cd /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/MolTransforms && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK 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/build/reproducible-path/rdkit-202503.1/Code/GraphMol/MolTransforms/test1.cpp -[ 54%] Building CXX object Code/GraphMol/Descriptors/CMakeFiles/Descriptors.dir/ConnectivityDescriptors.cpp.o +[ 54%] Linking CXX executable substructTestCatch +cd /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/Substruct && /usr/bin/cmake -E cmake_link_script CMakeFiles/substructTestCatch.dir/link.txt --verbose=1 +/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/substructTestCatch.dir/link.d CMakeFiles/substructTestCatch.dir/catch_tests.cpp.o -o substructTestCatch ../../RDGeneral/librdkitCatch.a ../../../lib/libRDKitFileParsers.so.1.2025.03.1 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54%] Built target substructTestCatch +[ 54%] Building CXX object Code/GraphMol/Descriptors/CMakeFiles/Descriptors.dir/Lipinski.cpp.o +cd /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/Descriptors && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DDescriptors_EXPORTS -DRDKIT_DESCRIPTORS_BUILD -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_BUILD_XYZ2MOL_SUPPORT -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202503.1/External -I/build/reproducible-path/rdkit-202503.1/Code -I/build/reproducible-path/rdkit-202503.1/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 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target rdfragcatalog 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=" @@ -5299,6 +5338,11 @@ make[4]: Entering directory '/build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu' [ 55%] Building CXX object Code/GraphMol/ForceFieldHelpers/MMFF/CMakeFiles/testMMFFForceFieldHelpers.dir/testMMFFHelpers.cpp.o cd /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/ForceFieldHelpers/MMFF && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_BUILD_XYZ2MOL_SUPPORT -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202503.1/External -I/build/reproducible-path/rdkit-202503.1/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/GraphMol/ForceFieldHelpers/MMFF/CMakeFiles/testMMFFForceFieldHelpers.dir/testMMFFHelpers.cpp.o -MF CMakeFiles/testMMFFForceFieldHelpers.dir/testMMFFHelpers.cpp.o.d -o CMakeFiles/testMMFFForceFieldHelpers.dir/testMMFFHelpers.cpp.o -c /build/reproducible-path/rdkit-202503.1/Code/GraphMol/ForceFieldHelpers/MMFF/testMMFFHelpers.cpp +[ 55%] 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 ../../../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' +[ 55%] Built target fileParsersCatchTest 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=" @@ -5307,8 +5351,6 @@ make[4]: Entering directory '/build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu' [ 55%] Building CXX object Code/GraphMol/ForceFieldHelpers/MMFF/CMakeFiles/testMMFFForceFieldHelpersMultiThread.dir/testMultiThread.cpp.o cd /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/ForceFieldHelpers/MMFF && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_BUILD_XYZ2MOL_SUPPORT -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202503.1/External -I/build/reproducible-path/rdkit-202503.1/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/GraphMol/ForceFieldHelpers/MMFF/CMakeFiles/testMMFFForceFieldHelpersMultiThread.dir/testMultiThread.cpp.o -MF CMakeFiles/testMMFFForceFieldHelpersMultiThread.dir/testMultiThread.cpp.o.d -o CMakeFiles/testMMFFForceFieldHelpersMultiThread.dir/testMultiThread.cpp.o -c /build/reproducible-path/rdkit-202503.1/Code/GraphMol/ForceFieldHelpers/MMFF/testMultiThread.cpp -[ 55%] 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_BUILD_XYZ2MOL_SUPPORT -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202503.1/External -I/build/reproducible-path/rdkit-202503.1/Code -I/build/reproducible-path/rdkit-202503.1/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/Descriptors/CMakeFiles/Descriptors.dir/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 [ 55%] 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 @@ -5322,83 +5364,89 @@ make[4]: Entering directory '/build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu' [ 55%] Building CXX object Code/GraphMol/ForceFieldHelpers/UFF/CMakeFiles/testUFFForceFieldHelpers.dir/testUFFHelpers.cpp.o 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_BUILD_XYZ2MOL_SUPPORT -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202503.1/External -I/build/reproducible-path/rdkit-202503.1/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/GraphMol/ForceFieldHelpers/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 -[ 56%] 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 +[ 55%] 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 +/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/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 /usr/lib/aarch64-linux-gnu/libboost_system.so.1.83.0 /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 molTransformsTestCatch -[ 56%] 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_BUILD_XYZ2MOL_SUPPORT -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202503.1/External -I/build/reproducible-path/rdkit-202503.1/Code -I/build/reproducible-path/rdkit-202503.1/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/Descriptors/CMakeFiles/Descriptors.dir/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 -[ 56%] Building CXX object Code/GraphMol/Descriptors/CMakeFiles/Descriptors.dir/AUTOCORR2D.cpp.o -cd /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/Descriptors && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DDescriptors_EXPORTS -DRDKIT_DESCRIPTORS_BUILD -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_BUILD_XYZ2MOL_SUPPORT -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202503.1/External -I/build/reproducible-path/rdkit-202503.1/Code -I/build/reproducible-path/rdkit-202503.1/External/boost-numeric-bindings -isystem /usr/include/eigen3 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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 /usr/lib/aarch64-linux-gnu/libmaeparser.so +[ 55%] 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 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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 -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/testMMFFForceFieldHelpersMultiThread.dir/link.d CMakeFiles/testMMFFForceFieldHelpersMultiThread.dir/testMultiThread.cpp.o -o 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 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testMMFFForceFieldHelpersMultiThread +[ 56%] Building CXX object Code/GraphMol/Descriptors/CMakeFiles/Descriptors.dir/OxidationNumbers.cpp.o +cd /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/Descriptors && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DDescriptors_EXPORTS -DRDKIT_DESCRIPTORS_BUILD -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_BUILD_XYZ2MOL_SUPPORT -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202503.1/External -I/build/reproducible-path/rdkit-202503.1/Code -I/build/reproducible-path/rdkit-202503.1/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 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CMakeFiles/Descriptors.dir/DCLV.cpp.o -c /build/reproducible-path/rdkit-202503.1/Code/GraphMol/Descriptors/DCLV.cpp +[ 57%] 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 +[ 57%] Building CXX object Code/GraphMol/Descriptors/CMakeFiles/Descriptors.dir/EEM.cpp.o +cd /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/Descriptors && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DDescriptors_EXPORTS -DRDKIT_DESCRIPTORS_BUILD -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_BUILD_XYZ2MOL_SUPPORT -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED 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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/Descriptors/CMakeFiles/Descriptors.dir/USRDescriptor.cpp.o -MF CMakeFiles/Descriptors.dir/USRDescriptor.cpp.o.d -o CMakeFiles/Descriptors.dir/USRDescriptor.cpp.o -c /build/reproducible-path/rdkit-202503.1/Code/GraphMol/Descriptors/USRDescriptor.cpp -[ 57%] Building CXX object Code/GraphMol/Descriptors/CMakeFiles/Descriptors.dir/AtomFeat.cpp.o -cd /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/Descriptors 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-Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/Descriptors/CMakeFiles/Descriptors.dir/AtomFeat.cpp.o -MF CMakeFiles/Descriptors.dir/AtomFeat.cpp.o.d -o CMakeFiles/Descriptors.dir/AtomFeat.cpp.o -c /build/reproducible-path/rdkit-202503.1/Code/GraphMol/Descriptors/AtomFeat.cpp -[ 57%] 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 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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_BUILD_XYZ2MOL_SUPPORT -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202503.1/External -I/build/reproducible-path/rdkit-202503.1/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 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-Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/Descriptors/CMakeFiles/Descriptors.dir/OxidationNumbers.cpp.o -MF CMakeFiles/Descriptors.dir/OxidationNumbers.cpp.o.d -o CMakeFiles/Descriptors.dir/OxidationNumbers.cpp.o -c /build/reproducible-path/rdkit-202503.1/Code/GraphMol/Descriptors/OxidationNumbers.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/testFingerprints.dir/link.d CMakeFiles/testFingerprints.dir/test1.cpp.o -o testFingerprints ../../../lib/libRDKitFingerprints.so.1.2025.03.1 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CMakeFiles/Descriptors.dir/EEM.cpp.o -c /build/reproducible-path/rdkit-202503.1/Code/GraphMol/Descriptors/EEM.cpp -[ 58%] 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 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../../../lib/libRDKitForceField.so.1.2025.03.1 ../../../lib/libRDKitOptimizer.so.1.2025.03.1 ../../../lib/libRDKitTrajectory.so.1.2025.03.1 ../../../lib/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 +[ 58%] 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 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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=" @@ -5478,13 +5495,8 @@ make[4]: Entering directory '/build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu' [ 58%] 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 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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/RDF.cpp.o -MF CMakeFiles/Descriptors.dir/RDF.cpp.o.d -o CMakeFiles/Descriptors.dir/RDF.cpp.o -c /build/reproducible-path/rdkit-202503.1/Code/GraphMol/Descriptors/RDF.cpp -[ 58%] Linking CXX executable testShapeHelpers -cd /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/ShapeHelpers && /usr/bin/cmake -E cmake_link_script CMakeFiles/testShapeHelpers.dir/link.txt --verbose=1 -/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. 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Code/GraphMol/MolDraw2D/CMakeFiles/MolDraw2D.dir/MolDraw2D.cpp.o cd /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/MolDraw2D && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DMolDraw2D_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_MOLDRAW2D_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_CAIRO_SUPPORT -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_FREETYPE_SUPPORT -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_BUILD_XYZ2MOL_SUPPORT -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202503.1/External -I/usr/include/freetype2 -I/build/reproducible-path/rdkit-202503.1/Code -I/build/reproducible-path/rdkit-202503.1/External/boost-numeric-bindings -isystem /usr/include/eigen3 -isystem /usr/include/cairo -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/MolDraw2D/CMakeFiles/MolDraw2D.dir/MolDraw2D.cpp.o -MF CMakeFiles/MolDraw2D.dir/MolDraw2D.cpp.o.d -o CMakeFiles/MolDraw2D.dir/MolDraw2D.cpp.o -c /build/reproducible-path/rdkit-202503.1/Code/GraphMol/MolDraw2D/MolDraw2D.cpp +[ 58%] 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 [ 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 -/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%] Building CXX object Code/GraphMol/Descriptors/CMakeFiles/Descriptors.dir/AUTOCORR3D.cpp.o +cd /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/Descriptors && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DDescriptors_EXPORTS -DRDKIT_DESCRIPTORS_BUILD -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_BUILD_XYZ2MOL_SUPPORT -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202503.1/External -I/build/reproducible-path/rdkit-202503.1/Code -I/build/reproducible-path/rdkit-202503.1/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong 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../../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' -[ 59%] Built target testUFFForceFieldHelpers +[ 59%] Built target molAlignCatchTest make -f Code/GraphMol/FMCS/CMakeFiles/FMCS.dir/build.make Code/GraphMol/FMCS/CMakeFiles/FMCS.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-202503.1/obj-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 /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FMCS /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FMCS/CMakeFiles/FMCS.dir/DependInfo.cmake "--color=" @@ -5506,34 +5522,41 @@ 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_BUILD_XYZ2MOL_SUPPORT -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202503.1/External -I/build/reproducible-path/rdkit-202503.1/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/FMCS/CMakeFiles/FMCS.dir/FMCS.cpp.o -MF CMakeFiles/FMCS.dir/FMCS.cpp.o.d -o CMakeFiles/FMCS.dir/FMCS.cpp.o -c /build/reproducible-path/rdkit-202503.1/Code/GraphMol/FMCS/FMCS.cpp -[ 59%] Building CXX object Code/GraphMol/MolDraw2D/CMakeFiles/MolDraw2D.dir/MolDraw2DSVG.cpp.o -cd /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/MolDraw2D && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DMolDraw2D_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_MOLDRAW2D_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_CAIRO_SUPPORT -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_FREETYPE_SUPPORT -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_BUILD_XYZ2MOL_SUPPORT -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202503.1/External -I/usr/include/freetype2 -I/build/reproducible-path/rdkit-202503.1/Code -I/build/reproducible-path/rdkit-202503.1/External/boost-numeric-bindings -isystem /usr/include/eigen3 -isystem /usr/include/cairo -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/MolDraw2D/CMakeFiles/MolDraw2D.dir/MolDraw2DSVG.cpp.o -MF CMakeFiles/MolDraw2D.dir/MolDraw2DSVG.cpp.o.d -o CMakeFiles/MolDraw2D.dir/MolDraw2DSVG.cpp.o -c /build/reproducible-path/rdkit-202503.1/Code/GraphMol/MolDraw2D/MolDraw2DSVG.cpp +/usr/bin/c++ -g -O2 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Code/GraphMol/Descriptors/CMakeFiles/Descriptors.dir/RDF.cpp.o +cd /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/Descriptors && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DDescriptors_EXPORTS -DRDKIT_DESCRIPTORS_BUILD -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_BUILD_XYZ2MOL_SUPPORT -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202503.1/External -I/build/reproducible-path/rdkit-202503.1/Code -I/build/reproducible-path/rdkit-202503.1/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong 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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' +[ 60%] Built target testMolCatalog [ 60%] Building CXX object Code/GraphMol/MolDraw2D/CMakeFiles/MolDraw2D.dir/MolDraw2DDetails.cpp.o cd /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/MolDraw2D && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DMolDraw2D_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_MOLDRAW2D_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_CAIRO_SUPPORT -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_FREETYPE_SUPPORT -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_BUILD_XYZ2MOL_SUPPORT -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202503.1/External -I/usr/include/freetype2 -I/build/reproducible-path/rdkit-202503.1/Code -I/build/reproducible-path/rdkit-202503.1/External/boost-numeric-bindings -isystem /usr/include/eigen3 -isystem /usr/include/cairo -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/MolDraw2D/CMakeFiles/MolDraw2D.dir/MolDraw2DDetails.cpp.o -MF CMakeFiles/MolDraw2D.dir/MolDraw2DDetails.cpp.o.d -o CMakeFiles/MolDraw2D.dir/MolDraw2DDetails.cpp.o -c /build/reproducible-path/rdkit-202503.1/Code/GraphMol/MolDraw2D/MolDraw2DDetails.cpp -[ 60%] Building CXX object Code/GraphMol/MolDraw2D/CMakeFiles/MolDraw2D.dir/MolDraw2DUtils.cpp.o -cd 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CMakeFiles/MolDraw2D.dir/MolDraw2DUtils.cpp.o -c /build/reproducible-path/rdkit-202503.1/Code/GraphMol/MolDraw2D/MolDraw2DUtils.cpp +[ 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 +/usr/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/rdDistGeom.dir/link.d -Wl,-z,relro -Wl,-z,now -shared -o ../../../../rdkit/Chem/rdDistGeom.so CMakeFiles/rdDistGeom.dir/rdDistGeom.cpp.o 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-I/build/reproducible-path/rdkit-202503.1/External -I/build/reproducible-path/rdkit-202503.1/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-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 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-isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/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%] 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 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CMakeFiles/RascalMCES.dir/RascalButinaCluster.cpp.o -c /build/reproducible-path/rdkit-202503.1/Code/GraphMol/RascalMCES/RascalButinaCluster.cpp -[ 61%] Linking CXX shared library ../../../lib/libRDKitMMPA.so +[ 62%] Built target testDistGeomHelpers +make -f Code/GraphMol/Deprotect/CMakeFiles/Deprotect.dir/build.make Code/GraphMol/Deprotect/CMakeFiles/Deprotect.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/Deprotect /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/Deprotect /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/Deprotect/CMakeFiles/Deprotect.dir/DependInfo.cmake "--color=" +make[4]: Leaving directory '/build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu' +make -f Code/GraphMol/Deprotect/CMakeFiles/Deprotect.dir/build.make Code/GraphMol/Deprotect/CMakeFiles/Deprotect.dir/build +make[4]: Entering directory '/build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu' +[ 62%] Building CXX object Code/GraphMol/Deprotect/CMakeFiles/Deprotect.dir/Deprotect.cpp.o +cd /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/Deprotect && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DDeprotect_EXPORTS -DRDKIT_DEPROTECT_BUILD -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_BUILD_XYZ2MOL_SUPPORT -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202503.1/External -I/build/reproducible-path/rdkit-202503.1/Code -I/build/reproducible-path/rdkit-202503.1/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/Deprotect/CMakeFiles/Deprotect.dir/Deprotect.cpp.o -MF CMakeFiles/Deprotect.dir/Deprotect.cpp.o.d -o CMakeFiles/Deprotect.dir/Deprotect.cpp.o -c /build/reproducible-path/rdkit-202503.1/Code/GraphMol/Deprotect/Deprotect.cpp +[ 62%] 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 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-mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/RascalMCES/CMakeFiles/RascalMCES.dir/PartitionSet.cpp.o -MF CMakeFiles/RascalMCES.dir/PartitionSet.cpp.o.d -o CMakeFiles/RascalMCES.dir/PartitionSet.cpp.o -c /build/reproducible-path/rdkit-202503.1/Code/GraphMol/RascalMCES/PartitionSet.cpp -[ 63%] Building CXX object Code/GraphMol/RascalMCES/CMakeFiles/RascalMCES.dir/RascalResult.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 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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/FMCS/CMakeFiles/FMCS.dir/SubstructMatchCustom.cpp.o -MF CMakeFiles/FMCS.dir/SubstructMatchCustom.cpp.o.d -o CMakeFiles/FMCS.dir/SubstructMatchCustom.cpp.o -c /build/reproducible-path/rdkit-202503.1/Code/GraphMol/FMCS/SubstructMatchCustom.cpp -[ 64%] Linking CXX executable molHashCatchTest +[ 62%] Built target MMPA +make -f Code/GraphMol/Trajectory/CMakeFiles/trajectoryTest.dir/build.make Code/GraphMol/Trajectory/CMakeFiles/trajectoryTest.dir/depend +make[4]: Entering directory '/build/reproducible-path/rdkit-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/Trajectory 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/build/reproducible-path/rdkit-202503.1/Code/GraphMol/Trajectory/trajectoryTest.cpp +[ 62%] 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_BUILD_XYZ2MOL_SUPPORT -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DRascalMCES_EXPORTS -I/build/reproducible-path/rdkit-202503.1/External -I/build/reproducible-path/rdkit-202503.1/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. 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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/MolEnumerator/CMakeFiles/MolEnumerator.dir/LinkNode.cpp.o -MF CMakeFiles/MolEnumerator.dir/LinkNode.cpp.o.d -o CMakeFiles/MolEnumerator.dir/LinkNode.cpp.o -c /build/reproducible-path/rdkit-202503.1/Code/GraphMol/MolEnumerator/LinkNode.cpp +[ 62%] Building CXX object 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 && 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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 +[ 62%] Linking CXX shared library ../../../lib/libRDKitFMCS.so +cd /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FMCS && /usr/bin/cmake -E cmake_link_script CMakeFiles/FMCS.dir/link.txt --verbose=1 +[ 62%] Building CXX object Code/GraphMol/RascalMCES/CMakeFiles/RascalMCES.dir/PartitionSet.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 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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/MolEnumerator/CMakeFiles/MolEnumerator.dir/RepeatUnit.cpp.o -MF CMakeFiles/MolEnumerator.dir/RepeatUnit.cpp.o.d -o CMakeFiles/MolEnumerator.dir/RepeatUnit.cpp.o -c /build/reproducible-path/rdkit-202503.1/Code/GraphMol/MolEnumerator/RepeatUnit.cpp [ 64%] Building CXX object Code/GraphMol/MolDraw2D/CMakeFiles/MolDraw2D.dir/DrawMolMCH.cpp.o cd /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/MolDraw2D && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB 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-MD -MT Code/GraphMol/MolDraw2D/CMakeFiles/MolDraw2D.dir/DrawMolMCH.cpp.o -MF CMakeFiles/MolDraw2D.dir/DrawMolMCH.cpp.o.d -o CMakeFiles/MolDraw2D.dir/DrawMolMCH.cpp.o -c /build/reproducible-path/rdkit-202503.1/Code/GraphMol/MolDraw2D/DrawMolMCH.cpp [ 64%] Building CXX object Code/GraphMol/MolDraw2D/CMakeFiles/MolDraw2D.dir/DrawMolMCHCircleAndLine.cpp.o cd /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/MolDraw2D && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DMolDraw2D_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_MOLDRAW2D_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_CAIRO_SUPPORT -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_FREETYPE_SUPPORT -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_BUILD_XYZ2MOL_SUPPORT -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202503.1/External -I/usr/include/freetype2 -I/build/reproducible-path/rdkit-202503.1/Code -I/build/reproducible-path/rdkit-202503.1/External/boost-numeric-bindings -isystem /usr/include/eigen3 -isystem /usr/include/cairo -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/MolDraw2D/CMakeFiles/MolDraw2D.dir/DrawMolMCHCircleAndLine.cpp.o -MF CMakeFiles/MolDraw2D.dir/DrawMolMCHCircleAndLine.cpp.o.d -o CMakeFiles/MolDraw2D.dir/DrawMolMCHCircleAndLine.cpp.o -c /build/reproducible-path/rdkit-202503.1/Code/GraphMol/MolDraw2D/DrawMolMCHCircleAndLine.cpp -make -f Code/GraphMol/Deprotect/CMakeFiles/Deprotect.dir/build.make 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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/Deprotect/CMakeFiles/Deprotect.dir/Deprotect.cpp.o -MF CMakeFiles/Deprotect.dir/Deprotect.cpp.o.d -o CMakeFiles/Deprotect.dir/Deprotect.cpp.o -c /build/reproducible-path/rdkit-202503.1/Code/GraphMol/Deprotect/Deprotect.cpp -[ 64%] Building CXX object Code/GraphMol/MolDraw2D/CMakeFiles/MolDraw2D.dir/DrawMolMCHLasso.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 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/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' -make -f Code/GraphMol/Trajectory/CMakeFiles/trajectoryTest.dir/build.make Code/GraphMol/Trajectory/CMakeFiles/trajectoryTest.dir/build +make -f Code/GraphMol/MolInterchange/CMakeFiles/molInterchangeCatchTest.dir/build.make Code/GraphMol/MolInterchange/CMakeFiles/molInterchangeCatchTest.dir/build make[4]: Entering directory '/build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu' -[ 64%] Building CXX object Code/GraphMol/Trajectory/CMakeFiles/trajectoryTest.dir/trajectoryTest.cpp.o -cd 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-Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/GraphMol/Trajectory/CMakeFiles/trajectoryTest.dir/trajectoryTest.cpp.o -MF CMakeFiles/trajectoryTest.dir/trajectoryTest.cpp.o.d -o CMakeFiles/trajectoryTest.dir/trajectoryTest.cpp.o -c /build/reproducible-path/rdkit-202503.1/Code/GraphMol/Trajectory/trajectoryTest.cpp -[ 65%] Building CXX object Code/GraphMol/MolEnumerator/CMakeFiles/MolEnumerator.dir/RepeatUnit.cpp.o -cd /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/MolEnumerator && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DMolEnumerator_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_MOLENUMERATOR_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_BUILD_XYZ2MOL_SUPPORT -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202503.1/External -I/build/reproducible-path/rdkit-202503.1/Code -I/build/reproducible-path/rdkit-202503.1/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/MolEnumerator/CMakeFiles/MolEnumerator.dir/RepeatUnit.cpp.o -MF CMakeFiles/MolEnumerator.dir/RepeatUnit.cpp.o.d -o CMakeFiles/MolEnumerator.dir/RepeatUnit.cpp.o -c /build/reproducible-path/rdkit-202503.1/Code/GraphMol/MolEnumerator/RepeatUnit.cpp -[ 65%] Building CXX object Code/GraphMol/MolDraw2D/CMakeFiles/MolDraw2D.dir/MolDraw2DJS.cpp.o -cd /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/MolDraw2D && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DMolDraw2D_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_MOLDRAW2D_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_CAIRO_SUPPORT -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_FREETYPE_SUPPORT -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_BUILD_XYZ2MOL_SUPPORT -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202503.1/External -I/usr/include/freetype2 -I/build/reproducible-path/rdkit-202503.1/Code -I/build/reproducible-path/rdkit-202503.1/External/boost-numeric-bindings -isystem /usr/include/eigen3 -isystem /usr/include/cairo -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/MolDraw2D/CMakeFiles/MolDraw2D.dir/MolDraw2DJS.cpp.o -MF CMakeFiles/MolDraw2D.dir/MolDraw2DJS.cpp.o.d -o CMakeFiles/MolDraw2D.dir/MolDraw2DJS.cpp.o -c /build/reproducible-path/rdkit-202503.1/Code/GraphMol/MolDraw2D/MolDraw2DJS.cpp -[ 65%] Building CXX object Code/GraphMol/MolDraw2D/CMakeFiles/MolDraw2D.dir/DrawTextJS.cpp.o -cd /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/MolDraw2D && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DMolDraw2D_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_MOLDRAW2D_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_CAIRO_SUPPORT -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_FREETYPE_SUPPORT -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_BUILD_XYZ2MOL_SUPPORT -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202503.1/External -I/usr/include/freetype2 -I/build/reproducible-path/rdkit-202503.1/Code -I/build/reproducible-path/rdkit-202503.1/External/boost-numeric-bindings -isystem /usr/include/eigen3 -isystem /usr/include/cairo -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/MolDraw2D/CMakeFiles/MolDraw2D.dir/DrawTextJS.cpp.o -MF CMakeFiles/MolDraw2D.dir/DrawTextJS.cpp.o.d -o CMakeFiles/MolDraw2D.dir/DrawTextJS.cpp.o -c /build/reproducible-path/rdkit-202503.1/Code/GraphMol/MolDraw2D/DrawTextJS.cpp -[ 66%] Building CXX object Code/GraphMol/MolDraw2D/CMakeFiles/MolDraw2D.dir/MolDraw2DCairo.cpp.o -cd /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/MolDraw2D && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DMolDraw2D_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_MOLDRAW2D_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_CAIRO_SUPPORT -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_FREETYPE_SUPPORT -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_BUILD_XYZ2MOL_SUPPORT -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202503.1/External -I/usr/include/freetype2 -I/build/reproducible-path/rdkit-202503.1/Code -I/build/reproducible-path/rdkit-202503.1/External/boost-numeric-bindings -isystem /usr/include/eigen3 -isystem /usr/include/cairo -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/MolDraw2D/CMakeFiles/MolDraw2D.dir/MolDraw2DCairo.cpp.o -MF CMakeFiles/MolDraw2D.dir/MolDraw2DCairo.cpp.o.d -o CMakeFiles/MolDraw2D.dir/MolDraw2DCairo.cpp.o -c /build/reproducible-path/rdkit-202503.1/Code/GraphMol/MolDraw2D/MolDraw2DCairo.cpp -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, - from /build/reproducible-path/rdkit-202503.1/Code/GraphMol/MolDraw2D/DrawText.cpp:13: -/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/DrawText.cpp:165:47: required from here - 165 | tl = mol_draw.getAtomCoords(std::make_pair(tl.x, tl.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) - | ^~~~~~~~~ -make -f Code/GraphMol/DetermineBonds/CMakeFiles/DetermineBonds.dir/build.make Code/GraphMol/DetermineBonds/CMakeFiles/DetermineBonds.dir/depend +[ 64%] 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_BUILD_XYZ2MOL_SUPPORT -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202503.1/External -I/build/reproducible-path/rdkit-202503.1/External/rapidjson-1.1.0/include -I/build/reproducible-path/rdkit-202503.1/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -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 +[ 64%] 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_BUILD_XYZ2MOL_SUPPORT -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202503.1/External -I/usr/include/freetype2 -I/build/reproducible-path/rdkit-202503.1/Code -I/build/reproducible-path/rdkit-202503.1/External/boost-numeric-bindings -isystem /usr/include/eigen3 -isystem /usr/include/cairo -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/MolDraw2D/CMakeFiles/MolDraw2D.dir/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 +[ 65%] Building CXX object Code/GraphMol/RascalMCES/CMakeFiles/RascalMCES.dir/RascalResult.cpp.o +cd /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/RascalMCES && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDKIT_RASCALMCES_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_BUILD_XYZ2MOL_SUPPORT -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DRascalMCES_EXPORTS -I/build/reproducible-path/rdkit-202503.1/External -I/build/reproducible-path/rdkit-202503.1/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/RascalMCES/CMakeFiles/RascalMCES.dir/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 +make -f Code/GraphMol/Wrap/CMakeFiles/rdmolops.dir/build.make Code/GraphMol/Wrap/CMakeFiles/rdmolops.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/DetermineBonds /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/DetermineBonds /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/DetermineBonds/CMakeFiles/DetermineBonds.dir/DependInfo.cmake "--color=" +cd /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202503.1 /build/reproducible-path/rdkit-202503.1/Code/GraphMol/Wrap /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/Wrap /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/Wrap/CMakeFiles/rdmolops.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu' -make -f Code/GraphMol/DetermineBonds/CMakeFiles/DetermineBonds.dir/build.make Code/GraphMol/DetermineBonds/CMakeFiles/DetermineBonds.dir/build +make -f Code/GraphMol/Wrap/CMakeFiles/rdmolops.dir/build.make Code/GraphMol/Wrap/CMakeFiles/rdmolops.dir/build make[4]: Entering directory '/build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu' -[ 66%] Building CXX object Code/GraphMol/DetermineBonds/CMakeFiles/DetermineBonds.dir/DetermineBonds.cpp.o -cd /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/DetermineBonds && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DDetermineBonds_EXPORTS -DRDKIT_DETERMINEBONDS_BUILD -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_BUILD_XYZ2MOL_SUPPORT -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202503.1/External -I/build/reproducible-path/rdkit-202503.1/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/DetermineBonds/CMakeFiles/DetermineBonds.dir/DetermineBonds.cpp.o -MF CMakeFiles/DetermineBonds.dir/DetermineBonds.cpp.o.d -o 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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/rdmolops.dir/rdmolops.cpp.o -MF CMakeFiles/rdmolops.dir/rdmolops.cpp.o.d -o CMakeFiles/rdmolops.dir/rdmolops.cpp.o -c /build/reproducible-path/rdkit-202503.1/Code/GraphMol/Wrap/rdmolops.cpp +[ 65%] Linking CXX shared library ../../../lib/libRDKitDetermineBonds.so +cd /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/DetermineBonds && /usr/bin/cmake -E cmake_link_script 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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 -MD -MT Code/GraphMol/Abbreviations/CMakeFiles/testAbbreviations.dir/catch_tests.cpp.o -MF CMakeFiles/testAbbreviations.dir/catch_tests.cpp.o.d -o CMakeFiles/testAbbreviations.dir/catch_tests.cpp.o -c /build/reproducible-path/rdkit-202503.1/Code/GraphMol/Abbreviations/catch_tests.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]', @@ -5724,198 +5775,166 @@ 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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 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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/testReactionFingerprints.dir/testReactionFingerprints.cpp.o -MF CMakeFiles/testReactionFingerprints.dir/testReactionFingerprints.cpp.o.d -o CMakeFiles/testReactionFingerprints.dir/testReactionFingerprints.cpp.o -c /build/reproducible-path/rdkit-202503.1/Code/GraphMol/ChemReactions/testReactionFingerprints.cpp -cd /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/MarvinParse && /usr/bin/c++ 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/usr/lib/aarch64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl /usr/lib/aarch64-linux-gnu/libmaeparser.so +make[4]: Leaving directory '/build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu' +[ 67%] Built target molInterchangeCatchTest +[ 67%] 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_BUILD_XYZ2MOL_SUPPORT -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202503.1/External -I/usr/include/freetype2 -I/build/reproducible-path/rdkit-202503.1/Code -I/build/reproducible-path/rdkit-202503.1/External/boost-numeric-bindings -isystem /usr/include/eigen3 -isystem /usr/include/cairo -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/MolDraw2D/CMakeFiles/MolDraw2D.dir/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 +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, + from /build/reproducible-path/rdkit-202503.1/Code/GraphMol/MolDraw2D/DrawText.cpp:13: +/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/DrawText.cpp:165:47: required from here + 165 | tl = mol_draw.getAtomCoords(std::make_pair(tl.x, tl.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) + | ^~~~~~~~~ +[ 67%] Linking CXX shared library ../../../lib/libRDKitMolProcessing.so cd /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/MolProcessing && /usr/bin/cmake -E cmake_link_script CMakeFiles/MolProcessing.dir/link.txt --verbose=1 /usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,--dependency-file=CMakeFiles/MolProcessing.dir/link.d -Wl,-z,relro -Wl,-z,now -shared -Wl,-soname,libRDKitMolProcessing.so.1 -o ../../../lib/libRDKitMolProcessing.so.1.2025.03.1 CMakeFiles/MolProcessing.dir/MolProcessing.cpp.o ../../../lib/libRDKitFileParsers.so.1.2025.03.1 ../../../lib/libRDKitFingerprints.so.1.2025.03.1 ../../../lib/libRDKitRDStreams.so.1.2025.03.1 ../../../lib/libRDKitChemTransforms.so.1.2025.03.1 ../../../lib/libRDKitDepictor.so.1.2025.03.1 /usr/lib/aarch64-linux-gnu/libcoordgen.so ../../../lib/libRDKitMolAlign.so.1.2025.03.1 ../../../lib/libRDKitMolTransforms.so.1.2025.03.1 ../../../lib/libRDKitEigenSolvers.so.1.2025.03.1 ../../../lib/libRDKitAlignment.so.1.2025.03.1 /usr/lib/aarch64-linux-gnu/libmaeparser.so ../../../lib/libRDKitSmilesParse.so.1.2025.03.1 ../../../lib/libRDKitSubgraphs.so.1.2025.03.1 ../../../lib/libRDKitSubstructMatch.so.1.2025.03.1 ../../../lib/libRDKitGenericGroups.so.1.2025.03.1 ../../../lib/libRDKitGraphMol.so.1.2025.03.1 ../../../lib/libRDKitRDGeometryLib.so.1.2025.03.1 ../../../lib/libRDKitDataStructs.so.1.2025.03.1 ../../../lib/libRDKitRDGeneral.so.1.2025.03.1 -ldl /usr/lib/aarch64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_iostreams.so.1.83.0 cd /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/MolProcessing && /usr/bin/cmake -E cmake_symlink_library ../../../lib/libRDKitMolProcessing.so.1.2025.03.1 ../../../lib/libRDKitMolProcessing.so.1 ../../../lib/libRDKitMolProcessing.so make[4]: Leaving directory '/build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu' -[ 68%] Built target MolProcessing +[ 67%] Built target MolProcessing +[ 67%] Building CXX object Code/GraphMol/MarvinParse/CMakeFiles/MarvinParser.dir/MarvinWriter.cpp.o +cd /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/MarvinParse && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DMarvinParser_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_MARVINPARSER_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_BUILD_XYZ2MOL_SUPPORT -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202503.1/External -I/build/reproducible-path/rdkit-202503.1/Code -I/build/reproducible-path/rdkit-202503.1/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/MarvinParse/CMakeFiles/MarvinParser.dir/MarvinWriter.cpp.o -MF CMakeFiles/MarvinParser.dir/MarvinWriter.cpp.o.d -o CMakeFiles/MarvinParser.dir/MarvinWriter.cpp.o -c /build/reproducible-path/rdkit-202503.1/Code/GraphMol/MarvinParse/MarvinWriter.cpp +[ 67%] Building CXX object Code/GraphMol/MolDraw2D/CMakeFiles/MolDraw2D.dir/DrawTextSVG.cpp.o +cd /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/MolDraw2D && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DMolDraw2D_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_MOLDRAW2D_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_CAIRO_SUPPORT -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_FREETYPE_SUPPORT -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_BUILD_XYZ2MOL_SUPPORT -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202503.1/External -I/usr/include/freetype2 -I/build/reproducible-path/rdkit-202503.1/Code -I/build/reproducible-path/rdkit-202503.1/External/boost-numeric-bindings -isystem /usr/include/eigen3 -isystem /usr/include/cairo -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/MolDraw2D/CMakeFiles/MolDraw2D.dir/DrawTextSVG.cpp.o -MF CMakeFiles/MolDraw2D.dir/DrawTextSVG.cpp.o.d -o CMakeFiles/MolDraw2D.dir/DrawTextSVG.cpp.o -c /build/reproducible-path/rdkit-202503.1/Code/GraphMol/MolDraw2D/DrawTextSVG.cpp +[ 67%] Building CXX object Code/GraphMol/MarvinParse/CMakeFiles/MarvinParser.dir/MarvinDefs.cpp.o +cd /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/MarvinParse && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DMarvinParser_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_MARVINPARSER_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_BUILD_XYZ2MOL_SUPPORT -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202503.1/External -I/build/reproducible-path/rdkit-202503.1/Code -I/build/reproducible-path/rdkit-202503.1/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 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-DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_FREETYPE_SUPPORT -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_BUILD_XYZ2MOL_SUPPORT -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202503.1/External -I/usr/include/freetype2 -I/build/reproducible-path/rdkit-202503.1/Code -I/build/reproducible-path/rdkit-202503.1/External/boost-numeric-bindings -isystem /usr/include/eigen3 -isystem /usr/include/cairo -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/MolDraw2D/CMakeFiles/MolDraw2D.dir/MolDraw2DJS.cpp.o -MF CMakeFiles/MolDraw2D.dir/MolDraw2DJS.cpp.o.d -o 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../../../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' +[ 68%] Built target testAbbreviations +[ 68%] Building CXX object Code/GraphMol/MolDraw2D/CMakeFiles/MolDraw2D.dir/DrawTextJS.cpp.o make -f Code/GraphMol/ChemReactions/CMakeFiles/testEnumeration.dir/build.make 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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 -[ 68%] Linking CXX executable molInterchangeCatchTest -cd /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/MolInterchange && /usr/bin/cmake -E cmake_link_script 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Code/GraphMol/MolDraw2D/CMakeFiles/MolDraw2D.dir/DrawTextFTSVG.cpp.o +cd /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/MolDraw2D && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DMolDraw2D_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_MOLDRAW2D_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_CAIRO_SUPPORT -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_FREETYPE_SUPPORT -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_BUILD_XYZ2MOL_SUPPORT -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202503.1/External -I/usr/include/freetype2 -I/build/reproducible-path/rdkit-202503.1/Code -I/build/reproducible-path/rdkit-202503.1/External/boost-numeric-bindings -isystem /usr/include/eigen3 -isystem /usr/include/cairo -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/MolDraw2D/CMakeFiles/MolDraw2D.dir/DrawTextFTSVG.cpp.o -MF CMakeFiles/MolDraw2D.dir/DrawTextFTSVG.cpp.o.d -o CMakeFiles/MolDraw2D.dir/DrawTextFTSVG.cpp.o -c /build/reproducible-path/rdkit-202503.1/Code/GraphMol/MolDraw2D/DrawTextFTSVG.cpp make -f Code/GraphMol/Descriptors/CMakeFiles/testAUTOCORR2D.dir/build.make Code/GraphMol/Descriptors/CMakeFiles/testAUTOCORR2D.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-202503.1/obj-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/Descriptors /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/Descriptors /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/Descriptors/CMakeFiles/testAUTOCORR2D.dir/DependInfo.cmake "--color=" @@ -5924,15 +5943,17 @@ make[4]: Entering directory '/build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu' [ 69%] Building CXX object Code/GraphMol/Descriptors/CMakeFiles/testAUTOCORR2D.dir/testAUTOCORR2D.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 -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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object Code/GraphMol/MolStandardize/CMakeFiles/MolStandardize.dir/Metal.cpp.o +cd /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/MolStandardize && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DMolStandardize_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_MOLSTANDARDIZE_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_BUILD_XYZ2MOL_SUPPORT -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202503.1/External -I/build/reproducible-path/rdkit-202503.1/Code -I/build/reproducible-path/rdkit-202503.1/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/MolStandardize/CMakeFiles/MolStandardize.dir/Metal.cpp.o -MF CMakeFiles/MolStandardize.dir/Metal.cpp.o.d -o CMakeFiles/MolStandardize.dir/Metal.cpp.o -c /build/reproducible-path/rdkit-202503.1/Code/GraphMol/MolStandardize/Metal.cpp +[ 69%] Building CXX object Code/GraphMol/MolDraw2D/CMakeFiles/MolDraw2D.dir/DrawTextFTJS.cpp.o +cd /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/MolDraw2D && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DMolDraw2D_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_MOLDRAW2D_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_CAIRO_SUPPORT -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_FREETYPE_SUPPORT -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_BUILD_XYZ2MOL_SUPPORT -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202503.1/External -I/usr/include/freetype2 -I/build/reproducible-path/rdkit-202503.1/Code -I/build/reproducible-path/rdkit-202503.1/External/boost-numeric-bindings -isystem /usr/include/eigen3 -isystem /usr/include/cairo -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/MolDraw2D/CMakeFiles/MolDraw2D.dir/DrawTextFTJS.cpp.o -MF CMakeFiles/MolDraw2D.dir/DrawTextFTJS.cpp.o.d -o CMakeFiles/MolDraw2D.dir/DrawTextFTJS.cpp.o -c /build/reproducible-path/rdkit-202503.1/Code/GraphMol/MolDraw2D/DrawTextFTJS.cpp [ 69%] Building CXX object Code/GraphMol/MolStandardize/CMakeFiles/MolStandardize.dir/Normalize.cpp.o cd /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/MolStandardize && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DMolStandardize_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_MOLSTANDARDIZE_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_BUILD_XYZ2MOL_SUPPORT -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202503.1/External -I/build/reproducible-path/rdkit-202503.1/Code -I/build/reproducible-path/rdkit-202503.1/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/MolStandardize/CMakeFiles/MolStandardize.dir/Normalize.cpp.o -MF CMakeFiles/MolStandardize.dir/Normalize.cpp.o.d -o CMakeFiles/MolStandardize.dir/Normalize.cpp.o -c /build/reproducible-path/rdkit-202503.1/Code/GraphMol/MolStandardize/Normalize.cpp [ 69%] Linking CXX executable testEnumeration cd /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/ChemReactions && /usr/bin/cmake -E cmake_link_script CMakeFiles/testEnumeration.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 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-DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DMolStandardize_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_MOLSTANDARDIZE_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_BUILD_XYZ2MOL_SUPPORT -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202503.1/External -I/build/reproducible-path/rdkit-202503.1/Code -I/build/reproducible-path/rdkit-202503.1/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/MolStandardize/CMakeFiles/MolStandardize.dir/Validate.cpp.o -MF CMakeFiles/MolStandardize.dir/Validate.cpp.o.d -o CMakeFiles/MolStandardize.dir/Validate.cpp.o -c /build/reproducible-path/rdkit-202503.1/Code/GraphMol/MolStandardize/Validate.cpp make -f Code/GraphMol/Descriptors/CMakeFiles/testATF.dir/build.make Code/GraphMol/Descriptors/CMakeFiles/testATF.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/Descriptors /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/Descriptors /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/Descriptors/CMakeFiles/testATF.dir/DependInfo.cmake "--color=" @@ -5941,28 +5962,40 @@ make[4]: Entering directory '/build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu' [ 69%] Building CXX object Code/GraphMol/Descriptors/CMakeFiles/testATF.dir/testATF.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 -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_BUILD_XYZ2MOL_SUPPORT -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202503.1/External -I/build/reproducible-path/rdkit-202503.1/Code -I/build/reproducible-path/rdkit-202503.1/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/GraphMol/Descriptors/CMakeFiles/testATF.dir/testATF.cpp.o -MF CMakeFiles/testATF.dir/testATF.cpp.o.d -o CMakeFiles/testATF.dir/testATF.cpp.o -c /build/reproducible-path/rdkit-202503.1/Code/GraphMol/Descriptors/testATF.cpp -[ 69%] Building CXX object Code/GraphMol/MolStandardize/CMakeFiles/MolStandardize.dir/Charge.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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../../../lib/libRDKitRDGeometryLib.so.1.2025.03.1 ../../../lib/libRDKitDataStructs.so.1.2025.03.1 ../../../lib/libRDKitEigenSolvers.so.1.2025.03.1 ../../../lib/libRDKitRDGeneral.so.1.2025.03.1 /usr/lib/aarch64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl make[4]: Leaving directory '/build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu' -[ 69%] Built target testAUTOCORR2D +[ 69%] Built target testATF +[ 69%] Building CXX object Code/GraphMol/MolStandardize/CMakeFiles/MolStandardize.dir/Fragment.cpp.o +cd /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/MolStandardize && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DMolStandardize_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_MOLSTANDARDIZE_BUILD -DRDK_64BIT_BUILD 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'/build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu' [ 69%] Building CXX object Code/GraphMol/Descriptors/CMakeFiles/testEEM.dir/testEEM.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 -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_BUILD_XYZ2MOL_SUPPORT -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202503.1/External -I/build/reproducible-path/rdkit-202503.1/Code -I/build/reproducible-path/rdkit-202503.1/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/GraphMol/Descriptors/CMakeFiles/testEEM.dir/testEEM.cpp.o -MF CMakeFiles/testEEM.dir/testEEM.cpp.o.d -o CMakeFiles/testEEM.dir/testEEM.cpp.o -c /build/reproducible-path/rdkit-202503.1/Code/GraphMol/Descriptors/testEEM.cpp -[ 69%] Building CXX object Code/GraphMol/MolStandardize/CMakeFiles/MolStandardize.dir/Fragment.cpp.o -cd /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/MolStandardize && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DMolStandardize_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_MOLSTANDARDIZE_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT 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/build/reproducible-path/rdkit-202503.1/Code/GraphMol/MolStandardize/Fragment.cpp +[ 69%] Linking CXX shared library ../../../lib/libRDKitMarvinParser.so +cd /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/MarvinParse && /usr/bin/cmake -E cmake_link_script CMakeFiles/MarvinParser.dir/link.txt --verbose=1 +/usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,--dependency-file=CMakeFiles/MarvinParser.dir/link.d -Wl,-z,relro -Wl,-z,now -shared -Wl,-soname,libRDKitMarvinParser.so.1 -o ../../../lib/libRDKitMarvinParser.so.1.2025.03.1 CMakeFiles/MarvinParser.dir/MarvinParser.cpp.o CMakeFiles/MarvinParser.dir/MarvinWriter.cpp.o CMakeFiles/MarvinParser.dir/MarvinDefs.cpp.o 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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/MarvinParse && /usr/bin/cmake -E cmake_symlink_library ../../../lib/libRDKitMarvinParser.so.1.2025.03.1 ../../../lib/libRDKitMarvinParser.so.1 ../../../lib/libRDKitMarvinParser.so +make[4]: Leaving directory '/build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu' +[ 69%] Built target MarvinParser [ 70%] Building CXX object Code/GraphMol/MolStandardize/CMakeFiles/MolStandardize.dir/FragmentCatalog/FragmentCatalogEntry.cpp.o cd /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/MolStandardize && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DMolStandardize_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_MOLSTANDARDIZE_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_BUILD_XYZ2MOL_SUPPORT -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202503.1/External -I/build/reproducible-path/rdkit-202503.1/Code -I/build/reproducible-path/rdkit-202503.1/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/MolStandardize/CMakeFiles/MolStandardize.dir/FragmentCatalog/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 [ 70%] Building CXX object Code/GraphMol/MolStandardize/CMakeFiles/MolStandardize.dir/FragmentCatalog/FragmentCatalogParams.cpp.o @@ -5995,16 +6032,25 @@ /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/testDescriptors.dir/link.d CMakeFiles/testDescriptors.dir/test.cpp.o -o testDescriptors ../../../lib/libRDKitDescriptors.so.1.2025.03.1 ../../../lib/libRDKitPartialCharges.so.1.2025.03.1 ../../../lib/libRDKitFileParsers.so.1.2025.03.1 ../../../lib/libRDKitChemTransforms.so.1.2025.03.1 ../../../lib/libRDKitDepictor.so.1.2025.03.1 /usr/lib/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 /usr/lib/aarch64-linux-gnu/libmaeparser.so ../../../lib/libRDKitSubgraphs.so.1.2025.03.1 ../../../lib/libRDKitSubstructMatch.so.1.2025.03.1 ../../../lib/libRDKitGenericGroups.so.1.2025.03.1 ../../../lib/libRDKitMolTransforms.so.1.2025.03.1 ../../../lib/libRDKitGraphMol.so.1.2025.03.1 ../../../lib/libRDKitRDGeometryLib.so.1.2025.03.1 ../../../lib/libRDKitDataStructs.so.1.2025.03.1 ../../../lib/libRDKitEigenSolvers.so.1.2025.03.1 ../../../lib/libRDKitRDGeneral.so.1.2025.03.1 /usr/lib/aarch64-linux-gnu/libboost_system.so.1.83.0 /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' [ 70%] Built target testDescriptors +[ 70%] Building CXX object Code/GraphMol/MolStandardize/CMakeFiles/MolStandardize.dir/FragmentCatalog/FragmentCatalogUtils.cpp.o +cd /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/MolStandardize && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DMolStandardize_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_MOLSTANDARDIZE_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_BUILD_XYZ2MOL_SUPPORT -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202503.1/External -I/build/reproducible-path/rdkit-202503.1/Code -I/build/reproducible-path/rdkit-202503.1/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/MolStandardize/CMakeFiles/MolStandardize.dir/FragmentCatalog/FragmentCatalogUtils.cpp.o -MF CMakeFiles/MolStandardize.dir/FragmentCatalog/FragmentCatalogUtils.cpp.o.d -o CMakeFiles/MolStandardize.dir/FragmentCatalog/FragmentCatalogUtils.cpp.o -c /build/reproducible-path/rdkit-202503.1/Code/GraphMol/MolStandardize/FragmentCatalog/FragmentCatalogUtils.cpp +[ 70%] 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 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'/build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu' +[ 72%] Built target testPBF make -f Code/GraphMol/Descriptors/CMakeFiles/test3D.dir/build.make Code/GraphMol/Descriptors/CMakeFiles/test3D.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-202503.1/obj-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/Descriptors /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/Descriptors /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/Descriptors/CMakeFiles/test3D.dir/DependInfo.cmake "--color=" @@ -6056,28 +6091,27 @@ make[4]: Entering directory '/build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu' [ 72%] Building CXX object 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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 -cd /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/MarvinParse && /usr/bin/cmake -E cmake_symlink_library ../../../lib/libRDKitMarvinParser.so.1.2025.03.1 ../../../lib/libRDKitMarvinParser.so.1 ../../../lib/libRDKitMarvinParser.so -make[4]: Leaving directory '/build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu' -[ 73%] Built target MarvinParser make -f Code/GraphMol/Descriptors/CMakeFiles/testAUTOCORR3D.dir/build.make Code/GraphMol/Descriptors/CMakeFiles/testAUTOCORR3D.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-202503.1/obj-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/Descriptors /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/Descriptors /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/Descriptors/CMakeFiles/testAUTOCORR3D.dir/DependInfo.cmake "--color=" @@ -6098,39 +6128,40 @@ make[4]: Entering directory '/build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu' [ 73%] Building CXX object Code/GraphMol/Descriptors/CMakeFiles/testAUTOCORR3D.dir/testAUTOCORR3D.cpp.o cd /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/Descriptors && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB 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make -f Code/GraphMol/MolDraw2D/CMakeFiles/moldraw2DTest1.dir/build.make Code/GraphMol/MolDraw2D/CMakeFiles/moldraw2DTest1.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-202503.1/obj-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/moldraw2DTest1.dir/DependInfo.cmake "--color=" @@ -6152,11 +6178,13 @@ make[4]: Entering directory '/build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu' [ 74%] Building CXX object Code/GraphMol/MolDraw2D/CMakeFiles/moldraw2DTest1.dir/test1.cpp.o cd 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../../../lib/libRDKitMolTransforms.so.1.2025.03.1 ../../../lib/libRDKitGraphMol.so.1.2025.03.1 ../../../lib/libRDKitRDGeometryLib.so.1.2025.03.1 ../../../lib/libRDKitDataStructs.so.1.2025.03.1 ../../../lib/libRDKitEigenSolvers.so.1.2025.03.1 ../../../lib/libRDKitRDGeneral.so.1.2025.03.1 /usr/lib/aarch64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl +/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/testGETAWAY.dir/link.d CMakeFiles/testGETAWAY.dir/testGETAWAY.cpp.o -o testGETAWAY ../../../lib/libRDKitDescriptors.so.1.2025.03.1 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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' -[ 75%] Built target testAUTOCORR3D +[ 75%] Built target testGETAWAY make -f Code/GraphMol/FMCS/CMakeFiles/testFMCS.dir/build.make Code/GraphMol/FMCS/CMakeFiles/testFMCS.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu' 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 /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FMCS /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FMCS/CMakeFiles/testFMCS.dir/DependInfo.cmake "--color=" @@ -6199,11 +6237,9 @@ make[4]: Entering directory '/build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu' [ 75%] Building CXX object Code/GraphMol/FMCS/CMakeFiles/testFMCS.dir/testFMCS_Unit.cpp.o cd /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FMCS && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_BUILD_XYZ2MOL_SUPPORT -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202503.1/External -I/build/reproducible-path/rdkit-202503.1/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/GraphMol/FMCS/CMakeFiles/testFMCS.dir/testFMCS_Unit.cpp.o -MF CMakeFiles/testFMCS.dir/testFMCS_Unit.cpp.o.d -o CMakeFiles/testFMCS.dir/testFMCS_Unit.cpp.o -c /build/reproducible-path/rdkit-202503.1/Code/GraphMol/FMCS/testFMCS_Unit.cpp -[ 75%] Linking CXX executable testCoulombMat -cd /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/Descriptors && /usr/bin/cmake -E cmake_link_script CMakeFiles/testCoulombMat.dir/link.txt --verbose=1 -/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/testCoulombMat.dir/link.d CMakeFiles/testCoulombMat.dir/testCoulombMat.cpp.o -o testCoulombMat ../../../lib/libRDKitDescriptors.so.1.2025.03.1 ../../../lib/libRDKitDistGeomHelpers.so.1.2025.03.1 ../../../lib/libRDKitPartialCharges.so.1.2025.03.1 ../../../lib/libRDKitFileParsers.so.1.2025.03.1 ../../../lib/libRDKitChemTransforms.so.1.2025.03.1 ../../../lib/libRDKitDepictor.so.1.2025.03.1 /usr/lib/aarch64-linux-gnu/libcoordgen.so /usr/lib/aarch64-linux-gnu/libmaeparser.so ../../../lib/libRDKitSubgraphs.so.1.2025.03.1 ../../../lib/libRDKitMolAlign.so.1.2025.03.1 ../../../lib/libRDKitMolTransforms.so.1.2025.03.1 ../../../lib/libRDKitDistGeometry.so.1.2025.03.1 ../../../lib/libRDKitForceFieldHelpers.so.1.2025.03.1 ../../../lib/libRDKitSmilesParse.so.1.2025.03.1 ../../../lib/libRDKitSubstructMatch.so.1.2025.03.1 ../../../lib/libRDKitGenericGroups.so.1.2025.03.1 ../../../lib/libRDKitEigenSolvers.so.1.2025.03.1 ../../../lib/libRDKitForceField.so.1.2025.03.1 ../../../lib/libRDKitOptimizer.so.1.2025.03.1 ../../../lib/libRDKitTrajectory.so.1.2025.03.1 ../../../lib/libRDKitGraphMol.so.1.2025.03.1 ../../../lib/libRDKitAlignment.so.1.2025.03.1 ../../../lib/libRDKitRDGeometryLib.so.1.2025.03.1 ../../../lib/libRDKitDataStructs.so.1.2025.03.1 ../../../lib/libRDKitRDGeneral.so.1.2025.03.1 /usr/lib/aarch64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl +/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/rxnTestCatch.dir/link.d CMakeFiles/rxnTestCatch.dir/catch_tests.cpp.o -o rxnTestCatch ../../RDGeneral/librdkitCatch.a ../../../lib/libRDKitChemReactions.so.1.2025.03.1 /usr/lib/libCatch2.a ../../../lib/libRDKitFilterCatalog.so.1.2025.03.1 ../../../lib/libRDKitCatalogs.so.1.2025.03.1 ../../../lib/libRDKitFingerprints.so.1.2025.03.1 ../../../lib/libRDKitSubgraphs.so.1.2025.03.1 ../../../lib/libRDKitFileParsers.so.1.2025.03.1 /usr/lib/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 make[4]: Leaving directory '/build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu' -[ 75%] Built target testCoulombMat +[ 75%] Built target rxnTestCatch make -f Code/GraphMol/FMCS/Wrap/CMakeFiles/rdFMCS.dir/build.make Code/GraphMol/FMCS/Wrap/CMakeFiles/rdFMCS.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/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=" @@ -6212,15 +6248,11 @@ make[4]: Entering directory '/build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu' [ 75%] 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_BUILD_XYZ2MOL_SUPPORT -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 -/build/reproducible-path/rdkit-202503.1/Code/GraphMol/Descriptors/Wrap/rdMolDescriptors.cpp: In function 'std::pair {anonymous}::{anonymous}::BCUT2D_list(const RDKit::ROMol&, boost::python::list)': -/build/reproducible-path/rdkit-202503.1/Code/GraphMol/Descriptors/Wrap/rdMolDescriptors.cpp:444:61: note: parameter passing for argument of type 'std::pair' when C++17 is enabled changed to match C++14 in GCC 10.1 - 444 | python::list atomprops) { - | ^ -[ 75%] Linking CXX executable test3D -cd /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/Descriptors && /usr/bin/cmake -E cmake_link_script CMakeFiles/test3D.dir/link.txt --verbose=1 -/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/test3D.dir/link.d CMakeFiles/test3D.dir/test3D.cpp.o -o test3D ../../../lib/libRDKitDescriptors.so.1.2025.03.1 ../../../lib/libRDKitPartialCharges.so.1.2025.03.1 ../../../lib/libRDKitFileParsers.so.1.2025.03.1 ../../../lib/libRDKitChemTransforms.so.1.2025.03.1 ../../../lib/libRDKitDepictor.so.1.2025.03.1 /usr/lib/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 /usr/lib/aarch64-linux-gnu/libmaeparser.so ../../../lib/libRDKitSubgraphs.so.1.2025.03.1 ../../../lib/libRDKitSubstructMatch.so.1.2025.03.1 ../../../lib/libRDKitGenericGroups.so.1.2025.03.1 ../../../lib/libRDKitMolTransforms.so.1.2025.03.1 ../../../lib/libRDKitGraphMol.so.1.2025.03.1 ../../../lib/libRDKitRDGeometryLib.so.1.2025.03.1 ../../../lib/libRDKitDataStructs.so.1.2025.03.1 ../../../lib/libRDKitEigenSolvers.so.1.2025.03.1 ../../../lib/libRDKitRDGeneral.so.1.2025.03.1 /usr/lib/aarch64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl +[ 75%] Linking CXX executable testCoulombMat +cd /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/Descriptors && /usr/bin/cmake -E cmake_link_script CMakeFiles/testCoulombMat.dir/link.txt --verbose=1 +/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/testCoulombMat.dir/link.d CMakeFiles/testCoulombMat.dir/testCoulombMat.cpp.o -o testCoulombMat ../../../lib/libRDKitDescriptors.so.1.2025.03.1 ../../../lib/libRDKitDistGeomHelpers.so.1.2025.03.1 ../../../lib/libRDKitPartialCharges.so.1.2025.03.1 ../../../lib/libRDKitFileParsers.so.1.2025.03.1 ../../../lib/libRDKitChemTransforms.so.1.2025.03.1 ../../../lib/libRDKitDepictor.so.1.2025.03.1 /usr/lib/aarch64-linux-gnu/libcoordgen.so /usr/lib/aarch64-linux-gnu/libmaeparser.so ../../../lib/libRDKitSubgraphs.so.1.2025.03.1 ../../../lib/libRDKitMolAlign.so.1.2025.03.1 ../../../lib/libRDKitMolTransforms.so.1.2025.03.1 ../../../lib/libRDKitDistGeometry.so.1.2025.03.1 ../../../lib/libRDKitForceFieldHelpers.so.1.2025.03.1 ../../../lib/libRDKitSmilesParse.so.1.2025.03.1 ../../../lib/libRDKitSubstructMatch.so.1.2025.03.1 ../../../lib/libRDKitGenericGroups.so.1.2025.03.1 ../../../lib/libRDKitEigenSolvers.so.1.2025.03.1 ../../../lib/libRDKitForceField.so.1.2025.03.1 ../../../lib/libRDKitOptimizer.so.1.2025.03.1 ../../../lib/libRDKitTrajectory.so.1.2025.03.1 ../../../lib/libRDKitGraphMol.so.1.2025.03.1 ../../../lib/libRDKitAlignment.so.1.2025.03.1 ../../../lib/libRDKitRDGeometryLib.so.1.2025.03.1 ../../../lib/libRDKitDataStructs.so.1.2025.03.1 ../../../lib/libRDKitRDGeneral.so.1.2025.03.1 /usr/lib/aarch64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl make[4]: Leaving directory '/build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu' -[ 75%] Built target test3D +[ 75%] Built target testCoulombMat make -f Code/GraphMol/FMCS/Test/CMakeFiles/FMCStest.dir/build.make Code/GraphMol/FMCS/Test/CMakeFiles/FMCStest.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-202503.1/obj-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 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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, @@ -6242,37 +6287,21 @@ /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) | ^~~~~~~~~ -[ 75%] 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 -/usr/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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../../../lib/libRDKitGenericGroups.so.1.2025.03.1 ../../../lib/libRDKitMolTransforms.so.1.2025.03.1 ../../../lib/libRDKitGraphMol.so.1.2025.03.1 ../../../lib/libRDKitRDGeometryLib.so.1.2025.03.1 ../../../lib/libRDKitDataStructs.so.1.2025.03.1 ../../../lib/libRDKitEigenSolvers.so.1.2025.03.1 ../../../lib/libRDKitRDGeneral.so.1.2025.03.1 /usr/lib/aarch64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl make[4]: Leaving directory '/build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu' -[ 75%] Built target moldraw2DRxnTest1 +[ 76%] Built target descriptorsTestCatch make -f Code/GraphMol/MMPA/Wrap/CMakeFiles/rdMMPA.dir/build.make Code/GraphMol/MMPA/Wrap/CMakeFiles/rdMMPA.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-202503.1/obj-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/Wrap /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/MMPA/Wrap /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/MMPA/Wrap/CMakeFiles/rdMMPA.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu' make -f Code/GraphMol/MMPA/Wrap/CMakeFiles/rdMMPA.dir/build.make Code/GraphMol/MMPA/Wrap/CMakeFiles/rdMMPA.dir/build make[4]: Entering directory '/build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu' -[ 75%] Building CXX object Code/GraphMol/MMPA/Wrap/CMakeFiles/rdMMPA.dir/rdMMPA.cpp.o +[ 76%] Building CXX object Code/GraphMol/MMPA/Wrap/CMakeFiles/rdMMPA.dir/rdMMPA.cpp.o cd /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/MMPA/Wrap && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_NUMPY_DYN_LINK -DBOOST_NUMPY_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_BUILD_XYZ2MOL_SUPPORT -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DrdMMPA_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/MMPA/Wrap/CMakeFiles/rdMMPA.dir/rdMMPA.cpp.o -MF CMakeFiles/rdMMPA.dir/rdMMPA.cpp.o.d -o CMakeFiles/rdMMPA.dir/rdMMPA.cpp.o -c /build/reproducible-path/rdkit-202503.1/Code/GraphMol/MMPA/Wrap/rdMMPA.cpp -[ 75%] Linking CXX shared library ../../../lib/libRDKitO3AAlign.so +[ 76%] Linking CXX shared library ../../../lib/libRDKitO3AAlign.so cd /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/MolAlign && /usr/bin/cmake -E cmake_link_script CMakeFiles/O3AAlign.dir/link.txt --verbose=1 -[ 76%] Linking CXX executable descriptorsTestCatch -cd /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/Descriptors && /usr/bin/cmake -E cmake_link_script CMakeFiles/descriptorsTestCatch.dir/link.txt --verbose=1 /usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,--dependency-file=CMakeFiles/O3AAlign.dir/link.d -Wl,-z,relro -Wl,-z,now -shared -Wl,-soname,libRDKitO3AAlign.so.1 -o ../../../lib/libRDKitO3AAlign.so.1.2025.03.1 CMakeFiles/O3AAlign.dir/O3AAlignMolecules.cpp.o ../../../lib/libRDKitDescriptors.so.1.2025.03.1 ../../../lib/libRDKitForceFieldHelpers.so.1.2025.03.1 ../../../lib/libRDKitPartialCharges.so.1.2025.03.1 ../../../lib/libRDKitFileParsers.so.1.2025.03.1 ../../../lib/libRDKitChemTransforms.so.1.2025.03.1 ../../../lib/libRDKitDepictor.so.1.2025.03.1 ../../../lib/libRDKitMolAlign.so.1.2025.03.1 ../../../lib/libRDKitAlignment.so.1.2025.03.1 ../../../lib/libRDKitMolTransforms.so.1.2025.03.1 /usr/lib/aarch64-linux-gnu/libcoordgen.so /usr/lib/aarch64-linux-gnu/libmaeparser.so ../../../lib/libRDKitSubgraphs.so.1.2025.03.1 ../../../lib/libRDKitEigenSolvers.so.1.2025.03.1 ../../../lib/libRDKitSubstructMatch.so.1.2025.03.1 ../../../lib/libRDKitGenericGroups.so.1.2025.03.1 ../../../lib/libRDKitSmilesParse.so.1.2025.03.1 ../../../lib/libRDKitForceField.so.1.2025.03.1 ../../../lib/libRDKitOptimizer.so.1.2025.03.1 ../../../lib/libRDKitTrajectory.so.1.2025.03.1 ../../../lib/libRDKitGraphMol.so.1.2025.03.1 ../../../lib/libRDKitRDGeometryLib.so.1.2025.03.1 ../../../lib/libRDKitDataStructs.so.1.2025.03.1 ../../../lib/libRDKitRDGeneral.so.1.2025.03.1 /usr/lib/aarch64-linux-gnu/libboost_system.so.1.83.0 /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 '/build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu' @@ -6285,9 +6314,11 @@ make[4]: Entering directory '/build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu' [ 76%] Building CXX object Code/GraphMol/RascalMCES/CMakeFiles/testRascalMCES.dir/mces_catch.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 -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_BUILD_XYZ2MOL_SUPPORT -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202503.1/External -I/build/reproducible-path/rdkit-202503.1/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/GraphMol/RascalMCES/CMakeFiles/testRascalMCES.dir/mces_catch.cpp.o -MF CMakeFiles/testRascalMCES.dir/mces_catch.cpp.o.d -o CMakeFiles/testRascalMCES.dir/mces_catch.cpp.o -c /build/reproducible-path/rdkit-202503.1/Code/GraphMol/RascalMCES/mces_catch.cpp -/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/descriptorsTestCatch.dir/link.d CMakeFiles/descriptorsTestCatch.dir/catch_tests.cpp.o -o descriptorsTestCatch ../../RDGeneral/librdkitCatch.a ../../../lib/libRDKitDescriptors.so.1.2025.03.1 ../../../lib/libRDKitFileParsers.so.1.2025.03.1 /usr/lib/libCatch2.a ../../../lib/libRDKitChemTransforms.so.1.2025.03.1 ../../../lib/libRDKitDepictor.so.1.2025.03.1 /usr/lib/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 /usr/lib/aarch64-linux-gnu/libmaeparser.so ../../../lib/libRDKitPartialCharges.so.1.2025.03.1 ../../../lib/libRDKitSubgraphs.so.1.2025.03.1 ../../../lib/libRDKitSubstructMatch.so.1.2025.03.1 ../../../lib/libRDKitGenericGroups.so.1.2025.03.1 ../../../lib/libRDKitMolTransforms.so.1.2025.03.1 ../../../lib/libRDKitGraphMol.so.1.2025.03.1 ../../../lib/libRDKitRDGeometryLib.so.1.2025.03.1 ../../../lib/libRDKitDataStructs.so.1.2025.03.1 ../../../lib/libRDKitEigenSolvers.so.1.2025.03.1 ../../../lib/libRDKitRDGeneral.so.1.2025.03.1 /usr/lib/aarch64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl +[ 76%] Linking CXX executable moldraw2DRxnTest1 +cd /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/MolDraw2D && /usr/bin/cmake -E cmake_link_script CMakeFiles/moldraw2DRxnTest1.dir/link.txt --verbose=1 +/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/moldraw2DRxnTest1.dir/link.d CMakeFiles/moldraw2DRxnTest1.dir/rxn_test1.cpp.o -o moldraw2DRxnTest1 ../../../lib/libRDKitMolDraw2D.so.1.2025.03.1 ../../../lib/libRDKitChemReactions.so.1.2025.03.1 ../../../lib/libRDKitFilterCatalog.so.1.2025.03.1 ../../../lib/libRDKitCatalogs.so.1.2025.03.1 ../../../lib/libRDKitFingerprints.so.1.2025.03.1 ../../../lib/libRDKitFileParsers.so.1.2025.03.1 /usr/lib/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 make[4]: Leaving directory '/build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu' -[ 76%] Built target descriptorsTestCatch +[ 76%] Built target moldraw2DRxnTest1 make -f Code/GraphMol/RascalMCES/CMakeFiles/testRascalCluster.dir/build.make Code/GraphMol/RascalMCES/CMakeFiles/testRascalCluster.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu' cd /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202503.1 /build/reproducible-path/rdkit-202503.1/Code/GraphMol/RascalMCES /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/RascalMCES /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/RascalMCES/CMakeFiles/testRascalCluster.dir/DependInfo.cmake "--color=" @@ -6296,11 +6327,11 @@ make[4]: Entering directory '/build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu' [ 76%] Building CXX object Code/GraphMol/RascalMCES/CMakeFiles/testRascalCluster.dir/mces_cluster_catch.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 -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_BUILD_XYZ2MOL_SUPPORT -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202503.1/External -I/build/reproducible-path/rdkit-202503.1/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/GraphMol/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 -[ 76%] Linking CXX executable FMCStest -cd /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FMCS/Test && /usr/bin/cmake -E cmake_link_script CMakeFiles/FMCStest.dir/link.txt --verbose=1 -/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/FMCStest.dir/link.d CMakeFiles/FMCStest.dir/testFMCS.cpp.o -o FMCStest ../../../../lib/libRDKitFMCS.so.1.2025.03.1 ../../../../lib/libRDKitFileParsers.so.1.2025.03.1 /usr/lib/aarch64-linux-gnu/libmaeparser.so ../../../../lib/libRDKitChemTransforms.so.1.2025.03.1 ../../../../lib/libRDKitDepictor.so.1.2025.03.1 /usr/lib/aarch64-linux-gnu/libcoordgen.so ../../../../lib/libRDKitMolAlign.so.1.2025.03.1 ../../../../lib/libRDKitMolTransforms.so.1.2025.03.1 ../../../../lib/libRDKitEigenSolvers.so.1.2025.03.1 ../../../../lib/libRDKitAlignment.so.1.2025.03.1 ../../../../lib/libRDKitSmilesParse.so.1.2025.03.1 ../../../../lib/libRDKitSubstructMatch.so.1.2025.03.1 ../../../../lib/libRDKitGenericGroups.so.1.2025.03.1 ../../../../lib/libRDKitGraphMol.so.1.2025.03.1 ../../../../lib/libRDKitRDGeometryLib.so.1.2025.03.1 ../../../../lib/libRDKitDataStructs.so.1.2025.03.1 ../../../../lib/libRDKitRDGeneral.so.1.2025.03.1 /usr/lib/aarch64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl +[ 76%] Linking CXX executable testMMPA +cd /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/MMPA && /usr/bin/cmake -E cmake_link_script CMakeFiles/testMMPA.dir/link.txt --verbose=1 +/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/testMMPA.dir/link.d CMakeFiles/testMMPA.dir/MMPA_UnitTest.cpp.o -o testMMPA ../../../lib/libRDKitMMPA.so.1.2025.03.1 ../../../lib/libRDKitFileParsers.so.1.2025.03.1 /usr/lib/aarch64-linux-gnu/libmaeparser.so ../../../lib/libRDKitChemTransforms.so.1.2025.03.1 ../../../lib/libRDKitDepictor.so.1.2025.03.1 /usr/lib/aarch64-linux-gnu/libcoordgen.so ../../../lib/libRDKitMolAlign.so.1.2025.03.1 ../../../lib/libRDKitSmilesParse.so.1.2025.03.1 ../../../lib/libRDKitSubstructMatch.so.1.2025.03.1 ../../../lib/libRDKitGenericGroups.so.1.2025.03.1 ../../../lib/libRDKitMolTransforms.so.1.2025.03.1 ../../../lib/libRDKitEigenSolvers.so.1.2025.03.1 ../../../lib/libRDKitAlignment.so.1.2025.03.1 ../../../lib/libRDKitGraphMol.so.1.2025.03.1 ../../../lib/libRDKitRDGeometryLib.so.1.2025.03.1 ../../../lib/libRDKitDataStructs.so.1.2025.03.1 ../../../lib/libRDKitRDGeneral.so.1.2025.03.1 /usr/lib/aarch64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl make[4]: Leaving directory '/build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu' -[ 76%] Built target FMCStest +[ 76%] Built target testMMPA make -f Code/GraphMol/RascalMCES/Wrap/CMakeFiles/rdRascalMCES.dir/build.make Code/GraphMol/RascalMCES/Wrap/CMakeFiles/rdRascalMCES.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu' cd /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202503.1 /build/reproducible-path/rdkit-202503.1/Code/GraphMol/RascalMCES/Wrap /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/RascalMCES/Wrap /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/RascalMCES/Wrap/CMakeFiles/rdRascalMCES.dir/DependInfo.cmake "--color=" @@ -6309,11 +6340,11 @@ make[4]: Entering directory '/build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu' [ 76%] Building CXX object Code/GraphMol/RascalMCES/Wrap/CMakeFiles/rdRascalMCES.dir/rdRascalMCES.cpp.o cd /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/RascalMCES/Wrap && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_NUMPY_DYN_LINK -DBOOST_NUMPY_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_BUILD_XYZ2MOL_SUPPORT -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DrdRascalMCES_EXPORTS -I/build/reproducible-path/rdkit-202503.1/External -I/build/reproducible-path/rdkit-202503.1/Code -I/usr/lib/aarch64-linux-gnu/python3-numpy/numpy/_core/include -isystem /usr/include/python3.13 -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/RascalMCES/Wrap/CMakeFiles/rdRascalMCES.dir/rdRascalMCES.cpp.o -MF CMakeFiles/rdRascalMCES.dir/rdRascalMCES.cpp.o.d -o CMakeFiles/rdRascalMCES.dir/rdRascalMCES.cpp.o -c /build/reproducible-path/rdkit-202503.1/Code/GraphMol/RascalMCES/Wrap/rdRascalMCES.cpp -[ 76%] Linking CXX executable testMMPA -cd /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/MMPA && /usr/bin/cmake -E cmake_link_script CMakeFiles/testMMPA.dir/link.txt --verbose=1 -/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/testMMPA.dir/link.d CMakeFiles/testMMPA.dir/MMPA_UnitTest.cpp.o -o testMMPA ../../../lib/libRDKitMMPA.so.1.2025.03.1 ../../../lib/libRDKitFileParsers.so.1.2025.03.1 /usr/lib/aarch64-linux-gnu/libmaeparser.so ../../../lib/libRDKitChemTransforms.so.1.2025.03.1 ../../../lib/libRDKitDepictor.so.1.2025.03.1 /usr/lib/aarch64-linux-gnu/libcoordgen.so ../../../lib/libRDKitMolAlign.so.1.2025.03.1 ../../../lib/libRDKitSmilesParse.so.1.2025.03.1 ../../../lib/libRDKitSubstructMatch.so.1.2025.03.1 ../../../lib/libRDKitGenericGroups.so.1.2025.03.1 ../../../lib/libRDKitMolTransforms.so.1.2025.03.1 ../../../lib/libRDKitEigenSolvers.so.1.2025.03.1 ../../../lib/libRDKitAlignment.so.1.2025.03.1 ../../../lib/libRDKitGraphMol.so.1.2025.03.1 ../../../lib/libRDKitRDGeometryLib.so.1.2025.03.1 ../../../lib/libRDKitDataStructs.so.1.2025.03.1 ../../../lib/libRDKitRDGeneral.so.1.2025.03.1 /usr/lib/aarch64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl +[ 76%] Linking CXX executable FMCStest +cd /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FMCS/Test && /usr/bin/cmake -E cmake_link_script CMakeFiles/FMCStest.dir/link.txt --verbose=1 +/usr/bin/c++ -g -O2 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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 make[4]: Leaving directory '/build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu' -[ 76%] Built target testMMPA +[ 76%] Built target FMCStest make -f Code/GraphMol/CIPLabeler/CMakeFiles/testCIPLabeler.dir/build.make Code/GraphMol/CIPLabeler/CMakeFiles/testCIPLabeler.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu' cd /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202503.1 /build/reproducible-path/rdkit-202503.1/Code/GraphMol/CIPLabeler /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/CIPLabeler /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/CIPLabeler/CMakeFiles/testCIPLabeler.dir/DependInfo.cmake "--color=" @@ -6340,205 +6371,208 @@ /usr/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/rdMMPA.dir/link.d -Wl,-z,relro -Wl,-z,now -shared -o ../../../../rdkit/Chem/rdMMPA.so CMakeFiles/rdMMPA.dir/rdMMPA.cpp.o ../../../../lib/libRDKitMMPA.so.1.2025.03.1 ../../../../lib/libRDKitRDBoost.so.1.2025.03.1 ../../../../lib/libRDKitFileParsers.so.1.2025.03.1 /usr/lib/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/libRDKitMolTransforms.so.1.2025.03.1 ../../../../lib/libRDKitEigenSolvers.so.1.2025.03.1 ../../../../lib/libRDKitAlignment.so.1.2025.03.1 ../../../../lib/libRDKitSmilesParse.so.1.2025.03.1 ../../../../lib/libRDKitGraphMol.so.1.2025.03.1 ../../../../lib/libRDKitRDGeometryLib.so.1.2025.03.1 ../../../../lib/libRDKitDataStructs.so.1.2025.03.1 /usr/lib/aarch64-linux-gnu/libboost_numpy313.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_python313.so.1.83.0 ../../../../lib/libRDKitRDGeneral.so.1.2025.03.1 /usr/lib/aarch64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl make[4]: Leaving directory '/build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu' [ 76%] Built target rdMMPA +[ 77%] Building CXX object Code/GraphMol/CIPLabeler/CMakeFiles/testCIPLabeler.dir/CIPMol.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_BUILD_XYZ2MOL_SUPPORT -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202503.1/External -I/build/reproducible-path/rdkit-202503.1/Code -I/build/reproducible-path/rdkit-202503.1/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/GraphMol/CIPLabeler/CMakeFiles/testCIPLabeler.dir/CIPMol.cpp.o -MF CMakeFiles/testCIPLabeler.dir/CIPMol.cpp.o.d -o CMakeFiles/testCIPLabeler.dir/CIPMol.cpp.o -c /build/reproducible-path/rdkit-202503.1/Code/GraphMol/CIPLabeler/CIPMol.cpp +[ 77%] Linking CXX shared module ../../../../rdkit/Chem/rdFMCS.so +cd /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FMCS/Wrap && /usr/bin/cmake -E cmake_link_script CMakeFiles/rdFMCS.dir/link.txt --verbose=1 +/usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=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/rdFMCS.dir/link.d -Wl,-z,relro -Wl,-z,now -shared -o ../../../../rdkit/Chem/rdFMCS.so CMakeFiles/rdFMCS.dir/rdFMCS.cpp.o ../../../../lib/libRDKitFMCS.so.1.2025.03.1 ../../../../lib/libRDKitRDBoost.so.1.2025.03.1 ../../../../lib/libRDKitFileParsers.so.1.2025.03.1 /usr/lib/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 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Code/GraphMol/CIPLabeler/CMakeFiles/testCIPLabeler.dir/CIPLabeler.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_BUILD_XYZ2MOL_SUPPORT -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202503.1/External -I/build/reproducible-path/rdkit-202503.1/Code -I/build/reproducible-path/rdkit-202503.1/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/GraphMol/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 +[ 77%] Building CXX object Code/GraphMol/CIPLabeler/CMakeFiles/testCIPLabeler.dir/Mancude.cpp.o +cd /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/CIPLabeler && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -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_BUILD_XYZ2MOL_SUPPORT -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202503.1/External -I/build/reproducible-path/rdkit-202503.1/Code -I/build/reproducible-path/rdkit-202503.1/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/GraphMol/CIPLabeler/CMakeFiles/testCIPLabeler.dir/Mancude.cpp.o -MF CMakeFiles/testCIPLabeler.dir/Mancude.cpp.o.d -o CMakeFiles/testCIPLabeler.dir/Mancude.cpp.o -c /build/reproducible-path/rdkit-202503.1/Code/GraphMol/CIPLabeler/Mancude.cpp +[ 77%] 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 +[ 77%] Linking CXX executable deprotectTest +cd /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/Deprotect && /usr/bin/cmake -E cmake_link_script CMakeFiles/deprotectTest.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 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CMakeFiles/testRascalMCES.dir/link.txt --verbose=1 +/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/testRascalMCES.dir/link.d CMakeFiles/testRascalMCES.dir/mces_catch.cpp.o -o testRascalMCES ../../RDGeneral/librdkitCatch.a ../../../lib/libRDKitRascalMCES.so.1.2025.03.1 /usr/lib/libCatch2.a ../../../lib/libRDKitFileParsers.so.1.2025.03.1 /usr/lib/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 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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/DetermineBonds/Wrap/CMakeFiles/rdDetermineBonds.dir/rdDetermineBonds.cpp.o -MF CMakeFiles/rdDetermineBonds.dir/rdDetermineBonds.cpp.o.d -o CMakeFiles/rdDetermineBonds.dir/rdDetermineBonds.cpp.o -c /build/reproducible-path/rdkit-202503.1/Code/GraphMol/DetermineBonds/Wrap/rdDetermineBonds.cpp -[ 77%] 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 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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/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 -f Code/GraphMol/MolStandardize/CMakeFiles/molTautomerTest.dir/build.make Code/GraphMol/MolStandardize/CMakeFiles/molTautomerTest.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu' cd 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CMakeFiles/molTautomerTest.dir/testTautomer.cpp.o.d -o CMakeFiles/molTautomerTest.dir/testTautomer.cpp.o -c /build/reproducible-path/rdkit-202503.1/Code/GraphMol/MolStandardize/testTautomer.cpp -[ 81%] 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 ../../../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' -[ 81%] Built target molChargeTest -[ 81%] Building CXX object Code/GraphMol/CIPLabeler/CMakeFiles/testCIPLabeler.dir/rules/Rule3.cpp.o -cd /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/CIPLabeler && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_CIPLABELER_BUILD -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_BUILD_XYZ2MOL_SUPPORT -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202503.1/External -I/build/reproducible-path/rdkit-202503.1/Code -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/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 -[ 81%] Building CXX object Code/GraphMol/Wrap/CMakeFiles/rdmolfiles.dir/SmilesWriter.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/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' +[ 81%] Built target molValidateTest [ 81%] 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 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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/CIPLabeler/CMakeFiles/testCIPLabeler.dir/rules/Rule4c.cpp.o -MF CMakeFiles/testCIPLabeler.dir/rules/Rule4c.cpp.o.d -o CMakeFiles/testCIPLabeler.dir/rules/Rule4c.cpp.o -c /build/reproducible-path/rdkit-202503.1/Code/GraphMol/CIPLabeler/rules/Rule4c.cpp -[ 81%] Building CXX object Code/GraphMol/CIPLabeler/CMakeFiles/testCIPLabeler.dir/rules/Rule5.cpp.o +[ 82%] Building CXX object 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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/GraphMol/Wrap/CMakeFiles/rdmolfiles.dir/MultithreadedSDMolSupplier.cpp.o -MF CMakeFiles/rdmolfiles.dir/MultithreadedSDMolSupplier.cpp.o.d -o CMakeFiles/rdmolfiles.dir/MultithreadedSDMolSupplier.cpp.o -c /build/reproducible-path/rdkit-202503.1/Code/GraphMol/Wrap/MultithreadedSDMolSupplier.cpp +[ 85%] Building CXX object Code/GraphMol/Wrap/CMakeFiles/rdchem.dir/SubstanceGroup.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 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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/MolStandardize/Wrap/CMakeFiles/rdMolStandardize.dir/Tautomer.cpp.o -MF CMakeFiles/rdMolStandardize.dir/Tautomer.cpp.o.d -o CMakeFiles/rdMolStandardize.dir/Tautomer.cpp.o -c /build/reproducible-path/rdkit-202503.1/Code/GraphMol/MolStandardize/Wrap/Tautomer.cpp make -f Code/GraphMol/MolProcessing/CMakeFiles/testMolProcessing.dir/build.make 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'/build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu' -[ 87%] Building CXX object Code/GraphMol/MolProcessing/CMakeFiles/testMolProcessing.dir/processing_tests.cpp.o +[ 88%] Building CXX object Code/GraphMol/MolProcessing/CMakeFiles/testMolProcessing.dir/processing_tests.cpp.o cd /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/MolProcessing && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_BUILD_XYZ2MOL_SUPPORT -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202503.1/External -I/build/reproducible-path/rdkit-202503.1/Code 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-DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DrdMolStandardize_EXPORTS -I/build/reproducible-path/rdkit-202503.1/External -I/build/reproducible-path/rdkit-202503.1/Code -I/build/reproducible-path/rdkit-202503.1/External/boost-numeric-bindings -I/usr/lib/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/Pipeline.cpp.o -MF CMakeFiles/rdMolStandardize.dir/Pipeline.cpp.o.d -o CMakeFiles/rdMolStandardize.dir/Pipeline.cpp.o -c /build/reproducible-path/rdkit-202503.1/Code/GraphMol/MolStandardize/Wrap/Pipeline.cpp make -f Code/GraphMol/MolProcessing/Wrap/CMakeFiles/rdMolProcessing.dir/build.make Code/GraphMol/MolProcessing/Wrap/CMakeFiles/rdMolProcessing.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu' cd /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202503.1 /build/reproducible-path/rdkit-202503.1/Code/GraphMol/MolProcessing/Wrap /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/MolProcessing/Wrap /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/MolProcessing/Wrap/CMakeFiles/rdMolProcessing.dir/DependInfo.cmake "--color=" @@ -6711,8 +6757,6 @@ make[4]: Entering directory '/build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu' [ 88%] Building CXX object Code/GraphMol/MolProcessing/Wrap/CMakeFiles/rdMolProcessing.dir/rdMolProcessing.cpp.o cd /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/MolProcessing/Wrap && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_NUMPY_DYN_LINK -DBOOST_NUMPY_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_BUILD_XYZ2MOL_SUPPORT -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DrdMolProcessing_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/MolProcessing/Wrap/CMakeFiles/rdMolProcessing.dir/rdMolProcessing.cpp.o -MF CMakeFiles/rdMolProcessing.dir/rdMolProcessing.cpp.o.d -o CMakeFiles/rdMolProcessing.dir/rdMolProcessing.cpp.o -c /build/reproducible-path/rdkit-202503.1/Code/GraphMol/MolProcessing/Wrap/rdMolProcessing.cpp -[ 88%] Building CXX object Code/GraphMol/MolStandardize/Wrap/CMakeFiles/rdMolStandardize.dir/Fragment.cpp.o -cd /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/MolStandardize/Wrap && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_NUMPY_DYN_LINK -DBOOST_NUMPY_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_BUILD_XYZ2MOL_SUPPORT -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DrdMolStandardize_EXPORTS -I/build/reproducible-path/rdkit-202503.1/External -I/build/reproducible-path/rdkit-202503.1/Code -I/build/reproducible-path/rdkit-202503.1/External/boost-numeric-bindings -I/usr/lib/aarch64-linux-gnu/python3-numpy/numpy/_core/include -isystem /usr/include/python3.13 -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/MolStandardize/Wrap/CMakeFiles/rdMolStandardize.dir/Fragment.cpp.o -MF CMakeFiles/rdMolStandardize.dir/Fragment.cpp.o.d -o CMakeFiles/rdMolStandardize.dir/Fragment.cpp.o -c /build/reproducible-path/rdkit-202503.1/Code/GraphMol/MolStandardize/Wrap/Fragment.cpp 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 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CMakeFiles/rdmolfiles.dir/SmilesMolSupplier.cpp.o CMakeFiles/rdmolfiles.dir/SmilesWriter.cpp.o CMakeFiles/rdmolfiles.dir/SDWriter.cpp.o CMakeFiles/rdmolfiles.dir/TDTWriter.cpp.o CMakeFiles/rdmolfiles.dir/PDBWriter.cpp.o CMakeFiles/rdmolfiles.dir/MultithreadedSmilesMolSupplier.cpp.o CMakeFiles/rdmolfiles.dir/MultithreadedSDMolSupplier.cpp.o ../../../lib/libRDKitMarvinParser.so.1.2025.03.1 ../../../lib/libRDKitRDBoost.so.1.2025.03.1 ../../../lib/libRDKitChemReactions.so.1.2025.03.1 ../../../lib/libRDKitFileParsers.so.1.2025.03.1 /usr/lib/aarch64-linux-gnu/libmaeparser.so ../../../lib/libRDKitChemTransforms.so.1.2025.03.1 ../../../lib/libRDKitDepictor.so.1.2025.03.1 /usr/lib/aarch64-linux-gnu/libcoordgen.so ../../../lib/libRDKitMolAlign.so.1.2025.03.1 ../../../lib/libRDKitMolTransforms.so.1.2025.03.1 ../../../lib/libRDKitEigenSolvers.so.1.2025.03.1 ../../../lib/libRDKitAlignment.so.1.2025.03.1 ../../../lib/libRDKitFilterCatalog.so.1.2025.03.1 ../../../lib/libRDKitCatalogs.so.1.2025.03.1 ../../../lib/libRDKitFingerprints.so.1.2025.03.1 ../../../lib/libRDKitSubstructMatch.so.1.2025.03.1 ../../../lib/libRDKitGenericGroups.so.1.2025.03.1 ../../../lib/libRDKitSmilesParse.so.1.2025.03.1 ../../../lib/libRDKitSubgraphs.so.1.2025.03.1 ../../../lib/libRDKitGraphMol.so.1.2025.03.1 ../../../lib/libRDKitRDGeometryLib.so.1.2025.03.1 ../../../lib/libRDKitDataStructs.so.1.2025.03.1 ../../../lib/libRDKitRDGeneral.so.1.2025.03.1 -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' -[ 88%] Built target rdmolfiles make -f Code/GraphMol/GenericGroups/CMakeFiles/testGenericGroups.dir/build.make Code/GraphMol/GenericGroups/CMakeFiles/testGenericGroups.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-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/GenericGroups /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/GenericGroups /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/GenericGroups/CMakeFiles/testGenericGroups.dir/DependInfo.cmake "--color=" @@ -6749,9 +6788,6 @@ cd /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/GenericGroups && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D 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../../../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 ../../../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' -[ 88%] Built target testMolProcessing make -f Code/GraphMol/ChemReactions/Wrap/CMakeFiles/rdChemReactions.dir/build.make Code/GraphMol/ChemReactions/Wrap/CMakeFiles/rdChemReactions.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu' cd /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202503.1 /build/reproducible-path/rdkit-202503.1/Code/GraphMol/ChemReactions/Wrap /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/ChemReactions/Wrap /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/ChemReactions/Wrap/CMakeFiles/rdChemReactions.dir/DependInfo.cmake "--color=" @@ -6760,25 +6796,19 @@ make[4]: Entering directory '/build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu' [ 88%] Building CXX object Code/GraphMol/ChemReactions/Wrap/CMakeFiles/rdChemReactions.dir/Enumerate.cpp.o cd /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/ChemReactions/Wrap && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_NUMPY_DYN_LINK -DBOOST_NUMPY_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_BUILD_XYZ2MOL_SUPPORT -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DrdChemReactions_EXPORTS -I/build/reproducible-path/rdkit-202503.1/External -I/build/reproducible-path/rdkit-202503.1/Code -I/build/reproducible-path/rdkit-202503.1/External/boost-numeric-bindings -I/usr/lib/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/ChemReactions/Wrap/CMakeFiles/rdChemReactions.dir/Enumerate.cpp.o -MF CMakeFiles/rdChemReactions.dir/Enumerate.cpp.o.d -o CMakeFiles/rdChemReactions.dir/Enumerate.cpp.o -c /build/reproducible-path/rdkit-202503.1/Code/GraphMol/ChemReactions/Wrap/Enumerate.cpp -[ 89%] Linking CXX executable molStandardizeCatchTest -cd /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/MolStandardize && /usr/bin/cmake -E cmake_link_script CMakeFiles/molStandardizeCatchTest.dir/link.txt --verbose=1 -[ 89%] Building CXX object Code/GraphMol/MolStandardize/Wrap/CMakeFiles/rdMolStandardize.dir/Normalize.cpp.o -cd /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/MolStandardize/Wrap && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_NUMPY_DYN_LINK -DBOOST_NUMPY_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_BUILD_XYZ2MOL_SUPPORT -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DrdMolStandardize_EXPORTS -I/build/reproducible-path/rdkit-202503.1/External -I/build/reproducible-path/rdkit-202503.1/Code 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&& /usr/bin/cmake -E cmake_link_script CMakeFiles/rdMolEnumerator.dir/link.txt --verbose=1 -/usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=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/rdMolEnumerator.dir/link.d -Wl,-z,relro -Wl,-z,now -shared -o ../../../../rdkit/Chem/rdMolEnumerator.so CMakeFiles/rdMolEnumerator.dir/rdMolEnumerator.cpp.o ../../../../lib/libRDKitMolEnumerator.so.1.2025.03.1 ../../../../lib/libRDKitRDBoost.so.1.2025.03.1 ../../../../lib/libRDKitChemReactions.so.1.2025.03.1 ../../../../lib/libRDKitFileParsers.so.1.2025.03.1 /usr/lib/aarch64-linux-gnu/libmaeparser.so ../../../../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 +/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/testMolProcessing.dir/link.d CMakeFiles/testMolProcessing.dir/processing_tests.cpp.o -o testMolProcessing ../../RDGeneral/librdkitCatch.a ../../../lib/libRDKitMolProcessing.so.1.2025.03.1 /usr/lib/libCatch2.a ../../../lib/libRDKitFileParsers.so.1.2025.03.1 ../../../lib/libRDKitChemTransforms.so.1.2025.03.1 ../../../lib/libRDKitDepictor.so.1.2025.03.1 /usr/lib/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 ../../../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' -[ 89%] Building CXX object Code/GraphMol/MolStandardize/Wrap/CMakeFiles/rdMolStandardize.dir/Metal.cpp.o -cd /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/MolStandardize/Wrap && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_NUMPY_DYN_LINK -DBOOST_NUMPY_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_BUILD_XYZ2MOL_SUPPORT -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DrdMolStandardize_EXPORTS -I/build/reproducible-path/rdkit-202503.1/External -I/build/reproducible-path/rdkit-202503.1/Code -I/build/reproducible-path/rdkit-202503.1/External/boost-numeric-bindings -I/usr/lib/aarch64-linux-gnu/python3-numpy/numpy/_core/include -isystem /usr/include/python3.13 -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/MolStandardize/Wrap/CMakeFiles/rdMolStandardize.dir/Metal.cpp.o -MF CMakeFiles/rdMolStandardize.dir/Metal.cpp.o.d -o CMakeFiles/rdMolStandardize.dir/Metal.cpp.o -c /build/reproducible-path/rdkit-202503.1/Code/GraphMol/MolStandardize/Wrap/Metal.cpp -[ 89%] Built target rdMolEnumerator +[ 88%] Built target testMolProcessing 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 /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/TautomerQuery /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/TautomerQuery/CMakeFiles/TautomerQuery.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu' make -f Code/GraphMol/TautomerQuery/CMakeFiles/TautomerQuery.dir/build.make Code/GraphMol/TautomerQuery/CMakeFiles/TautomerQuery.dir/build make[4]: Entering directory '/build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu' -[ 89%] Building CXX object Code/GraphMol/TautomerQuery/CMakeFiles/TautomerQuery.dir/TautomerQuery.cpp.o +[ 88%] Building CXX object Code/GraphMol/TautomerQuery/CMakeFiles/TautomerQuery.dir/TautomerQuery.cpp.o cd /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/TautomerQuery && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDKIT_TAUTOMERQUERY_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_BUILD_XYZ2MOL_SUPPORT -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DTautomerQuery_EXPORTS -I/build/reproducible-path/rdkit-202503.1/External -I/build/reproducible-path/rdkit-202503.1/Code -I/build/reproducible-path/rdkit-202503.1/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/TautomerQuery/CMakeFiles/TautomerQuery.dir/TautomerQuery.cpp.o -MF CMakeFiles/TautomerQuery.dir/TautomerQuery.cpp.o.d -o CMakeFiles/TautomerQuery.dir/TautomerQuery.cpp.o -c /build/reproducible-path/rdkit-202503.1/Code/GraphMol/TautomerQuery/TautomerQuery.cpp +[ 89%] Linking CXX executable molStandardizeCatchTest +cd /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/MolStandardize && /usr/bin/cmake -E cmake_link_script CMakeFiles/molStandardizeCatchTest.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong 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../../../lib/libRDKitMolAlign.so.1.2025.03.1 ../../../lib/libRDKitMolTransforms.so.1.2025.03.1 ../../../lib/libRDKitEigenSolvers.so.1.2025.03.1 ../../../lib/libRDKitAlignment.so.1.2025.03.1 ../../../lib/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' [ 89%] Built target molStandardizeCatchTest @@ -6790,50 +6820,31 @@ make[4]: Entering directory '/build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu' [ 89%] Building CXX object Code/GraphMol/MolAlign/CMakeFiles/testO3AAlign.dir/testO3AAlign.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_BUILD_XYZ2MOL_SUPPORT -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202503.1/External -I/build/reproducible-path/rdkit-202503.1/Code -I/build/reproducible-path/rdkit-202503.1/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/GraphMol/MolAlign/CMakeFiles/testO3AAlign.dir/testO3AAlign.cpp.o -MF CMakeFiles/testO3AAlign.dir/testO3AAlign.cpp.o.d -o CMakeFiles/testO3AAlign.dir/testO3AAlign.cpp.o -c /build/reproducible-path/rdkit-202503.1/Code/GraphMol/MolAlign/testO3AAlign.cpp -[ 89%] Building CXX object Code/GraphMol/MolStandardize/Wrap/CMakeFiles/rdMolStandardize.dir/Tautomer.cpp.o -cd /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/MolStandardize/Wrap && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_NUMPY_DYN_LINK -DBOOST_NUMPY_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT 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../../../../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 +[ 90%] Linking CXX executable testMolEnumerator +cd /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/MolEnumerator && /usr/bin/cmake -E cmake_link_script CMakeFiles/testMolEnumerator.dir/link.txt --verbose=1 +/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/testMolEnumerator.dir/link.d CMakeFiles/testMolEnumerator.dir/enumerator_catch.cpp.o -o testMolEnumerator ../../RDGeneral/librdkitCatch.a ../../../lib/libRDKitMolEnumerator.so.1.2025.03.1 /usr/lib/libCatch2.a ../../../lib/libRDKitChemReactions.so.1.2025.03.1 ../../../lib/libRDKitFileParsers.so.1.2025.03.1 /usr/lib/aarch64-linux-gnu/libmaeparser.so ../../../lib/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/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 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-Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/ChemReactions/Wrap/CMakeFiles/rdChemReactions.dir/rdChemReactions.cpp.o -MF CMakeFiles/rdChemReactions.dir/rdChemReactions.cpp.o.d -o CMakeFiles/rdChemReactions.dir/rdChemReactions.cpp.o -c /build/reproducible-path/rdkit-202503.1/Code/GraphMol/ChemReactions/Wrap/rdChemReactions.cpp +[ 90%] 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 +[ 90%] Linking CXX shared module ../../../../rdkit/Chem/rdMolEnumerator.so +cd /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/MolEnumerator/Wrap && /usr/bin/cmake -E cmake_link_script CMakeFiles/rdMolEnumerator.dir/link.txt --verbose=1 +/usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=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/rdMolEnumerator.dir/link.d -Wl,-z,relro -Wl,-z,now -shared -o ../../../../rdkit/Chem/rdMolEnumerator.so CMakeFiles/rdMolEnumerator.dir/rdMolEnumerator.cpp.o ../../../../lib/libRDKitMolEnumerator.so.1.2025.03.1 ../../../../lib/libRDKitRDBoost.so.1.2025.03.1 ../../../../lib/libRDKitChemReactions.so.1.2025.03.1 ../../../../lib/libRDKitFileParsers.so.1.2025.03.1 /usr/lib/aarch64-linux-gnu/libmaeparser.so ../../../../lib/libRDKitFilterCatalog.so.1.2025.03.1 ../../../../lib/libRDKitCatalogs.so.1.2025.03.1 ../../../../lib/libRDKitFingerprints.so.1.2025.03.1 ../../../../lib/libRDKitSubgraphs.so.1.2025.03.1 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Leaving directory '/build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu' +[ 90%] Built target rdMolEnumerator make -f Code/GraphMol/MolAlign/Wrap/CMakeFiles/rdMolAlign.dir/build.make Code/GraphMol/MolAlign/Wrap/CMakeFiles/rdMolAlign.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-202503.1/obj-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/Wrap /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/MolAlign/Wrap /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/MolAlign/Wrap/CMakeFiles/rdMolAlign.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu' make -f 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-DrdMolAlign_EXPORTS -I/build/reproducible-path/rdkit-202503.1/External -I/build/reproducible-path/rdkit-202503.1/Code -I/build/reproducible-path/rdkit-202503.1/External/boost-numeric-bindings -I/usr/lib/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/MolAlign/Wrap/CMakeFiles/rdMolAlign.dir/rdMolAlign.cpp.o -MF CMakeFiles/rdMolAlign.dir/rdMolAlign.cpp.o.d -o CMakeFiles/rdMolAlign.dir/rdMolAlign.cpp.o -c /build/reproducible-path/rdkit-202503.1/Code/GraphMol/MolAlign/Wrap/rdMolAlign.cpp -[ 89%] 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 -In file included from /usr/include/c++/14/bits/stl_algobase.h:64, - from /usr/include/c++/14/string:51, - from /build/reproducible-path/rdkit-202503.1/Code/RDGeneral/Invariant.h:17, - from /build/reproducible-path/rdkit-202503.1/Code/Numerics/Matrix.h:14, - from /build/reproducible-path/rdkit-202503.1/Code/Numerics/SquareMatrix.h:14, - from /build/reproducible-path/rdkit-202503.1/Code/Geometry/Transform3D.h:16, - from /build/reproducible-path/rdkit-202503.1/Code/GraphMol/MolAlign/AlignMolecules.h:14, - from /build/reproducible-path/rdkit-202503.1/Code/GraphMol/MolAlign/testO3AAlign.cpp:11: -/usr/include/c++/14/bits/stl_pair.h: In instantiation of 'constexpr std::pair::type>::__type, typename std::__strip_reference_wrapper::type>::__type> std::make_pair(_T1&&, _T2&&) [with _T1 = double&; _T2 = double&; typename __strip_reference_wrapper::type>::__type = double; typename decay<_Tp>::type = double; typename __strip_reference_wrapper::type>::__type = double; typename decay<_Tp2>::type = double]': -/build/reproducible-path/rdkit-202503.1/Code/GraphMol/MolAlign/testO3AAlign.cpp:643:37: required from here - 643 | oscores.push_back(std::make_pair(rmsd, score)); - | ~~~~~~~~~~~~~~^~~~~~~~~~~~~ -/usr/include/c++/14/bits/stl_pair.h:1132:5: note: parameter passing for argument of type 'std::pair' when C++17 is enabled changed to match C++14 in GCC 10.1 - 1132 | make_pair(_T1&& __x, _T2&& __y) - | ^~~~~~~~~ /usr/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 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/usr/lib/aarch64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl +[ 90%] Building CXX object Code/GraphMol/MolAlign/Wrap/CMakeFiles/rdMolAlign.dir/rdMolAlign.cpp.o make[4]: Leaving directory '/build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu' -[ 89%] Built target rdchem -[ 89%] Building CXX object Code/GraphMol/ChemReactions/Wrap/CMakeFiles/rdChemReactions.dir/rdChemReactions.cpp.o -cd /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/ChemReactions/Wrap && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_NUMPY_DYN_LINK -DBOOST_NUMPY_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_BUILD_XYZ2MOL_SUPPORT -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS 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/build/reproducible-path/rdkit-202503.1/Code/GraphMol/ChemReactions/Wrap/rdChemReactions.cpp -[ 90%] Linking CXX executable testMolEnumerator -cd /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/MolEnumerator && /usr/bin/cmake -E cmake_link_script CMakeFiles/testMolEnumerator.dir/link.txt --verbose=1 -/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/testMolEnumerator.dir/link.d CMakeFiles/testMolEnumerator.dir/enumerator_catch.cpp.o -o testMolEnumerator ../../RDGeneral/librdkitCatch.a ../../../lib/libRDKitMolEnumerator.so.1.2025.03.1 /usr/lib/libCatch2.a ../../../lib/libRDKitChemReactions.so.1.2025.03.1 ../../../lib/libRDKitFileParsers.so.1.2025.03.1 /usr/lib/aarch64-linux-gnu/libmaeparser.so ../../../lib/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/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 -make[4]: Leaving directory '/build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu' -[ 90%] Built target testMolEnumerator -[ 90%] Building CXX object Code/GraphMol/MolStandardize/Wrap/CMakeFiles/rdMolStandardize.dir/Pipeline.cpp.o -cd /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/MolStandardize/Wrap && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_NUMPY_DYN_LINK -DBOOST_NUMPY_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_BUILD_XYZ2MOL_SUPPORT -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DrdMolStandardize_EXPORTS -I/build/reproducible-path/rdkit-202503.1/External -I/build/reproducible-path/rdkit-202503.1/Code -I/build/reproducible-path/rdkit-202503.1/External/boost-numeric-bindings -I/usr/lib/aarch64-linux-gnu/python3-numpy/numpy/_core/include -isystem /usr/include/python3.13 -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/MolStandardize/Wrap/CMakeFiles/rdMolStandardize.dir/Pipeline.cpp.o -MF CMakeFiles/rdMolStandardize.dir/Pipeline.cpp.o.d -o CMakeFiles/rdMolStandardize.dir/Pipeline.cpp.o -c /build/reproducible-path/rdkit-202503.1/Code/GraphMol/MolStandardize/Wrap/Pipeline.cpp +cd /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/MolAlign/Wrap && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_NUMPY_DYN_LINK -DBOOST_NUMPY_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_BUILD_XYZ2MOL_SUPPORT -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DrdMolAlign_EXPORTS -I/build/reproducible-path/rdkit-202503.1/External -I/build/reproducible-path/rdkit-202503.1/Code -I/build/reproducible-path/rdkit-202503.1/External/boost-numeric-bindings -I/usr/lib/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/MolAlign/Wrap/CMakeFiles/rdMolAlign.dir/rdMolAlign.cpp.o -MF CMakeFiles/rdMolAlign.dir/rdMolAlign.cpp.o.d -o CMakeFiles/rdMolAlign.dir/rdMolAlign.cpp.o -c /build/reproducible-path/rdkit-202503.1/Code/GraphMol/MolAlign/Wrap/rdMolAlign.cpp +[ 90%] Built target rdchem make -f Code/GraphMol/ScaffoldNetwork/CMakeFiles/testScaffoldNetwork.dir/build.make Code/GraphMol/ScaffoldNetwork/CMakeFiles/testScaffoldNetwork.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu' cd /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202503.1 /build/reproducible-path/rdkit-202503.1/Code/GraphMol/ScaffoldNetwork /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/ScaffoldNetwork /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/ScaffoldNetwork/CMakeFiles/testScaffoldNetwork.dir/DependInfo.cmake "--color=" @@ -6850,53 +6861,95 @@ make[4]: Entering directory '/build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu' [ 90%] 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 -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_BUILD_XYZ2MOL_SUPPORT -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DrdScaffoldNetwork_EXPORTS -I/build/reproducible-path/rdkit-202503.1/External -I/build/reproducible-path/rdkit-202503.1/Code -I/build/reproducible-path/rdkit-202503.1/External/boost-numeric-bindings -I/usr/lib/aarch64-linux-gnu/python3-numpy/numpy/_core/include -isystem /usr/include/python3.13 -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/ScaffoldNetwork/Wrap/CMakeFiles/rdScaffoldNetwork.dir/rdScaffoldNetwork.cpp.o -MF CMakeFiles/rdScaffoldNetwork.dir/rdScaffoldNetwork.cpp.o.d -o CMakeFiles/rdScaffoldNetwork.dir/rdScaffoldNetwork.cpp.o -c /build/reproducible-path/rdkit-202503.1/Code/GraphMol/ScaffoldNetwork/Wrap/rdScaffoldNetwork.cpp -[ 90%] 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 +In file included from /usr/include/c++/14/bits/stl_algobase.h:64, + from /usr/include/c++/14/string:51, + from /build/reproducible-path/rdkit-202503.1/Code/RDGeneral/Invariant.h:17, + from /build/reproducible-path/rdkit-202503.1/Code/Numerics/Matrix.h:14, + from /build/reproducible-path/rdkit-202503.1/Code/Numerics/SquareMatrix.h:14, + from /build/reproducible-path/rdkit-202503.1/Code/Geometry/Transform3D.h:16, + from /build/reproducible-path/rdkit-202503.1/Code/GraphMol/MolAlign/AlignMolecules.h:14, + from /build/reproducible-path/rdkit-202503.1/Code/GraphMol/MolAlign/testO3AAlign.cpp:11: +/usr/include/c++/14/bits/stl_pair.h: In instantiation of 'constexpr std::pair::type>::__type, typename std::__strip_reference_wrapper::type>::__type> std::make_pair(_T1&&, _T2&&) [with _T1 = double&; _T2 = double&; typename __strip_reference_wrapper::type>::__type = double; typename decay<_Tp>::type = double; typename __strip_reference_wrapper::type>::__type = double; typename decay<_Tp2>::type = double]': +/build/reproducible-path/rdkit-202503.1/Code/GraphMol/MolAlign/testO3AAlign.cpp:643:37: required from here + 643 | oscores.push_back(std::make_pair(rmsd, score)); + | ~~~~~~~~~~~~~~^~~~~~~~~~~~~ +/usr/include/c++/14/bits/stl_pair.h:1132:5: note: parameter passing for argument of type 'std::pair' when C++17 is enabled changed to match C++14 in GCC 10.1 + 1132 | make_pair(_T1&& __x, _T2&& __y) + | ^~~~~~~~~ +[ 90%] 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 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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 && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202503.1 /build/reproducible-path/rdkit-202503.1/Code/GraphMol/TautomerQuery/Wrap /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/TautomerQuery/Wrap /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/TautomerQuery/Wrap/CMakeFiles/rdTautomerQuery.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 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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 -f Code/GraphMol/TautomerQuery/Wrap/CMakeFiles/rdTautomerQuery.dir/build.make Code/GraphMol/TautomerQuery/Wrap/CMakeFiles/rdTautomerQuery.dir/depend +make -f Code/GraphMol/TautomerQuery/CMakeFiles/tautomerQueryTestCatch.dir/build.make Code/GraphMol/TautomerQuery/CMakeFiles/tautomerQueryTestCatch.dir/build make[4]: Leaving directory '/build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu' make[4]: Entering directory '/build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu' -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/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' -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 /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/GeneralizedSubstruct/CMakeFiles/GeneralizedSubstruct.dir/DependInfo.cmake "--color=" -[ 91%] Building CXX object Code/GraphMol/TautomerQuery/Wrap/CMakeFiles/rdTautomerQuery.dir/rdTautomerQuery.cpp.o +[ 90%] Building CXX object Code/GraphMol/TautomerQuery/CMakeFiles/tautomerQueryTestCatch.dir/catch_tests.cpp.o +cd /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/TautomerQuery && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_BUILD_XYZ2MOL_SUPPORT -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202503.1/External -I/build/reproducible-path/rdkit-202503.1/Code -I/build/reproducible-path/rdkit-202503.1/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/GraphMol/TautomerQuery/CMakeFiles/tautomerQueryTestCatch.dir/catch_tests.cpp.o -MF CMakeFiles/tautomerQueryTestCatch.dir/catch_tests.cpp.o.d -o CMakeFiles/tautomerQueryTestCatch.dir/catch_tests.cpp.o -c /build/reproducible-path/rdkit-202503.1/Code/GraphMol/TautomerQuery/catch_tests.cpp +[ 90%] Building CXX object Code/GraphMol/TautomerQuery/Wrap/CMakeFiles/rdTautomerQuery.dir/rdTautomerQuery.cpp.o cd /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/TautomerQuery/Wrap && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_NUMPY_DYN_LINK -DBOOST_NUMPY_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_BUILD_XYZ2MOL_SUPPORT -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DrdTautomerQuery_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/TautomerQuery/Wrap/CMakeFiles/rdTautomerQuery.dir/rdTautomerQuery.cpp.o -MF CMakeFiles/rdTautomerQuery.dir/rdTautomerQuery.cpp.o.d -o CMakeFiles/rdTautomerQuery.dir/rdTautomerQuery.cpp.o -c /build/reproducible-path/rdkit-202503.1/Code/GraphMol/TautomerQuery/Wrap/rdTautomerQuery.cpp -make[4]: Leaving directory '/build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu' -make -f Code/GraphMol/GeneralizedSubstruct/CMakeFiles/GeneralizedSubstruct.dir/build.make Code/GraphMol/GeneralizedSubstruct/CMakeFiles/GeneralizedSubstruct.dir/build -make[4]: Entering directory '/build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu' -[ 91%] Building CXX object Code/GraphMol/GeneralizedSubstruct/CMakeFiles/GeneralizedSubstruct.dir/XQMol.cpp.o +[ 90%] 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 -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DGeneralizedSubstruct_EXPORTS -DRDKIT_DYN_LINK 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CMakeFiles/GeneralizedSubstruct.dir/XQMol.cpp.o.d -o CMakeFiles/GeneralizedSubstruct.dir/XQMol.cpp.o -c /build/reproducible-path/rdkit-202503.1/Code/GraphMol/GeneralizedSubstruct/XQMol.cpp -[ 91%] Linking CXX executable cxsmilesTest -cd /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/SmilesParse && /usr/bin/cmake -E cmake_link_script CMakeFiles/cxsmilesTest.dir/link.txt --verbose=1 -[ 91%] Linking CXX executable testO3AAlign -cd /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/MolAlign && /usr/bin/cmake -E cmake_link_script CMakeFiles/testO3AAlign.dir/link.txt --verbose=1 -/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/cxsmilesTest.dir/link.d CMakeFiles/cxsmilesTest.dir/cxsmiles_test.cpp.o -o cxsmilesTest ../../RDGeneral/librdkitCatch.a ../../../lib/libRDKitMarvinParser.so.1.2025.03.1 /usr/lib/libCatch2.a ../../../lib/libRDKitChemReactions.so.1.2025.03.1 ../../../lib/libRDKitFileParsers.so.1.2025.03.1 /usr/lib/aarch64-linux-gnu/libmaeparser.so ../../../lib/libRDKitChemTransforms.so.1.2025.03.1 ../../../lib/libRDKitDepictor.so.1.2025.03.1 /usr/lib/aarch64-linux-gnu/libcoordgen.so ../../../lib/libRDKitMolAlign.so.1.2025.03.1 ../../../lib/libRDKitMolTransforms.so.1.2025.03.1 ../../../lib/libRDKitEigenSolvers.so.1.2025.03.1 ../../../lib/libRDKitAlignment.so.1.2025.03.1 ../../../lib/libRDKitFilterCatalog.so.1.2025.03.1 ../../../lib/libRDKitCatalogs.so.1.2025.03.1 ../../../lib/libRDKitFingerprints.so.1.2025.03.1 ../../../lib/libRDKitSmilesParse.so.1.2025.03.1 ../../../lib/libRDKitSubstructMatch.so.1.2025.03.1 ../../../lib/libRDKitGenericGroups.so.1.2025.03.1 ../../../lib/libRDKitSubgraphs.so.1.2025.03.1 ../../../lib/libRDKitGraphMol.so.1.2025.03.1 ../../../lib/libRDKitRDGeometryLib.so.1.2025.03.1 ../../../lib/libRDKitDataStructs.so.1.2025.03.1 ../../../lib/libRDKitRDGeneral.so.1.2025.03.1 /usr/lib/aarch64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl +[ 91%] 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 +In file included from /usr/include/boost/python/override.hpp:13, + from /usr/include/boost/python/wrapper.hpp:8, + from /usr/include/boost/python/object/value_holder.hpp:15, + from /usr/include/boost/python/object/class_metadata.hpp:14, + from /usr/include/boost/python/class.hpp:23, + from /usr/include/boost/python/suite/indexing/indexing_suite.hpp:9, + from /usr/include/boost/python/suite/indexing/map_indexing_suite.hpp:9, + from /build/reproducible-path/rdkit-202503.1/Code/GraphMol/MolStandardize/Wrap/Tautomer.cpp:11: +In member function 'boost::python::converter::extract_rvalue::result_type boost::python::converter::extract_rvalue::operator()() const [with T = long int]', + inlined from 'boost::python::extract::operator result_type() const [with T = long int]' at /usr/include/boost/python/extract.hpp:136:23, + inlined from 'static void boost::python::detail::slice_helper::base_get_slice_data(Container&, PySliceObject*, Index&, Index&) [with Container = std::vector; DerivedPolicies = boost::python::detail::final_vector_derived_policies, false>; ProxyHandler = boost::python::detail::proxy_helper, boost::python::detail::final_vector_derived_policies, false>, boost::python::detail::container_element, long unsigned int, boost::python::detail::final_vector_derived_policies, false> >, long unsigned int>; Data = RDKit::MolStandardize::TautomerScoringFunctions::SubstructTerm; Index = long unsigned int]' at /usr/include/boost/python/suite/indexing/detail/indexing_suite_detail.hpp:617:27: +/usr/include/boost/python/extract.hpp:185:11: warning: '*(long int*)((char*)& + offsetof(boost::python::extract,boost::python::extract::.boost::python::converter::extract_rvalue::m_data.boost::python::converter::rvalue_from_python_data::.boost::python::converter::rvalue_from_python_storage::storage))' may be used uninitialized [-Wmaybe-uninitialized] + 185 | ); + | ^ +In file included from /usr/include/boost/python/suite/indexing/indexing_suite.hpp:12: +/usr/include/boost/python/suite/indexing/detail/indexing_suite_detail.hpp: In static member function 'static void boost::python::detail::slice_helper::base_get_slice_data(Container&, PySliceObject*, Index&, Index&) [with Container = std::vector; DerivedPolicies = boost::python::detail::final_vector_derived_policies, false>; ProxyHandler = boost::python::detail::proxy_helper, boost::python::detail::final_vector_derived_policies, false>, boost::python::detail::container_element, long unsigned int, boost::python::detail::final_vector_derived_policies, false> >, long unsigned int>; Data = RDKit::MolStandardize::TautomerScoringFunctions::SubstructTerm; Index = long unsigned int]': +/usr/include/boost/python/suite/indexing/detail/indexing_suite_detail.hpp:617:27: note: '' declared here + 617 | long to = extract( slice->stop); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ +In member function 'boost::python::converter::extract_rvalue::result_type boost::python::converter::extract_rvalue::operator()() const [with T = long int]', + inlined from 'boost::python::extract::operator result_type() const [with T = long int]' at /usr/include/boost/python/extract.hpp:136:23, + inlined from 'static void boost::python::detail::slice_helper::base_get_slice_data(Container&, PySliceObject*, Index&, Index&) [with Container = std::vector; DerivedPolicies = boost::python::detail::final_vector_derived_policies, false>; ProxyHandler = boost::python::detail::proxy_helper, boost::python::detail::final_vector_derived_policies, false>, boost::python::detail::container_element, long unsigned int, boost::python::detail::final_vector_derived_policies, false> >, long unsigned int>; Data = RDKit::MolStandardize::TautomerScoringFunctions::SubstructTerm; Index = long unsigned int]' at /usr/include/boost/python/suite/indexing/detail/indexing_suite_detail.hpp:603:29: +/usr/include/boost/python/extract.hpp:185:11: warning: '*(long int*)((char*)& + offsetof(boost::python::extract,boost::python::extract::.boost::python::converter::extract_rvalue::m_data.boost::python::converter::rvalue_from_python_data::.boost::python::converter::rvalue_from_python_storage::storage))' may be used uninitialized [-Wmaybe-uninitialized] + 185 | ); + | ^ +/usr/include/boost/python/suite/indexing/detail/indexing_suite_detail.hpp: In static member function 'static void boost::python::detail::slice_helper::base_get_slice_data(Container&, PySliceObject*, Index&, Index&) [with Container = std::vector; DerivedPolicies = boost::python::detail::final_vector_derived_policies, false>; ProxyHandler = boost::python::detail::proxy_helper, boost::python::detail::final_vector_derived_policies, false>, boost::python::detail::container_element, long unsigned int, boost::python::detail::final_vector_derived_policies, false> >, long unsigned int>; Data = RDKit::MolStandardize::TautomerScoringFunctions::SubstructTerm; Index = long unsigned int]': +/usr/include/boost/python/suite/indexing/detail/indexing_suite_detail.hpp:603:29: note: '' declared here + 603 | long from = extract( slice->start); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ +/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 ../../../lib/libRDKitChemReactions.so.1.2025.03.1 ../../../lib/libRDKitFileParsers.so.1.2025.03.1 /usr/lib/aarch64-linux-gnu/libmaeparser.so ../../../lib/libRDKitChemTransforms.so.1.2025.03.1 ../../../lib/libRDKitDepictor.so.1.2025.03.1 /usr/lib/aarch64-linux-gnu/libcoordgen.so ../../../lib/libRDKitMolAlign.so.1.2025.03.1 ../../../lib/libRDKitMolTransforms.so.1.2025.03.1 ../../../lib/libRDKitEigenSolvers.so.1.2025.03.1 ../../../lib/libRDKitAlignment.so.1.2025.03.1 ../../../lib/libRDKitFilterCatalog.so.1.2025.03.1 ../../../lib/libRDKitCatalogs.so.1.2025.03.1 ../../../lib/libRDKitFingerprints.so.1.2025.03.1 ../../../lib/libRDKitSubstructMatch.so.1.2025.03.1 ../../../lib/libRDKitGenericGroups.so.1.2025.03.1 ../../../lib/libRDKitSmilesParse.so.1.2025.03.1 ../../../lib/libRDKitSubgraphs.so.1.2025.03.1 ../../../lib/libRDKitGraphMol.so.1.2025.03.1 ../../../lib/libRDKitRDGeometryLib.so.1.2025.03.1 ../../../lib/libRDKitDataStructs.so.1.2025.03.1 ../../../lib/libRDKitRDGeneral.so.1.2025.03.1 /usr/lib/aarch64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl make[4]: Leaving directory '/build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu' -[ 91%] Built target cxsmilesTest +[ 91%] Built target testMrvToMol 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 /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/RGroupDecomposition/CMakeFiles/RGroupDecomposition.dir/DependInfo.cmake "--color=" @@ -6905,11 +6958,6 @@ make[4]: Entering directory '/build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu' [ 91%] Building CXX object Code/GraphMol/RGroupDecomposition/CMakeFiles/RGroupDecomposition.dir/RGroupDecomp.cpp.o cd /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/RGroupDecomposition && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDKIT_RGROUPDECOMPOSITION_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_BUILD_XYZ2MOL_SUPPORT -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DRGroupDecomposition_EXPORTS -I/build/reproducible-path/rdkit-202503.1/External -I/build/reproducible-path/rdkit-202503.1/Code -I/build/reproducible-path/rdkit-202503.1/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/RGroupDecomposition/CMakeFiles/RGroupDecomposition.dir/RGroupDecomp.cpp.o -MF 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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' -[ 91%] Built target testO3AAlign -[ 91%] Building CXX object Code/GraphMol/GeneralizedSubstruct/CMakeFiles/GeneralizedSubstruct.dir/TextIO.cpp.o -cd /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/GeneralizedSubstruct && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DGeneralizedSubstruct_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_GENERALIZEDSUBSTRUCT_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_BUILD_XYZ2MOL_SUPPORT -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS 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/usr/lib/aarch64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl +make[4]: Leaving 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' +[ 91%] Built target rdMolStandardize +[ 91%] Built target cxsmilesTest [ 91%] 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 -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDKIT_RGROUPDECOMPOSITION_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_BUILD_XYZ2MOL_SUPPORT -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS 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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/RGroupDecomposition/CMakeFiles/RGroupDecomposition.dir/RGroupCore.cpp.o -MF CMakeFiles/RGroupDecomposition.dir/RGroupCore.cpp.o.d -o CMakeFiles/RGroupDecomposition.dir/RGroupCore.cpp.o -c /build/reproducible-path/rdkit-202503.1/Code/GraphMol/RGroupDecomposition/RGroupCore.cpp [ 92%] Linking CXX shared module ../../../../rdkit/Chem/rdMolAlign.so cd 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../../../../lib/libRDKitFileParsers.so.1.2025.03.1 ../../../../lib/libRDKitChemTransforms.so.1.2025.03.1 ../../../../lib/libRDKitDepictor.so.1.2025.03.1 ../../../../lib/libRDKitMolAlign.so.1.2025.03.1 ../../../../lib/libRDKitAlignment.so.1.2025.03.1 ../../../../lib/libRDKitMolTransforms.so.1.2025.03.1 ../../../../lib/libRDKitEigenSolvers.so.1.2025.03.1 /usr/lib/aarch64-linux-gnu/libcoordgen.so /usr/lib/aarch64-linux-gnu/libmaeparser.so ../../../../lib/libRDKitSubgraphs.so.1.2025.03.1 ../../../../lib/libRDKitForceFieldHelpers.so.1.2025.03.1 ../../../../lib/libRDKitSmilesParse.so.1.2025.03.1 ../../../../lib/libRDKitSubstructMatch.so.1.2025.03.1 ../../../../lib/libRDKitGenericGroups.so.1.2025.03.1 ../../../../lib/libRDKitForceField.so.1.2025.03.1 ../../../../lib/libRDKitOptimizer.so.1.2025.03.1 ../../../../lib/libRDKitTrajectory.so.1.2025.03.1 ../../../../lib/libRDKitGraphMol.so.1.2025.03.1 ../../../../lib/libRDKitRDGeometryLib.so.1.2025.03.1 ../../../../lib/libRDKitDataStructs.so.1.2025.03.1 /usr/lib/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 rdMolAlign -[ 92%] Building CXX object Code/GraphMol/RGroupDecomposition/CMakeFiles/RGroupDecomposition.dir/RGroupCore.cpp.o -cd /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/RGroupDecomposition && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDKIT_RGROUPDECOMPOSITION_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_BUILD_XYZ2MOL_SUPPORT -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DRGroupDecomposition_EXPORTS -I/build/reproducible-path/rdkit-202503.1/External -I/build/reproducible-path/rdkit-202503.1/Code -I/build/reproducible-path/rdkit-202503.1/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/RGroupDecomposition/CMakeFiles/RGroupDecomposition.dir/RGroupCore.cpp.o -MF CMakeFiles/RGroupDecomposition.dir/RGroupCore.cpp.o.d -o CMakeFiles/RGroupDecomposition.dir/RGroupCore.cpp.o -c /build/reproducible-path/rdkit-202503.1/Code/GraphMol/RGroupDecomposition/RGroupCore.cpp +[ 92%] Building CXX object Code/GraphMol/RGroupDecomposition/CMakeFiles/RGroupDecomposition.dir/RGroupDecompParams.cpp.o +cd /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/RGroupDecomposition && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDKIT_RGROUPDECOMPOSITION_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_BUILD_XYZ2MOL_SUPPORT -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DRGroupDecomposition_EXPORTS -I/build/reproducible-path/rdkit-202503.1/External -I/build/reproducible-path/rdkit-202503.1/Code -I/build/reproducible-path/rdkit-202503.1/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/RGroupDecomposition/CMakeFiles/RGroupDecomposition.dir/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 [ 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 CMakeFiles/tautomerQueryTestCatch.dir/catch_tests.cpp.o -o tautomerQueryTestCatch ../../RDGeneral/librdkitCatch.a ../../../lib/libRDKitTautomerQuery.so.1.2025.03.1 /usr/lib/libCatch2.a ../../../lib/libRDKitMolStandardize.so.1.2025.03.1 ../../../lib/libRDKitChemReactions.so.1.2025.03.1 ../../../lib/libRDKitFilterCatalog.so.1.2025.03.1 ../../../lib/libRDKitCatalogs.so.1.2025.03.1 ../../../lib/libRDKitFingerprints.so.1.2025.03.1 ../../../lib/libRDKitSubgraphs.so.1.2025.03.1 ../../../lib/libRDKitFileParsers.so.1.2025.03.1 /usr/lib/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 tautomerQueryTestCatch -[ 92%] Building CXX object Code/GraphMol/RGroupDecomposition/CMakeFiles/RGroupDecomposition.dir/RGroupDecompParams.cpp.o -cd /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/RGroupDecomposition && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDKIT_RGROUPDECOMPOSITION_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_BUILD_XYZ2MOL_SUPPORT -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DRGroupDecomposition_EXPORTS -I/build/reproducible-path/rdkit-202503.1/External -I/build/reproducible-path/rdkit-202503.1/Code -I/build/reproducible-path/rdkit-202503.1/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/RGroupDecomposition/CMakeFiles/RGroupDecomposition.dir/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 -In file included from /usr/include/boost/python/override.hpp:13, - from /usr/include/boost/python/wrapper.hpp:8, - from /usr/include/boost/python/object/value_holder.hpp:15, - from /usr/include/boost/python/object/class_metadata.hpp:14, - from /usr/include/boost/python/class.hpp:23, - from /usr/include/boost/python/suite/indexing/indexing_suite.hpp:9, - from /usr/include/boost/python/suite/indexing/map_indexing_suite.hpp:9, - from /build/reproducible-path/rdkit-202503.1/Code/GraphMol/MolStandardize/Wrap/Tautomer.cpp:11: -In member function 'boost::python::converter::extract_rvalue::result_type boost::python::converter::extract_rvalue::operator()() const [with T = long int]', - inlined from 'boost::python::extract::operator result_type() const [with T = long int]' at /usr/include/boost/python/extract.hpp:136:23, - inlined from 'static void boost::python::detail::slice_helper::base_get_slice_data(Container&, PySliceObject*, Index&, Index&) [with Container = std::vector; DerivedPolicies = boost::python::detail::final_vector_derived_policies, false>; ProxyHandler = boost::python::detail::proxy_helper, boost::python::detail::final_vector_derived_policies, false>, boost::python::detail::container_element, long unsigned int, boost::python::detail::final_vector_derived_policies, false> >, long unsigned int>; Data = RDKit::MolStandardize::TautomerScoringFunctions::SubstructTerm; Index = long unsigned int]' at /usr/include/boost/python/suite/indexing/detail/indexing_suite_detail.hpp:617:27: -/usr/include/boost/python/extract.hpp:185:11: warning: '*(long int*)((char*)& + offsetof(boost::python::extract,boost::python::extract::.boost::python::converter::extract_rvalue::m_data.boost::python::converter::rvalue_from_python_data::.boost::python::converter::rvalue_from_python_storage::storage))' may be used uninitialized [-Wmaybe-uninitialized] - 185 | ); - | ^ -In file included from /usr/include/boost/python/suite/indexing/indexing_suite.hpp:12: -/usr/include/boost/python/suite/indexing/detail/indexing_suite_detail.hpp: In static member function 'static void boost::python::detail::slice_helper::base_get_slice_data(Container&, PySliceObject*, Index&, Index&) [with Container = std::vector; DerivedPolicies = boost::python::detail::final_vector_derived_policies, false>; ProxyHandler = boost::python::detail::proxy_helper, boost::python::detail::final_vector_derived_policies, false>, boost::python::detail::container_element, long unsigned int, boost::python::detail::final_vector_derived_policies, false> >, long unsigned int>; Data = RDKit::MolStandardize::TautomerScoringFunctions::SubstructTerm; Index = long unsigned int]': -/usr/include/boost/python/suite/indexing/detail/indexing_suite_detail.hpp:617:27: note: '' declared here - 617 | long to = extract( slice->stop); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ -In member function 'boost::python::converter::extract_rvalue::result_type boost::python::converter::extract_rvalue::operator()() const [with T = long int]', - inlined from 'boost::python::extract::operator result_type() const [with T = long int]' at /usr/include/boost/python/extract.hpp:136:23, - inlined from 'static void boost::python::detail::slice_helper::base_get_slice_data(Container&, PySliceObject*, Index&, Index&) [with Container = std::vector; DerivedPolicies = boost::python::detail::final_vector_derived_policies, false>; ProxyHandler = boost::python::detail::proxy_helper, boost::python::detail::final_vector_derived_policies, false>, boost::python::detail::container_element, long unsigned int, boost::python::detail::final_vector_derived_policies, false> >, long unsigned int>; Data = RDKit::MolStandardize::TautomerScoringFunctions::SubstructTerm; Index = long unsigned int]' at /usr/include/boost/python/suite/indexing/detail/indexing_suite_detail.hpp:603:29: -/usr/include/boost/python/extract.hpp:185:11: warning: '*(long int*)((char*)& + offsetof(boost::python::extract,boost::python::extract::.boost::python::converter::extract_rvalue::m_data.boost::python::converter::rvalue_from_python_data::.boost::python::converter::rvalue_from_python_storage::storage))' may be used uninitialized [-Wmaybe-uninitialized] - 185 | ); - | ^ -/usr/include/boost/python/suite/indexing/detail/indexing_suite_detail.hpp: In static member function 'static void boost::python::detail::slice_helper::base_get_slice_data(Container&, PySliceObject*, Index&, Index&) [with Container = std::vector; DerivedPolicies = boost::python::detail::final_vector_derived_policies, false>; ProxyHandler = boost::python::detail::proxy_helper, boost::python::detail::final_vector_derived_policies, false>, boost::python::detail::container_element, long unsigned int, boost::python::detail::final_vector_derived_policies, false> >, long unsigned int>; Data = RDKit::MolStandardize::TautomerScoringFunctions::SubstructTerm; Index = long unsigned int]': -/usr/include/boost/python/suite/indexing/detail/indexing_suite_detail.hpp:603:29: note: '' declared here - 603 | long from = extract( slice->start); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ -[ 92%] Linking CXX shared module ../../../../rdkit/Chem/rdTautomerQuery.so -cd /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/TautomerQuery/Wrap && /usr/bin/cmake -E cmake_link_script CMakeFiles/rdTautomerQuery.dir/link.txt --verbose=1 -[ 92%] Linking CXX shared module ../../../../rdkit/Chem/Scaffolds/rdScaffoldNetwork.so -cd /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/ScaffoldNetwork/Wrap && /usr/bin/cmake -E cmake_link_script CMakeFiles/rdScaffoldNetwork.dir/link.txt --verbose=1 -/usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -g -fwrapv -O2 -Wl,--dependency-file=CMakeFiles/rdTautomerQuery.dir/link.d -Wl,-z,relro -Wl,-z,now -shared -o ../../../../rdkit/Chem/rdTautomerQuery.so CMakeFiles/rdTautomerQuery.dir/rdTautomerQuery.cpp.o ../../../../lib/libRDKitTautomerQuery.so.1.2025.03.1 ../../../../lib/libRDKitRDBoost.so.1.2025.03.1 ../../../../lib/libRDKitMolStandardize.so.1.2025.03.1 ../../../../lib/libRDKitChemReactions.so.1.2025.03.1 ../../../../lib/libRDKitFilterCatalog.so.1.2025.03.1 ../../../../lib/libRDKitCatalogs.so.1.2025.03.1 ../../../../lib/libRDKitFingerprints.so.1.2025.03.1 ../../../../lib/libRDKitSubgraphs.so.1.2025.03.1 ../../../../lib/libRDKitFileParsers.so.1.2025.03.1 /usr/lib/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 /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 rdTautomerQuery [ 93%] Building CXX object Code/GraphMol/RGroupDecomposition/CMakeFiles/RGroupDecomposition.dir/RGroupScore.cpp.o cd /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/RGroupDecomposition && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK 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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 +[ 93%] Linking CXX shared library ../../../lib/libRDKitGeneralizedSubstruct.so +cd /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/GeneralizedSubstruct && /usr/bin/cmake -E cmake_link_script CMakeFiles/GeneralizedSubstruct.dir/link.txt --verbose=1 /usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC 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../../../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' @@ -7043,69 +7074,57 @@ make -f Code/GraphMol/SynthonSpaceSearch/CMakeFiles/SynthonSpaceSearch.dir/build.make Code/GraphMol/SynthonSpaceSearch/CMakeFiles/SynthonSpaceSearch.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu' cd /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202503.1 /build/reproducible-path/rdkit-202503.1/Code/GraphMol/SynthonSpaceSearch /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/SynthonSpaceSearch /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/SynthonSpaceSearch/CMakeFiles/SynthonSpaceSearch.dir/DependInfo.cmake "--color=" -make[4]: Leaving directory '/build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu' -make -f 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-DSynthonSpaceSearch_EXPORTS -I/build/reproducible-path/rdkit-202503.1/External -I/build/reproducible-path/rdkit-202503.1/Code -I/build/reproducible-path/rdkit-202503.1/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/SynthonSpaceSearch/CMakeFiles/SynthonSpaceSearch.dir/SynthonSpaceSearch_details.cpp.o -MF CMakeFiles/SynthonSpaceSearch.dir/SynthonSpaceSearch_details.cpp.o.d -o CMakeFiles/SynthonSpaceSearch.dir/SynthonSpaceSearch_details.cpp.o -c /build/reproducible-path/rdkit-202503.1/Code/GraphMol/SynthonSpaceSearch/SynthonSpaceSearch_details.cpp make -f Code/GraphMol/SubstructLibrary/CMakeFiles/SubstructLibrary.dir/build.make Code/GraphMol/SubstructLibrary/CMakeFiles/SubstructLibrary.dir/depend +make -f Code/GraphMol/GeneralizedSubstruct/CMakeFiles/generalizedSubstructCatch.dir/build.make Code/GraphMol/GeneralizedSubstruct/CMakeFiles/generalizedSubstructCatch.dir/depend +make -f Code/GraphMol/GeneralizedSubstruct/Wrap/CMakeFiles/rdGeneralizedSubstruct.dir/build.make Code/GraphMol/GeneralizedSubstruct/Wrap/CMakeFiles/rdGeneralizedSubstruct.dir/depend make[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 -[ 94%] Building CXX object Code/GraphMol/SynthonSpaceSearch/CMakeFiles/SynthonSpaceSearch.dir/SynthonSpace.cpp.o -cd /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/SynthonSpaceSearch && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDKIT_SYNTHONSPACESEARCH_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_BUILD_XYZ2MOL_SUPPORT -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DSynthonSpaceSearch_EXPORTS -I/build/reproducible-path/rdkit-202503.1/External -I/build/reproducible-path/rdkit-202503.1/Code 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-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/Synthon.cpp.o -MF CMakeFiles/SynthonSpaceSearch.dir/Synthon.cpp.o.d -o CMakeFiles/SynthonSpaceSearch.dir/Synthon.cpp.o -c /build/reproducible-path/rdkit-202503.1/Code/GraphMol/SynthonSpaceSearch/Synthon.cpp -[ 94%] 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 -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDKIT_SUBSTRUCTLIBRARY_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_BUILD_XYZ2MOL_SUPPORT -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DSubstructLibrary_EXPORTS -I/build/reproducible-path/rdkit-202503.1/External -I/build/reproducible-path/rdkit-202503.1/Code -I/build/reproducible-path/rdkit-202503.1/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. 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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/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=" make[4]: Leaving directory '/build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu' make -f Code/GraphMol/GeneralizedSubstruct/CMakeFiles/generalizedSubstructCatch.dir/build.make Code/GraphMol/GeneralizedSubstruct/CMakeFiles/generalizedSubstructCatch.dir/build make[4]: Entering directory '/build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu' -[ 94%] Building CXX object Code/GraphMol/GeneralizedSubstruct/CMakeFiles/generalizedSubstructCatch.dir/catch_tests.cpp.o -cd /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/GeneralizedSubstruct && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_BUILD_XYZ2MOL_SUPPORT -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202503.1/External -I/build/reproducible-path/rdkit-202503.1/Code -I/build/reproducible-path/rdkit-202503.1/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection 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Code/GraphMol/GeneralizedSubstruct/CMakeFiles/generalizedSubstructCatch.dir/catch_tests.cpp.o +cd /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/GeneralizedSubstruct && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_BUILD_XYZ2MOL_SUPPORT -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202503.1/External -I/build/reproducible-path/rdkit-202503.1/Code -I/build/reproducible-path/rdkit-202503.1/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection 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/build/reproducible-path/rdkit-202503.1/Code/PgSQL/rdkit/adapter.cpp -[ 95%] Building CXX object Code/GraphMol/SynthonSpaceSearch/CMakeFiles/SynthonSpaceSearch.dir/SynthonSpaceSubstructureSearcher.cpp.o -cd /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/SynthonSpaceSearch && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDKIT_SYNTHONSPACESEARCH_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_BUILD_XYZ2MOL_SUPPORT -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DSynthonSpaceSearch_EXPORTS -I/build/reproducible-path/rdkit-202503.1/External -I/build/reproducible-path/rdkit-202503.1/Code -I/build/reproducible-path/rdkit-202503.1/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/SynthonSpaceSearch/CMakeFiles/SynthonSpaceSearch.dir/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 -[ 95%] Linking CXX shared library ../../../lib/libRDKitRGroupDecomposition.so -cd /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/RGroupDecomposition && /usr/bin/cmake -E cmake_link_script CMakeFiles/RGroupDecomposition.dir/link.txt --verbose=1 -/usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,--dependency-file=CMakeFiles/RGroupDecomposition.dir/link.d -Wl,-z,relro -Wl,-z,now -shared -Wl,-soname,libRDKitRGroupDecomposition.so.1 -o ../../../lib/libRDKitRGroupDecomposition.so.1.2025.03.1 CMakeFiles/RGroupDecomposition.dir/RGroupDecomp.cpp.o CMakeFiles/RGroupDecomposition.dir/RGroupDecompData.cpp.o CMakeFiles/RGroupDecomposition.dir/RGroupData.cpp.o CMakeFiles/RGroupDecomposition.dir/RGroupUtils.cpp.o CMakeFiles/RGroupDecomposition.dir/RGroupCore.cpp.o CMakeFiles/RGroupDecomposition.dir/RGroupDecompParams.cpp.o CMakeFiles/RGroupDecomposition.dir/RGroupScore.cpp.o CMakeFiles/RGroupDecomposition.dir/RGroupFingerprintScore.cpp.o CMakeFiles/RGroupDecomposition.dir/RGroupGa.cpp.o CMakeFiles/RGroupDecomposition.dir/RGroupDecompJSONParsers.cpp.o ../../../lib/libRDKitFMCS.so.1.2025.03.1 ../../../lib/libRDKitga.so.1.2025.03.1 ../../../lib/libRDKitMolEnumerator.so.1.2025.03.1 ../../../lib/libRDKitTautomerQuery.so.1.2025.03.1 ../../../lib/libRDKitMolStandardize.so.1.2025.03.1 ../../../lib/libRDKitChemReactions.so.1.2025.03.1 ../../../lib/libRDKitFingerprints.so.1.2025.03.1 ../../../lib/libRDKitFileParsers.so.1.2025.03.1 ../../../lib/libRDKitChemTransforms.so.1.2025.03.1 ../../../lib/libRDKitDepictor.so.1.2025.03.1 /usr/lib/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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Leaving directory '/build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu' -[ 95%] Built target RGroupDecomposition +cd /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/SynthonSpaceSearch && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDKIT_SYNTHONSPACESEARCH_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_BUILD_XYZ2MOL_SUPPORT -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DSynthonSpaceSearch_EXPORTS -I/build/reproducible-path/rdkit-202503.1/External -I/build/reproducible-path/rdkit-202503.1/Code -I/build/reproducible-path/rdkit-202503.1/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 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-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/SynthonSet.cpp.o -MF CMakeFiles/SynthonSpaceSearch.dir/SynthonSet.cpp.o.d -o CMakeFiles/SynthonSpaceSearch.dir/SynthonSet.cpp.o -c /build/reproducible-path/rdkit-202503.1/Code/GraphMol/SynthonSpaceSearch/SynthonSet.cpp +[ 95%] Building CXX object 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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/SynthonSpaceSearch/CMakeFiles/SynthonSpaceSearch.dir/Synthon.cpp.o -MF CMakeFiles/SynthonSpaceSearch.dir/Synthon.cpp.o.d -o CMakeFiles/SynthonSpaceSearch.dir/Synthon.cpp.o -c /build/reproducible-path/rdkit-202503.1/Code/GraphMol/SynthonSpaceSearch/Synthon.cpp [ 95%] Building C object Code/PgSQL/rdkit/CMakeFiles/rdkit.dir/bfp_op.c.o cd /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/PgSQL/rdkit && /usr/bin/cc -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKITVER=\"007600\" -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_CAIRO_SUPPORT -DRDK_BUILD_COORDGEN_SUPPORT 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-Wno-unused-function -fno-strict-aliasing -fPIC -fPIC -MD -MT Code/PgSQL/rdkit/CMakeFiles/rdkit.dir/bfp_op.c.o -MF CMakeFiles/rdkit.dir/bfp_op.c.o.d -o CMakeFiles/rdkit.dir/bfp_op.c.o -c /build/reproducible-path/rdkit-202503.1/Code/PgSQL/rdkit/bfp_op.c [ 95%] Building C object Code/PgSQL/rdkit/CMakeFiles/rdkit.dir/cache.c.o cd /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/PgSQL/rdkit && /usr/bin/cc -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKITVER=\"007600\" -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_CAIRO_SUPPORT -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_FREETYPE_SUPPORT -DRDK_BUILD_INCHI_SUPPORT -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_MOLINTERCHANGE_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_BUILD_XYZ2MOL_SUPPORT -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_TOOLKIT_VERSION=\"2025.03.1\" -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -Drdkit_EXPORTS -I/build/reproducible-path/rdkit-202503.1/External -I/build/reproducible-path/rdkit-202503.1/Code -I/usr/include/postgresql -I/usr/include/postgresql/17/server -I/build/reproducible-path/rdkit-202503.1/External/boost-numeric-bindings -I/usr/include/freetype2 -isystem /usr/include/eigen3 -isystem /usr/include/cairo -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -fPIC -fPIC -MD -MT Code/PgSQL/rdkit/CMakeFiles/rdkit.dir/cache.c.o -MF CMakeFiles/rdkit.dir/cache.c.o.d -o CMakeFiles/rdkit.dir/cache.c.o -c /build/reproducible-path/rdkit-202503.1/Code/PgSQL/rdkit/cache.c -[ 95%] Building C object Code/PgSQL/rdkit/CMakeFiles/rdkit.dir/guc.c.o -cd /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/PgSQL/rdkit && /usr/bin/cc -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKITVER=\"007600\" -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_CAIRO_SUPPORT -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_FREETYPE_SUPPORT -DRDK_BUILD_INCHI_SUPPORT -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_MOLINTERCHANGE_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_BUILD_XYZ2MOL_SUPPORT -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_TOOLKIT_VERSION=\"2025.03.1\" -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -Drdkit_EXPORTS -I/build/reproducible-path/rdkit-202503.1/External -I/build/reproducible-path/rdkit-202503.1/Code -I/usr/include/postgresql -I/usr/include/postgresql/17/server -I/build/reproducible-path/rdkit-202503.1/External/boost-numeric-bindings -I/usr/include/freetype2 -isystem /usr/include/eigen3 -isystem /usr/include/cairo -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -fPIC -fPIC -MD -MT Code/PgSQL/rdkit/CMakeFiles/rdkit.dir/guc.c.o -MF CMakeFiles/rdkit.dir/guc.c.o.d -o CMakeFiles/rdkit.dir/guc.c.o -c /build/reproducible-path/rdkit-202503.1/Code/PgSQL/rdkit/guc.c -[ 95%] Building CXX object Code/GraphMol/SynthonSpaceSearch/CMakeFiles/SynthonSpaceSearch.dir/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 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/build/reproducible-path/rdkit-202503.1/Code/GraphMol/SynthonSpaceSearch/SynthonSpaceSearcher.cpp /build/reproducible-path/rdkit-202503.1/Code/PgSQL/rdkit/adapter.cpp: In function 'void* makeAvalonBFP(CROMol, bool, unsigned int)': /build/reproducible-path/rdkit-202503.1/Code/PgSQL/rdkit/adapter.cpp:1636:38: warning: unused parameter 'data' [-Wunused-parameter] 1636 | extern "C" CBfp makeAvalonBFP(CROMol data, bool isQuery, @@ -7116,6 +7135,12 @@ /build/reproducible-path/rdkit-202503.1/Code/PgSQL/rdkit/adapter.cpp:1637:44: warning: unused parameter 'bitFlags' [-Wunused-parameter] 1637 | unsigned int bitFlags) { | ~~~~~~~~~~~~~^~~~~~~~ +[ 95%] Linking CXX shared library ../../../lib/libRDKitRGroupDecomposition.so +cd /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/RGroupDecomposition && /usr/bin/cmake -E cmake_link_script CMakeFiles/RGroupDecomposition.dir/link.txt --verbose=1 +/usr/bin/c++ -fPIC -g -O2 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Code/GraphMol/RGroupDecomposition/CMakeFiles/testRGroupDecomp.dir/build.make Code/GraphMol/RGroupDecomposition/CMakeFiles/testRGroupDecomp.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu' cd /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202503.1 /build/reproducible-path/rdkit-202503.1/Code/GraphMol/RGroupDecomposition /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/RGroupDecomposition /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/RGroupDecomposition/CMakeFiles/testRGroupDecomp.dir/DependInfo.cmake "--color=" @@ -7124,13 +7149,8 @@ make[4]: Entering directory '/build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu' [ 95%] Building CXX object Code/GraphMol/RGroupDecomposition/CMakeFiles/testRGroupDecomp.dir/testRGroupDecomp.cpp.o cd /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/RGroupDecomposition && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_BUILD_XYZ2MOL_SUPPORT -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202503.1/External -I/build/reproducible-path/rdkit-202503.1/Code -I/build/reproducible-path/rdkit-202503.1/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat 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-DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKITVER=\"007600\" -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_CAIRO_SUPPORT -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_FREETYPE_SUPPORT -DRDK_BUILD_INCHI_SUPPORT -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_MOLINTERCHANGE_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_BUILD_XYZ2MOL_SUPPORT -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_TOOLKIT_VERSION=\"2025.03.1\" -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -Drdkit_EXPORTS -I/build/reproducible-path/rdkit-202503.1/External -I/build/reproducible-path/rdkit-202503.1/Code -I/usr/include/postgresql -I/usr/include/postgresql/17/server -I/build/reproducible-path/rdkit-202503.1/External/boost-numeric-bindings -I/usr/include/freetype2 -isystem /usr/include/eigen3 -isystem /usr/include/cairo -g -O2 -Werror=implicit-function-declaration 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/build/reproducible-path/rdkit-202503.1/Code/GraphMol/RGroupDecomposition/testRGroupInternals.cpp -[ 95%] Linking CXX shared module ../../../../rdkit/Chem/rdGeneralizedSubstruct.so -cd /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/GeneralizedSubstruct/Wrap && /usr/bin/cmake -E cmake_link_script CMakeFiles/rdGeneralizedSubstruct.dir/link.txt --verbose=1 -/usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -g -fwrapv -O2 -Wl,--dependency-file=CMakeFiles/rdGeneralizedSubstruct.dir/link.d -Wl,-z,relro -Wl,-z,now -shared -o ../../../../rdkit/Chem/rdGeneralizedSubstruct.so 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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/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 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../../../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' -[ 95%] Built target generalizedSubstructCatch +[ 95%] Building C object Code/PgSQL/rdkit/CMakeFiles/rdkit.dir/mol_op.c.o +cd /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/PgSQL/rdkit && /usr/bin/cc -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKITVER=\"007600\" -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_CAIRO_SUPPORT -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_FREETYPE_SUPPORT -DRDK_BUILD_INCHI_SUPPORT -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_MOLINTERCHANGE_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_BUILD_XYZ2MOL_SUPPORT -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED 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/build/reproducible-path/rdkit-202503.1/Code/PgSQL/rdkit/mol_op.c make -f Code/GraphMol/RGroupDecomposition/CMakeFiles/rgroupCatchTests.dir/build.make Code/GraphMol/RGroupDecomposition/CMakeFiles/rgroupCatchTests.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/rgroupCatchTests.dir/DependInfo.cmake "--color=" @@ -7163,10 +7171,13 @@ make[4]: Entering directory '/build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu' [ 95%] Building CXX object Code/GraphMol/RGroupDecomposition/CMakeFiles/rgroupCatchTests.dir/catch_rgd.cpp.o cd /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/RGroupDecomposition && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_BUILD_XYZ2MOL_SUPPORT -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202503.1/External -I/build/reproducible-path/rdkit-202503.1/Code -I/build/reproducible-path/rdkit-202503.1/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/GraphMol/RGroupDecomposition/CMakeFiles/rgroupCatchTests.dir/catch_rgd.cpp.o -MF CMakeFiles/rgroupCatchTests.dir/catch_rgd.cpp.o.d -o CMakeFiles/rgroupCatchTests.dir/catch_rgd.cpp.o -c /build/reproducible-path/rdkit-202503.1/Code/GraphMol/RGroupDecomposition/catch_rgd.cpp -[ 95%] Building C object Code/PgSQL/rdkit/CMakeFiles/rdkit.dir/mol_op.c.o -cd /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/PgSQL/rdkit && /usr/bin/cc -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKITVER=\"007600\" -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_CAIRO_SUPPORT -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_FREETYPE_SUPPORT 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-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 +[ 95%] 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 +[ 95%] Linking CXX shared module ../../../../rdkit/Chem/rdGeneralizedSubstruct.so +cd /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/GeneralizedSubstruct/Wrap && /usr/bin/cmake -E cmake_link_script CMakeFiles/rdGeneralizedSubstruct.dir/link.txt --verbose=1 +/usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -g -fwrapv -O2 -Wl,--dependency-file=CMakeFiles/rdGeneralizedSubstruct.dir/link.d 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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/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 [ 96%] Building C object Code/PgSQL/rdkit/CMakeFiles/rdkit.dir/bfp_gin.c.o cd /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/PgSQL/rdkit && /usr/bin/cc -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKITVER=\"007600\" -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_CAIRO_SUPPORT -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_FREETYPE_SUPPORT -DRDK_BUILD_INCHI_SUPPORT -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_MOLINTERCHANGE_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_BUILD_XYZ2MOL_SUPPORT -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_TOOLKIT_VERSION=\"2025.03.1\" -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -Drdkit_EXPORTS -I/build/reproducible-path/rdkit-202503.1/External -I/build/reproducible-path/rdkit-202503.1/Code -I/usr/include/postgresql -I/usr/include/postgresql/17/server -I/build/reproducible-path/rdkit-202503.1/External/boost-numeric-bindings -I/usr/include/freetype2 -isystem /usr/include/eigen3 -isystem /usr/include/cairo -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -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 [ 96%] Building C object Code/PgSQL/rdkit/CMakeFiles/rdkit.dir/bitstring.c.o @@ -7187,61 +7218,71 @@ cd /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/PgSQL/rdkit && /usr/bin/cc -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKITVER=\"007600\" -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_CAIRO_SUPPORT -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_FREETYPE_SUPPORT -DRDK_BUILD_INCHI_SUPPORT -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_MOLINTERCHANGE_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_BUILD_XYZ2MOL_SUPPORT -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_TOOLKIT_VERSION=\"2025.03.1\" -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -Drdkit_EXPORTS -I/build/reproducible-path/rdkit-202503.1/External -I/build/reproducible-path/rdkit-202503.1/Code -I/usr/include/postgresql -I/usr/include/postgresql/17/server -I/build/reproducible-path/rdkit-202503.1/External/boost-numeric-bindings -I/usr/include/freetype2 -isystem /usr/include/eigen3 -isystem /usr/include/cairo -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -fPIC -fPIC -MD -MT Code/PgSQL/rdkit/CMakeFiles/rdkit.dir/rdkit_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 [ 96%] Building C object Code/PgSQL/rdkit/CMakeFiles/rdkit.dir/rxn_op.c.o cd /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/PgSQL/rdkit && /usr/bin/cc -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKITVER=\"007600\" -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_CAIRO_SUPPORT -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_FREETYPE_SUPPORT -DRDK_BUILD_INCHI_SUPPORT -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_MOLINTERCHANGE_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_BUILD_XYZ2MOL_SUPPORT -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_TOOLKIT_VERSION=\"2025.03.1\" -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -Drdkit_EXPORTS -I/build/reproducible-path/rdkit-202503.1/External -I/build/reproducible-path/rdkit-202503.1/Code -I/usr/include/postgresql -I/usr/include/postgresql/17/server -I/build/reproducible-path/rdkit-202503.1/External/boost-numeric-bindings -I/usr/include/freetype2 -isystem /usr/include/eigen3 -isystem /usr/include/cairo -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -fPIC -fPIC -MD -MT Code/PgSQL/rdkit/CMakeFiles/rdkit.dir/rxn_op.c.o -MF CMakeFiles/rdkit.dir/rxn_op.c.o.d -o CMakeFiles/rdkit.dir/rxn_op.c.o -c /build/reproducible-path/rdkit-202503.1/Code/PgSQL/rdkit/rxn_op.c -[ 96%] 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 [ 96%] Building C object Code/PgSQL/rdkit/CMakeFiles/rdkit.dir/sfp_op.c.o cd /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/PgSQL/rdkit && /usr/bin/cc -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKITVER=\"007600\" -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_CAIRO_SUPPORT -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_FREETYPE_SUPPORT -DRDK_BUILD_INCHI_SUPPORT -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_MOLINTERCHANGE_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_BUILD_XYZ2MOL_SUPPORT -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_TOOLKIT_VERSION=\"2025.03.1\" -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -Drdkit_EXPORTS -I/build/reproducible-path/rdkit-202503.1/External -I/build/reproducible-path/rdkit-202503.1/Code -I/usr/include/postgresql -I/usr/include/postgresql/17/server -I/build/reproducible-path/rdkit-202503.1/External/boost-numeric-bindings -I/usr/include/freetype2 -isystem /usr/include/eigen3 -isystem /usr/include/cairo -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -fPIC -fPIC -MD -MT Code/PgSQL/rdkit/CMakeFiles/rdkit.dir/sfp_op.c.o -MF CMakeFiles/rdkit.dir/sfp_op.c.o.d -o CMakeFiles/rdkit.dir/sfp_op.c.o -c /build/reproducible-path/rdkit-202503.1/Code/PgSQL/rdkit/sfp_op.c +[ 96%] Building CXX object Code/GraphMol/SynthonSpaceSearch/CMakeFiles/SynthonSpaceSearch.dir/SynthonSpaceRascalSearcher.cpp.o +cd /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/SynthonSpaceSearch && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDKIT_SYNTHONSPACESEARCH_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_BUILD_XYZ2MOL_SUPPORT -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DSynthonSpaceSearch_EXPORTS -I/build/reproducible-path/rdkit-202503.1/External -I/build/reproducible-path/rdkit-202503.1/Code -I/build/reproducible-path/rdkit-202503.1/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/SynthonSpaceSearch/CMakeFiles/SynthonSpaceSearch.dir/SynthonSpaceRascalSearcher.cpp.o -MF CMakeFiles/SynthonSpaceSearch.dir/SynthonSpaceRascalSearcher.cpp.o.d -o CMakeFiles/SynthonSpaceSearch.dir/SynthonSpaceRascalSearcher.cpp.o -c /build/reproducible-path/rdkit-202503.1/Code/GraphMol/SynthonSpaceSearch/SynthonSpaceRascalSearcher.cpp [ 96%] Linking CXX shared library librdkit.so cd /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/PgSQL/rdkit && /usr/bin/cmake -E cmake_link_script CMakeFiles/rdkit.dir/link.txt --verbose=1 +/usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,--dependency-file=CMakeFiles/rdkit.dir/link.d -Wl,-z,relro -Wl,-z,now -shared -Wl,-soname,librdkit.so -o librdkit.so CMakeFiles/rdkit.dir/adapter.cpp.o CMakeFiles/rdkit.dir/bfp_op.c.o CMakeFiles/rdkit.dir/cache.c.o CMakeFiles/rdkit.dir/guc.c.o CMakeFiles/rdkit.dir/low_gist.c.o CMakeFiles/rdkit.dir/mol_op.c.o CMakeFiles/rdkit.dir/rdkit_gist.c.o CMakeFiles/rdkit.dir/bfp_gist.c.o CMakeFiles/rdkit.dir/bfp_gin.c.o CMakeFiles/rdkit.dir/bitstring.c.o CMakeFiles/rdkit.dir/rdkit_io.c.o CMakeFiles/rdkit.dir/rxn_op.c.o CMakeFiles/rdkit.dir/sfp_op.c.o -L/build/reproducible-path/rdkit-202503.1/Code/PgSQL/rdkit/lib 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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/libRDKitAlignment.so.1.2025.03.1 /usr/lib/aarch64-linux-gnu/libmaeparser.so ../../../lib/libRDKitSmilesParse.so.1.2025.03.1 ../../../lib/libRDKitSubgraphs.so.1.2025.03.1 ../../../lib/libRDKitSubstructMatch.so.1.2025.03.1 ../../../lib/libRDKitGenericGroups.so.1.2025.03.1 ../../../lib/libRDKitGraphMol.so.1.2025.03.1 ../../../lib/libRDKitRDGeometryLib.so.1.2025.03.1 ../../../lib/libRDKitDataStructs.so.1.2025.03.1 ../../../lib/libRDKitEigenSolvers.so.1.2025.03.1 ../../../lib/libRDKitRDGeneral.so.1.2025.03.1 -ldl /usr/lib/aarch64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_iostreams.so.1.83.0 +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 +cd /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/PgSQL/rdkit && /usr/bin/cmake -E copy_directory /build/reproducible-path/rdkit-202503.1/Code/PgSQL/rdkit/expected /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/PgSQL/rdkit/expected +make[4]: Leaving directory '/build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu' +[ 96%] Built target rdkit +[ 96%] Building CXX object Code/GraphMol/SynthonSpaceSearch/CMakeFiles/SynthonSpaceSearch.dir/SynthonSpaceHitSet.cpp.o +cd /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/SynthonSpaceSearch && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDKIT_SYNTHONSPACESEARCH_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_BUILD_XYZ2MOL_SUPPORT -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DSynthonSpaceSearch_EXPORTS -I/build/reproducible-path/rdkit-202503.1/External -I/build/reproducible-path/rdkit-202503.1/Code -I/build/reproducible-path/rdkit-202503.1/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/SynthonSpaceSearch/CMakeFiles/SynthonSpaceSearch.dir/SynthonSpaceHitSet.cpp.o -MF CMakeFiles/SynthonSpaceSearch.dir/SynthonSpaceHitSet.cpp.o.d -o CMakeFiles/SynthonSpaceSearch.dir/SynthonSpaceHitSet.cpp.o -c /build/reproducible-path/rdkit-202503.1/Code/GraphMol/SynthonSpaceSearch/SynthonSpaceHitSet.cpp +[ 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 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Code/GraphMol/SynthonSpaceSearch/CMakeFiles/SynthonSpaceSearch.dir/SearchResults.cpp.o +cd /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/SynthonSpaceSearch && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDKIT_SYNTHONSPACESEARCH_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_BUILD_XYZ2MOL_SUPPORT -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DSynthonSpaceSearch_EXPORTS -I/build/reproducible-path/rdkit-202503.1/External -I/build/reproducible-path/rdkit-202503.1/Code -I/build/reproducible-path/rdkit-202503.1/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/SynthonSpaceSearch/CMakeFiles/SynthonSpaceSearch.dir/SearchResults.cpp.o -MF CMakeFiles/SynthonSpaceSearch.dir/SearchResults.cpp.o.d -o CMakeFiles/SynthonSpaceSearch.dir/SearchResults.cpp.o -c /build/reproducible-path/rdkit-202503.1/Code/GraphMol/SynthonSpaceSearch/SearchResults.cpp +[ 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 +[ 96%] Building CXX object Code/GraphMol/SynthonSpaceSearch/CMakeFiles/SynthonSpaceSearch.dir/MemoryMappedFileReader.cpp.o +cd 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/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 -f Code/GraphMol/RGroupDecomposition/Wrap/CMakeFiles/rdRGroupDecomposition.dir/build.make Code/GraphMol/RGroupDecomposition/Wrap/CMakeFiles/rdRGroupDecomposition.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/Wrap /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/RGroupDecomposition/Wrap 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Code/GraphMol/SubstructLibrary/Wrap/CMakeFiles/rdSubstructLibrary.dir/rdSubstructLibrary.cpp.o -MF CMakeFiles/rdSubstructLibrary.dir/rdSubstructLibrary.cpp.o.d -o CMakeFiles/rdSubstructLibrary.dir/rdSubstructLibrary.cpp.o -c /build/reproducible-path/rdkit-202503.1/Code/GraphMol/SubstructLibrary/Wrap/rdSubstructLibrary.cpp -[ 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 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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 -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' -[ 97%] Built target testRGroupDecompInternals +[ 97%] Built target rgroupCatchTests [ 98%] Linking CXX shared library ../../../lib/libRDKitSynthonSpaceSearch.so cd /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/SynthonSpaceSearch && /usr/bin/cmake -E cmake_link_script CMakeFiles/SynthonSpaceSearch.dir/link.txt --verbose=1 /usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,--dependency-file=CMakeFiles/SynthonSpaceSearch.dir/link.d -Wl,-z,relro -Wl,-z,now -shared -Wl,-soname,libRDKitSynthonSpaceSearch.so.1 -o ../../../lib/libRDKitSynthonSpaceSearch.so.1.2025.03.1 CMakeFiles/SynthonSpaceSearch.dir/SynthonSpaceSearch_details.cpp.o CMakeFiles/SynthonSpaceSearch.dir/SynthonSpace.cpp.o CMakeFiles/SynthonSpaceSearch.dir/SynthonSet.cpp.o CMakeFiles/SynthonSpaceSearch.dir/Synthon.cpp.o CMakeFiles/SynthonSpaceSearch.dir/SynthonSpaceSearcher.cpp.o CMakeFiles/SynthonSpaceSearch.dir/SynthonSpaceSubstructureSearcher.cpp.o CMakeFiles/SynthonSpaceSearch.dir/SynthonSpaceFingerprintSearcher.cpp.o CMakeFiles/SynthonSpaceSearch.dir/SynthonSpaceRascalSearcher.cpp.o CMakeFiles/SynthonSpaceSearch.dir/SynthonSpaceHitSet.cpp.o CMakeFiles/SynthonSpaceSearch.dir/SearchResults.cpp.o CMakeFiles/SynthonSpaceSearch.dir/MemoryMappedFileReader.cpp.o ../../../lib/libRDKitRascalMCES.so.1.2025.03.1 ../../../lib/libRDKitGeneralizedSubstruct.so.1.2025.03.1 ../../../lib/libRDKitMolEnumerator.so.1.2025.03.1 ../../../lib/libRDKitTautomerQuery.so.1.2025.03.1 ../../../lib/libRDKitMolStandardize.so.1.2025.03.1 ../../../lib/libRDKitChemReactions.so.1.2025.03.1 ../../../lib/libRDKitFileParsers.so.1.2025.03.1 /usr/lib/aarch64-linux-gnu/libmaeparser.so ../../../lib/libRDKitChemTransforms.so.1.2025.03.1 ../../../lib/libRDKitFingerprints.so.1.2025.03.1 ../../../lib/libRDKitDepictor.so.1.2025.03.1 /usr/lib/aarch64-linux-gnu/libcoordgen.so ../../../lib/libRDKitMolAlign.so.1.2025.03.1 ../../../lib/libRDKitMolTransforms.so.1.2025.03.1 ../../../lib/libRDKitEigenSolvers.so.1.2025.03.1 ../../../lib/libRDKitAlignment.so.1.2025.03.1 ../../../lib/libRDKitFilterCatalog.so.1.2025.03.1 ../../../lib/libRDKitSmilesParse.so.1.2025.03.1 ../../../lib/libRDKitSubstructMatch.so.1.2025.03.1 ../../../lib/libRDKitGenericGroups.so.1.2025.03.1 ../../../lib/libRDKitSubgraphs.so.1.2025.03.1 ../../../lib/libRDKitGraphMol.so.1.2025.03.1 ../../../lib/libRDKitRDGeometryLib.so.1.2025.03.1 ../../../lib/libRDKitDataStructs.so.1.2025.03.1 ../../../lib/libRDKitCatalogs.so.1.2025.03.1 ../../../lib/libRDKitRDGeneral.so.1.2025.03.1 /usr/lib/aarch64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl @@ -7250,38 +7291,33 @@ [ 98%] Built target SynthonSpaceSearch make -f Code/GraphMol/SynthonSpaceSearch/CMakeFiles/testSynthonSpaceSubstructureSearch.dir/build.make Code/GraphMol/SynthonSpaceSearch/CMakeFiles/testSynthonSpaceSubstructureSearch.dir/depend make -f Code/GraphMol/SynthonSpaceSearch/CMakeFiles/testSynthonSpaceRascalSearch.dir/build.make Code/GraphMol/SynthonSpaceSearch/CMakeFiles/testSynthonSpaceRascalSearch.dir/depend -make -f Code/GraphMol/SynthonSpaceSearch/Wrap/CMakeFiles/rdSynthonSpaceSearch.dir/build.make Code/GraphMol/SynthonSpaceSearch/Wrap/CMakeFiles/rdSynthonSpaceSearch.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu' +cd /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202503.1 /build/reproducible-path/rdkit-202503.1/Code/GraphMol/SynthonSpaceSearch /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/SynthonSpaceSearch /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/SynthonSpaceSearch/CMakeFiles/testSynthonSpaceSubstructureSearch.dir/DependInfo.cmake "--color=" +make -f Code/GraphMol/SynthonSpaceSearch/Wrap/CMakeFiles/rdSynthonSpaceSearch.dir/build.make Code/GraphMol/SynthonSpaceSearch/Wrap/CMakeFiles/rdSynthonSpaceSearch.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu' +cd /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202503.1 /build/reproducible-path/rdkit-202503.1/Code/GraphMol/SynthonSpaceSearch /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/SynthonSpaceSearch /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/SynthonSpaceSearch/CMakeFiles/testSynthonSpaceRascalSearch.dir/DependInfo.cmake "--color=" make[4]: Entering directory '/build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu' -cd /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202503.1 /build/reproducible-path/rdkit-202503.1/Code/GraphMol/SynthonSpaceSearch /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=" 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=" -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]: Leaving directory '/build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu' -make -f Code/GraphMol/SynthonSpaceSearch/Wrap/CMakeFiles/rdSynthonSpaceSearch.dir/build.make Code/GraphMol/SynthonSpaceSearch/Wrap/CMakeFiles/rdSynthonSpaceSearch.dir/build -make[4]: Entering directory '/build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu' make[4]: Entering directory '/build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu' 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' +make[4]: Leaving directory '/build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu' +make -f Code/GraphMol/SynthonSpaceSearch/Wrap/CMakeFiles/rdSynthonSpaceSearch.dir/build.make Code/GraphMol/SynthonSpaceSearch/Wrap/CMakeFiles/rdSynthonSpaceSearch.dir/build +make[4]: Entering directory '/build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu' [ 98%] Building CXX object Code/GraphMol/SynthonSpaceSearch/CMakeFiles/testSynthonSpaceSubstructureSearch.dir/substructure_search_catch_tests.cpp.o -cd /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/SynthonSpaceSearch && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_BUILD_XYZ2MOL_SUPPORT -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202503.1/External -I/build/reproducible-path/rdkit-202503.1/Code -I/build/reproducible-path/rdkit-202503.1/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/GraphMol/SynthonSpaceSearch/CMakeFiles/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 [ 98%] Building CXX object Code/GraphMol/SynthonSpaceSearch/Wrap/CMakeFiles/rdSynthonSpaceSearch.dir/rdSynthonSpaceSearch.cpp.o -cd /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/SynthonSpaceSearch/Wrap && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_NUMPY_DYN_LINK -DBOOST_NUMPY_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_BUILD_XYZ2MOL_SUPPORT -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -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 [ 98%] Building CXX object Code/GraphMol/SynthonSpaceSearch/CMakeFiles/testSynthonSpaceRascalSearch.dir/rascal_search_catch_tests.cpp.o +cd /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/SynthonSpaceSearch/Wrap && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_NUMPY_DYN_LINK -DBOOST_NUMPY_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_BUILD_XYZ2MOL_SUPPORT -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -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 cd /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/SynthonSpaceSearch && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_BUILD_XYZ2MOL_SUPPORT -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202503.1/External -I/build/reproducible-path/rdkit-202503.1/Code -I/build/reproducible-path/rdkit-202503.1/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/GraphMol/SynthonSpaceSearch/CMakeFiles/testSynthonSpaceRascalSearch.dir/rascal_search_catch_tests.cpp.o -MF CMakeFiles/testSynthonSpaceRascalSearch.dir/rascal_search_catch_tests.cpp.o.d -o CMakeFiles/testSynthonSpaceRascalSearch.dir/rascal_search_catch_tests.cpp.o -c /build/reproducible-path/rdkit-202503.1/Code/GraphMol/SynthonSpaceSearch/rascal_search_catch_tests.cpp -[ 98%] 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[4]: Leaving directory '/build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu' -[ 98%] Built target gaExample -[ 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 +cd /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/SynthonSpaceSearch && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_BUILD_XYZ2MOL_SUPPORT -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202503.1/External -I/build/reproducible-path/rdkit-202503.1/Code -I/build/reproducible-path/rdkit-202503.1/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/GraphMol/SynthonSpaceSearch/CMakeFiles/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 +[ 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' -[ 98%] Built target rgroupCatchTests +[ 98%] Built target rdRGroupDecomposition [ 99%] 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 @@ -7292,33 +7328,28 @@ /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/substructLibraryTest.dir/link.d CMakeFiles/substructLibraryTest.dir/substructLibraryTest.cpp.o -o substructLibraryTest ../../../lib/libRDKitSubstructLibrary.so.1.2025.03.1 ../../../lib/libRDKitGeneralizedSubstruct.so.1.2025.03.1 ../../../lib/libRDKitTautomerQuery.so.1.2025.03.1 ../../../lib/libRDKitMolStandardize.so.1.2025.03.1 ../../../lib/libRDKitMolEnumerator.so.1.2025.03.1 ../../../lib/libRDKitChemReactions.so.1.2025.03.1 ../../../lib/libRDKitFileParsers.so.1.2025.03.1 /usr/lib/aarch64-linux-gnu/libmaeparser.so ../../../lib/libRDKitFilterCatalog.so.1.2025.03.1 ../../../lib/libRDKitChemTransforms.so.1.2025.03.1 ../../../lib/libRDKitDepictor.so.1.2025.03.1 /usr/lib/aarch64-linux-gnu/libcoordgen.so ../../../lib/libRDKitMolAlign.so.1.2025.03.1 ../../../lib/libRDKitMolTransforms.so.1.2025.03.1 ../../../lib/libRDKitEigenSolvers.so.1.2025.03.1 ../../../lib/libRDKitAlignment.so.1.2025.03.1 ../../../lib/libRDKitFingerprints.so.1.2025.03.1 ../../../lib/libRDKitSmilesParse.so.1.2025.03.1 ../../../lib/libRDKitSubstructMatch.so.1.2025.03.1 ../../../lib/libRDKitGenericGroups.so.1.2025.03.1 ../../../lib/libRDKitSubgraphs.so.1.2025.03.1 ../../../lib/libRDKitGraphMol.so.1.2025.03.1 ../../../lib/libRDKitRDGeometryLib.so.1.2025.03.1 ../../../lib/libRDKitCatalogs.so.1.2025.03.1 ../../../lib/libRDKitDataStructs.so.1.2025.03.1 ../../../lib/libRDKitRDGeneral.so.1.2025.03.1 /usr/lib/aarch64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl make[4]: Leaving directory '/build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu' [ 99%] Built target substructLibraryTest -[ 99%] Linking CXX shared module ../../../../rdkit/Chem/rdRGroupDecomposition.so -cd /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/RGroupDecomposition/Wrap && /usr/bin/cmake -E cmake_link_script CMakeFiles/rdRGroupDecomposition.dir/link.txt --verbose=1 [100%] 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++ -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' -[100%] Built target rdRGroupDecomposition /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' [100%] Built target testSynthonSpaceRascalSearch -[100%] Linking CXX executable testSynthonSpaceSubstructureSearch -cd /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/SynthonSpaceSearch && /usr/bin/cmake -E cmake_link_script CMakeFiles/testSynthonSpaceSubstructureSearch.dir/link.txt --verbose=1 -/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 +[100%] Linking CXX executable testRGroupDecomp +cd /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/RGroupDecomposition && /usr/bin/cmake -E cmake_link_script CMakeFiles/testRGroupDecomp.dir/link.txt --verbose=1 +/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/testRGroupDecomp.dir/link.d CMakeFiles/testRGroupDecomp.dir/testRGroupDecomp.cpp.o -o testRGroupDecomp ../../../lib/libRDKitRGroupDecomposition.so.1.2025.03.1 ../../../lib/libRDKitFMCS.so.1.2025.03.1 ../../../lib/libRDKitga.so.1.2025.03.1 ../../../lib/libRDKitMolEnumerator.so.1.2025.03.1 ../../../lib/libRDKitTautomerQuery.so.1.2025.03.1 ../../../lib/libRDKitMolStandardize.so.1.2025.03.1 ../../../lib/libRDKitChemReactions.so.1.2025.03.1 ../../../lib/libRDKitFingerprints.so.1.2025.03.1 ../../../lib/libRDKitFileParsers.so.1.2025.03.1 ../../../lib/libRDKitChemTransforms.so.1.2025.03.1 ../../../lib/libRDKitDepictor.so.1.2025.03.1 /usr/lib/aarch64-linux-gnu/libcoordgen.so ../../../lib/libRDKitMolAlign.so.1.2025.03.1 ../../../lib/libRDKitMolTransforms.so.1.2025.03.1 ../../../lib/libRDKitEigenSolvers.so.1.2025.03.1 ../../../lib/libRDKitAlignment.so.1.2025.03.1 /usr/lib/aarch64-linux-gnu/libmaeparser.so ../../../lib/libRDKitFilterCatalog.so.1.2025.03.1 ../../../lib/libRDKitSubstructMatch.so.1.2025.03.1 ../../../lib/libRDKitGenericGroups.so.1.2025.03.1 ../../../lib/libRDKitSmilesParse.so.1.2025.03.1 ../../../lib/libRDKitSubgraphs.so.1.2025.03.1 ../../../lib/libRDKitGraphMol.so.1.2025.03.1 ../../../lib/libRDKitRDGeometryLib.so.1.2025.03.1 ../../../lib/libRDKitDataStructs.so.1.2025.03.1 ../../../lib/libRDKitCatalogs.so.1.2025.03.1 ../../../lib/libRDKitRDGeneral.so.1.2025.03.1 /usr/lib/aarch64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl make[4]: Leaving directory '/build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu' -[100%] Built target testSynthonSpaceSubstructureSearch +[100%] Built target testRGroupDecomp [100%] 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' [100%] Built target rdSynthonSpaceSearch -[100%] Linking CXX executable testRGroupDecomp -cd /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/RGroupDecomposition && /usr/bin/cmake -E cmake_link_script CMakeFiles/testRGroupDecomp.dir/link.txt --verbose=1 -/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/testRGroupDecomp.dir/link.d CMakeFiles/testRGroupDecomp.dir/testRGroupDecomp.cpp.o -o testRGroupDecomp ../../../lib/libRDKitRGroupDecomposition.so.1.2025.03.1 ../../../lib/libRDKitFMCS.so.1.2025.03.1 ../../../lib/libRDKitga.so.1.2025.03.1 ../../../lib/libRDKitMolEnumerator.so.1.2025.03.1 ../../../lib/libRDKitTautomerQuery.so.1.2025.03.1 ../../../lib/libRDKitMolStandardize.so.1.2025.03.1 ../../../lib/libRDKitChemReactions.so.1.2025.03.1 ../../../lib/libRDKitFingerprints.so.1.2025.03.1 ../../../lib/libRDKitFileParsers.so.1.2025.03.1 ../../../lib/libRDKitChemTransforms.so.1.2025.03.1 ../../../lib/libRDKitDepictor.so.1.2025.03.1 /usr/lib/aarch64-linux-gnu/libcoordgen.so ../../../lib/libRDKitMolAlign.so.1.2025.03.1 ../../../lib/libRDKitMolTransforms.so.1.2025.03.1 ../../../lib/libRDKitEigenSolvers.so.1.2025.03.1 ../../../lib/libRDKitAlignment.so.1.2025.03.1 /usr/lib/aarch64-linux-gnu/libmaeparser.so ../../../lib/libRDKitFilterCatalog.so.1.2025.03.1 ../../../lib/libRDKitSubstructMatch.so.1.2025.03.1 ../../../lib/libRDKitGenericGroups.so.1.2025.03.1 ../../../lib/libRDKitSmilesParse.so.1.2025.03.1 ../../../lib/libRDKitSubgraphs.so.1.2025.03.1 ../../../lib/libRDKitGraphMol.so.1.2025.03.1 ../../../lib/libRDKitRDGeometryLib.so.1.2025.03.1 ../../../lib/libRDKitDataStructs.so.1.2025.03.1 ../../../lib/libRDKitCatalogs.so.1.2025.03.1 ../../../lib/libRDKitRDGeneral.so.1.2025.03.1 /usr/lib/aarch64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl +[100%] Linking CXX executable testSynthonSpaceSubstructureSearch +cd /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/SynthonSpaceSearch && /usr/bin/cmake -E cmake_link_script CMakeFiles/testSynthonSpaceSubstructureSearch.dir/link.txt --verbose=1 +/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' -[100%] Built target testRGroupDecomp +[100%] Built target testSynthonSpaceSubstructureSearch [100%] Linking CXX shared module ../../../../rdkit/Chem/rdSubstructLibrary.so cd /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/SubstructLibrary/Wrap && /usr/bin/cmake -E cmake_link_script CMakeFiles/rdSubstructLibrary.dir/link.txt --verbose=1 /usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -g -fwrapv -O2 -Wl,--dependency-file=CMakeFiles/rdSubstructLibrary.dir/link.d -Wl,-z,relro -Wl,-z,now -shared -o ../../../../rdkit/Chem/rdSubstructLibrary.so CMakeFiles/rdSubstructLibrary.dir/rdSubstructLibrary.cpp.o CMakeFiles/rdSubstructLibrary.dir/SubstructLibraryWrap.cpp.o ../../../../lib/libRDKitSubstructLibrary.so.1.2025.03.1 ../../../../lib/libRDKitRDBoost.so.1.2025.03.1 ../../../../lib/libRDKitGeneralizedSubstruct.so.1.2025.03.1 ../../../../lib/libRDKitMolEnumerator.so.1.2025.03.1 ../../../../lib/libRDKitTautomerQuery.so.1.2025.03.1 ../../../../lib/libRDKitMolStandardize.so.1.2025.03.1 ../../../../lib/libRDKitChemReactions.so.1.2025.03.1 ../../../../lib/libRDKitFileParsers.so.1.2025.03.1 /usr/lib/aarch64-linux-gnu/libmaeparser.so ../../../../lib/libRDKitFilterCatalog.so.1.2025.03.1 ../../../../lib/libRDKitChemTransforms.so.1.2025.03.1 ../../../../lib/libRDKitDepictor.so.1.2025.03.1 /usr/lib/aarch64-linux-gnu/libcoordgen.so ../../../../lib/libRDKitMolAlign.so.1.2025.03.1 ../../../../lib/libRDKitMolTransforms.so.1.2025.03.1 ../../../../lib/libRDKitEigenSolvers.so.1.2025.03.1 ../../../../lib/libRDKitAlignment.so.1.2025.03.1 ../../../../lib/libRDKitFingerprints.so.1.2025.03.1 ../../../../lib/libRDKitSubgraphs.so.1.2025.03.1 ../../../../lib/libRDKitSubstructMatch.so.1.2025.03.1 ../../../../lib/libRDKitGenericGroups.so.1.2025.03.1 ../../../../lib/libRDKitSmilesParse.so.1.2025.03.1 ../../../../lib/libRDKitGraphMol.so.1.2025.03.1 ../../../../lib/libRDKitRDGeometryLib.so.1.2025.03.1 ../../../../lib/libRDKitCatalogs.so.1.2025.03.1 ../../../../lib/libRDKitDataStructs.so.1.2025.03.1 /usr/lib/aarch64-linux-gnu/libboost_numpy313.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_python313.so.1.83.0 ../../../../lib/libRDKitRDGeneral.so.1.2025.03.1 /usr/lib/aarch64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl @@ -12987,7 +13018,7 @@ 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 @@ -15204,36 +15235,47 @@ 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: [02:19:03] Testing Github940: property dictionaries leaking memory -3: [02:19:03] done +3: [11:05:59] Testing Github940: property dictionaries leaking memory +3: [11:05:59] done 3: Testing RDValue 3: Testing RDAny 3: dict set int vect 3: dict get int vect -3: static boost any:0.000645 s -3: dynamic boost any:0.002973 s -3: static RDAny:0.000375 s -3: dynamic RDAny:0.002903 s +3: static boost any:0.000646 s +3: dynamic boost any:0.003025 s +3: static RDAny:0.000366 s +3: dynamic RDAny:0.002953 s 3: static RDValue:1e-06 s -3: dynamic RDValue:0.00045 s +3: dynamic RDValue:0.000451 s +3: deleted! +3: [11:05:59] ------------------------------------- +3: [11:05:59] Testing String Pickle Roundtrips. +3: [11:05:59] done +3: [11:05:59] ------------------------------------- +3: [11:05:59] Testing conversion of vect to string. +3: [11:05:59] done +3: [11:05:59] ------------------------------------- +3: [11:05:59] Testing returning const references. +3: [11:05:59] any cast +3: [11:05:59] done: 0.002465 300000 +3: [11:05:59] copy +3: [11:05:59] done: 0.002477 300000 +3: [11:05:59] ref +3: [11:05:59] done: 0.002489 300000 +3: [11:05:59] dict +3: [11:05:59] done: 0.006183 300000 +3: [11:05:59] ref with hasVal +3: [11:05:59] done: 0.003936 300000 +3: [11:05:59] done +3: [11:05:59] ------------------------------------- +3: [11:05:59] Testing dict update. +3: [11:05:59] done +3: deleted! +3: deleted! +3: deleted! +3: deleted! +3: deleted! 3: deleted! -3: [02:19:03] ------------------------------------- -3: [02:19:03] Testing String Pickle Roundtrips. -3: [02:19:03] done -3: [02:19:03] ------------------------------------- -3: [02:19:03] Testing conversion of vect to string. -3: [02:19:03] done -3: [02:19:03] ------------------------------------- -3: [02:19:03] Testing returning const references. -3: [02:19:03] any cast -3: [02:19:03] done: 0.002477 300000 -3: [02:19:03] copy -3: [02:19:03] done: 0.002608 300000 -3: [02:19:03] ref -3: [02:19:03] done: 0.002598 300000 -3: [02:19:03] dict -3: [02:19:03] done: 0.005935 300000 -3: [02:19:03] ref with hasVal 4: -- running tests -- 4: min: -2147483648 -2147483648 4: min: 0 0 @@ -15246,48 +15288,48 @@ 4: == unsigned int 4: == bool 4: == std::string -5: [02:19:03] +5: [11:05:59] 5: ----------------------------------------- -5: [02:19:03] Finished: testPushAndPop() -5: [02:19:03] +5: [11:05:59] Finished: testPushAndPop() +5: [11:05:59] 5: ----------------------------------------- -5: [02:19:03] +5: [11:05:59] 5: ----------------------------------------- -6: Randomness seeded to: 198666950 +6: Randomness seeded to: 4259170493 6: =============================================================================== 6: All tests passed (32 assertions in 2 test cases) 6: -7: [02:19:03] should not be silent -7: [02:19:03] should not be silent -7: Randomness seeded to: 1900715104 -7: [02:19:03] should not be silent -7: [02:19:03] should not be silent -7: [02:19:03] should not be silent -7: [02:19:03] should not be silent -7: [02:19:03] should not be silent -7: [02:19:03] should not be silent -7: [02:19:03] should not be silent -7: [02:19:03] should not be silent +7: [11:05:59] should not be silent +7: [11:05:59] should not be silent +7: Randomness seeded to: 3053627737 +7: [11:05:59] should not be silent +7: [11:05:59] should not be silent +7: [11:05:59] should not be silent +7: [11:05:59] should not be silent +7: [11:05:59] should not be silent +7: [11:05:59] should not be silent +7: [11:05:59] should not be silent +7: [11:05:59] should not be silent 7: =============================================================================== 7: All tests passed (26 assertions in 3 test cases) 7: -8: [02:19:03] pass -8: [02:19:03] v3 4 -8: [02:19:03] v4 5 -8: [02:19:03] SPARSE ----------------------------------- -8: [02:19:03] Set 10: 0 -8: [02:19:03] Set 11: 0 -8: [02:19:03] Set 14: 0 -8: [02:19:03] Set 10: 1 -8: [02:19:03] Get 14: 1 -8: [02:19:03] Num: 20 -8: [02:19:03] NumOn: 3 -8: [02:19:03] NumOff: 17 +8: [11:05:59] pass +8: [11:05:59] v3 4 +8: [11:05:59] v4 5 +8: [11:05:59] SPARSE ----------------------------------- +8: [11:05:59] Set 10: 0 +8: [11:05:59] Set 11: 0 +8: [11:05:59] Set 14: 0 +8: [11:05:59] Set 10: 1 +8: [11:05:59] Get 14: 1 +8: [11:05:59] Num: 20 +8: [11:05:59] NumOn: 3 +8: [11:05:59] NumOff: 17 8: 10, 11, 14, -8: [02:19:03] t2[19]: 0 -8: [02:19:03] t2[14]: 1 -8: [02:19:03] t2[19]: 0 -8: [02:19:03] t2[14]: 0 +8: [11:05:59] t2[19]: 0 +8: [11:05:59] t2[14]: 1 +8: [11:05:59] t2[19]: 0 +8: [11:05:59] t2[14]: 0 8: t1: 10, 11, 14, 8: t2: 10, 11, 15, 17, 8: t1|t2: 10, 11, 14, 15, 17, @@ -15295,20 +15337,20 @@ 8: t1^t2: 14, 15, 17, 8: ~t1: 0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 12, 13, 15, 16, 17, 18, 19, 8: except -8: [02:19:03] Explicit ---------------------------------- -8: [02:19:03] Set 10: 0 -8: [02:19:03] Set 11: 0 -8: [02:19:03] Set 14: 0 -8: [02:19:03] Set 10: 1 -8: [02:19:03] Get 14: 1 -8: [02:19:03] Num: 20 -8: [02:19:03] NumOn: 3 -8: [02:19:03] NumOff: 17 +8: [11:05:59] Explicit ---------------------------------- +8: [11:05:59] Set 10: 0 +8: [11:05:59] Set 11: 0 +8: [11:05:59] Set 14: 0 +8: [11:05:59] Set 10: 1 +8: [11:05:59] Get 14: 1 +8: [11:05:59] Num: 20 +8: [11:05:59] NumOn: 3 +8: [11:05:59] NumOff: 17 8: 10, 11, 14, -8: [02:19:03] t2[19]: 0 -8: [02:19:03] t2[14]: 1 -8: [02:19:03] t2[19]: 0 -8: [02:19:03] t2[14]: 0 +8: [11:05:59] t2[19]: 0 +8: [11:05:59] t2[14]: 1 +8: [11:05:59] t2[19]: 0 +8: [11:05:59] t2[14]: 0 8: t1: 10, 11, 14, 8: t2: 10, 11, 15, 17, 8: t1|t2: 10, 11, 14, 15, 17, @@ -15316,50 +15358,44 @@ 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: [02:19:03] Done -8: [02:19:03] Test DiscreteValue Vectors 1 ---------------------------- -8: [02:19:03] Expected failure: Value out of range -8: [02:19:03] Expected failure: Value out of range -8: [02:19:03] Expected failure: Value out of range -8: [02:19:03] Expected failure: Value out of range -8: [02:19:03] Expected failure: Value out of range -8: [02:19:03] Test DiscreteValue Vectors 2 ------------------------------ -8: [02:19:03] Test DiscreteValue Vectors 3 --------------------------- -8: [02:19:03] Test DiscreteValue Operations ----------------------------- -8: [02:19:03] Test DiscreteValue Operations 2 -------------------------- -8: [02:19:03] Test SparseIntVect ------------------------------------ -8: [02:19:03] Test SparseIntVect Serialization -------------------------- -8: [02:19:03] Test BitVect Serialization ------------------------------- -8: [02:19:03] Test BitVect to FPS ------------------------------- -8: [02:19:03] Test BitVect to binary string ------------------------------- -8: [02:19:03] Test Similarity Measures BitVect ------------------------------- -8: [02:19:03] Test Similarity Measures SparseBitVect ------------------------------- -8: [02:19:03] Test BitVect with all ones ------------------------------- -8: [02:19:03] Test Explicit BitVects: Concatenation Operation ------------------------------- -8: [02:19:03] Test bitmap operations ------------------------------- -8: [02:19:03] Test bitmaps as properties ------------------------------- -8: [02:19:03] Test #3944: SparseIntVect copy constructor and assignment operators not clearing existing data------------------------------- -8: [02:19:03] Test RealValue Vectors 1: Constructors and Accessing Values ------------------------------- -8: [02:19:03] Test RealValue Vectors 2: L1Norm ------------------------------- -8: [02:19:03] Test RealValue Vectors 3: Pickles ------------------------------- -8: [02:19:03] Test RealValue Vectors 4: Vector Operations ------------------------------- - 1/238 Test #4: testRDValue ............................ Passed 0.03 sec - 2/238 Test #6: dictTestsCatch ......................... Passed 0.02 sec - 3/238 Test #7: logTestsCatch .......................... Passed 0.02 sec - 4/238 Test #8: testDataStructs ........................ Passed 0.02 sec -3: [02:19:03] done: 0.003833 300000 -3: [02:19:03] done -3: [02:19:03] ------------------------------------- -3: [02:19:03] Testing dict update. -3: [02:19:03] done -3: deleted! -3: deleted! -3: deleted! -3: deleted! -3: deleted! -3: deleted! - 5/238 Test #3: testDict ............................... Passed 0.03 sec - 6/238 Test #9: testFPB ................................ Passed 0.02 sec +8: [11:05:59] Done +8: [11:05:59] Test DiscreteValue Vectors 1 ---------------------------- +8: [11:05:59] Expected failure: Value out of range +8: [11:05:59] Expected failure: Value out of range +8: [11:05:59] Expected failure: Value out of range +8: [11:05:59] Expected failure: Value out of range +8: [11:05:59] Expected failure: Value out of range +8: [11:05:59] Test DiscreteValue Vectors 2 ------------------------------ +8: [11:05:59] Test DiscreteValue Vectors 3 --------------------------- +8: [11:05:59] Test DiscreteValue Operations ----------------------------- +8: [11:05:59] Test DiscreteValue Operations 2 -------------------------- +8: [11:05:59] Test SparseIntVect ------------------------------------ +8: [11:05:59] Test SparseIntVect Serialization -------------------------- +8: [11:05:59] Test BitVect Serialization ------------------------------- +8: [11:05:59] Test BitVect to FPS ------------------------------- +8: [11:05:59] Test BitVect to binary string ------------------------------- +8: [11:05:59] Test Similarity Measures BitVect ------------------------------- +8: [11:05:59] Test Similarity Measures SparseBitVect ------------------------------- +8: [11:05:59] Test BitVect with all ones ------------------------------- +8: [11:05:59] Test Explicit BitVects: Concatenation Operation ------------------------------- +8: [11:05:59] Test bitmap operations ------------------------------- +8: [11:05:59] Test bitmaps as properties ------------------------------- +8: [11:05:59] Test #3944: SparseIntVect copy constructor and assignment operators not clearing existing data------------------------------- +8: [11:05:59] Test RealValue Vectors 1: Constructors and Accessing Values ------------------------------- +8: [11:05:59] Test RealValue Vectors 2: L1Norm ------------------------------- +8: [11:05:59] Test RealValue Vectors 3: Pickles ------------------------------- +8: [11:05:59] Test RealValue Vectors 4: Vector Operations ------------------------------- + 1/238 Test #3: testDict ............................... Passed 0.04 sec + 2/238 Test #4: testRDValue ............................ Passed 0.04 sec + 3/238 Test #6: dictTestsCatch ......................... Passed 0.03 sec + 4/238 Test #7: logTestsCatch .......................... Passed 0.03 sec + 5/238 Test #8: testDataStructs ........................ Passed 0.03 sec +11: Randomness seeded to: 2824097974 +11: =============================================================================== +11: All tests passed (3 assertions in 1 test case) +11: + 6/238 Test #11: catchDataStructs ....................... Passed 0.02 sec + 7/238 Test #9: testFPB ................................ Passed 0.03 sec test 13 Start 13: pyDiscreteValueVect @@ -15396,12 +15432,13 @@ 18: Test command: /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/Geometry/testGrid 18: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/Geometry 18: Test timeout computed to be: 1500 -11: Randomness seeded to: 2331846185 -11: =============================================================================== -11: All tests passed (3 assertions in 1 test case) -11: - 7/238 Test #11: catchDataStructs ....................... Passed 0.03 sec - 8/238 Test #10: testMultiFPB ........................... Passed 0.03 sec +test 19 + Start 19: testRealValueGrid + +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 + 8/238 Test #10: testMultiFPB ........................... Passed 0.06 sec 1: core 1: RDKit 2D 1: @@ -15568,6 +15605,12 @@ 1: 10 1 1 0 1: M END 1: +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 1: core+sidechain 1: RDKit 2D 1: @@ -15795,18 +15838,6 @@ 1: 5 7 1 0 1: M END 1: -test 19 - Start 19: testRealValueGrid - -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 -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 1: templated 1: RDKit 2D 1: @@ -15879,8 +15910,8 @@ 17: testPointOps2D 17: **************************************** 17: test12D -17: ref1: 1.42652 2.5567 ref2: 0.101864 1.5044 -17: pt1: 0.114511 1.67276 pt2: 2.79798 2.03038 +17: ref1: 3.97439 3.18682 ref2: 1.42617 3.87136 +17: pt1: 2.04663 3.7983 pt2: 1.24704 0.00116718 17: **************************************** 17: test23D 17: **************************************** @@ -15895,7 +15926,7 @@ 17: **************************************** 17: testFromQuaternion 17: **************************************** - 9/238 Test #17: testTransforms ......................... Passed 0.03 sec + 9/238 Test #17: testTransforms ......................... Passed 0.04 sec test 21 Start 21: testPyGeometry @@ -15919,41 +15950,24 @@ 18: --------------------------------- 18: testUniformGridIndexing 18: - 10/238 Test #18: testGrid ............................... Passed 0.04 sec -20: Randomness seeded to: 1684044956 +20: Randomness seeded to: 1424707884 20: =============================================================================== 20: All tests passed (50 assertions in 5 test cases) 20: + 10/238 Test #18: testGrid ............................... Passed 0.05 sec + 11/238 Test #20: geometryTestsCatch ..................... Passed 0.03 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 - 11/238 Test #20: geometryTestsCatch ..................... Passed 0.02 sec -22: [02:19:03] ----------------------------------------- -22: [02:19:03] Testing RDNumerics: vectors and matrices Code -22: [02:19:03] --------------------------------------- -22: [02:19:03] test1Vector 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: [02:19:03] --------------------------------------- -22: [02:19:03] test2Matrix -22: [02:19:03] --------------------------------------- -22: [02:19:03] test3SquareMatrix -22: [02:19:03] --------------------------------------- -22: [02:19:03] test4SymmMatrix - 12/238 Test #22: testMatrices ........................... Passed 0.01 sec -test 24 - Start 24: testAlignment - -24: Test command: /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/Numerics/Alignment/testAlignment -24: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/Numerics/Alignment -24: Test timeout computed to be: 1500 19: *********************************************************** 19: Testing RealValueGrid3D 19: --------------------------------- @@ -15968,6 +15982,34 @@ 19: --------------------------------- 19: test4UniformRealValueGrid3DOps 19: +22: [11:05:59] ----------------------------------------- +22: [11:05:59] Testing RDNumerics: vectors and matrices Code +22: [11:05:59] --------------------------------------- +22: [11:05:59] test1Vector +22: [11:05:59] --------------------------------------- +22: [11:05:59] test2Matrix +22: [11:05:59] --------------------------------------- +22: [11:05:59] test3SquareMatrix +22: [11:05:59] --------------------------------------- +22: [11:05:59] test4SymmMatrix + 12/238 Test #19: testRealValueGrid ...................... Passed 0.05 sec + 13/238 Test #22: testMatrices ........................... Passed 0.01 sec +test 24 + Start 24: testAlignment + +24: Test command: /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/Numerics/Alignment/testAlignment +24: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/Numerics/Alignment +24: Test timeout computed to be: 1500 +test 25 + Start 25: pyAlignment + +25: Test command: /usr/bin/python3 "/build/reproducible-path/rdkit-202503.1/Code/Numerics/Alignment/Wrap/testAlignment.py" +25: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/Numerics/Alignment/Wrap +25: Test timeout computed to be: 1500 +23: Randomness seeded to: 2083867192 +23: =============================================================================== +23: All tests passed (76 assertions in 3 test cases) +23: 24: ----------------------------------------- 24: Testing Alignment Code 24: --------------------------------------- @@ -15979,25 +16021,14 @@ 24: --------------------------------------- 24: testReflection 24: --------------------------------------- - 13/238 Test #19: testRealValueGrid ...................... Passed 0.05 sec -test 25 - Start 25: pyAlignment - -25: Test command: /usr/bin/python3 "/build/reproducible-path/rdkit-202503.1/Code/Numerics/Alignment/Wrap/testAlignment.py" -25: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/Numerics/Alignment/Wrap -25: Test timeout computed to be: 1500 - 14/238 Test #24: testAlignment .......................... Passed 0.02 sec + 14/238 Test #23: testConrec ............................. Passed 0.02 sec + 15/238 Test #24: testAlignment .......................... Passed 0.01 sec test 26 Start 26: testOptimizer 26: Test command: /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/Numerics/Optimizer/testOptimizer 26: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/Numerics/Optimizer 26: Test timeout computed to be: 1500 -23: Randomness seeded to: 2804141433 -23: =============================================================================== -23: All tests passed (76 assertions in 3 test cases) -23: - 15/238 Test #23: testConrec ............................. Passed 0.03 sec test 27 Start 27: ForceFieldsCatch @@ -16017,6 +16048,10 @@ 28: Test command: /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/ForceField/UFF/testUFFForceField 28: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/ForceField/UFF 28: Test timeout computed to be: 1500 +27: Randomness seeded to: 889101841 +27: =============================================================================== +27: All tests passed (20 assertions in 2 test cases) +27: 28: ------------------------------------- 28: Unit tests for force field basics. 28: done @@ -16063,10 +16098,6 @@ 28: done 28: ------------------------------------- 28: Unit tests for all UFF constraint terms. -27: Randomness seeded to: 2318727772 -27: =============================================================================== -27: All tests passed (20 assertions in 2 test cases) -27: 17/238 Test #27: ForceFieldsCatch ....................... Passed 0.03 sec test 29 Start 29: testMMFFForceField @@ -16074,14 +16105,6 @@ 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 -29: ------------------------------------- -29: Official MMFF validation suite. -28: done -28: ------------------------------------- -28: Unit tests for copying UFF ForceFields. -28: done -28: ------------------------------------- -28: Unit test for UFF butane scan. 1: cyclosporine a 1: RDKit 2D 1: @@ -16322,6 +16345,11 @@ 1: 9 10 1 0 1: M END 1: +29: ------------------------------------- +29: Official MMFF validation suite. +28: done +28: ------------------------------------- +28: Unit tests for copying UFF ForceFields. 1: admntn 1: RDKit 2D 1: @@ -16350,6 +16378,9 @@ 1: 10 2 1 0 1: M END 1: +28: done +28: ------------------------------------- +28: Unit test for UFF butane scan. 1: github 4845 - nan coordinates but no crash 1: RDKit 2D 1: @@ -16442,7 +16473,7 @@ 1: 30 11 1 0 1: M END 1: - 18/238 Test #1: testCoordGen ........................... Passed 0.21 sec + 18/238 Test #1: testCoordGen ........................... Passed 0.24 sec test 30 Start 30: pyForceFieldConstraints @@ -16451,6 +16482,11 @@ 30: Test timeout computed to be: 1500 29: 29: Computing MMFF94 energies for /build/reproducible-path/rdkit-202503.1/Code/ForceField/MMFF/test_data/MMFF94_dative.sdf... +13: ...... +13: ---------------------------------------------------------------------- +13: Ran 6 tests in 0.008s +13: +13: OK 14: ...... 14: ---------------------------------------------------------------------- 14: Ran 6 tests in 0.001s @@ -16458,39 +16494,28 @@ 14: OK 15: ......... 15: ---------------------------------------------------------------------- -15: Ran 9 tests in 0.006s +15: Ran 9 tests in 0.005s 15: 15: OK -25: ..... -25: ---------------------------------------------------------------------- -25: Ran 5 tests in 0.001s -25: -25: OK -25: Testing Alignment Wrapper code: -13: ...... -13: ---------------------------------------------------------------------- -13: Ran 6 tests in 0.012s -13: -13: OK 28: done - 19/238 Test #28: testUFFForceField ...................... Passed 0.16 sec + 19/238 Test #28: testUFFForceField ...................... Passed 0.17 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 +25: ..... +25: ---------------------------------------------------------------------- +25: Ran 5 tests in 0.002s +25: +25: OK +25: Testing Alignment Wrapper code: 16: ......... 16: ---------------------------------------------------------------------- -16: Ran 9 tests in 0.022s +16: Ran 9 tests in 0.032s 16: 16: OK -21: .................... -21: ---------------------------------------------------------------------- -21: Ran 20 tests in 0.024s -21: -21: OK -21: Testing Geometry wrapper 31: *********************************************************** 31: test1 31: *********************************************************** @@ -16502,63 +16527,67 @@ 31: 1 1 1 0 31: *********************************************************** 31: - 20/238 Test #31: testDistGeom ........................... Passed 0.01 sec + 20/238 Test #31: testDistGeom ........................... Passed 0.03 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 - 21/238 Test #14: pyRealValueVect ........................ Passed 0.27 sec +21: .................... +21: ---------------------------------------------------------------------- +21: Ran 20 tests in 0.027s +21: +21: OK +21: Testing Geometry wrapper + 21/238 Test #13: pyDiscreteValueVect .................... Passed 0.31 sec + 22/238 Test #15: pySparseIntVect ........................ Passed 0.30 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 - 22/238 Test #15: pySparseIntVect ........................ Passed 0.27 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 -33: -33: -33: -33: COPY - 23/238 Test #33: graphmolcpTest ......................... Passed 0.01 sec + 23/238 Test #25: pyAlignment ............................ Passed 0.23 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 - 24/238 Test #13: pyDiscreteValueVect .................... Passed 0.29 sec - 25/238 Test #25: pyAlignment ............................ Passed 0.21 sec +2: .... +2: ---------------------------------------------------------------------- +2: Ran 4 tests in 0.016s +2: +2: OK +33: +33: +33: +33: COPY +34: [11:05:59] ---------------------- Test1 + 24/238 Test #14: pyRealValueVect ........................ Passed 0.32 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 -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 -34: [02:19:03] ---------------------- Test1 -34: [02:19:03] Done! -34: [02:19:03] ---------------------- Test2 -34: [02:19:03] Done! -34: [02:19:03] ---------------------- Test3 -34: [02:19:03] Done! -34: [02:19:03] ---------------------- Test4 -34: [02:19:03] Done! -34: [02:19:03] ---------------------- Test5 -34: [02:19:03] Done! -34: [02:19:03] +34: [11:05:59] Done! +34: [11:05:59] ---------------------- Test2 +34: [11:05:59] Done! +34: [11:05:59] ---------------------- Test3 +34: [11:05:59] Done! +34: [11:05:59] ---------------------- Test4 +34: [11:05:59] Done! +34: [11:05:59] ---------------------- Test5 +34: [11:05:59] Done! +34: [11:05:59] 34: 34: **** 34: Pre-condition Violation @@ -16570,55 +16599,62 @@ 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# 0x0000AAAAC3B63610 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/graphmolqueryTest -34: 4# 0x0000AAAAC3B60A88 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/graphmolqueryTest -34: 5# 0x0000FFFF971D229C in /lib/aarch64-linux-gnu/libc.so.6 +34: 3# 0x0000AAAAEAA23610 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/graphmolqueryTest +34: 4# 0x0000AAAAEAA20A88 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/graphmolqueryTest +34: 5# 0x0000FFFF946E229C in /lib/aarch64-linux-gnu/libc.so.6 34: 6# __libc_start_main in /lib/aarch64-linux-gnu/libc.so.6 -34: 7# 0x0000AAAAC3B60B70 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/graphmolqueryTest +34: 7# 0x0000AAAAEAA20B70 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/graphmolqueryTest 34: ---------- 34: **** 34: -34: [02:19:03] Done! -34: [02:19:03] ---------------------- Test issue 2892580 -34: [02:19:03] Done! -34: [02:19:03] ---------------------- Test github issue 53: query molecules not matching [R] -34: [02:19:03] Done! -34: [02:19:03] ---------------------- Test queries using qualifiers instead of == -34: [02:19:03] Done! -34: [02:19:03] ---------------------- Test Github issue 165: radicals not used in atom-atom matching -34: [02:19:03] Done! -34: [02:19:03] ---------------------- Test extra atom queries -34: [02:19:03] Done! -34: [02:19:03] ---------------------- Test extra bond queries -34: [02:19:03] Done! -34: [02:19:03] ---------------------- Test num heteroatom neighbor queries -34: [02:19:03] Done! -34: [02:19:03] ---------------------- Test atom type queries -34: [02:19:03] Done! -34: [02:19:03] ---------------------- Test Github #2471: dummy atom queries are flagged as complex -34: [02:19:03] Done! -34: [02:19:03] ---------------------- Testing hasBondTypeQuery() and hasComplexBondTypeQuery() -34: [02:19:03] Done! - 26/238 Test #21: testPyGeometry ......................... Passed 0.26 sec +34: [11:05:59] Done! +34: [11:05:59] ---------------------- Test issue 2892580 +34: [11:05:59] Done! +34: [11:05:59] ---------------------- Test github issue 53: query molecules not matching [R] +34: [11:05:59] Done! +34: [11:05:59] ---------------------- Test queries using qualifiers instead of == +34: [11:05:59] Done! +34: [11:05:59] ---------------------- Test Github issue 165: radicals not used in atom-atom matching +34: [11:05:59] Done! +34: [11:05:59] ---------------------- Test extra atom queries +34: [11:05:59] Done! +34: [11:05:59] ---------------------- Test extra bond queries +34: [11:05:59] Done! +34: [11:05:59] ---------------------- Test num heteroatom neighbor queries +34: [11:05:59] Done! +34: [11:05:59] ---------------------- Test atom type queries +34: [11:05:59] Done! +34: [11:05:59] ---------------------- Test Github #2471: dummy atom queries are flagged as complex +34: [11:05:59] Done! +34: [11:05:59] ---------------------- Testing hasBondTypeQuery() and hasComplexBondTypeQuery() +34: [11:05:59] Done! + 25/238 Test #34: graphmolqueryTest ...................... Passed 0.03 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 + 26/238 Test #21: testPyGeometry ......................... Passed 0.29 sec + 27/238 Test #33: graphmolcpTest ......................... Passed 0.04 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 - 27/238 Test #34: graphmolqueryTest ...................... Passed 0.02 sec -2: .... -2: ---------------------------------------------------------------------- -2: Ran 4 tests in 0.018s -2: -2: OK - 28/238 Test #16: pyFPB .................................. Passed 0.30 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 +36: -------------------------- +36: -------------------------- +36: C/C=C/C(C)Cl +37: [11:05:59] ------------------------------------- +37: [11:05:59] Testing String Pickle Roundtrips. + 28/238 Test #16: pyFPB .................................. Passed 0.35 sec test 40 Start 40: hanoiTest @@ -16629,130 +16665,91 @@ 35: 1 1 1 35: 2 1 0.75 35: path: 2 -35: [02:19:03] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 10 ignored -35: [02:19:03] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 10 ignored -36: -------------------------- -36: -------------------------- -36: C/C=C/C(C)Cl -35: [02:19:03] Explicit valence for atom # 0 B, 5, is greater than permitted -35: [02:19:03] Explicit valence for atom # 1 C, 5, is greater than permitted -35: [02:19:03] Explicit valence for atom # 1 C, 5, is greater than permitted -35: [02:19:03] Explicit valence for atom # 1 C, 5, is greater than permitted -35: [02:19:03] Explicit valence for atom # 1 Si, 7, is greater than permitted -37: [02:19:03] ------------------------------------- -37: [02:19:03] Testing String Pickle Roundtrips. -38: [02:19:03] done - 29/238 Test #38: graphmoltestPicklerGlobalSetting ....... Passed 0.02 sec +36: [11:05:59] Conflicting single bond directions around double bond at index 2. +36: [11:05:59] BondStereo set to STEREONONE and single bond directions set to NONE. +36: [11:05:59] Conflicting single bond directions around double bond at index 4. +36: [11:05:59] BondStereo set to STEREONONE and single bond directions set to NONE. +36: [11:05:59] Conflicting single bond directions around double bond at index 15. +36: [11:05:59] BondStereo set to STEREONONE and single bond directions set to NONE. +36: [11:05:59] Conflicting single bond directions around double bond at index 2. +36: [11:05:59] BondStereo set to STEREONONE and single bond directions set to NONE. +36: [11:05:59] Conflicting single bond directions around double bond at index 1. +36: [11:05:59] BondStereo set to STEREONONE and single bond directions set to NONE. + 29/238 Test #2: pyCoordGen ............................. Passed 0.41 sec test 41 Start 41: graphmolMemTest1 41: Test command: /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/graphmolMemTest1 41: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol 41: Test timeout computed to be: 1500 - 30/238 Test #39: graphmolIterTest ....................... Passed 0.02 sec +35: [11:05:59] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 10 ignored +35: [11:05:59] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 10 ignored +38: [11:05:59] done + 30/238 Test #38: graphmoltestPicklerGlobalSetting ....... Passed 0.02 sec +36: -------------------------------------------------- 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: [02:19:03] Testing the hanoi sort -40: [02:19:03] populating vectors - 31/238 Test #41: graphmolMemTest1 ....................... Passed 0.02 sec +35: [11:05:59] Explicit valence for atom # 0 B, 5, is greater than permitted +35: [11:05:59] Explicit valence for atom # 1 C, 5, is greater than permitted +35: [11:05:59] Explicit valence for atom # 1 C, 5, is greater than permitted +35: [11:05:59] Explicit valence for atom # 1 C, 5, is greater than permitted +35: [11:05:59] Explicit valence for atom # 1 Si, 7, is greater than permitted + 31/238 Test #36: graphmoltestChirality .................. Passed 0.04 sec test 43 Start 43: molBundleTest 43: Test command: /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/molBundleTest 43: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol 43: Test timeout computed to be: 1500 -36: [02:19:03] Conflicting single bond directions around double bond at index 2. -36: [02:19:03] BondStereo set to STEREONONE and single bond directions set to NONE. -36: [02:19:03] Conflicting single bond directions around double bond at index 4. -36: [02:19:03] BondStereo set to STEREONONE and single bond directions set to NONE. -36: [02:19:03] Conflicting single bond directions around double bond at index 15. -36: [02:19:03] BondStereo set to STEREONONE and single bond directions set to NONE. -36: [02:19:03] Conflicting single bond directions around double bond at index 2. -36: [02:19:03] BondStereo set to STEREONONE and single bond directions set to NONE. -36: [02:19:03] Conflicting single bond directions around double bond at index 1. -36: [02:19:03] BondStereo set to STEREONONE and single bond directions set to NONE. - 32/238 Test #2: pyCoordGen ............................. Passed 0.39 sec + 32/238 Test #41: graphmolMemTest1 ....................... Passed 0.01 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 - 33/238 Test #43: molBundleTest .......................... Passed 0.02 sec +40: [11:05:59] Testing the hanoi sort +40: [11:05:59] populating vectors + 33/238 Test #39: graphmolIterTest ....................... Passed 0.03 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 -36: -------------------------------------------------- -37: [02:19:03] done -37: [02:19:03] ------------------------------------- -37: [02:19:03] Testing reading existing pickle file (v2). - 34/238 Test #36: graphmoltestChirality .................. Passed 0.07 sec +37: [11:05:59] done +37: [11:05:59] ------------------------------------- +37: [11:05:59] Testing reading existing pickle file (v2). + 34/238 Test #43: molBundleTest .......................... Passed 0.03 sec test 46 Start 46: graphmolTestsCatch 46: Test command: /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch 46: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol 46: Test timeout computed to be: 1500 -35: smi: Cc1ccc(S(=O)(=O)/N=C2\CC(=N\C(C)(C)C)/C2=N\C(C)(C)C)cc1 - 35/238 Test #45: test-valgrind .......................... Passed 0.01 sec +30: ...[11:05:59] Molecule does not have explicit Hs. Consider calling AddHs() + 35/238 Test #44: testSGroup ............................. Passed 0.04 sec + 36/238 Test #45: test-valgrind .......................... Passed 0.03 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 - 36/238 Test #44: testSGroup ............................. Passed 0.03 sec test 48 Start 48: graphmolSGroupCatch 48: Test command: /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/graphmolSGroupCatch 48: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol 48: Test timeout computed to be: 1500 -46: Randomness seeded to: 3794540237 -46: [02:19:03] WARNING: not removing hydrogen atom without neighbors -46: [02:19:03] WARNING: could not find number of expected rings. Switching to an approximate ring finding algorithm. -46: [02:19:03] WARNING: could not find number of expected rings. Switching to an approximate ring finding algorithm. -46: [02:19:03] WARNING: could not find number of expected rings. Switching to an approximate ring finding algorithm. -46: [02:19:03] WARNING: could not find number of expected rings. Switching to an approximate ring finding algorithm. -46: [02:19:03] WARNING: could not find number of expected rings. Switching to an approximate ring finding algorithm. -35: [02:19:03] non-ring atom 0 marked aromatic -35: [02:19:03] non-ring atom 0 marked aromatic -46: [02:19:03] Explicit valence for atom # 1 N, 5, is greater than permitted -46: [02:19:03] Explicit valence for atom # 1 N, 6, is greater than permitted -30: ...[02:19:03] Molecule does not have explicit Hs. Consider calling AddHs() -46: [02:19:03] Explicit valence for atom # 1 N, 5, is greater than permitted -46: [02:19:03] Explicit valence for atom # 1 N, 5, is greater than permitted -46: [02:19:03] Explicit valence for atom # 2 O, 3, is greater than permitted -46: [02:19:03] Explicit valence for atom # 2 O, 3, is greater than permitted -46: [02:19:03] non-ring atom 2 marked aromatic -46: [02:19:03] non-ring atom 2 marked aromatic -46: [02:19:03] Can't kekulize mol. Unkekulized atoms: 0 1 2 3 4 -46: [02:19:03] Can't kekulize mol. Unkekulized atoms: 0 1 2 3 4 -46: [02:19:03] Can't kekulize mol. Unkekulized atoms: 1 2 3 -46: [02:19:03] Can't kekulize mol. Unkekulized atoms: 1 2 3 -46: [02:19:03] Can't kekulize mol. Unkekulized atoms: 0 1 2 -46: [02:19:03] Can't kekulize mol. Unkekulized atoms: 0 1 2 -46: [02:19:03] Explicit valence for atom # 1 O, 3, is greater than permitted -46: [02:19:03] Explicit valence for atom # 4 F, 2, is greater than permitted -46: [02:19:03] Can't kekulize mol. Unkekulized atoms: 6 7 8 -46: [02:19:03] Explicit valence for atom # 1 C, 5, is greater than permitted -46: [02:19:03] WARNING: not removing hydrogen atom with dummy atom neighbors -46: [02:19:03] WARNING: not removing hydrogen atom with dummy atom neighbors -46: [02:19:03] WARNING: not removing hydrogen atom with wedged bond -46: [02:19:03] WARNING: not removing hydrogen atom without neighbors -46: [02:19:03] WARNING: not removing hydrogen atom without neighbors -35: [02:19:03] Conflicting single bond directions around double bond at index 17. -35: [02:19:03] BondStereo set to STEREONONE and single bond directions set to NONE. -37: [02:19:03] done -37: [02:19:03] ------------------------------------- -37: [02:19:03] Testing combining molecules using pickles. +35: smi: Cc1ccc(S(=O)(=O)/N=C2\CC(=N\C(C)(C)C)/C2=N\C(C)(C)C)cc1 +37: [11:05:59] done +37: [11:05:59] ------------------------------------- +37: [11:05:59] 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 @@ -16769,30 +16766,149 @@ 37: 4 4->5 order: 1 37: 5 5->6 order: 1 37: 6 6->3 order: 1 -37: [02:19:03] done -37: [02:19:03] ------------------------------------- -37: [02:19:03] Testing Issue164: Roundtrip Pickle Failure. +37: [11:05:59] done +37: [11:05:59] ------------------------------------- +37: [11:05:59] Testing Issue164: Roundtrip Pickle Failure. +37: [11:05:59] done +37: [11:05:59] ------------------------------------- +37: [11:05:59] Testing Issue219: Pickle Failure with Conformations. +37: [11:05:59] done +37: [11:05:59] ------------------------------------- +37: [11:05:59] Testing Issue220: Pickle problems with bond stereochemistry. +37: [11:05:59] done +37: [11:05:59] ------------------------------------- +37: [11:05:59] Testing query serialization. +37: [11:05:59] C=[$(C=O)] +37: [11:05:59] S(=O)(=O)-[C&H2][F,Br,I,Cl] S(=O)(=O)-[C&H2][F,Br,I,Cl] +37: [11:05:59] done +37: [11:05:59] ------------------------------------- +37: [11:05:59] Testing radical handling in pickles. +37: [11:05:59] done +37: [11:05:59] done +37: [11:05:59] ------------------------------------- +37: [11:05:59] Testing sf.net issue 2788233. +37: [11:05:59] done +37: [11:05:59] ------------------------------------- +37: [11:05:59] Testing sf.net issue 3202580. +37: mass! 13.0034 +37: [11:05:59] done +37: [11:05:59] ------------------------------------- +37: [11:05:59] Testing sf.net issue 3316407. +35: [11:05:59] non-ring atom 0 marked aromatic +37: [11:05:59] done +37: [11:05:59] ------------------------------------- +37: [11:05:59] Testing sf.net issue 3496759. +35: [11:05:59] non-ring atom 0 marked aromatic +37: smi match: *C *C +37: smi match: **=* **=* +37: smi match: [N-]=[N+]=NC=O [N-]=[N+]=NC=O +46: Randomness seeded to: 4164447098 +37: smi match: *OS(=O)OC *OS(=O)OC +37: smi match: *S(=O)(=O)OC *S(=O)(=O)OC +46: [11:05:59] WARNING: not removing hydrogen atom without neighbors +37: smi match: O=COC=O O=COC=O +37: smi match: OO OO +46: [11:05:59] WARNING: could not find number of expected rings. Switching to an approximate ring finding algorithm. +37: smi match: O=COc1c(F)c(F)c(F)c(F)c1F O=COc1c(F)c(F)c(F)c(F)c1F +46: [11:05:59] WARNING: could not find number of expected rings. Switching to an approximate ring finding algorithm. +37: smi match: O=COc1ccc(N(=O)=O)cc1 O=COc1ccc(N(=O)=O)cc1 +46: [11:05:59] WARNING: could not find number of expected rings. Switching to an approximate ring finding algorithm. +37: smi match: nnnOC=O nnnOC=O +37: smi match: *=C=N *=C=N +37: smi match: OS(=O)(=O)C(F)(F)F OS(=O)(=O)C(F)(F)F +37: smi match: SP(S)=S SP(S)=S +37: smi match: NP(N)(N)=O NP(N)(N)=O +37: smi match: cN=[N+]=[N-] cN=[N+]=[N-] +46: [11:05:59] WARNING: could not find number of expected rings. Switching to an approximate ring finding algorithm. +37: smi match: *CC=O *CC=O +37: smi match: NNC=O NNC=O +37: smi match: * * +37: smi match: C=P C=P +37: smi match: CC(=N)Cl CC(=N)Cl +37: smi match: N=O N=O +46: [11:05:59] WARNING: could not find number of expected rings. Switching to an approximate ring finding algorithm. +37: smi match: ** ** +37: smi match: N=C=N N=C=N +37: smi match: [C-]#[NH+] [C-]#[NH+] +37: smi match: O=CON(C=O)C=O O=CON(C=O)C=O +37: smi match: N#CC[OH] N#CC[OH] +37: smi match: N#CC=O N#CC=O +37: smi match: N#CS(=O)=O N#CS(=O)=O +46: [11:05:59] Explicit valence for atom # 1 N, 5, is greater than permitted +46: [11:05:59] Explicit valence for atom # 1 N, 6, is greater than permitted +46: [11:05:59] Explicit valence for atom # 1 N, 5, is greater than permitted +35: [11:05:59] Conflicting single bond directions around double bond at index 17. +35: [11:05:59] BondStereo set to STEREONONE and single bond directions set to NONE. +46: [11:05:59] Explicit valence for atom # 1 N, 5, is greater than permitted +46: [11:05:59] Explicit valence for atom # 2 O, 3, is greater than permitted +46: [11:05:59] Explicit valence for atom # 2 O, 3, is greater than permitted +46: [11:05:59] non-ring atom 2 marked aromatic +46: [11:05:59] non-ring atom 2 marked aromatic +46: [11:05:59] Can't kekulize mol. Unkekulized atoms: 0 1 2 3 4 +46: [11:05:59] Can't kekulize mol. Unkekulized atoms: 0 1 2 3 4 +46: [11:05:59] Can't kekulize mol. Unkekulized atoms: 1 2 3 +46: [11:05:59] Can't kekulize mol. Unkekulized atoms: 1 2 3 +46: [11:05:59] Can't kekulize mol. Unkekulized atoms: 0 1 2 +46: [11:05:59] Can't kekulize mol. Unkekulized atoms: 0 1 2 +46: [11:05:59] Explicit valence for atom # 1 O, 3, is greater than permitted +46: [11:05:59] Explicit valence for atom # 4 F, 2, is greater than permitted +46: [11:05:59] Can't kekulize mol. Unkekulized atoms: 6 7 8 +35: starting ring finding +46: [11:05:59] Explicit valence for atom # 1 C, 5, is greater than permitted +46: [11:05:59] WARNING: not removing hydrogen atom with dummy atom neighbors +46: [11:05:59] WARNING: not removing hydrogen atom with dummy atom neighbors +35: done +46: [11:05:59] WARNING: not removing hydrogen atom with wedged bond +46: [11:05:59] WARNING: not removing hydrogen atom without neighbors +46: [11:05:59] WARNING: not removing hydrogen atom without neighbors +35: starting ring finding +37: smi match: CCOP(=O)(C#N)OCC CCOP(=O)(C#N)OCC +37: smi match: N#CN=N N#CN=N +37: smi match: N=NCC=O N=NCC=O +37: smi match: CCCCCCC CCCCCCC +35: done +37: smi match: OCCOCCO OCCOCCO +37: smi match: SS SS +35: starting ring finding +46: [11:05:59] WARNING: not removing hydrogen atom without neighbors +46: [11:05:59] WARNING: not removing hydrogen atom without neighbors +46: [11:05:59] Unreasonable formal charge on atom # 0. +35: done +37: smi match: [SH] [SH] +35: C/C=N/c1ccc(cc1)c1cc2cc(c1)c1ccc(cc1)N=Cc1ccc(cc1)c1cc(cc(c1)c1ccc(cc1)C)c1ccc(cc1)C=Nc1ccc(cc1)c1cc(cc(c1)c1ccc(cc1)/N=C/C)c1ccc(cc1)N=Cc1ccc(cc1)c1cc(c3ccc(C=Nc4ccc(c5cc6c7ccc(N=Cc8ccc(c9cc(c%10ccc(C=Nc%11ccc2cc%11)cc%10)cc(c9)c2ccc(cc2)C=Nc2ccc(cc2)c2cc(cc(c2)c2ccc(cc2)N=Cc2ccc(cc2)c2cc(cc(c2)c2ccc(cc2)C)c2ccc(cc2)C=Nc2ccc(cc2)c2cc(c9ccc(N=Cc%10ccc(c%11cc(c%12ccc(C=Nc%13ccc(c(c6)c5)cc%13)cc%12)cc(c%11)c5ccc(cc5)C)cc%10)cc9)cc(c2)c2ccc(cc2)/N=C/C)c2ccc(cc2)/N=C/C)cc8)cc7)cc4)cc3)cc(c1)c1ccc(cc1)C +35: starting sanitization +37: smi match: *1CC1 *1CC1 +37: smi match: [OH]ccc([OH])c[OH] [OH]ccc([OH])c[OH] +37: smi match: [OH]cc([OH])c[OH] [OH]cc([OH])c[OH] +37: smi match: NC(=S)N=N NC(=S)N=N +37: smi match: N#CS N#CS +37: smi match: cC[N+] cC[N+] +37: smi match: C*C=S C*C=S 32: ...... 32: ---------------------------------------------------------------------- -32: Ran 6 tests in 0.003s +32: Ran 6 tests in 0.001s +37: smi match: N[CH2]C#N N[CH2]C#N 32: 32: OK -46: [02:19:03] WARNING: not removing hydrogen atom without neighbors -46: [02:19:03] WARNING: not removing hydrogen atom without neighbors -46: [02:19:03] Unreasonable formal charge on atom # 0. -37: [02:19:03] done -48: Randomness seeded to: 3066547698 -48: =============================================================================== -48: All tests passed (136 assertions in 8 test cases) -48: -37: [02:19:03] ------------------------------------- -37: [02:19:03] Testing Issue219: Pickle Failure with Conformations. -46: [02:19:03] +37: smi match: O=C1CCO1 O=C1CCO1 +37: smi match: O=P([OH])OP(=O)[OH] O=P([OH])OP(=O)[OH] +37: smi match: O=C1CCN1 O=C1CCN1 +37: smi match: O=C1C~CC(=O)C~C1 O=C1C~CC(=O)C~C1 +37: smi match: C=CC=CC=CC=C C=CC=CC=CC=C +37: smi match: C1CCC(OC2CCC3CCCCC3C2)OC1 C1CCC(OC2CCC3CCCCC3C2)OC1 +37: smi match: O=C1NCC2CCCCC21 O=C1NCC2CCCCC21 +37: smi match: O=C1CCCC(=O)N1 O=C1CCCC(=O)N1 +37: smi match: C1CCC(C2CCCO2)OC1 C1CCC(C2CCCO2)OC1 +37: smi match: [OH]C1Cc2c([OH])cc([OH])cc2OC1c1ccc([OH])c([OH])c1 [OH]C1Cc2c([OH])cc([OH])cc2OC1c1ccc([OH])c([OH])c1 +37: smi match: C1CC2CCC(O1)O2 C1CC2CCC(O1)O2 +37: smi match: cN(=O)~O cN(=O)~O +37: smi match: *[CH2]N1C(=O)CCC1=O *[CH2]N1C(=O)CCC1=O +37: smi match: N~NC=O N~NC=O +37: smi match: *=N~C *=N~C +37: smi match: CO*(=O)=O CO*(=O)=O +46: [11:05:59] 46: 46: **** -37: [02:19:03] done -37: [02:19:03] ------------------------------------- -37: [02:19:03] Testing Issue220: Pickle problems with bond stereochemistry. 46: Pre-condition Violation 46: no atom 46: Violation occurred on line 181 in file ./Code/GraphMol/ROMol.cpp @@ -16802,25 +16918,22 @@ 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# 0x0000AAAADA46C1A4 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch -46: 4# 0x0000AAAADA4B83CC in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch -46: 5# 0x0000AAAADA4B8D80 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch -46: 6# 0x0000AAAADA4B91B4 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch -46: 7# 0x0000AAAADA48C598 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch -46: 8# 0x0000AAAADA48CAE4 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch -46: 9# 0x0000AAAADA40E090 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch -46: 10# 0x0000FFFFB204229C in /lib/aarch64-linux-gnu/libc.so.6 +46: 3# 0x0000AAAAC3A9C1A4 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch +46: 4# 0x0000AAAAC3AE83CC in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch +46: 5# 0x0000AAAAC3AE8D80 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch +46: 6# 0x0000AAAAC3AE91B4 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch +46: 7# 0x0000AAAAC3ABC598 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch +46: 8# 0x0000AAAAC3ABCAE4 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch +46: 9# 0x0000AAAAC3A3E090 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch +46: 10# 0x0000FFFF8369229C in /lib/aarch64-linux-gnu/libc.so.6 46: 11# __libc_start_main in /lib/aarch64-linux-gnu/libc.so.6 -46: 12# 0x0000AAAADA40E170 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch +46: 12# 0x0000AAAAC3A3E170 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch 46: ---------- 46: **** 46: -37: [02:19:03] done -46: [02:19:03] +46: [11:05:59] 46: 46: **** -37: [02:19:03] ------------------------------------- -37: [02:19:03] Testing query serialization. 46: Pre-condition Violation 46: no owner 46: Violation occurred on line 153 in file ./Code/GraphMol/Atom.h @@ -16830,20 +16943,20 @@ 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# 0x0000AAAADA46C218 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch -46: 4# 0x0000AAAADA4B83CC in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch -46: 5# 0x0000AAAADA4B8D80 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch -46: 6# 0x0000AAAADA4B91B4 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch -46: 7# 0x0000AAAADA48C598 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch -46: 8# 0x0000AAAADA48CAE4 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch -46: 9# 0x0000AAAADA40E090 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch -46: 10# 0x0000FFFFB204229C in /lib/aarch64-linux-gnu/libc.so.6 +46: 3# 0x0000AAAAC3A9C218 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch +46: 4# 0x0000AAAAC3AE83CC in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch +46: 5# 0x0000AAAAC3AE8D80 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch +46: 6# 0x0000AAAAC3AE91B4 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch +46: 7# 0x0000AAAAC3ABC598 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch +46: 8# 0x0000AAAAC3ABCAE4 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch +46: 9# 0x0000AAAAC3A3E090 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch +46: 10# 0x0000FFFF8369229C in /lib/aarch64-linux-gnu/libc.so.6 46: 11# __libc_start_main in /lib/aarch64-linux-gnu/libc.so.6 -46: 12# 0x0000AAAADA40E170 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch +46: 12# 0x0000AAAAC3A3E170 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch 46: ---------- 46: **** 46: -46: [02:19:03] +46: [11:05:59] 46: 46: **** 46: Pre-condition Violation @@ -16855,20 +16968,20 @@ 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# 0x0000AAAADA46C298 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch -46: 4# 0x0000AAAADA4B83CC in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch -46: 5# 0x0000AAAADA4B8D80 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch -46: 6# 0x0000AAAADA4B91B4 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch -46: 7# 0x0000AAAADA48C598 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch -46: 8# 0x0000AAAADA48CAE4 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch -46: 9# 0x0000AAAADA40E090 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch -46: 10# 0x0000FFFFB204229C in /lib/aarch64-linux-gnu/libc.so.6 +46: 3# 0x0000AAAAC3A9C298 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch +46: 4# 0x0000AAAAC3AE83CC in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch +46: 5# 0x0000AAAAC3AE8D80 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch +46: 6# 0x0000AAAAC3AE91B4 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch +46: 7# 0x0000AAAAC3ABC598 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch +46: 8# 0x0000AAAAC3ABCAE4 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch +46: 9# 0x0000AAAAC3A3E090 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch +46: 10# 0x0000FFFF8369229C in /lib/aarch64-linux-gnu/libc.so.6 46: 11# __libc_start_main in /lib/aarch64-linux-gnu/libc.so.6 -46: 12# 0x0000AAAADA40E170 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch +46: 12# 0x0000AAAAC3A3E170 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch 46: ---------- 46: **** 46: -46: [02:19:03] +46: [11:05:59] 46: 46: **** 46: Pre-condition Violation @@ -16880,20 +16993,20 @@ 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# 0x0000AAAADA46C360 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch -46: 4# 0x0000AAAADA4B83CC in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch -46: 5# 0x0000AAAADA4B8D80 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch -46: 6# 0x0000AAAADA4B91B4 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch -46: 7# 0x0000AAAADA48C598 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch -46: 8# 0x0000AAAADA48CAE4 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch -46: 9# 0x0000AAAADA40E090 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch -46: 10# 0x0000FFFFB204229C in /lib/aarch64-linux-gnu/libc.so.6 +46: 3# 0x0000AAAAC3A9C360 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch +46: 4# 0x0000AAAAC3AE83CC in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch +46: 5# 0x0000AAAAC3AE8D80 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch +46: 6# 0x0000AAAAC3AE91B4 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch +46: 7# 0x0000AAAAC3ABC598 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch +46: 8# 0x0000AAAAC3ABCAE4 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch +46: 9# 0x0000AAAAC3A3E090 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch +46: 10# 0x0000FFFF8369229C in /lib/aarch64-linux-gnu/libc.so.6 46: 11# __libc_start_main in /lib/aarch64-linux-gnu/libc.so.6 -46: 12# 0x0000AAAADA40E170 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch +46: 12# 0x0000AAAAC3A3E170 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch 46: ---------- 46: **** 46: -46: [02:19:03] +46: [11:05:59] 46: 46: **** 46: Pre-condition Violation @@ -16905,20 +17018,20 @@ 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# 0x0000AAAADA46C3D8 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch -46: 4# 0x0000AAAADA4B83CC in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch -46: 5# 0x0000AAAADA4B8D80 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch -46: 6# 0x0000AAAADA4B91B4 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch -46: 7# 0x0000AAAADA48C598 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch -46: 8# 0x0000AAAADA48CAE4 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch -46: 9# 0x0000AAAADA40E090 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch -46: 10# 0x0000FFFFB204229C in /lib/aarch64-linux-gnu/libc.so.6 +46: 3# 0x0000AAAAC3A9C3D8 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch +46: 4# 0x0000AAAAC3AE83CC in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch +46: 5# 0x0000AAAAC3AE8D80 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch +46: 6# 0x0000AAAAC3AE91B4 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch +46: 7# 0x0000AAAAC3ABC598 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch +46: 8# 0x0000AAAAC3ABCAE4 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch +46: 9# 0x0000AAAAC3A3E090 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch +46: 10# 0x0000FFFF8369229C in /lib/aarch64-linux-gnu/libc.so.6 46: 11# __libc_start_main in /lib/aarch64-linux-gnu/libc.so.6 -46: 12# 0x0000AAAADA40E170 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch +46: 12# 0x0000AAAAC3A3E170 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch 46: ---------- 46: **** 46: -46: [02:19:03] +46: [11:05:59] 46: 46: **** 46: Pre-condition Violation @@ -16930,21 +17043,20 @@ 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# 0x0000AAAADA46C45C in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch -46: 4# 0x0000AAAADA4B83CC in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch -46: 5# 0x0000AAAADA4B8D80 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch -46: 6# 0x0000AAAADA4B91B4 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch -46: 7# 0x0000AAAADA48C598 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch -46: 8# 0x0000AAAADA48CAE4 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch -46: 9# 0x0000AAAADA40E090 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch -46: 10# 0x0000FFFFB204229C in /lib/aarch64-linux-gnu/libc.so.6 +46: 3# 0x0000AAAAC3A9C45C in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch +46: 4# 0x0000AAAAC3AE83CC in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch +46: 5# 0x0000AAAAC3AE8D80 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch +46: 6# 0x0000AAAAC3AE91B4 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch +46: 7# 0x0000AAAAC3ABC598 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch +46: 8# 0x0000AAAAC3ABCAE4 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch +46: 9# 0x0000AAAAC3A3E090 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch +46: 10# 0x0000FFFF8369229C in /lib/aarch64-linux-gnu/libc.so.6 46: 11# __libc_start_main in /lib/aarch64-linux-gnu/libc.so.6 -46: 12# 0x0000AAAADA40E170 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch +46: 12# 0x0000AAAAC3A3E170 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch 46: ---------- 46: **** 46: - 37/238 Test #48: graphmolSGroupCatch .................... Passed 0.02 sec -46: [02:19:03] +46: [11:05:59] 46: 46: **** 46: Pre-condition Violation @@ -16956,20 +17068,20 @@ 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# 0x0000AAAADA46CB70 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch -46: 4# 0x0000AAAADA4B83CC in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch -46: 5# 0x0000AAAADA4B8D80 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch -46: 6# 0x0000AAAADA4B91B4 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch -46: 7# 0x0000AAAADA48C598 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch -46: 8# 0x0000AAAADA48CAE4 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch -46: 9# 0x0000AAAADA40E090 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch -46: 10# 0x0000FFFFB204229C in /lib/aarch64-linux-gnu/libc.so.6 +46: 3# 0x0000AAAAC3A9CB70 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch +46: 4# 0x0000AAAAC3AE83CC in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch +46: 5# 0x0000AAAAC3AE8D80 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch +46: 6# 0x0000AAAAC3AE91B4 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch +46: 7# 0x0000AAAAC3ABC598 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch +46: 8# 0x0000AAAAC3ABCAE4 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch +46: 9# 0x0000AAAAC3A3E090 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch +46: 10# 0x0000FFFF8369229C in /lib/aarch64-linux-gnu/libc.so.6 46: 11# __libc_start_main in /lib/aarch64-linux-gnu/libc.so.6 -46: 12# 0x0000AAAADA40E170 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch +46: 12# 0x0000AAAAC3A3E170 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch 46: ---------- 46: **** 46: -46: [02:19:03] +46: [11:05:59] 46: 46: **** 46: Pre-condition Violation @@ -16981,20 +17093,20 @@ 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# 0x0000AAAADA46C58C in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch -46: 4# 0x0000AAAADA4B83CC in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch -46: 5# 0x0000AAAADA4B8D80 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch -46: 6# 0x0000AAAADA4B91B4 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch -46: 7# 0x0000AAAADA48C598 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch -46: 8# 0x0000AAAADA48CAE4 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch -46: 9# 0x0000AAAADA40E090 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch -46: 10# 0x0000FFFFB204229C in /lib/aarch64-linux-gnu/libc.so.6 +46: 3# 0x0000AAAAC3A9C58C in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch +46: 4# 0x0000AAAAC3AE83CC in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch +46: 5# 0x0000AAAAC3AE8D80 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch +46: 6# 0x0000AAAAC3AE91B4 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch +46: 7# 0x0000AAAAC3ABC598 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch +46: 8# 0x0000AAAAC3ABCAE4 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch +46: 9# 0x0000AAAAC3A3E090 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch +46: 10# 0x0000FFFF8369229C in /lib/aarch64-linux-gnu/libc.so.6 46: 11# __libc_start_main in /lib/aarch64-linux-gnu/libc.so.6 -46: 12# 0x0000AAAADA40E170 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch +46: 12# 0x0000AAAAC3A3E170 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch 46: ---------- 46: **** 46: -46: [02:19:03] +46: [11:05:59] 46: 46: **** 46: Pre-condition Violation @@ -17006,20 +17118,20 @@ 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# 0x0000AAAADA46C610 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch -46: 4# 0x0000AAAADA4B83CC in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch -46: 5# 0x0000AAAADA4B8D80 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch -46: 6# 0x0000AAAADA4B91B4 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch -46: 7# 0x0000AAAADA48C598 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch -46: 8# 0x0000AAAADA48CAE4 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch -46: 9# 0x0000AAAADA40E090 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch -46: 10# 0x0000FFFFB204229C in /lib/aarch64-linux-gnu/libc.so.6 +46: 3# 0x0000AAAAC3A9C610 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch +46: 4# 0x0000AAAAC3AE83CC in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch +46: 5# 0x0000AAAAC3AE8D80 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch +46: 6# 0x0000AAAAC3AE91B4 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch +46: 7# 0x0000AAAAC3ABC598 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch +46: 8# 0x0000AAAAC3ABCAE4 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch +46: 9# 0x0000AAAAC3A3E090 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch +46: 10# 0x0000FFFF8369229C in /lib/aarch64-linux-gnu/libc.so.6 46: 11# __libc_start_main in /lib/aarch64-linux-gnu/libc.so.6 -46: 12# 0x0000AAAADA40E170 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch +46: 12# 0x0000AAAAC3A3E170 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch 46: ---------- 46: **** 46: -46: [02:19:03] +46: [11:05:59] 46: 46: **** 46: Pre-condition Violation @@ -17031,20 +17143,20 @@ 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# 0x0000AAAADA46CB54 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch -46: 4# 0x0000AAAADA4B83CC in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch -46: 5# 0x0000AAAADA4B8D80 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch -46: 6# 0x0000AAAADA4B91B4 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch -46: 7# 0x0000AAAADA48C598 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch -46: 8# 0x0000AAAADA48CAE4 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch -46: 9# 0x0000AAAADA40E090 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch -46: 10# 0x0000FFFFB204229C in /lib/aarch64-linux-gnu/libc.so.6 +46: 3# 0x0000AAAAC3A9CB54 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch +46: 4# 0x0000AAAAC3AE83CC in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch +46: 5# 0x0000AAAAC3AE8D80 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch +46: 6# 0x0000AAAAC3AE91B4 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch +46: 7# 0x0000AAAAC3ABC598 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch +46: 8# 0x0000AAAAC3ABCAE4 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch +46: 9# 0x0000AAAAC3A3E090 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch +46: 10# 0x0000FFFF8369229C in /lib/aarch64-linux-gnu/libc.so.6 46: 11# __libc_start_main in /lib/aarch64-linux-gnu/libc.so.6 -46: 12# 0x0000AAAADA40E170 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch +46: 12# 0x0000AAAAC3A3E170 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch 46: ---------- 46: **** 46: -46: [02:19:03] +46: [11:05:59] 46: 46: **** 46: Pre-condition Violation @@ -17056,20 +17168,20 @@ 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# 0x0000AAAADA46C800 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch -46: 4# 0x0000AAAADA4B83CC in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch -46: 5# 0x0000AAAADA4B8D80 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch -46: 6# 0x0000AAAADA4B91B4 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch -46: 7# 0x0000AAAADA48C598 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch -46: 8# 0x0000AAAADA48CAE4 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch -46: 9# 0x0000AAAADA40E090 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch -46: 10# 0x0000FFFFB204229C in /lib/aarch64-linux-gnu/libc.so.6 +46: 3# 0x0000AAAAC3A9C800 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch +46: 4# 0x0000AAAAC3AE83CC in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch +46: 5# 0x0000AAAAC3AE8D80 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch +46: 6# 0x0000AAAAC3AE91B4 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch +46: 7# 0x0000AAAAC3ABC598 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch +46: 8# 0x0000AAAAC3ABCAE4 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch +46: 9# 0x0000AAAAC3A3E090 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch +46: 10# 0x0000FFFF8369229C in /lib/aarch64-linux-gnu/libc.so.6 46: 11# __libc_start_main in /lib/aarch64-linux-gnu/libc.so.6 -46: 12# 0x0000AAAADA40E170 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch +46: 12# 0x0000AAAAC3A3E170 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch 46: ---------- 46: **** 46: -46: [02:19:03] +46: [11:05:59] 46: 46: **** 46: Pre-condition Violation @@ -17081,38 +17193,24 @@ 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# 0x0000AAAADA46CB34 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch -46: 4# 0x0000AAAADA4B83CC in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch -46: 5# 0x0000AAAADA4B8D80 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch -46: 6# 0x0000AAAADA4B91B4 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch -46: 7# 0x0000AAAADA48C598 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch -46: 8# 0x0000AAAADA48CAE4 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch -46: 9# 0x0000AAAADA40E090 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch -46: 10# 0x0000FFFFB204229C in /lib/aarch64-linux-gnu/libc.so.6 +46: 3# 0x0000AAAAC3A9CB34 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch +46: 4# 0x0000AAAAC3AE83CC in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch +46: 5# 0x0000AAAAC3AE8D80 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch +46: 6# 0x0000AAAAC3AE91B4 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch +46: 7# 0x0000AAAAC3ABC598 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch +46: 8# 0x0000AAAAC3ABCAE4 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch +46: 9# 0x0000AAAAC3A3E090 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch +46: 10# 0x0000FFFF8369229C in /lib/aarch64-linux-gnu/libc.so.6 46: 11# __libc_start_main in /lib/aarch64-linux-gnu/libc.so.6 -46: 12# 0x0000AAAADA40E170 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch +46: 12# 0x0000AAAAC3A3E170 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch 46: ---------- 46: **** 46: -46: [02:19:03] WARNING: could not find number of expected rings. Switching to an approximate ring finding algorithm. -35: starting ring finding -35: done -35: starting ring finding -35: done -35: starting ring finding -35: done -35: C/C=N/c1ccc(cc1)c1cc2cc(c1)c1ccc(cc1)N=Cc1ccc(cc1)c1cc(cc(c1)c1ccc(cc1)C)c1ccc(cc1)C=Nc1ccc(cc1)c1cc(cc(c1)c1ccc(cc1)/N=C/C)c1ccc(cc1)N=Cc1ccc(cc1)c1cc(c3ccc(C=Nc4ccc(c5cc6c7ccc(N=Cc8ccc(c9cc(c%10ccc(C=Nc%11ccc2cc%11)cc%10)cc(c9)c2ccc(cc2)C=Nc2ccc(cc2)c2cc(cc(c2)c2ccc(cc2)N=Cc2ccc(cc2)c2cc(cc(c2)c2ccc(cc2)C)c2ccc(cc2)C=Nc2ccc(cc2)c2cc(c9ccc(N=Cc%10ccc(c%11cc(c%12ccc(C=Nc%13ccc(c(c6)c5)cc%13)cc%12)cc(c%11)c5ccc(cc5)C)cc%10)cc9)cc(c2)c2ccc(cc2)/N=C/C)c2ccc(cc2)/N=C/C)cc8)cc7)cc4)cc3)cc(c1)c1ccc(cc1)C -35: starting sanitization -test 49 - Start 49: graphmolAdjustQueryCatch - -49: Test command: /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/graphmolAdjustQueryCatch -49: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol -49: Test timeout computed to be: 1500 -46: [02:19:03] WARNING: could not find number of expected rings. Switching to an approximate ring finding algorithm. -46: [02:19:03] WARNING: not removing hydrogen atom without neighbors -46: [02:19:03] Explicit valence for atom # 1 F greater than permitted -46: [02:19:03] +46: [11:05:59] WARNING: could not find number of expected rings. Switching to an approximate ring finding algorithm. +46: [11:05:59] WARNING: could not find number of expected rings. Switching to an approximate ring finding algorithm. +46: [11:05:59] WARNING: not removing hydrogen atom without neighbors +46: [11:05:59] Explicit valence for atom # 1 F greater than permitted +46: [11:05:59] 46: 46: **** 46: Pre-condition Violation @@ -17124,20 +17222,20 @@ 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# 0x0000AAAADA41AB6C in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch -46: 4# 0x0000AAAADA4B83CC in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch -46: 5# 0x0000AAAADA4B8D80 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch -46: 6# 0x0000AAAADA4B91B4 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch -46: 7# 0x0000AAAADA48C598 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch -46: 8# 0x0000AAAADA48CAE4 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch -46: 9# 0x0000AAAADA40E090 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch -46: 10# 0x0000FFFFB204229C in /lib/aarch64-linux-gnu/libc.so.6 +46: 3# 0x0000AAAAC3A4AB6C in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch +46: 4# 0x0000AAAAC3AE83CC in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch +46: 5# 0x0000AAAAC3AE8D80 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch +46: 6# 0x0000AAAAC3AE91B4 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch +46: 7# 0x0000AAAAC3ABC598 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch +46: 8# 0x0000AAAAC3ABCAE4 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch +46: 9# 0x0000AAAAC3A3E090 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch +46: 10# 0x0000FFFF8369229C in /lib/aarch64-linux-gnu/libc.so.6 46: 11# __libc_start_main in /lib/aarch64-linux-gnu/libc.so.6 -46: 12# 0x0000AAAADA40E170 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch +46: 12# 0x0000AAAAC3A3E170 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch 46: ---------- 46: **** 46: -46: [02:19:03] +46: [11:05:59] 46: 46: **** 46: Pre-condition Violation @@ -17149,20 +17247,20 @@ 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# 0x0000AAAADA41ABF8 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch -46: 4# 0x0000AAAADA4B83CC in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch -46: 5# 0x0000AAAADA4B8D80 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch -46: 6# 0x0000AAAADA4B91B4 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch -46: 7# 0x0000AAAADA48C598 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch -46: 8# 0x0000AAAADA48CAE4 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch -46: 9# 0x0000AAAADA40E090 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch -46: 10# 0x0000FFFFB204229C in /lib/aarch64-linux-gnu/libc.so.6 +46: 3# 0x0000AAAAC3A4ABF8 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch +46: 4# 0x0000AAAAC3AE83CC in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch +46: 5# 0x0000AAAAC3AE8D80 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch +46: 6# 0x0000AAAAC3AE91B4 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch +46: 7# 0x0000AAAAC3ABC598 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch +46: 8# 0x0000AAAAC3ABCAE4 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch +46: 9# 0x0000AAAAC3A3E090 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch +46: 10# 0x0000FFFF8369229C in /lib/aarch64-linux-gnu/libc.so.6 46: 11# __libc_start_main in /lib/aarch64-linux-gnu/libc.so.6 -46: 12# 0x0000AAAADA40E170 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch +46: 12# 0x0000AAAAC3A3E170 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch 46: ---------- 46: **** 46: -46: [02:19:03] +46: [11:05:59] 46: 46: **** 46: Pre-condition Violation @@ -17174,22 +17272,23 @@ 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# 0x0000AAAADA41A7BC in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch -46: 4# 0x0000AAAADA4B83CC in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch -46: 5# 0x0000AAAADA4B8D80 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch -46: 6# 0x0000AAAADA4B91B4 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch -46: 7# 0x0000AAAADA48C598 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch -46: 8# 0x0000AAAADA48CAE4 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch -46: 9# 0x0000AAAADA40E090 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch -46: 10# 0x0000FFFFB204229C in /lib/aarch64-linux-gnu/libc.so.6 +46: 3# 0x0000AAAAC3A4A7BC in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch +46: 4# 0x0000AAAAC3AE83CC in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch +46: 5# 0x0000AAAAC3AE8D80 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch +46: 6# 0x0000AAAAC3AE91B4 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch +46: 7# 0x0000AAAAC3ABC598 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch +46: 8# 0x0000AAAAC3ABCAE4 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch +46: 9# 0x0000AAAAC3A3E090 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch +46: 10# 0x0000FFFF8369229C in /lib/aarch64-linux-gnu/libc.so.6 46: 11# __libc_start_main in /lib/aarch64-linux-gnu/libc.so.6 -46: 12# 0x0000AAAADA40E170 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch +46: 12# 0x0000AAAAC3A3E170 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch 46: ---------- 46: **** 46: -46: [02:19:03] +46: [11:05:59] 46: 46: **** +35: done 46: Pre-condition Violation 46: plain bonds have no query 46: Violation occurred on line 228 in file ./Code/GraphMol/Bond.cpp @@ -17199,149 +17298,40 @@ 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# 0x0000AAAADA41A848 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch -46: 4# 0x0000AAAADA4B83CC in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch -46: 5# 0x0000AAAADA4B8D80 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch -46: 6# 0x0000AAAADA4B91B4 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch -46: 7# 0x0000AAAADA48C598 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch -46: 8# 0x0000AAAADA48CAE4 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch -46: 9# 0x0000AAAADA40E090 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch -46: 10# 0x0000FFFFB204229C in /lib/aarch64-linux-gnu/libc.so.6 +46: 3# 0x0000AAAAC3A4A848 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch +46: 4# 0x0000AAAAC3AE83CC in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch +46: 5# 0x0000AAAAC3AE8D80 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch +46: 6# 0x0000AAAAC3AE91B4 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch +46: 7# 0x0000AAAAC3ABC598 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch +46: 8# 0x0000AAAAC3ABCAE4 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch +46: 9# 0x0000AAAAC3A3E090 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch +46: 10# 0x0000FFFF8369229C in /lib/aarch64-linux-gnu/libc.so.6 46: 11# __libc_start_main in /lib/aarch64-linux-gnu/libc.so.6 -46: 12# 0x0000AAAADA40E170 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch +46: 12# 0x0000AAAAC3A3E170 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch 46: ---------- 46: **** 46: -46: [02:19:03] Can't kekulize mol. Unkekulized atoms: 0 1 2 3 4 -46: [02:19:03] Can't kekulize mol. Unkekulized atoms: 0 1 2 3 4 -46: [02:19:03] Can't kekulize mol. Unkekulized atoms: 6 7 8 9 10 -46: [02:19:03] Can't kekulize mol. Unkekulized atoms: 6 7 8 9 10 -46: [02:19:03] Can't kekulize mol. Unkekulized atoms: 0 1 2 3 4 -46: [02:19:03] Unusual charge on atom 0 number of radical electrons set to zero -46: [02:19:03] Unusual charge on atom 0 number of radical electrons set to zero -46: [02:19:03] Unusual charge on atom 0 number of radical electrons set to zero -46: [02:19:03] non-ring atom 0 marked aromatic -46: [02:19:03] non-ring atom 0 marked aromatic -46: [02:19:03] Explicit valence for atom # 1 C, 5, is greater than permitted -46: [02:19:03] Explicit valence for atom # 9 C, 5, is greater than permitted -46: [02:19:03] Explicit valence for atom # 3 N, 4, is greater than permitted -46: [02:19:03] Explicit valence for atom # 15 C, 5, is greater than permitted -46: [02:19:03] Explicit valence for atom # 11 C, 5, is greater than permitted -46: [02:19:03] Explicit valence for atom # 9 C, 5, is greater than permitted -46: [02:19:03] Explicit valence for atom # 9 C, 5, is greater than permitted -46: [02:19:03] Explicit valence for atom # 9 C, 6, is greater than permitted -46: [02:19:03] Can't kekulize mol. Unkekulized atoms: 0 1 2 3 4 -46: [02:19:03] Can't kekulize mol. Unkekulized atoms: 7 -46: [02:19:03] Can't kekulize mol. Unkekulized atoms: 3 -46: [02:19:03] Can't kekulize mol. Unkekulized atoms: 3 7 -46: [02:19:03] Can't kekulize mol. Unkekulized atoms: 3 7 -46: [02:19:03] WARNING: could not find number of expected rings. Switching to an approximate ring finding algorithm. -35: done -35: starting sanitization -37: [02:19:03] C=[$(C=O)] -37: [02:19:03] S(=O)(=O)-[C&H2][F,Br,I,Cl] S(=O)(=O)-[C&H2][F,Br,I,Cl] -37: [02:19:03] done -37: [02:19:03] ------------------------------------- -37: [02:19:03] Testing radical handling in pickles. -37: [02:19:03] done -37: [02:19:03] done -37: [02:19:03] ------------------------------------- -37: [02:19:03] Testing sf.net issue 2788233. -37: [02:19:03] done -37: [02:19:03] ------------------------------------- -37: [02:19:03] Testing sf.net issue 3202580. -37: mass! 13.0034 -37: [02:19:03] done -37: [02:19:03] ------------------------------------- -37: [02:19:03] Testing sf.net issue 3316407. -37: [02:19:03] done -37: [02:19:03] ------------------------------------- -37: [02:19:03] Testing sf.net issue 3496759. -37: smi match: *C *C -37: smi match: **=* **=* -37: smi match: [N-]=[N+]=NC=O [N-]=[N+]=NC=O -37: smi match: *OS(=O)OC *OS(=O)OC -37: smi match: *S(=O)(=O)OC *S(=O)(=O)OC -37: smi match: O=COC=O O=COC=O -37: smi match: OO OO -37: smi match: O=COc1c(F)c(F)c(F)c(F)c1F O=COc1c(F)c(F)c(F)c(F)c1F -37: smi match: O=COc1ccc(N(=O)=O)cc1 O=COc1ccc(N(=O)=O)cc1 -37: smi match: nnnOC=O nnnOC=O -37: smi match: *=C=N *=C=N -37: smi match: OS(=O)(=O)C(F)(F)F OS(=O)(=O)C(F)(F)F -37: smi match: SP(S)=S SP(S)=S -37: smi match: NP(N)(N)=O NP(N)(N)=O -37: smi match: cN=[N+]=[N-] cN=[N+]=[N-] -37: smi match: *CC=O *CC=O -37: smi match: NNC=O NNC=O -37: smi match: * * -37: smi match: C=P C=P -37: smi match: CC(=N)Cl CC(=N)Cl -37: smi match: N=O N=O -37: smi match: ** ** -37: smi match: N=C=N N=C=N -37: smi match: [C-]#[NH+] [C-]#[NH+] -37: smi match: O=CON(C=O)C=O O=CON(C=O)C=O -37: smi match: N#CC[OH] N#CC[OH] -37: smi match: N#CC=O N#CC=O -37: smi match: N#CS(=O)=O N#CS(=O)=O -37: smi match: CCOP(=O)(C#N)OCC CCOP(=O)(C#N)OCC -37: smi match: N#CN=N N#CN=N -37: smi match: N=NCC=O N=NCC=O -37: smi match: CCCCCCC CCCCCCC -37: smi match: OCCOCCO OCCOCCO -37: smi match: SS SS -37: smi match: [SH] [SH] -37: smi match: *1CC1 *1CC1 -37: smi match: [OH]ccc([OH])c[OH] [OH]ccc([OH])c[OH] -37: smi match: [OH]cc([OH])c[OH] [OH]cc([OH])c[OH] -37: smi match: NC(=S)N=N NC(=S)N=N -37: smi match: N#CS N#CS -37: smi match: cC[N+] cC[N+] -37: smi match: C*C=S C*C=S -37: smi match: N[CH2]C#N N[CH2]C#N -37: smi match: O=C1CCO1 O=C1CCO1 -37: smi match: O=P([OH])OP(=O)[OH] O=P([OH])OP(=O)[OH] -37: smi match: O=C1CCN1 O=C1CCN1 -37: smi match: O=C1C~CC(=O)C~C1 O=C1C~CC(=O)C~C1 -37: smi match: C=CC=CC=CC=C C=CC=CC=CC=C -37: smi match: C1CCC(OC2CCC3CCCCC3C2)OC1 C1CCC(OC2CCC3CCCCC3C2)OC1 -37: smi match: O=C1NCC2CCCCC21 O=C1NCC2CCCCC21 -37: smi match: O=C1CCCC(=O)N1 O=C1CCCC(=O)N1 -37: smi match: C1CCC(C2CCCO2)OC1 C1CCC(C2CCCO2)OC1 -37: smi match: [OH]C1Cc2c([OH])cc([OH])cc2OC1c1ccc([OH])c([OH])c1 [OH]C1Cc2c([OH])cc([OH])cc2OC1c1ccc([OH])c([OH])c1 -37: smi match: C1CC2CCC(O1)O2 C1CC2CCC(O1)O2 -37: smi match: cN(=O)~O cN(=O)~O -37: smi match: *[CH2]N1C(=O)CCC1=O *[CH2]N1C(=O)CCC1=O -37: smi match: N~NC=O N~NC=O -37: smi match: *=N~C *=N~C -37: smi match: CO*(=O)=O CO*(=O)=O 37: smi match: * * 37: smi match: * * +35: starting sanitization 37: smi match: *C=C *C=C 37: smi match: N#CS N#CS 37: smi match: *C=S *C=S +46: [11:05:59] Can't kekulize mol. Unkekulized atoms: 0 1 2 3 4 +46: [11:05:59] Can't kekulize mol. Unkekulized atoms: 0 1 2 3 4 37: smi match: *N *N +46: [11:05:59] Can't kekulize mol. Unkekulized atoms: 6 7 8 9 10 +46: [11:05:59] Can't kekulize mol. Unkekulized atoms: 6 7 8 9 10 37: smi match: *C(=C)C=O *C(=C)C=O 37: smi match: *C#C *C#C 37: smi match: N#CCO N#CCO 37: smi match: O=N(=O)CCO O=N(=O)CCO 37: smi match: N=CS N=CS 37: smi match: O=CNC(O)C=O O=CNC(O)C=O +46: [11:05:59] Can't kekulize mol. Unkekulized atoms: 0 1 2 3 4 37: smi match: C=C(C=O)C=O C=C(C=O)C=O 37: smi match: N=CC=O N=CC=O 37: smi match: *C(C=O)C=O *C(C=O)C=O -47: Randomness seeded to: 4252682187 -47: =============================================================================== -47: All tests passed (62 assertions in 6 test cases) -47: - 38/238 Test #47: graphmolOrganometallicsCatch ........... Passed 0.05 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 37: smi match: *C(C=O)=C(*)C=O *C(C=O)=C(*)C=O 37: smi match: O=CC=CC=O O=CC=CC=O 37: smi match: O=CN(O)C=O O=CN(O)C=O @@ -17355,8 +17345,32 @@ 37: smi match: S=CS S=CS 37: smi match: C=O C=O 37: smi match: *C=N *C=N +35: done 37: smi match: CCCCCCC CCCCCCC +46: [11:05:59] Unusual charge on atom 0 number of radical electrons set to zero 37: smi match: CN=O CN=O +46: [11:05:59] Unusual charge on atom 0 number of radical electrons set to zero +46: [11:05:59] Unusual charge on atom 0 number of radical electrons set to zero +35: starting ring finding +46: [11:05:59] non-ring atom 0 marked aromatic +35: done +46: [11:05:59] non-ring atom 0 marked aromatic +35: starting ring finding +35: done +46: [11:05:59] Explicit valence for atom # 1 C, 5, is greater than permitted +46: [11:05:59] Explicit valence for atom # 9 C, 5, is greater than permitted +46: [11:05:59] Explicit valence for atom # 3 N, 4, is greater than permitted +35: smiles: CC[C@]1(C(=O)c([nH])n)CC[C@](C)(O)CC1 +46: [11:05:59] Explicit valence for atom # 15 C, 5, is greater than permitted +46: [11:05:59] Explicit valence for atom # 11 C, 5, is greater than permitted +46: [11:05:59] Explicit valence for atom # 9 C, 5, is greater than permitted +46: [11:05:59] Explicit valence for atom # 9 C, 5, is greater than permitted +46: [11:05:59] Explicit valence for atom # 9 C, 6, is greater than permitted +46: [11:05:59] Can't kekulize mol. Unkekulized atoms: 0 1 2 3 4 +46: [11:05:59] Can't kekulize mol. Unkekulized atoms: 7 +46: [11:05:59] Can't kekulize mol. Unkekulized atoms: 3 +46: [11:05:59] Can't kekulize mol. Unkekulized atoms: 3 7 +46: [11:05:59] Can't kekulize mol. Unkekulized atoms: 3 7 37: smi match: CS(=O)(=O)O CS(=O)(=O)O 37: smi match: O=C1CCO1 O=C1CCO1 37: smi match: C=C(S)[SH]=O C=C(S)[SH]=O @@ -17368,27 +17382,33 @@ 37: smi match: C=CC(=S)S C=CC(=S)S 37: smi match: *C=C(*)C=C *C=C(*)C=C 37: smi match: C=CC=N C=CC=N +48: Randomness seeded to: 2385333801 +48: =============================================================================== +48: All tests passed (136 assertions in 8 test cases) +48: 37: smi match: *N(*)C=C *N(*)C=C 37: smi match: C=CN(=O)=O C=CN(=O)=O 37: smi match: C=CN(O)=O C=CN(O)=O 37: smi match: C=CO C=CO 37: smi match: C=COC=O C=COC=O +46: [11:05:59] WARNING: could not find number of expected rings. Switching to an approximate ring finding algorithm. 37: smi match: C=CS C=CS 37: smi match: C=C[SH](=O)=O C=C[SH](=O)=O 37: smi match: C=NCO C=NCO 37: smi match: C=NC=O C=NC=O 37: smi match: C=NN C=NN 37: smi match: C=NN=C C=NN=C + 37/238 Test #48: graphmolSGroupCatch .................... Passed 0.04 sec 37: smi match: C=NO C=NO -46: [02:19:03] WARNING: could not find number of expected rings. Switching to an approximate ring finding algorithm. -35: done -35: starting ring finding -35: done -35: starting ring finding -35: done 37: smi match: C=NOC=O C=NOC=O 37: smi match: C=N=O C=N=O 37: smi match: N#CS N#CS +test 49 + Start 49: graphmolAdjustQueryCatch + +49: Test command: /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/graphmolAdjustQueryCatch +49: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol +49: Test timeout computed to be: 1500 37: smi match: *CN=O *CN=O 37: smi match: NCN NCN 37: smi match: ON=CCN=O ON=CCN=O @@ -17398,7 +17418,6 @@ 37: smi match: NC=S NC=S 37: smi match: NC(N)=S NC(N)=S 37: smi match: C=CN C=CN -35: smiles: CC[C@]1(C(=O)c([nH])n)CC[C@](C)(O)CC1 37: smi match: NOC=O NOC=O 37: smi match: C1CN1 C1CN1 37: smi match: O=C1NNNN1 O=C1NNNN1 @@ -17437,13 +17456,6 @@ 37: smi match: C1COCOC1 C1COCOC1 37: smi match: C=S C=S 37: smi match: c=S c=S - 39/238 Test #32: pyDistGeom ............................. Passed 0.17 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 37: smi match: S=CS S=CS 37: smi match: C=CN(=O)=O C=CN(=O)=O 37: smi match: C=CN(=O)O C=CN(=O)O @@ -17461,13 +17473,11 @@ 37: smi match: N=C(=N)S N=C(=N)S 37: smi match: O=N=O O=N=O 37: smi match: O=NO O=NO -35: [02:19:03] WARNING: not removing hydrogen atom with dummy atom neighbors 37: smi match: ONO ONO 37: smi match: C1SCS1 C1SCS1 37: smi match: N=C=S N=C=S 37: smi match: N=C=N N=C=N 37: smi match: C1N=N1 C1N=N1 -35: ------------------------------- 37: smi match: *CS *CS 37: smi match: SC(S)=C(S)S SC(S)=C(S)S 37: smi match: N=CC=NO N=CC=NO @@ -17483,7 +17493,6 @@ 37: smi match: C1COCO1 C1COCO1 37: smi match: C=NN[SH](=O)=O C=NN[SH](=O)=O 37: smi match: O=CC=O O=CC=O -35: [02:19:03] Explicit valence for atom # 0 N, 4, is greater than permitted 37: smi match: O=CNOC=O O=CNOC=O 37: smi match: O=C1C=CC(=O)C=C1 O=C1C=CC(=O)C=C1 37: smi match: ONO ONO @@ -17500,11 +17509,35 @@ 37: smi match: OCS OCS 37: smi match: C1NO1 C1NO1 37: smi match: COS(C)(=O)=O COS(C)(=O)=O +35: [11:05:59] WARNING: not removing hydrogen atom with dummy atom neighbors +35: ------------------------------- +35: [11:05:59] Explicit valence for atom # 0 N, 4, is greater than permitted +35: [11:05:59] Can't kekulize mol. Unkekulized atoms: 0 1 2 3 4 +35: [11:05:59] Can't kekulize mol. Unkekulized atoms: 6 7 8 9 10 +35: [11:05:59] Can't kekulize mol. Unkekulized atoms: 0 1 2 3 4 +35: [11:05:59] WARNING: merging explicit H queries involved in ORs is not supported. This query will not be merged +35: [11:05:59] WARNING: merging explicit H queries involved in ORs is not supported. This query will not be merged +35: [11:05:59] WARNING: merging explicit H queries involved in ORs is not supported. This query will not be merged +35: [11:05:59] WARNING: merging explicit H queries involved in ORs is not supported. This query will not be merged +35: [11:05:59] WARNING: merging explicit H queries involved in ORs is not supported. This query will not be merged +35: +46: [11:05:59] WARNING: could not find number of expected rings. Switching to an approximate ring finding algorithm. +47: Randomness seeded to: 3535698829 +47: =============================================================================== +47: All tests passed (62 assertions in 6 test cases) +47: + 38/238 Test #47: graphmolOrganometallicsCatch ........... Passed 0.07 sec 37: smi match: C1CO1 C1CO1 37: smi match: *c1-c-c-ccN1 *c1-c-c-ccN1 37: smi match: *C(*)=C *C(*)=C 37: smi match: N#[NH+] N#[NH+] 37: smi match: C#NO C#NO +test 50 + Start 50: chiralityTestsCatch + +50: Test command: /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/chiralityTestsCatch +50: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol +50: Test timeout computed to be: 1500 37: smi match: OOO OOO 37: smi match: OO OO 37: smi match: O~Cl(~O)~O O~Cl(~O)~O @@ -17513,6 +17546,7 @@ 37: smi match: *N *N 37: smi match: *P *P 37: smi match: *S *S +35: [11:05:59] WARNING: not removing hydrogen atom with dummy atom neighbors 37: smi match: *C(*)(*)C=C *C(*)(*)C=C 37: smi match: *C(*)(*)C=C *C(*)(*)C=C 37: smi match: *C(*)C=C *C(*)C=C @@ -17546,31 +17580,18 @@ 37: smi match: *C(*)C=O *C(*)C=O 37: smi match: *CC=O *CC=O 37: smi match: *C(*)(*)[SH](=O)=O *C(*)(*)[SH](=O)=O + 39/238 Test #32: pyDistGeom ............................. Passed 0.19 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 37: smi match: *C(*)(*)[SH](=O)=O *C(*)(*)[SH](=O)=O 37: smi match: *C(*)[SH](=O)=O *C(*)[SH](=O)=O 37: smi match: *C[SH](=O)=O *C[SH](=O)=O 37: smi match: * * 37: smi match: *1CC1 *1CC1 -46: [02:19:03] Explicit valence for atom # 1 O, 3, is greater than permitted -46: [02:19:03] WARNING: merging explicit H queries involved in ORs is not supported. This query will not be merged -46: [02:19:03] WARNING: merging explicit H queries involved in ORs is not supported. This query will not be merged -46: [02:19:03] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -46: [02:19:03] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -46: [02:19:03] Invalid value for molAttachPoint: 4 on atom 1. Not expanding this atttachment point. -46: [02:19:03] Invalid value for _fromAttachPoint: -1 on atom 0. Not collapsing this atom -46: [02:19:03] Invalid value for _fromAttachPoint: 4 on atom 0. Not collapsing this atom -46: [02:19:03] non-ring atom 0 marked aromatic -46: [02:19:03] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored -46: [02:19:03] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored -35: [02:19:03] Can't kekulize mol. Unkekulized atoms: 0 1 2 3 4 -35: [02:19:03] Can't kekulize mol. Unkekulized atoms: 6 7 8 9 10 -35: [02:19:03] Can't kekulize mol. Unkekulized atoms: 0 1 2 3 4 -35: [02:19:03] WARNING: merging explicit H queries involved in ORs is not supported. This query will not be merged -35: [02:19:03] WARNING: merging explicit H queries involved in ORs is not supported. This query will not be merged -35: [02:19:03] WARNING: merging explicit H queries involved in ORs is not supported. This query will not be merged -35: [02:19:03] WARNING: merging explicit H queries involved in ORs is not supported. This query will not be merged -35: [02:19:03] WARNING: merging explicit H queries involved in ORs is not supported. This query will not be merged -35: 37: smi match: O=COC=O O=COC=O 37: smi match: N=C=O N=C=O 37: smi match: N=C=S N=C=S @@ -17587,7 +17608,6 @@ 37: smi match: N~N~O N~N~O 37: smi match: *N(~O)(~O)~O *N(~O)(~O)~O 37: smi match: *[N+](=C)[O-] *[N+](=C)[O-] -35: [02:19:03] WARNING: not removing hydrogen atom with dummy atom neighbors 37: smi match: * * 37: smi match: *C(*)NCN(*)* *C(*)NCN(*)* 37: smi match: *OCC#N *OCC#N @@ -17597,14 +17617,21 @@ 37: smi match: * * 37: smi match: O=CON1C(=O)CCC1=O O=CON1C(=O)CCC1=O 37: smi match: O=COn1ccnc1 O=COn1ccnc1 +46: [11:05:59] Explicit valence for atom # 1 O, 3, is greater than permitted +46: [11:05:59] WARNING: merging explicit H queries involved in ORs is not supported. This query will not be merged +46: [11:05:59] WARNING: merging explicit H queries involved in ORs is not supported. This query will not be merged +46: [11:05:59] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +46: [11:05:59] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +46: [11:05:59] Invalid value for molAttachPoint: 4 on atom 1. Not expanding this atttachment point. +46: [11:05:59] Invalid value for _fromAttachPoint: -1 on atom 0. Not collapsing this atom +46: [11:05:59] Invalid value for _fromAttachPoint: 4 on atom 0. Not collapsing this atom +46: [11:05:59] non-ring atom 0 marked aromatic +46: [11:05:59] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored +46: [11:05:59] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored 37: smi match: O=COc1c(F)c(F)c(F)c(F)c1F O=COc1c(F)c(F)c(F)c(F)c1F 37: smi match: CC(C)(C)S CC(C)(C)S 37: smi match: [CH2][CH]~[CH]~[CH]~[CH]~[CH]~[CH]~[CH]~[CH]~[CH]~[CH]~C [CH2][CH]~[CH]~[CH]~[CH]~[CH]~[CH]~[CH]~[CH]~[CH]~[CH]~C 37: smi match: [CH]=O [CH]=O -49: Randomness seeded to: 3502774858 -49: =============================================================================== -49: All tests passed (292 assertions in 12 test cases) -49: 37: smi match: C~[CH2]~[CH2]~[CH2]~[CH2]~[CH2]~C C~[CH2]~[CH2]~[CH2]~[CH2]~[CH2]~C 37: smi match: SS SS 37: smi match: [SH] [SH] @@ -17612,25 +17639,19 @@ 37: smi match: * * 37: smi match: C[nH3+] C[nH3+] 37: smi match: cC(=N)[NH2] cC(=N)[NH2] - 40/238 Test #49: graphmolAdjustQueryCatch ............... Passed 0.04 sec 37: smi match: O=CN[OH] O=CN[OH] 37: smi match: NN NN -test 52 - Start 52: moliteratorTestsCatch - -52: Test command: /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/moliteratorTestsCatch -52: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol -52: Test timeout computed to be: 1500 37: smi match: * * 37: smi match: *OP(=O)O* *OP(=O)O* 37: smi match: * * 37: smi match: * * 37: smi match: * * -46: [02:19:03] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 37: smi match: *N=C(*)* *N=C(*)* 37: smi match: *C(*)(*)C=O *C(*)(*)C=O 37: smi match: CSC=O CSC=O 37: smi match: * * +40: [11:05:59] sorting (hanoi sort) vectors +46: [11:05:59] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 37: smi match: O=CCl O=CCl 37: smi match: *** *** 37: smi match: *C=O *C=O @@ -17643,9 +17664,11 @@ 37: smi match: *C *C 37: smi match: C#C C#C 37: smi match: *[CH]C=C *[CH]C=C +46: [11:05:59] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 37: smi match: cCC(=O)[OH] cCC(=O)[OH] 37: smi match: *C(*)(*)C(=O)[OH] *C(*)(*)C(=O)[OH] 37: smi match: CC(=O)C(=O)[OH] CC(=O)C(=O)[OH] +46: [11:05:59] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 37: smi match: C=CC(=O)[OH] C=CC(=O)[OH] 37: smi match: N#CC(=O)[OH] N#CC(=O)[OH] 37: smi match: O=C([OH])CN(~O)~O O=C([OH])CN(~O)~O @@ -17655,8 +17678,6 @@ 37: smi match: *=CC#N *=CC#N 37: smi match: *C[OH] *C[OH] 37: smi match: ** ** -50: Randomness seeded to: 2441336255 -50: [02:19:03] unable to set wavy bonds for double bonds: 3 37: smi match: *C[OH] *C[OH] 37: smi match: *C(*)=O *C(*)=O 37: smi match: * * @@ -17672,50 +17693,42 @@ 37: smi match: N~N~N N~N~N 37: smi match: *N=N* *N=N* 37: smi match: *CC[OH] *CC[OH] -46: [02:19:03] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +46: [11:05:59] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 2 ignored +46: [11:05:59] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 2 ignored 37: smi match: *CC[OH] *CC[OH] +46: [11:05:59] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 37: smi match: *=CCC(=O)[OH] *=CCC(=O)[OH] 37: smi match: O=C([OH])CC[OH] O=C([OH])CC[OH] 37: smi match: *CCC(=O)[OH] *CCC(=O)[OH] 37: smi match: CC(=O)CC(=O)[OH] CC(=O)CC(=O)[OH] -52: Randomness seeded to: 1883359409 -52: =============================================================================== -52: All tests passed (14 assertions in 4 test cases) -52: 37: smi match: *OC(=O)CC(C)=O *OC(=O)CC(C)=O 37: smi match: *OC(*)=O *OC(*)=O - 41/238 Test #52: moliteratorTestsCatch .................. Passed 0.01 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 37: smi match: *C(=O)[OH] *C(=O)[OH] 37: smi match: O=C[OH] O=C[OH] +46: [11:05:59] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored +46: [11:05:59] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored 37: smi match: *OC(=O)O* *OC(=O)O* 37: smi match: * * 37: smi match: *OC(=O)Cl *OC(=O)Cl 37: smi match: *C#N *C#N +46: [11:05:59] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored +46: [11:05:59] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored 37: smi match: NCC(=O)NCC=O NCC(=O)NCC=O 37: smi match: SS SS 37: smi match: * * 37: smi match: *=* *=* +46: [11:05:59] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +50: Randomness seeded to: 3578678242 +50: [11:05:59] unable to set wavy bonds for double bonds: 3 37: smi match: *=* *=* 37: smi match: *=* *=* -46: [02:19:03] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 37: smi match: *=* *=* -46: [02:19:03] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 2 ignored -46: [02:19:03] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 2 ignored 37: smi match: C1CO1 C1CO1 37: smi match: *OC(*)=O *OC(*)=O 37: smi match: * * -40: [02:19:03] sorting (hanoi sort) vectors 37: smi match: *O*[OH] *O*[OH] 37: smi match: COC(C)(C)O COC(C)(C)O -50: [02:19:03] WARNING: not removing hydrogen atom with neighbor that has non-tetrahedral stereochemistry 37: smi match: *[OH] *[OH] -50: [02:19:03] WARNING: not removing hydrogen atom with neighbor that has non-tetrahedral stereochemistry 37: smi match: ** ** 37: smi match: C=N[NH2] C=N[NH2] 37: smi match: C=NC=O C=NC=O @@ -17727,6 +17740,17 @@ 37: smi match: *C(*)=O *C(*)=O 37: smi match: C~C~C~C~C~C~C C~C~C~C~C~C~C 37: smi match: *~*=O *~*=O +49: Randomness seeded to: 815944458 +49: =============================================================================== +49: All tests passed (292 assertions in 12 test cases) +49: + 40/238 Test #49: graphmolAdjustQueryCatch ............... Passed 0.07 sec +test 52 + Start 52: moliteratorTestsCatch + +52: Test command: /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/moliteratorTestsCatch +52: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol +52: Test timeout computed to be: 1500 37: smi match: *~*=O *~*=O 37: smi match: OC(=O)CC(=O)[OH] OC(=O)CC(=O)[OH] 37: smi match: * * @@ -17736,21 +17760,10 @@ 37: smi match: OC(=O)C(O)=O OC(=O)C(O)=O 37: smi match: C=NO C=NO 37: smi match: O~O O~O -53: Randomness seeded to: 1038916370 -53: =============================================================================== -53: All tests passed (10 assertions in 1 test case) -53: 37: smi match: c[OH] c[OH] 37: smi match: O=P(~[OH])~O O=P(~[OH])~O 37: smi match: CO~P(=O)~O CO~P(=O)~O - 42/238 Test #53: queryTestsCatch ........................ Passed 0.01 sec 37: smi match: O=P(~[OH])(~O)~O O=P(~[OH])(~O)~O -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 37: smi match: CO~P(=O)(~O)~O CO~P(=O)(~O)~O 37: smi match: O=P(~O)~O O=P(~O)~O 37: smi match: O=P(~O)(~O)~O O=P(~O)(~O)~O @@ -17771,98 +17784,136 @@ 37: smi match: * * 37: smi match: C[SH] C[SH] 37: smi match: c[SH] c[SH] +50: [11:05:59] WARNING: not removing hydrogen atom with neighbor that has non-tetrahedral stereochemistry +50: [11:05:59] WARNING: not removing hydrogen atom with neighbor that has non-tetrahedral stereochemistry 37: smi match: NC(N)=S NC(N)=S 37: smi match: * * 37: smi match: ***** ***** 37: smi match: NC(N)=O NC(N)=O -37: [02:19:03] done -37: [02:19:03] ------------------------------------- -37: [02:19:03] Testing sf.net issue 280. -37: [02:19:03] done -37: [02:19:03] ------------------------------------- -37: [02:19:03] Testing sf.net issue 285. -37: [02:19:03] done -37: [02:19:03] done -37: [02:19:03] done -37: [02:19:03] done -37: [02:19:03] done -37: [02:19:03] done -37: [02:19:03] done -37: [02:19:03] ------------------------------------- -37: [02:19:03] Testing Github2441: Add RDProps interface to Conformers. -37: [02:19:03] done -37: [02:19:03] ------------------------------------- -37: [02:19:03] Testing Issue2510: Pickle Confs as double. -37: [02:19:03] done -37: [02:19:03] ------------------------------------- -37: [02:19:03] Testing Github #2465: Negative atom-map numbers cause depickling to fail. -37: [02:19:03] done -37: [02:19:03] ------------------------------------- -37: [02:19:03] Testing loading pickled mols with conformers -37: [02:19:03] done -37: [02:19:03] ------------------------------------- -37: [02:19:03] Testing conformer reading/writing options -37: [02:19:03] done -37: [02:19:03] ------------------------------------- -37: [02:19:03] Testing property reading options -37: [02:19:03] done -37: [02:19:03] ------------------------------------- -37: [02:19:03] Testing property reading options -37: [02:19:03] done -37: [02:19:03] ------------------------------------- -37: [02:19:03] Testing boost::serialization integration -37: [02:19:03] done -37: [02:19:03] ------------------------------------- -37: [02:19:03] Testing github issue 6036 -46: [02:19:03] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -46: [02:19:03] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored -46: [02:19:03] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored -46: [02:19:03] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored -46: [02:19:03] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored - 43/238 Test #37: graphmoltestPickler .................... Passed 0.19 sec +37: [11:05:59] done +37: [11:05:59] ------------------------------------- +37: [11:05:59] Testing sf.net issue 280. +37: [11:05:59] done +37: [11:05:59] ------------------------------------- +37: [11:05:59] Testing sf.net issue 285. +37: [11:05:59] done +37: [11:05:59] done +37: [11:05:59] done +37: [11:05:59] done +37: [11:05:59] done +37: [11:05:59] done +37: [11:05:59] done +37: [11:05:59] ------------------------------------- +37: [11:05:59] Testing Github2441: Add RDProps interface to Conformers. +37: [11:05:59] done +37: [11:05:59] ------------------------------------- +37: [11:05:59] Testing Issue2510: Pickle Confs as double. +37: [11:05:59] done +37: [11:05:59] ------------------------------------- +37: [11:05:59] Testing Github #2465: Negative atom-map numbers cause depickling to fail. +37: [11:05:59] done +37: [11:05:59] ------------------------------------- +37: [11:05:59] Testing loading pickled mols with conformers +37: [11:05:59] done +37: [11:05:59] ------------------------------------- +37: [11:05:59] Testing conformer reading/writing options +37: [11:05:59] done +37: [11:05:59] ------------------------------------- +37: [11:05:59] Testing property reading options +37: [11:05:59] done +37: [11:05:59] ------------------------------------- +37: [11:05:59] Testing property reading options +37: [11:05:59] done +37: [11:05:59] ------------------------------------- +37: [11:05:59] Testing boost::serialization integration +37: [11:05:59] done +37: [11:05:59] ------------------------------------- +37: [11:05:59] Testing github issue 6036 + 41/238 Test #37: graphmoltestPickler .................... Passed 0.22 sec +test 53 + Start 53: queryTestsCatch + +53: Test command: /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/queryTestsCatch +53: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol +53: Test timeout computed to be: 1500 +50: [11:05:59] Warning: ambiguous stereochemistry - zero-length (or near zero-length) bond - at atom 1 ignored. +50: [11:05:59] Warning: ambiguous stereochemistry - zero-length (or near zero-length) bond - at atom 1 ignored. +52: Randomness seeded to: 2641447639 +52: =============================================================================== +52: All tests passed (14 assertions in 4 test cases) +52: + 42/238 Test #52: moliteratorTestsCatch .................. Passed 0.02 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: [11:05:59] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +46: [11:05:59] Explicit valence for atom # 0 Al, 6, is greater than permitted +46: [11:05:59] Explicit valence for atom # 0 Al, 6, is greater than permitted +46: [11:05:59] Explicit valence for atom # 1 Si, 6, is greater than permitted +46: [11:05:59] Explicit valence for atom # 1 Si, 6, is greater than permitted +46: [11:05:59] Explicit valence for atom # 0 P, 6, is greater than permitted +46: [11:05:59] Explicit valence for atom # 0 P, 6, is greater than permitted +46: [11:05:59] Explicit valence for atom # 0 P, 7, is greater than permitted +46: [11:05:59] Explicit valence for atom # 0 P, 7, is greater than permitted +46: [11:05:59] Explicit valence for atom # 1 As, 6, is greater than permitted +46: [11:05:59] Explicit valence for atom # 1 As, 6, is greater than permitted +46: [11:05:59] Explicit valence for atom # 1 As, 7, is greater than permitted +46: [11:05:59] Explicit valence for atom # 1 As, 7, is greater than permitted +46: [11:05:59] Explicit valence for atom # 0 Sb, 6, is greater than permitted +46: [11:05:59] Explicit valence for atom # 0 Sb, 6, is greater than permitted +46: [11:05:59] Explicit valence for atom # 0 Sb, 7, is greater than permitted +46: [11:05:59] Explicit valence for atom # 0 Sb, 7, is greater than permitted +46: [11:05:59] Explicit valence for atom # 1 Bi, 6, is greater than permitted +46: [11:05:59] Explicit valence for atom # 1 Bi, 6, is greater than permitted +46: [11:05:59] Explicit valence for atom # 1 Bi, 8, is greater than permitted +46: [11:05:59] Explicit valence for atom # 1 Bi, 8, is greater than permitted +46: =============================================================================== +46: All tests passed (4479 assertions in 107 test cases) +46: +50: [11:05:59] Warning: ambiguous stereochemistry - overlapping neighbors - at atom 2 ignored + 43/238 Test #46: graphmolTestsCatch ..................... Passed 0.17 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: [02:19:03] Warning: ambiguous stereochemistry - zero-length (or near zero-length) bond - at atom 1 ignored. -50: [02:19:03] Warning: ambiguous stereochemistry - zero-length (or near zero-length) bond - at atom 1 ignored. -46: [02:19:03] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -50: [02:19:03] Warning: ambiguous stereochemistry - overlapping neighbors - at atom 2 ignored -54: Randomness seeded to: 706099648 -54: =============================================================================== -54: All tests passed (6 assertions in 1 test case) -54: - 44/238 Test #54: molbundleTestsCatch .................... Passed 0.02 sec +50: =============================================================================== +50: All tests passed (2295 assertions in 80 test cases) +50: + 44/238 Test #50: chiralityTestsCatch .................... Passed 0.10 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 -50: =============================================================================== -50: All tests passed (2295 assertions in 80 test cases) -50: - 45/238 Test #50: chiralityTestsCatch .................... Passed 0.08 sec +53: Randomness seeded to: 2825872842 +53: =============================================================================== +53: All tests passed (10 assertions in 1 test case) +53: + 45/238 Test #53: queryTestsCatch ........................ Passed 0.03 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 -55: Randomness seeded to: 1627721576 -55: =============================================================================== -55: All tests passed (45 assertions in 4 test cases) -55: - 46/238 Test #55: pickleTestsCatch ....................... Passed 0.02 sec +54: Randomness seeded to: 2268398396 +54: =============================================================================== +54: All tests passed (6 assertions in 1 test case) +54: + 46/238 Test #54: molbundleTestsCatch .................... Passed 0.03 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 -56: Randomness seeded to: 567592993 +56: Randomness seeded to: 469570169 56: =============================================================================== 56: All tests passed (7 assertions in 2 test cases) 56: @@ -17873,283 +17924,95 @@ 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 -58: [02:19:03] WARNING: not removing hydrogen atom without neighbors -58: [02:19:03] WARNING: not removing hydrogen atom without neighbors -57: Randomness seeded to: 1453212509 -57: =============================================================================== -57: All tests passed (230 assertions in 7 test cases) -57: -58: [02:19:03] WARNING: not removing hydrogen atom without neighbors -58: [02:19:03] WARNING: not removing hydrogen atom without neighbors -58: [02:19:03] WARNING: not removing hydrogen atom without neighbors -58: [02:19:03] WARNING: not removing hydrogen atom without neighbors -58: [02:19:03] WARNING: not removing hydrogen atom without neighbors -58: [02:19:03] WARNING: not removing hydrogen atom without neighbors -58: [02:19:03] WARNING: not removing hydrogen atom without neighbors -58: [02:19:03] WARNING: not removing hydrogen atom without neighbors -59: [02:19:03] SMILES Parse Error: Failed parsing SMILES 'CO' for input: 'CO' -46: [02:19:03] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -59: [02:19:03] SMILES Parse Error: Failed parsing SMILES 'C-O' for input: 'C-O' -59: [02:19:03] SMILES Parse Error: syntax error while parsing: - -59: [02:19:03] SMILES Parse Error: check for mistakes around position 1: -59: [02:19:03] - -59: [02:19:03] ^ -59: [02:19:03] SMILES Parse Error: Failed parsing SMILES '-' for input: '-' -59: [02:19:03] SMILES Parse Error: Failed parsing SMILES '[Bg]' for input: '[Bg]' -59: [02:19:03] SMILES Parse Error: Failed parsing SMILES 'C' for input: 'C' -59: [02:19:03] SMILES Parse Error: Failed parsing SMILES 'C-O' for input: 'C-O' -59: [02:19:03] SMILES Parse Error: Failed parsing SMILES '*' for input: '*' -59: [02:19:03] SMARTS Parse Error: Failed parsing SMARTS 'CO' for input: 'CO' -59: [02:19:03] SMARTS Parse Error: Failed parsing SMARTS 'C-O' for input: 'C-O' -59: [02:19:03] SMARTS Parse Error: Failed parsing SMARTS '-' for input: '-' -59: [02:19:03] SMARTS Parse Error: Failed parsing SMARTS '[Bg]' for input: '[Bg]' -59: [02:19:03] SMARTS Parse Error: Failed parsing SMARTS 'C' for input: 'C' -59: [02:19:03] SMARTS Parse Error: Failed parsing SMARTS '-O' for input: '-O' -59: [02:19:03] SMARTS Parse Error: Failed parsing SMARTS '*' for input: '*' -58: [02:19:03] WARNING: not removing hydrogen atom without neighbors -58: [02:19:03] Invalid chiral specification on atom 0 -58: [02:19:03] Invalid chiral specification on atom 0 -58: [02:19:03] Invalid chiral specification on atom 0 -58: [02:19:03] Invalid chiral specification on atom 0 -58: [02:19:03] Invalid chiral specification on atom 0 - 48/238 Test #57: molopsTestsCatch ....................... Passed 0.03 sec - 49/238 Test #59: smiTest2 ............................... Passed 0.01 sec +55: Randomness seeded to: 1205188478 +55: =============================================================================== +55: All tests passed (45 assertions in 4 test cases) +55: + 48/238 Test #55: pickleTestsCatch ....................... Passed 0.03 sec test 60 Start 60: cxsmilesTest 60: Test command: /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/SmilesParse/cxsmilesTest 60: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/SmilesParse 60: Test timeout computed to be: 1500 +59: [11:05:59] SMILES Parse Error: Failed parsing SMILES 'CO' for input: 'CO' +59: [11:05:59] SMILES Parse Error: Failed parsing SMILES 'C-O' for input: 'C-O' +59: [11:05:59] SMILES Parse Error: syntax error while parsing: - +59: [11:05:59] SMILES Parse Error: check for mistakes around position 1: +59: [11:05:59] - +59: [11:05:59] ^ +59: [11:05:59] SMILES Parse Error: Failed parsing SMILES '-' for input: '-' +59: [11:05:59] SMILES Parse Error: Failed parsing SMILES '[Bg]' for input: '[Bg]' +59: [11:05:59] SMILES Parse Error: Failed parsing SMILES 'C' for input: 'C' +59: [11:05:59] SMILES Parse Error: Failed parsing SMILES 'C-O' for input: 'C-O' +59: [11:05:59] SMILES Parse Error: Failed parsing SMILES '*' for input: '*' +59: [11:05:59] SMARTS Parse Error: Failed parsing SMARTS 'CO' for input: 'CO' +59: [11:05:59] SMARTS Parse Error: Failed parsing SMARTS 'C-O' for input: 'C-O' +59: [11:05:59] SMARTS Parse Error: Failed parsing SMARTS '-' for input: '-' +59: [11:05:59] SMARTS Parse Error: Failed parsing SMARTS '[Bg]' for input: '[Bg]' +59: [11:05:59] SMARTS Parse Error: Failed parsing SMARTS 'C' for input: 'C' +59: [11:05:59] SMARTS Parse Error: Failed parsing SMARTS '-O' for input: '-O' +59: [11:05:59] SMARTS Parse Error: Failed parsing SMARTS '*' for input: '*' + 49/238 Test #59: smiTest2 ............................... Passed 0.01 sec test 61 Start 61: smaTest1 61: Test command: /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/SmilesParse/smaTest1 61: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/SmilesParse 61: Test timeout computed to be: 1500 -46: [02:19:03] Explicit valence for atom # 0 Al, 6, is greater than permitted -46: [02:19:03] Explicit valence for atom # 0 Al, 6, is greater than permitted -46: [02:19:03] Explicit valence for atom # 1 Si, 6, is greater than permitted -46: [02:19:03] Explicit valence for atom # 1 Si, 6, is greater than permitted -46: [02:19:03] Explicit valence for atom # 0 P, 6, is greater than permitted -46: [02:19:03] Explicit valence for atom # 0 P, 6, is greater than permitted -46: [02:19:03] Explicit valence for atom # 0 P, 7, is greater than permitted -46: [02:19:03] Explicit valence for atom # 0 P, 7, is greater than permitted -46: [02:19:03] Explicit valence for atom # 1 As, 6, is greater than permitted -46: [02:19:03] Explicit valence for atom # 1 As, 6, is greater than permitted -46: [02:19:03] Explicit valence for atom # 1 As, 7, is greater than permitted -46: [02:19:03] Explicit valence for atom # 1 As, 7, is greater than permitted -46: [02:19:03] Explicit valence for atom # 0 Sb, 6, is greater than permitted -46: [02:19:03] Explicit valence for atom # 0 Sb, 6, is greater than permitted -46: [02:19:03] Explicit valence for atom # 0 Sb, 7, is greater than permitted -46: [02:19:03] Explicit valence for atom # 0 Sb, 7, is greater than permitted -46: [02:19:03] Explicit valence for atom # 1 Bi, 6, is greater than permitted -46: [02:19:03] Explicit valence for atom # 1 Bi, 6, is greater than permitted -46: [02:19:03] Explicit valence for atom # 1 Bi, 8, is greater than permitted -46: [02:19:03] Explicit valence for atom # 1 Bi, 8, is greater than permitted -46: =============================================================================== -46: All tests passed (4479 assertions in 107 test cases) -46: - 50/238 Test #46: graphmolTestsCatch ..................... Passed 0.18 sec +58: [11:05:59] WARNING: not removing hydrogen atom without neighbors +58: [11:05:59] WARNING: not removing hydrogen atom without neighbors +58: [11:06:00] WARNING: not removing hydrogen atom without neighbors +58: [11:06:00] WARNING: not removing hydrogen atom without neighbors +58: [11:06:00] WARNING: not removing hydrogen atom without neighbors +58: [11:06:00] WARNING: not removing hydrogen atom without neighbors +58: [11:06:00] WARNING: not removing hydrogen atom without neighbors +58: [11:06:00] WARNING: not removing hydrogen atom without neighbors +58: [11:06:00] WARNING: not removing hydrogen atom without neighbors +58: [11:06:00] WARNING: not removing hydrogen atom without neighbors +58: [11:06:00] WARNING: not removing hydrogen atom without neighbors +58: [11:06:00] Invalid chiral specification on atom 0 +58: [11:06:00] Invalid chiral specification on atom 0 +58: [11:06:00] Invalid chiral specification on atom 0 +58: [11:06:00] Invalid chiral specification on atom 0 +58: [11:06:00] Invalid chiral specification on atom 0 +58: [11:06:00] SMILES Parse Error: unclosed ring for input: 'C1.C11.C' +58: [11:06:00] SMILES Parse Error: unclosed ring for input: 'C1C.CC11CCC' +57: Randomness seeded to: 314292938 +57: =============================================================================== +57: All tests passed (230 assertions in 7 test cases) +57: + 50/238 Test #57: molopsTestsCatch ....................... Passed 0.04 sec test 62 Start 62: smiTestCatch 62: Test command: /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/SmilesParse/smiTestCatch 62: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/SmilesParse 62: Test timeout computed to be: 1500 -58: [02:19:03] SMILES Parse Error: unclosed ring for input: 'C1.C11.C' -58: [02:19:03] SMILES Parse Error: unclosed ring for input: 'C1C.CC11CCC' -62: Randomness seeded to: 3570044102 -62: [02:19:03] SMILES Parse Error: unclosed ring for input: 'c1ccccc' -62: [02:19:03] Can't kekulize mol. Unkekulized atoms: 0 1 2 3 4 -62: [02:19:03] SMARTS Parse Error: unclosed ring for input: 'c1ccccc' -62: [02:19:03] SMARTS Parse Error: unclosed ring for input: 'C1C' -62: [02:19:03] Can't kekulize mol. Unkekulized atoms: 0 1 2 3 4 -62: [02:19:03] SMARTS Parse Error: syntax error while parsing: C)foo -62: [02:19:03] SMARTS Parse Error: Failed parsing SMARTS 'C)foo' for input: 'C)foo' +30: ......[11:06:00] Molecule does not have explicit Hs. Consider calling AddHs() +62: Randomness seeded to: 2188644501 +62: [11:06:00] SMILES Parse Error: unclosed ring for input: 'c1ccccc' +62: [11:06:00] Can't kekulize mol. Unkekulized atoms: 0 1 2 3 4 +62: [11:06:00] SMARTS Parse Error: unclosed ring for input: 'c1ccccc' 58: --C1CCC2(CC1)CCCCC2CCC1CCCC1 -62: [02:19:03] SMARTS Parse Error: syntax error while parsing: CCC |$foo;;bar$| -62: [02:19:03] SMARTS Parse Error: Failed parsing SMARTS 'CCC |$foo;;bar$|' for input: 'CCC |$foo;;bar$|' -62: [02:19:03] unrecognized CXSMILES CONNECT value: 'EU'. Assuming 'eu' -61: [02:19:03] SMARTS Parse Error: syntax error while parsing: [C:10H3]CC -61: [02:19:03] SMARTS Parse Error: Failed parsing SMARTS '[C:10H3]CC' for input: '[C:10H3]CC' -61: [02:19:03] SMARTS Parse Error: syntax error while parsing: [C:10:3]ON -61: [02:19:03] SMARTS Parse Error: Failed parsing SMARTS '[C:10:3]ON' for input: '[C:10:3]ON' -61: [02:19:03] WARNING: merging explicit H queries involved in ORs is not supported. This query will not be merged -61: [02:19:03] WARNING: merging explicit H queries involved in ORs is not supported. This query will not be merged - 51/238 Test #61: smaTest1 ............................... Passed 0.07 sec +62: [11:06:00] SMARTS Parse Error: unclosed ring for input: 'C1C' +62: [11:06:00] Can't kekulize mol. Unkekulized atoms: 0 1 2 3 4 +62: [11:06:00] SMARTS Parse Error: syntax error while parsing: C)foo +62: [11:06:00] SMARTS Parse Error: Failed parsing SMARTS 'C)foo' for input: 'C)foo' +62: [11:06:00] SMARTS Parse Error: syntax error while parsing: CCC |$foo;;bar$| +62: [11:06:00] SMARTS Parse Error: Failed parsing SMARTS 'CCC |$foo;;bar$|' for input: 'CCC |$foo;;bar$|' 58: smi: ClC1CCCCC1 58: smi: ClC1CCCCC1 58: smi: ClC1CCCCC1Br -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 58: smi: c1ccccc1 58: smi: c1ccncc1 58: smi: c1cc[nH]c1 58: smi: c1cc[nH]c1 58: smi: c1cc[pH]c1 -58: [02:19:03] WARNING: could not find number of expected rings. Switching to an approximate ring finding algorithm. -58: [02:19:03] 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: [02:19:03] SMILES Parse Error: syntax error while parsing: c%()ccccc%() -58: [02:19:03] SMILES Parse Error: check for mistakes around position 4: -58: [02:19:03] c%()ccccc%() -58: [02:19:03] ~~~^ -58: [02:19:03] SMILES Parse Error: Failed parsing SMILES 'c%()ccccc%()' for input: 'c%()ccccc%()' -58: [02:19:03] SMILES Parse Error: syntax error while parsing: c%(100000)ccccc%(100000) -58: [02:19:03] SMILES Parse Error: check for mistakes around position 9: -58: [02:19:03] c%(100000)ccccc%(100000) -58: [02:19:03] ~~~~~~~~^ -58: [02:19:03] SMILES Parse Error: Failed parsing SMILES 'c%(100000)ccccc%(100000)' for input: 'c%(100000)ccccc%(100000)' -58: [02:19:03] SMILES Parse Error: duplicated ring closure 1 bonds atom 2 to itself for input: 'C1CC111' -58: [02:19:03] SMILES Parse Error: ring closure 1 duplicates bond between atom 0 and atom 1 for input: 'C1C1' -58: [02:19:03] SMILES Parse Error: syntax error while parsing: COc(c1)cccc1C# -58: [02:19:03] SMILES Parse Error: check for mistakes around position 14: -58: [02:19:03] COc(c1)cccc1C# -58: [02:19:03] ~~~~~~~~~~~~~^ -58: [02:19:03] SMILES Parse Error: Failed parsing SMILES 'COc(c1)cccc1C#' for input: 'COc(c1)cccc1C#' -58: [02:19:03] SMARTS Parse Error: syntax error while parsing: COc(c1)cccc1C# -58: [02:19:03] SMARTS Parse Error: Failed parsing SMARTS 'COc(c1)cccc1C#' for input: 'COc(c1)cccc1C#' -58: [02:19:03] SMILES Parse Error: syntax error while parsing: COc(c1)cccc1C# -58: [02:19:03] SMILES Parse Error: check for mistakes around position 14: -58: [02:19:03] COc(c1)cccc1C# -58: [02:19:03] ~~~~~~~~~~~~~^ -58: [02:19:03] SMILES Parse Error: Failed parsing SMILES 'COc(c1)cccc1C#' for input: 'COc(c1)cccc1C#' -58: [02:19:03] SMARTS Parse Error: syntax error while parsing: COc(c1)cccc1C# -58: [02:19:03] SMARTS Parse Error: Failed parsing SMARTS 'COc(c1)cccc1C#' for input: 'COc(c1)cccc1C#' -58: [02:19:03] SMILES Parse Error: syntax error while parsing: COc(c1)cccc1C# -58: [02:19:03] SMILES Parse Error: check for mistakes around position 14: -58: [02:19:03] COc(c1)cccc1C# -58: [02:19:03] ~~~~~~~~~~~~~^ -58: [02:19:03] SMILES Parse Error: Failed parsing SMILES 'COc(c1)cccc1C#' for input: 'COc(c1)cccc1C#' -58: [02:19:03] SMARTS Parse Error: syntax error while parsing: COc(c1)cccc1C# -58: [02:19:03] 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: [02:19:03] SMILES Parse Error: extra close parentheses while parsing: C) -58: [02:19:03] SMILES Parse Error: check for mistakes around position 2: -58: [02:19:03] C) -58: [02:19:03] ~^ -58: [02:19:03] SMILES Parse Error: Failed parsing SMILES 'C)' for input: 'C)' - 52/238 Test #58: smiTest1 ............................... Passed 0.11 sec -63: Randomness seeded to: 190614079 -63: [02:19:03] WARNING: not removing hydrogen atom with neighbor that has non-tetrahedral stereochemistry -test 64 - Start 64: v2smiTestCatch - -64: Test command: /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/SmilesParse/v2smiTestCatch -64: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/SmilesParse -64: Test timeout computed to be: 1500 -63: [02:19:03] WARNING: not removing hydrogen atom with neighbor that has non-tetrahedral stereochemistry -63: [02:19:03] WARNING: not removing hydrogen atom with neighbor that has non-tetrahedral stereochemistry -63: [02:19:03] WARNING: not removing hydrogen atom with neighbor that has non-tetrahedral stereochemistry -63: [02:19:03] WARNING: not removing hydrogen atom with neighbor that has non-tetrahedral stereochemistry -63: [02:19:03] WARNING: not removing hydrogen atom with neighbor that has non-tetrahedral stereochemistry -62: [02:19:03] w block attempts to set wedging on bond 0 more than once. -62: [02:19:03] improperly formatted w block -64: Randomness seeded to: 4150570578 -64: =============================================================================== -64: All tests passed (14 assertions in 2 test cases) -64: - 53/238 Test #64: v2smiTestCatch ......................... Passed 0.01 sec -test 65 - Start 65: testDepictor - -65: Test command: /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/Depictor/testDepictor -65: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/Depictor -65: Test timeout computed to be: 1500 -62: [02:19:03] atom 3 is not associated with bond 1(1-2) in w block -63: [02:19:03] WARNING: not removing hydrogen atom with neighbor that has non-tetrahedral stereochemistry -63: [02:19:03] WARNING: not removing hydrogen atom with neighbor that has non-tetrahedral stereochemistry -30: ......[02:19:03] Molecule does not have explicit Hs. Consider calling AddHs() -63: [02:19:03] ignoring non-tetrahedral stereo specification since setAllowNontetrahedralChirality() is false. -63: =============================================================================== -63: All tests passed (308 assertions in 9 test cases) -63: - 54/238 Test #63: nontetrahedralCatch .................... Passed 0.05 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 -62: [02:19:03] -62: -62: **** -62: Range Error -62: idx -62: Violation occurred on line 209 in file ./Code/GraphMol/ROMol.cpp -62: Failed Expression: 20 < 20 -62: ---------- -62: Stacktrace: -62: 0# Invar::Invariant::toString[abi:cxx11]() const in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu//lib/libRDKitRDGeneral.so.1 -62: 1# Invar::operator<<(std::ostream&, Invar::Invariant const&) in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu//lib/libRDKitRDGeneral.so.1 -62: 2# RDKit::ROMol::getAtomWithIdx(unsigned int) in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu//lib/libRDKitGraphMol.so.1 -62: 3# RDKit::Canon::canonicalizeFragment(RDKit::ROMol&, int, std::vector >&, std::vector > const&, std::vector >&, boost::dynamic_bitset > const*, std::vector, std::allocator >, std::allocator, std::allocator > > > const*, bool, bool, bool) in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu//lib/libRDKitGraphMol.so.1 -62: 4# RDKit::SmilesWrite::FragmentSmilesConstruct(RDKit::ROMol&, int, std::vector >&, std::vector > const&, RDKit::SmilesWriteParams const&, std::vector >&, std::vector >&, boost::dynamic_bitset > const*, boost::dynamic_bitset > const*, std::vector, std::allocator >, std::allocator, std::allocator > > > const*, std::vector, std::allocator >, std::allocator, std::allocator > > > const*) in /build/reproducible-path/rdkit-202503.1/obj-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# 0x0000AAAAE6D29F8C in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/SmilesParse/smiTestCatch -62: 8# 0x0000AAAAE6D7A9EC in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/SmilesParse/smiTestCatch -62: 9# 0x0000AAAAE6D7B3A0 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/SmilesParse/smiTestCatch -62: 10# 0x0000AAAAE6D7B7D4 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/SmilesParse/smiTestCatch -62: 11# 0x0000AAAAE6D4FB98 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/SmilesParse/smiTestCatch -62: 12# 0x0000AAAAE6D500E4 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/SmilesParse/smiTestCatch -62: 13# 0x0000AAAAE6CE57D0 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/SmilesParse/smiTestCatch -62: 14# 0x0000FFFF9B95229C in /lib/aarch64-linux-gnu/libc.so.6 -62: 15# __libc_start_main in /lib/aarch64-linux-gnu/libc.so.6 -62: 16# 0x0000AAAAE6CE58B0 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/SmilesParse/smiTestCatch -62: ---------- -62: **** -62: -35: [02:19:03] Maximum BFS search size exceeded. -35: This is likely due to a highly symmetric fused ring system. -62: [02:19:03] -62: -62: **** -62: Range Error -62: idx -62: Violation occurred on line 209 in file ./Code/GraphMol/ROMol.cpp -62: Failed Expression: 20 < 20 -62: ---------- -62: Stacktrace: -62: 0# Invar::Invariant::toString[abi:cxx11]() const in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu//lib/libRDKitRDGeneral.so.1 -62: 1# Invar::operator<<(std::ostream&, Invar::Invariant const&) in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu//lib/libRDKitRDGeneral.so.1 -62: 2# RDKit::ROMol::getAtomWithIdx(unsigned int) in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu//lib/libRDKitGraphMol.so.1 -62: 3# RDKit::Canon::canonicalizeFragment(RDKit::ROMol&, int, std::vector >&, std::vector > const&, std::vector >&, boost::dynamic_bitset > const*, std::vector, std::allocator >, std::allocator, std::allocator > > > const*, bool, bool, bool) in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu//lib/libRDKitGraphMol.so.1 -62: 4# RDKit::SmilesWrite::FragmentSmilesConstruct(RDKit::ROMol&, int, std::vector >&, std::vector > const&, RDKit::SmilesWriteParams const&, std::vector >&, std::vector >&, boost::dynamic_bitset > const*, boost::dynamic_bitset > const*, std::vector, std::allocator >, std::allocator, std::allocator > > > const*, std::vector, std::allocator >, std::allocator, std::allocator > > > const*) in /build/reproducible-path/rdkit-202503.1/obj-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# 0x0000AAAAE6D29F8C in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/SmilesParse/smiTestCatch -62: 8# 0x0000AAAAE6D7A9EC in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/SmilesParse/smiTestCatch -62: 9# 0x0000AAAAE6D7B3A0 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/SmilesParse/smiTestCatch -62: 10# 0x0000AAAAE6D7B7D4 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/SmilesParse/smiTestCatch -62: 11# 0x0000AAAAE6D4FB98 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/SmilesParse/smiTestCatch -62: 12# 0x0000AAAAE6D500E4 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/SmilesParse/smiTestCatch -62: 13# 0x0000AAAAE6CE57D0 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/SmilesParse/smiTestCatch -62: 14# 0x0000FFFF9B95229C in /lib/aarch64-linux-gnu/libc.so.6 -62: 15# __libc_start_main in /lib/aarch64-linux-gnu/libc.so.6 -62: 16# 0x0000AAAAE6CE58B0 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/SmilesParse/smiTestCatch -62: ---------- -62: **** -62: -62: [02:19:03] SMARTS Parse Error: unclosed ring for input: 'C1.C2.C3.C4.C5' -62: [02:19:03] SMILES Parse Error: unclosed ring for input: 'C1.C2.C3.C4.C5' -62: [02:19:03] SMARTS Parse Error: syntax error while parsing: C1C)foo -62: [02:19:03] SMARTS Parse Error: Failed parsing SMARTS 'C1C)foo' for input: 'C1C)foo' -62: [02:19:03] SMILES Parse Error: extra close parentheses while parsing: C1C)foo -62: [02:19:03] SMILES Parse Error: check for mistakes around position 4: -62: [02:19:03] C1C)foo -62: [02:19:03] ~~~^ -62: [02:19:03] SMILES Parse Error: Failed parsing SMILES 'C1C)foo' for input: 'C1C)foo' -60: Randomness seeded to: 932430545 +62: [11:06:00] unrecognized CXSMILES CONNECT value: 'EU'. Assuming 'eu' +58: [11:06:00] WARNING: could not find number of expected rings. Switching to an approximate ring finding algorithm. +58: [11:06:00] WARNING: could not find number of expected rings. Switching to an approximate ring finding algorithm. +60: Randomness seeded to: 3615571034 60: Test 60: 60: ShortAtropisomerNoCoords.cxsmi @@ -18210,26 +18073,76 @@ 60: 60: BMS-986142_atrop5.cxsmi 60: -60: [02:19:03] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored -60: [02:19:03] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored -62: =============================================================================== -62: All tests passed (1588 assertions in 69 test cases) -62: -60: [02:19:03] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored -60: [02:19:03] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored -60: [02:19:03] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored -60: [02:19:03] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored - 55/238 Test #62: smiTestCatch ........................... Passed 0.13 sec -test 67 - Start 67: pyDepictor +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 +60: [11:06:00] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored +58: [11:06:00] SMILES Parse Error: syntax error while parsing: c%()ccccc%() +58: [11:06:00] SMILES Parse Error: check for mistakes around position 4: +58: [11:06:00] c%()ccccc%() +58: [11:06:00] ~~~^ +58: [11:06:00] SMILES Parse Error: Failed parsing SMILES 'c%()ccccc%()' for input: 'c%()ccccc%()' +58: [11:06:00] SMILES Parse Error: syntax error while parsing: c%(100000)ccccc%(100000) +58: [11:06:00] SMILES Parse Error: check for mistakes around position 9: +58: [11:06:00] c%(100000)ccccc%(100000) +58: [11:06:00] ~~~~~~~~^ +58: [11:06:00] SMILES Parse Error: Failed parsing SMILES 'c%(100000)ccccc%(100000)' for input: 'c%(100000)ccccc%(100000)' +60: [11:06:00] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored +58: [11:06:00] SMILES Parse Error: duplicated ring closure 1 bonds atom 2 to itself for input: 'C1CC111' +60: [11:06:00] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored +60: [11:06:00] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored +58: [11:06:00] SMILES Parse Error: ring closure 1 duplicates bond between atom 0 and atom 1 for input: 'C1C1' +60: [11:06:00] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored +60: [11:06:00] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored +60: [11:06:00] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored +60: [11:06:00] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored +61: [11:06:00] SMARTS Parse Error: syntax error while parsing: [C:10H3]CC +61: [11:06:00] SMARTS Parse Error: Failed parsing SMARTS '[C:10H3]CC' for input: '[C:10H3]CC' +61: [11:06:00] SMARTS Parse Error: syntax error while parsing: [C:10:3]ON +61: [11:06:00] SMARTS Parse Error: Failed parsing SMARTS '[C:10:3]ON' for input: '[C:10:3]ON' +61: [11:06:00] WARNING: merging explicit H queries involved in ORs is not supported. This query will not be merged +61: [11:06:00] WARNING: merging explicit H queries involved in ORs is not supported. This query will not be merged +35: [11:06:00] Maximum BFS search size exceeded. +35: This is likely due to a highly symmetric fused ring system. +60: [11:06:00] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored +60: [11:06:00] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored +58: [11:06:00] SMILES Parse Error: syntax error while parsing: COc(c1)cccc1C# +58: [11:06:00] SMILES Parse Error: check for mistakes around position 14: +58: [11:06:00] COc(c1)cccc1C# +58: [11:06:00] ~~~~~~~~~~~~~^ +58: [11:06:00] SMILES Parse Error: Failed parsing SMILES 'COc(c1)cccc1C#' for input: 'COc(c1)cccc1C#' +58: [11:06:00] SMARTS Parse Error: syntax error while parsing: COc(c1)cccc1C# +58: [11:06:00] SMARTS Parse Error: Failed parsing SMARTS 'COc(c1)cccc1C#' for input: 'COc(c1)cccc1C#' +58: [11:06:00] SMILES Parse Error: syntax error while parsing: COc(c1)cccc1C# +58: [11:06:00] SMILES Parse Error: check for mistakes around position 14: +58: [11:06:00] COc(c1)cccc1C# +58: [11:06:00] ~~~~~~~~~~~~~^ +58: [11:06:00] SMILES Parse Error: Failed parsing SMILES 'COc(c1)cccc1C#' for input: 'COc(c1)cccc1C#' +58: [11:06:00] SMARTS Parse Error: syntax error while parsing: COc(c1)cccc1C# +58: [11:06:00] SMARTS Parse Error: Failed parsing SMARTS 'COc(c1)cccc1C#' for input: 'COc(c1)cccc1C#' +58: [11:06:00] SMILES Parse Error: syntax error while parsing: COc(c1)cccc1C# +58: [11:06:00] SMILES Parse Error: check for mistakes around position 14: +58: [11:06:00] COc(c1)cccc1C# +58: [11:06:00] ~~~~~~~~~~~~~^ +58: [11:06:00] SMILES Parse Error: Failed parsing SMILES 'COc(c1)cccc1C#' for input: 'COc(c1)cccc1C#' +58: [11:06:00] SMARTS Parse Error: syntax error while parsing: COc(c1)cccc1C# +58: [11:06:00] 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: [11:06:00] SMILES Parse Error: extra close parentheses while parsing: C) +58: [11:06:00] SMILES Parse Error: check for mistakes around position 2: +58: [11:06:00] C) +58: [11:06:00] ~^ +58: [11:06:00] SMILES Parse Error: Failed parsing SMILES 'C)' for input: 'C)' + 51/238 Test #58: smiTest1 ............................... Passed 0.11 sec +test 63 + Start 63: nontetrahedralCatch -67: Test command: /usr/bin/python3 "/build/reproducible-path/rdkit-202503.1/Code/GraphMol/Depictor/Wrap/testDepictor.py" -67: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/Depictor/Wrap -67: Test timeout computed to be: 1500 -60: [02:19:03] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored -60: [02:19:03] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored -60: [02:19:03] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored -60: [02:19:03] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored +63: Test command: /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/SmilesParse/nontetrahedralCatch +63: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/SmilesParse +63: Test timeout computed to be: 1500 60: Test 60: 60: BMS-986142_atrop6.cxsmi @@ -18238,20 +18151,43 @@ 60: 60: BMS-986142_atropBad1.cxsmi 60: -60: [02:19:03] The 2 defining bonds for an atropisomer are co-planar - atoms are: 6 7 -60: [02:19:03] The 2 defining bonds for an atropisomer are co-planar - atoms are: 6 7 -60: [02:19:03] The 2 defining bonds for an atropisomer are co-planar - atoms are: 6 7 -60: [02:19:03] The 2 defining bonds for an atropisomer are co-planar - atoms are: 6 7 -60: [02:19:03] The 2 defining bonds for an atropisomer are co-planar - atoms are: 6 7 +60: [11:06:00] The 2 defining bonds for an atropisomer are co-planar - atoms are: 6 7 +60: [11:06:00] The 2 defining bonds for an atropisomer are co-planar - atoms are: 6 7 +60: [11:06:00] The 2 defining bonds for an atropisomer are co-planar - atoms are: 6 7 +60: [11:06:00] The 2 defining bonds for an atropisomer are co-planar - atoms are: 6 7 +60: [11:06:00] The 2 defining bonds for an atropisomer are co-planar - atoms are: 6 7 + 52/238 Test #61: smaTest1 ............................... Passed 0.10 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: Test 60: 60: BMS-986142_atropBad2.cxsmi 60: -60: [02:19:03] The bonds on one end of an atropisomer are both UP or both DOWN - atoms are: 6 7 -60: [02:19:03] The bonds on one end of an atropisomer are both UP or both DOWN - atoms are: 6 7 -60: [02:19:03] The bonds on one end of an atropisomer are both UP or both DOWN - atoms are: 6 7 -60: [02:19:03] The bonds on one end of an atropisomer are both UP or both DOWN - atoms are: 6 7 -60: [02:19:03] The bonds on one end of an atropisomer are both UP or both DOWN - atoms are: 6 7 +60: [11:06:00] The bonds on one end of an atropisomer are both UP or both DOWN - atoms are: 6 7 +60: [11:06:00] The bonds on one end of an atropisomer are both UP or both DOWN - atoms are: 6 7 +60: [11:06:00] The bonds on one end of an atropisomer are both UP or both DOWN - atoms are: 6 7 +60: [11:06:00] The bonds on one end of an atropisomer are both UP or both DOWN - atoms are: 6 7 +60: [11:06:00] The bonds on one end of an atropisomer are both UP or both DOWN - atoms are: 6 7 +64: Randomness seeded to: 1373460811 +64: =============================================================================== +64: All tests passed (14 assertions in 2 test cases) +64: + 53/238 Test #64: v2smiTestCatch ......................... Passed 0.01 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 +63: Randomness seeded to: 30765263 +62: [11:06:00] w block attempts to set wedging on bond 0 more than once. +62: [11:06:00] improperly formatted w block +62: [11:06:00] atom 3 is not associated with bond 1(1-2) in w block +63: [11:06:00] WARNING: not removing hydrogen atom with neighbor that has non-tetrahedral stereochemistry 60: Test 60: 60: JDQ443_3d.cxsmi @@ -18276,22 +18212,45 @@ 60: 60: JDQ443_atropBad1.cxsmi 60: -60: [02:19:03] The 2 defining bonds for an atropisomer are co-planar - atoms are: 2 3 -60: [02:19:03] The 2 defining bonds for an atropisomer are co-planar - atoms are: 2 3 -60: [02:19:03] The 2 defining bonds for an atropisomer are co-planar - atoms are: 2 3 -60: [02:19:03] The 2 defining bonds for an atropisomer are co-planar - atoms are: 2 3 -60: [02:19:03] The 2 defining bonds for an atropisomer are co-planar - atoms are: 2 3 -66: Randomness seeded to: 3732736271 -66: =============================================================================== -66: All tests passed (580 assertions in 18 test cases) -66: - 56/238 Test #66: depictorCatch .......................... Passed 0.09 sec -test 68 - Start 68: testMrvToMol - -68: Test command: /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/MarvinParse/testMrvToMol -68: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/MarvinParse -68: Test timeout computed to be: 1500 +60: [11:06:00] The 2 defining bonds for an atropisomer are co-planar - atoms are: 2 3 +60: [11:06:00] The 2 defining bonds for an atropisomer are co-planar - atoms are: 2 3 +60: [11:06:00] The 2 defining bonds for an atropisomer are co-planar - atoms are: 2 3 +60: [11:06:00] The 2 defining bonds for an atropisomer are co-planar - atoms are: 2 3 +60: [11:06:00] The 2 defining bonds for an atropisomer are co-planar - atoms are: 2 3 +63: [11:06:00] WARNING: not removing hydrogen atom with neighbor that has non-tetrahedral stereochemistry +63: [11:06:00] WARNING: not removing hydrogen atom with neighbor that has non-tetrahedral stereochemistry +63: [11:06:00] WARNING: not removing hydrogen atom with neighbor that has non-tetrahedral stereochemistry +62: [11:06:00] +62: +62: **** +62: Range Error +62: idx +62: Violation occurred on line 209 in file ./Code/GraphMol/ROMol.cpp +62: Failed Expression: 20 < 20 +62: ---------- +62: Stacktrace: +62: 0# Invar::Invariant::toString[abi:cxx11]() const in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu//lib/libRDKitRDGeneral.so.1 +62: 1# Invar::operator<<(std::ostream&, Invar::Invariant const&) in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu//lib/libRDKitRDGeneral.so.1 +62: 2# RDKit::ROMol::getAtomWithIdx(unsigned int) in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu//lib/libRDKitGraphMol.so.1 +62: 3# RDKit::Canon::canonicalizeFragment(RDKit::ROMol&, int, std::vector >&, std::vector > const&, std::vector >&, boost::dynamic_bitset > const*, std::vector, std::allocator >, std::allocator, std::allocator > > > const*, bool, bool, bool) in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu//lib/libRDKitGraphMol.so.1 +62: 4# RDKit::SmilesWrite::FragmentSmilesConstruct(RDKit::ROMol&, int, std::vector >&, std::vector > const&, RDKit::SmilesWriteParams const&, std::vector >&, std::vector >&, boost::dynamic_bitset > const*, boost::dynamic_bitset > const*, std::vector, std::allocator >, std::allocator, std::allocator > > > const*, std::vector, std::allocator >, std::allocator, std::allocator > > > const*) in /build/reproducible-path/rdkit-202503.1/obj-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# 0x0000AAAABACC9F8C in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/SmilesParse/smiTestCatch +62: 8# 0x0000AAAABAD1A9EC in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/SmilesParse/smiTestCatch +62: 9# 0x0000AAAABAD1B3A0 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/SmilesParse/smiTestCatch +62: 10# 0x0000AAAABAD1B7D4 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/SmilesParse/smiTestCatch +62: 11# 0x0000AAAABACEFB98 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/SmilesParse/smiTestCatch +62: 12# 0x0000AAAABACF00E4 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/SmilesParse/smiTestCatch +62: 13# 0x0000AAAABAC857D0 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/SmilesParse/smiTestCatch +62: 14# 0x0000FFFFA67E229C in /lib/aarch64-linux-gnu/libc.so.6 +62: 15# __libc_start_main in /lib/aarch64-linux-gnu/libc.so.6 +62: 16# 0x0000AAAABAC858B0 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/SmilesParse/smiTestCatch +62: ---------- +62: **** +62: +63: [11:06:00] WARNING: not removing hydrogen atom with neighbor that has non-tetrahedral stereochemistry +63: [11:06:00] WARNING: not removing hydrogen atom with neighbor that has non-tetrahedral stereochemistry 60: Test 60: 60: RP-6306_atrop1.cxsmi @@ -18312,16 +18271,19 @@ 60: 60: RP-6306_atrop5.cxsmi 60: -60: [02:19:03] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored -60: [02:19:03] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored -60: [02:19:03] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored -60: [02:19:03] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored -60: [02:19:03] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored -60: [02:19:03] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored -60: [02:19:03] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored -60: [02:19:03] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored -60: [02:19:03] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored -60: [02:19:03] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored +60: [11:06:00] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored +60: [11:06:00] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored +60: [11:06:00] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored +60: [11:06:00] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored +60: [11:06:00] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored +60: [11:06:00] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored +60: [11:06:00] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored +60: [11:06:00] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored +60: [11:06:00] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored +60: [11:06:00] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored +62: [11:06:00] +62: +62: **** 60: Test 60: 60: RP-6306_atrop6.cxsmi @@ -18330,30 +18292,78 @@ 60: 60: RP-6306_atropBad1.cxsmi 60: -60: [02:19:03] The 2 defining bonds for an atropisomer are co-planar - atoms are: 4 5 -60: [02:19:03] The 2 defining bonds for an atropisomer are co-planar - atoms are: 4 5 -60: [02:19:03] The 2 defining bonds for an atropisomer are co-planar - atoms are: 4 5 -60: [02:19:03] The 2 defining bonds for an atropisomer are co-planar - atoms are: 4 5 -60: [02:19:03] The 2 defining bonds for an atropisomer are co-planar - atoms are: 4 5 +60: [11:06:00] The 2 defining bonds for an atropisomer are co-planar - atoms are: 4 5 +60: [11:06:00] The 2 defining bonds for an atropisomer are co-planar - atoms are: 4 5 +62: Range Error +62: idx +62: Violation occurred on line 209 in file ./Code/GraphMol/ROMol.cpp +62: Failed Expression: 20 < 20 +62: ---------- +62: Stacktrace: +62: 0# Invar::Invariant::toString[abi:cxx11]() const in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu//lib/libRDKitRDGeneral.so.1 +62: 1# Invar::operator<<(std::ostream&, Invar::Invariant const&) in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu//lib/libRDKitRDGeneral.so.1 +62: 2# RDKit::ROMol::getAtomWithIdx(unsigned int) in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu//lib/libRDKitGraphMol.so.1 +62: 3# RDKit::Canon::canonicalizeFragment(RDKit::ROMol&, int, std::vector >&, std::vector > const&, std::vector >&, boost::dynamic_bitset > const*, std::vector, std::allocator >, std::allocator, std::allocator > > > const*, bool, bool, bool) in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu//lib/libRDKitGraphMol.so.1 +62: 4# RDKit::SmilesWrite::FragmentSmilesConstruct(RDKit::ROMol&, int, std::vector >&, std::vector > const&, RDKit::SmilesWriteParams const&, std::vector >&, std::vector >&, boost::dynamic_bitset > const*, boost::dynamic_bitset > const*, std::vector, std::allocator >, std::allocator, std::allocator > > > const*, std::vector, std::allocator >, std::allocator, std::allocator > > > const*) in /build/reproducible-path/rdkit-202503.1/obj-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# 0x0000AAAABACC9F8C in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/SmilesParse/smiTestCatch +62: 8# 0x0000AAAABAD1A9EC in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/SmilesParse/smiTestCatch +62: 9# 0x0000AAAABAD1B3A0 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/SmilesParse/smiTestCatch +62: 10# 0x0000AAAABAD1B7D4 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/SmilesParse/smiTestCatch +62: 11# 0x0000AAAABACEFB98 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/SmilesParse/smiTestCatch +62: 12# 0x0000AAAABACF00E4 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/SmilesParse/smiTestCatch +62: 13# 0x0000AAAABAC857D0 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/SmilesParse/smiTestCatch +62: 14# 0x0000FFFFA67E229C in /lib/aarch64-linux-gnu/libc.so.6 +62: 15# __libc_start_main in /lib/aarch64-linux-gnu/libc.so.6 +62: 16# 0x0000AAAABAC858B0 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/SmilesParse/smiTestCatch +62: ---------- +62: **** +62: +62: [11:06:00] SMARTS Parse Error: unclosed ring for input: 'C1.C2.C3.C4.C5' +62: [11:06:00] SMILES Parse Error: unclosed ring for input: 'C1.C2.C3.C4.C5' +62: [11:06:00] SMARTS Parse Error: syntax error while parsing: C1C)foo +62: [11:06:00] SMARTS Parse Error: Failed parsing SMARTS 'C1C)foo' for input: 'C1C)foo' +62: [11:06:00] SMILES Parse Error: extra close parentheses while parsing: C1C)foo +62: [11:06:00] SMILES Parse Error: check for mistakes around position 4: +62: [11:06:00] C1C)foo +62: [11:06:00] ~~~^ +62: [11:06:00] SMILES Parse Error: Failed parsing SMILES 'C1C)foo' for input: 'C1C)foo' +60: [11:06:00] The 2 defining bonds for an atropisomer are co-planar - atoms are: 4 5 +60: [11:06:00] The 2 defining bonds for an atropisomer are co-planar - atoms are: 4 5 +60: [11:06:00] The 2 defining bonds for an atropisomer are co-planar - atoms are: 4 5 60: Test 60: 60: RP-6306_atropBad2.cxsmi 60: -60: [02:19:03] The bonds on one end of an atropisomer are both UP or both DOWN - atoms are: 4 5 -60: [02:19:03] The bonds on one end of an atropisomer are both UP or both DOWN - atoms are: 4 5 -68: Using new chirality perception -68: Test -68: -68: rxnStereoMarkedCrossed.mrv -68: -68: Test -68: -68: 145323811.mol -68: -60: [02:19:03] The bonds on one end of an atropisomer are both UP or both DOWN - atoms are: 4 5 -60: [02:19:03] The bonds on one end of an atropisomer are both UP or both DOWN - atoms are: 4 5 -60: [02:19:03] The bonds on one end of an atropisomer are both UP or both DOWN - atoms are: 4 5 -68: [02:19:03] unsupported number of radical electrons 5 +60: [11:06:00] The bonds on one end of an atropisomer are both UP or both DOWN - atoms are: 4 5 +60: [11:06:00] The bonds on one end of an atropisomer are both UP or both DOWN - atoms are: 4 5 +63: [11:06:00] WARNING: not removing hydrogen atom with neighbor that has non-tetrahedral stereochemistry +63: [11:06:00] WARNING: not removing hydrogen atom with neighbor that has non-tetrahedral stereochemistry +60: [11:06:00] The bonds on one end of an atropisomer are both UP or both DOWN - atoms are: 4 5 +60: [11:06:00] The bonds on one end of an atropisomer are both UP or both DOWN - atoms are: 4 5 +60: [11:06:00] The bonds on one end of an atropisomer are both UP or both DOWN - atoms are: 4 5 +62: =============================================================================== +62: All tests passed (1588 assertions in 69 test cases) +62: + 54/238 Test #62: smiTestCatch ........................... Passed 0.13 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: [11:06:00] ignoring non-tetrahedral stereo specification since setAllowNontetrahedralChirality() is false. +63: =============================================================================== +63: All tests passed (308 assertions in 9 test cases) +63: + 55/238 Test #63: nontetrahedralCatch .................... Passed 0.06 sec +test 67 + Start 67: pyDepictor + +67: Test command: /usr/bin/python3 "/build/reproducible-path/rdkit-202503.1/Code/GraphMol/Depictor/Wrap/testDepictor.py" +67: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/Depictor/Wrap +67: Test timeout computed to be: 1500 60: Test 60: 60: RP-6306_3d.cxsmi @@ -18378,81 +18388,34 @@ 60: 60: Sotorasib_atrop5.cxsmi 60: -60: [02:19:03] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 13 ignored -60: [02:19:03] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 13 ignored -60: [02:19:03] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 13 ignored -60: [02:19:03] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 13 ignored -60: [02:19:03] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 13 ignored -60: [02:19:03] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 13 ignored -60: [02:19:03] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 13 ignored -60: [02:19:03] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 13 ignored -68: Test -68: -68: NewChiralTest.sdf -68: -68: Test -68: -68: NewChiralTest.sdf -68: -68: Test -68: -68: NewChiralTestNoChiral.sdf -68: -68: Test -68: -68: NewChiralTestNoChiral.sdf -68: -68: Test -68: -68: NewChiralTestAllChiral.sdf -68: -68: Test -68: -68: NewChiralTestAllChiral.sdf -68: -68: Test -68: -68: vendor839.sdf -68: -68: Test -68: -68: ProblemShort.mol -68: -60: [02:19:03] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 13 ignored -60: [02:19:03] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 13 ignored +60: [11:06:00] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 13 ignored +60: [11:06:00] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 13 ignored +60: [11:06:00] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 13 ignored +60: [11:06:00] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 13 ignored +60: [11:06:00] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 13 ignored +60: [11:06:00] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 13 ignored +60: [11:06:00] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 13 ignored +60: [11:06:00] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 13 ignored +60: [11:06:00] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 13 ignored +60: [11:06:00] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 13 ignored 60: Test 60: 60: Sotorasib_atropBad1.cxsmi 60: -68: [02:19:03] For a MultipleSgroup expansion, the matching orphaned bond was not found -68: The multiple sgroup will be ignored -60: [02:19:03] The 2 defining bonds for an atropisomer are co-planar - atoms are: 13 14 -60: [02:19:03] The 2 defining bonds for an atropisomer are co-planar - atoms are: 13 14 -60: [02:19:04] The 2 defining bonds for an atropisomer are co-planar - atoms are: 13 14 -60: [02:19:04] The 2 defining bonds for an atropisomer are co-planar - atoms are: 13 14 -60: [02:19:04] The 2 defining bonds for an atropisomer are co-planar - atoms are: 13 14 +60: [11:06:00] The 2 defining bonds for an atropisomer are co-planar - atoms are: 13 14 +60: [11:06:00] The 2 defining bonds for an atropisomer are co-planar - atoms are: 13 14 +60: [11:06:00] The 2 defining bonds for an atropisomer are co-planar - atoms are: 13 14 +60: [11:06:00] The 2 defining bonds for an atropisomer are co-planar - atoms are: 13 14 +60: [11:06:00] The 2 defining bonds for an atropisomer are co-planar - atoms are: 13 14 60: Test 60: 60: Sotorasib_atropBad2.cxsmi 60: -60: [02:19:04] The bonds on one end of an atropisomer are both UP or both DOWN - atoms are: 13 14 -60: [02:19:04] The bonds on one end of an atropisomer are both UP or both DOWN - atoms are: 13 14 -60: [02:19:04] The bonds on one end of an atropisomer are both UP or both DOWN - atoms are: 13 14 -60: [02:19:04] The bonds on one end of an atropisomer are both UP or both DOWN - atoms are: 13 14 -60: [02:19:04] The bonds on one end of an atropisomer are both UP or both DOWN - atoms are: 13 14 -30: ... -30: ---------------------------------------------------------------------- -30: Ran 12 tests in 0.521s -30: -30: OK -65: [02:19:04] Warning: stereochemistry around double bond may be incorrect in depiction. -35: [02:19:04] 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 +60: [11:06:00] The bonds on one end of an atropisomer are both UP or both DOWN - atoms are: 13 14 +60: [11:06:00] The bonds on one end of an atropisomer are both UP or both DOWN - atoms are: 13 14 +60: [11:06:00] The bonds on one end of an atropisomer are both UP or both DOWN - atoms are: 13 14 +60: [11:06:00] The bonds on one end of an atropisomer are both UP or both DOWN - atoms are: 13 14 +60: [11:06:00] 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 @@ -18477,39 +18440,115 @@ 60: 60: ZM374979_atropBad1.cxsmi 60: -60: [02:19:04] The 2 defining bonds for an atropisomer are co-planar - atoms are: 0 31 -60: [02:19:04] The 2 defining bonds for an atropisomer are co-planar - atoms are: 0 31 -35: [02:19:04] ----------------------- -35: Testing isRingFused -60: [02:19:04] The 2 defining bonds for an atropisomer are co-planar - atoms are: 0 31 -60: [02:19:04] The 2 defining bonds for an atropisomer are co-planar - atoms are: 0 31 - 57/238 Test #35: graphmolMolOpsTest ..................... Passed 0.62 sec +60: [11:06:00] The 2 defining bonds for an atropisomer are co-planar - atoms are: 0 31 +60: [11:06:00] The 2 defining bonds for an atropisomer are co-planar - atoms are: 0 31 +60: [11:06:00] The 2 defining bonds for an atropisomer are co-planar - atoms are: 0 31 +60: [11:06:00] The 2 defining bonds for an atropisomer are co-planar - atoms are: 0 31 +60: [11:06:00] The 2 defining bonds for an atropisomer are co-planar - atoms are: 0 31 +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: [11:06:00] The 2 defining bonds for an atropisomer are co-planar - atoms are: 11 12 +60: [11:06:00] The 2 defining bonds for an atropisomer are co-planar - atoms are: 11 12 +60: [11:06:00] The 2 defining bonds for an atropisomer are co-planar - atoms are: 11 12 +60: [11:06:00] The 2 defining bonds for an atropisomer are co-planar - atoms are: 11 12 +60: [11:06:00] The 2 defining bonds for an atropisomer are co-planar - atoms are: 11 12 +30: ... +30: ---------------------------------------------------------------------- +30: Ran 12 tests in 0.493s +30: +30: OK +66: Randomness seeded to: 1320779667 +66: =============================================================================== +66: All tests passed (580 assertions in 18 test cases) +66: + 56/238 Test #66: depictorCatch .......................... Passed 0.12 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 + 57/238 Test #30: pyForceFieldConstraints ................ Passed 0.71 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 -60: [02:19:04] The 2 defining bonds for an atropisomer are co-planar - atoms are: 0 31 - 58/238 Test #65: testDepictor ........................... Passed 0.27 sec +35: [11:06:00] Maximum BFS search size exceeded. +35: This is likely due to a highly symmetric fused ring system. +65: [11:06:00] Warning: stereochemistry around double bond may be incorrect in depiction. +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: [11:06:00] ----------------------- +35: Testing isRingFused + 58/238 Test #35: graphmolMolOpsTest ..................... Passed 0.61 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 - 59/238 Test #30: pyForceFieldConstraints ................ Passed 0.76 sec +68: Using new chirality perception +68: Test +68: +68: rxnStereoMarkedCrossed.mrv +68: +68: Test +68: +68: 145323811.mol +68: +70: [11:06:00] ---- Running with POSIX locale ----- + 59/238 Test #65: testDepictor ........................... Passed 0.22 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 -70: [02:19:04] ---- Running with POSIX locale ----- -71: Randomness seeded to: 1437400233 +68: [11:06:00] unsupported number of radical electrons 5 +69: *************************************** +69: *************************************** +70: [11:06:00] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +70: [11:06:00] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +69: [11:06:00] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +69: [11:06:00] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +70: [11:06:00] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +70: [11:06:00] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +70: [11:06:00] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +70: [11:06:00] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +71: Randomness seeded to: 3197646367 71: =============================================================================== 71: All tests passed (15 assertions in 3 test cases) 71: +70: [11:06:00] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored +70: [11:06:00] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored +70: [11:06:00] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored 60/238 Test #71: testSquiggleDoubleBonds ................ Passed 0.02 sec test 72 Start 72: testMolSupplier @@ -18517,179 +18556,205 @@ 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: *************************************** -69: *************************************** -69: [02:19:04] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -69: [02:19:04] 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: [02:19:04] The 2 defining bonds for an atropisomer are co-planar - atoms are: 11 12 -60: [02:19:04] The 2 defining bonds for an atropisomer are co-planar - atoms are: 11 12 -60: [02:19:04] The 2 defining bonds for an atropisomer are co-planar - atoms are: 11 12 -60: [02:19:04] The 2 defining bonds for an atropisomer are co-planar - atoms are: 11 12 -60: [02:19:04] The 2 defining bonds for an atropisomer are co-planar - atoms are: 11 12 -70: [02:19:04] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -70: [02:19:04] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -70: [02:19:04] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -70: [02:19:04] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -70: [02:19:04] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -70: [02:19:04] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -69: [02:19:04] bond with order 0 found on line 7. This is not part of the MDL specification. -72: [02:19:04] +70: [11:06:00] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored +70: [11:06:00] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored +70: [11:06:00] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored +70: [11:06:00] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored +70: [11:06:00] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored +70: [11:06:00] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored +70: [11:06:00] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored +70: [11:06:00] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored +70: [11:06:00] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored +69: [11:06:00] bond with order 0 found on line 7. This is not part of the MDL specification. +70: [11:06:00] The bonds on one end of an atropisomer are both UP or both DOWN - atoms are: 7 29 +70: [11:06:00] The bonds on one end of an atropisomer are both UP or both DOWN - atoms are: 7 29 +70: [11:06:00] The bonds on one end of an atropisomer are both UP or both DOWN - atoms are: 7 29 +68: Test +68: +68: NewChiralTest.sdf +68: +68: Test +68: +68: NewChiralTest.sdf +68: +68: Test +68: +68: NewChiralTestNoChiral.sdf +68: +68: Test +68: +68: NewChiralTestNoChiral.sdf +68: +68: Test +68: +68: NewChiralTestAllChiral.sdf +68: +68: Test +68: +68: NewChiralTestAllChiral.sdf +68: +68: Test +68: +68: vendor839.sdf +68: +68: Test +68: +68: ProblemShort.mol +68: +70: [11:06:00] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +70: [11:06:00] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +68: [11:06:00] For a MultipleSgroup expansion, the matching orphaned bond was not found +68: The multiple sgroup will be ignored +70: [11:06:00] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +70: [11:06:00] The 2 defining bonds for an atropisomer are co-planar - atoms are: 17 21 +70: [11:06:00] The 2 defining bonds for an atropisomer are co-planar - atoms are: 17 21 +70: [11:06:00] The 2 defining bonds for an atropisomer are co-planar - atoms are: 17 21 +70: [11:06:00] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 2 ignored +70: [11:06:00] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 2 ignored +70: [11:06:00] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 2 ignored +70: [11:06:00] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 2 ignored +70: [11:06:00] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 2 ignored +70: [11:06:00] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 2 ignored +70: [11:06:00] The bonds on one end of an atropisomer are both UP or both DOWN - atoms are: 2 8 +70: [11:06:00] The bonds on one end of an atropisomer are both UP or both DOWN - atoms are: 2 8 +70: [11:06:00] The bonds on one end of an atropisomer are both UP or both DOWN - atoms are: 2 8 +70: [11:06:00] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 2 ignored +70: [11:06:00] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 2 ignored +70: [11:06:00] The 2 defining bonds for an atropisomer are co-planar - atoms are: 2 8 +72: [11:06:00] 72: ----------------------------------------- -70: [02:19:04] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored -70: [02:19:04] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored -70: [02:19:04] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored -70: [02:19:04] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored -70: [02:19:04] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored -70: [02:19:04] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored -70: [02:19:04] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored -70: [02:19:04] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored -70: [02:19:04] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored -70: [02:19:04] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored -70: [02:19:04] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored -70: [02:19:04] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored -70: [02:19:04] The bonds on one end of an atropisomer are both UP or both DOWN - atoms are: 7 29 -70: [02:19:04] The bonds on one end of an atropisomer are both UP or both DOWN - atoms are: 7 29 -70: [02:19:04] The bonds on one end of an atropisomer are both UP or both DOWN - atoms are: 7 29 -69: [02:19:04] Skipping unrecognized collection type at line 26: MDLV30/HILITE BONDS=(1 7) -69: [02:19:04] Skipping unrecognized collection type at line 27: MDLV30/HILITE ATOMS=(1 7) -69: [02:19:04] Warning: molecule is tagged as 3D, but all Z coords are zero and 2D stereo markers have been found, marking the mol as 2D. -72: [02:19:04] Ignoring invalid chirality label: '2_bad_chirality' -70: [02:19:04] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -70: [02:19:04] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +70: [11:06:00] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 2 ignored +70: [11:06:00] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 2 ignored +70: [11:06:00] The 2 defining bonds for an atropisomer are co-planar - atoms are: 2 8 +70: [11:06:00] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 2 ignored +70: [11:06:00] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 2 ignored +70: [11:06:00] The 2 defining bonds for an atropisomer are co-planar - atoms are: 2 8 +70: [11:06:00] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +70: [11:06:00] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +69: [11:06:00] Skipping unrecognized collection type at line 26: MDLV30/HILITE BONDS=(1 7) +69: [11:06:00] Skipping unrecognized collection type at line 27: MDLV30/HILITE ATOMS=(1 7) +70: [11:06:00] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +69: [11:06:00] Warning: molecule is tagged as 3D, but all Z coords are zero and 2D stereo markers have been found, marking the mol as 2D. +70: [11:06:00] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored +70: [11:06:00] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored +70: [11:06:00] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored +70: [11:06:00] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored +70: [11:06:00] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored +70: [11:06:00] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored +70: [11:06:00] The 2 defining bonds for an atropisomer are co-planar - atoms are: 7 20 +70: [11:06:00] The 2 defining bonds for an atropisomer are co-planar - atoms are: 7 20 +70: [11:06:00] The 2 defining bonds for an atropisomer are co-planar - atoms are: 7 20 +70: [11:06:00] The bonds on one end of an atropisomer are both UP or both DOWN - atoms are: 7 20 +70: [11:06:00] The bonds on one end of an atropisomer are both UP or both DOWN - atoms are: 7 20 +70: [11:06:00] The bonds on one end of an atropisomer are both UP or both DOWN - atoms are: 7 20 69: generating smiles -70: [02:19:04] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +70: [11:06:00] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +70: [11:06:00] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +70: [11:06:00] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 69: smiles: c12n(C3OC(COP(OC4C(O)C(n5c(=O)[nH]c(=O)cc5)OC4COP(OC4C(O)C(n5c(=O)nc(N)cc5)OC4COP(OC4C(O)C(n5c6c(cc5)c(=O)[nH]c(N)n6)OC4COP(OC4C(O)C(n5c(=O)nc(N)cc5)OC4COP(OC4C(O)C(n5c6c(nc5)c(N)ncn6)OC4COP(OC4C(O)C(n5c6c(cc5)c(=O)[nH]c(N)n6)OC4COP(OC4C(O)C(n5c(=O)[nH]c(=O)cc5)OC4COP(OC4C(O)C(n5c(=O)nc(N)cc5)OC4COP(OC4C(O)C(n5c6c(nc5)c(N)ncn6)OC4COP(OC4C(O)C(n5c6c(nc5)c(N)ncn6)OC4CO)(=O)S)(=O)S)(=O)S)(S)=O)(S)=O)(=O)S)(=O)S)(S)=O)(=O)S)(S)=O)C(OP(S)(=O)OCC(COP(OC4C(O)C(n5c6c(cc5)c(=O)[nH]c(N)n6)OC4COP(OC4C(O)C(n5c(=O)[nH]c(=O)cc5)OC4COP(OC4C(O)C(n5c(=O)nc(N)cc5)OC4COP(OC4C(O)C(n5c6c(cc5)c(=O)[nH]c(N)n6)OC4COP(OC4C(O)C(n5c(=O)nc(N)cc5)OC4COP(OC4C(O)C(n5c6c(nc5)c(N)ncn6)OC4COP(OC4C(O)C(n5c6c(cc5)c(=O)[nH]c(N)n6)OC4COP(OC4C(O)C(n5c(=O)[nH]c(=O)cc5)OC4COP(OC4C(O)C(n5c(=O)nc(N)cc5)OC4COP(OC4C(O)C(n5c6c(nc5)c(N)ncn6)OC4COP(OC4C(O)C(n5c6c(nc5)c(N)ncn6)OC4CO)(=O)S)(=O)S)(=O)S)(S)=O)(S)=O)(=O)S)(=O)S)(S)=O)(=O)S)(S)=O)(S)=O)O)C3O)ccc1c(=O)[nH]c(N)n2 69: converting back -67: ..............[02:19:04] SMILES Parse Error: syntax error while parsing: invalidsmiles -67: [02:19:04] SMILES Parse Error: check for mistakes around position 1: -67: [02:19:04] invalidsmiles -67: [02:19:04] ^ -67: [02:19:04] SMILES Parse Error: Failed parsing SMILES 'invalidsmiles' for input: 'invalidsmiles' 69: check isomorphism -70: [02:19:04] The 2 defining bonds for an atropisomer are co-planar - atoms are: 17 21 -70: [02:19:04] The 2 defining bonds for an atropisomer are co-planar - atoms are: 17 21 -70: [02:19:04] The 2 defining bonds for an atropisomer are co-planar - atoms are: 17 21 -70: [02:19:04] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 2 ignored -70: [02:19:04] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 2 ignored -70: [02:19:04] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 2 ignored -70: [02:19:04] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 2 ignored -70: [02:19:04] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 2 ignored -70: [02:19:04] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 2 ignored -70: [02:19:04] The bonds on one end of an atropisomer are both UP or both DOWN - atoms are: 2 8 -70: [02:19:04] The bonds on one end of an atropisomer are both UP or both DOWN - atoms are: 2 8 -70: [02:19:04] The bonds on one end of an atropisomer are both UP or both DOWN - atoms are: 2 8 -70: [02:19:04] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 2 ignored -70: [02:19:04] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 2 ignored -70: [02:19:04] The 2 defining bonds for an atropisomer are co-planar - atoms are: 2 8 -70: [02:19:04] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 2 ignored -70: [02:19:04] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 2 ignored -70: [02:19:04] The 2 defining bonds for an atropisomer are co-planar - atoms are: 2 8 -70: [02:19:04] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 2 ignored -70: [02:19:04] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 2 ignored -70: [02:19:04] The 2 defining bonds for an atropisomer are co-planar - atoms are: 2 8 -70: [02:19:04] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -70: [02:19:04] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -70: [02:19:04] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -70: [02:19:04] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored -70: [02:19:04] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored -70: [02:19:04] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored -70: [02:19:04] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored -70: [02:19:04] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored -70: [02:19:04] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored -70: [02:19:04] The 2 defining bonds for an atropisomer are co-planar - atoms are: 7 20 -70: [02:19:04] The 2 defining bonds for an atropisomer are co-planar - atoms are: 7 20 -70: [02:19:04] The 2 defining bonds for an atropisomer are co-planar - atoms are: 7 20 -72: [02:19:04] Finished: testMolSup() -72: [02:19:04] ----------------------------------------- -72: -72: [02:19:04] ----------------------------------------- -70: [02:19:04] The bonds on one end of an atropisomer are both UP or both DOWN - atoms are: 7 20 -70: [02:19:04] The bonds on one end of an atropisomer are both UP or both DOWN - atoms are: 7 20 -70: [02:19:04] The bonds on one end of an atropisomer are both UP or both DOWN - atoms are: 7 20 -70: [02:19:04] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -72: [02:19:04] Finished: testRandMolSup() -70: [02:19:04] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -72: [02:19:04] ----------------------------------------- -72: -72: [02:19:04] ----------------------------------------- -70: [02:19:04] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -67: ..... -67: ---------------------------------------------------------------------- -67: Ran 19 tests in 0.225s -67: -67: OK -70: [02:19:04] The 2 defining bonds for an atropisomer are co-planar - atoms are: 0 31 -70: [02:19:04] The 2 defining bonds for an atropisomer are co-planar - atoms are: 0 31 -70: [02:19:04] The 2 defining bonds for an atropisomer are co-planar - atoms are: 0 31 -70: [02:19:04] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -70: [02:19:04] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -70: [02:19:04] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -70: [02:19:04] The 2 defining bonds for an atropisomer are co-planar - atoms are: 15 16 -70: [02:19:04] The 2 defining bonds for an atropisomer are co-planar - atoms are: 15 16 -70: [02:19:04] The 2 defining bonds for an atropisomer are co-planar - atoms are: 15 16 -72: [02:19:04] Finished: testSmilesSup() -72: [02:19:04] ----------------------------------------- -72: -72: [02:19:04] ----------------------------------------- -72: [02:19:04] ------------------------------------------------------ -72: [02:19:04] SMILES Parse Error: syntax error while parsing: fail -72: [02:19:04] SMILES Parse Error: check for mistakes around position 1: -72: [02:19:04] fail -72: [02:19:04] ^ -72: [02:19:04] SMILES Parse Error: Failed parsing SMILES 'fail' for input: 'fail' -72: [02:19:04] ERROR: Smiles parse error on line 3 -72: [02:19:04] ERROR: Cannot create molecule from : 'fail' -72: [02:19:04] ------------------------------------------------------ -72: [02:19:04] ------------------------------------------------------ -72: [02:19:04] >>> This may result in an infinite loop. It should finish almost immediately: -72: [02:19:04] <<< done. -72: [02:19:04] Finished: testSmilesSupFromText() -72: [02:19:04] ----------------------------------------- -72: -72: [02:19:04] ----------------------------------------- -72: [02:19:04] Finished: testSmilesWriter() -72: [02:19:04] ----------------------------------------- -72: -72: [02:19:04] ----------------------------------------- - 61/238 Test #67: pyDepictor ............................. Passed 0.45 sec +70: [11:06:00] The 2 defining bonds for an atropisomer are co-planar - atoms are: 0 31 +70: [11:06:00] The 2 defining bonds for an atropisomer are co-planar - atoms are: 0 31 +70: [11:06:00] The 2 defining bonds for an atropisomer are co-planar - atoms are: 0 31 +70: [11:06:00] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +70: [11:06:00] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +70: [11:06:00] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +72: [11:06:00] Ignoring invalid chirality label: '2_bad_chirality' +70: [11:06:00] The 2 defining bonds for an atropisomer are co-planar - atoms are: 15 16 +70: [11:06:00] The 2 defining bonds for an atropisomer are co-planar - atoms are: 15 16 +70: [11:06:00] The 2 defining bonds for an atropisomer are co-planar - atoms are: 15 16 +70: [11:06:00] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +70: [11:06:00] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +70: Atropisomers- 1 hits 3 misses +70: Final results: +70: Found atropisomers in TestMultInSDF.sdf - 1 hits 4 misses + 61/238 Test #70: testAtropisomers ....................... Passed 0.16 sec test 73 Start 73: testGeneralFileReader 73: Test command: /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/testGeneralFileReader 73: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers 73: Test timeout computed to be: 1500 -72: [02:19:04] Finished: testSDWriter() -72: [02:19:04] ----------------------------------------- +72: [11:06:00] Finished: testMolSup() +72: [11:06:00] ----------------------------------------- +72: +72: [11:06:00] ----------------------------------------- +72: [11:06:00] Finished: testRandMolSup() +72: [11:06:00] ----------------------------------------- 72: -72: [02:19:04] ----------------------------------------- -72: [02:19:04] Finished: testSDSupplierEnding() -72: [02:19:04] ----------------------------------------- +72: [11:06:00] ----------------------------------------- +73: [11:06:00] +73: ----------------------------------------- +73: [11:06:00] Finished: testDetermineFormat() +73: [11:06:00] ----------------------------------------- +73: +73: [11:06:00] +73: ----------------------------------------- +73: [11:06:00] Finished: testSdf() +73: [11:06:00] ----------------------------------------- +73: +73: [11:06:00] +73: ----------------------------------------- +72: [11:06:00] Finished: testSmilesSup() +72: [11:06:00] ----------------------------------------- +72: +72: [11:06:00] ----------------------------------------- +72: [11:06:00] ------------------------------------------------------ +72: [11:06:00] SMILES Parse Error: syntax error while parsing: fail +72: [11:06:00] SMILES Parse Error: check for mistakes around position 1: +72: [11:06:00] fail +72: [11:06:00] ^ +72: [11:06:00] SMILES Parse Error: Failed parsing SMILES 'fail' for input: 'fail' +72: [11:06:00] ERROR: Smiles parse error on line 3 +72: [11:06:00] ERROR: Cannot create molecule from : 'fail' +73: [11:06:00] Finished: testSmi() +73: [11:06:00] ----------------------------------------- +73: +73: [11:06:00] +73: ----------------------------------------- +72: [11:06:00] ------------------------------------------------------ +72: [11:06:00] ------------------------------------------------------ +72: [11:06:00] >>> This may result in an infinite loop. It should finish almost immediately: +72: [11:06:00] <<< done. +72: [11:06:00] Finished: testSmilesSupFromText() +72: [11:06:00] ----------------------------------------- +72: +72: [11:06:00] ----------------------------------------- +72: [11:06:00] Finished: testSmilesWriter() +72: [11:06:00] ----------------------------------------- +72: +72: [11:06:00] ----------------------------------------- +67: ..............[11:06:00] SMILES Parse Error: syntax error while parsing: invalidsmiles +67: [11:06:00] SMILES Parse Error: check for mistakes around position 1: +67: [11:06:00] invalidsmiles +67: [11:06:00] ^ +67: [11:06:00] SMILES Parse Error: Failed parsing SMILES 'invalidsmiles' for input: 'invalidsmiles' +72: [11:06:00] Finished: testSDWriter() +72: [11:06:00] ----------------------------------------- +72: +72: [11:06:00] ----------------------------------------- +72: [11:06:00] Finished: testSDSupplierEnding() +72: [11:06:00] ----------------------------------------- +72: +72: [11:06:00] ----------------------------------------- +72: [11:06:00] Finished: testSuppliersEmptyFile() +72: [11:06:00] ----------------------------------------- +72: +72: [11:06:00] ----------------------------------------- +72: [11:06:00] Finished: testCisTrans() +72: [11:06:00] ----------------------------------------- +72: +72: [11:06:00] ----------------------------------------- +72: [11:06:00] Finished: testStereoRound() +72: [11:06:00] ----------------------------------------- +72: +72: [11:06:00] ----------------------------------------- +72: [11:06:00] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +72: [11:06:00] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +72: [11:06:00] Finished: testIssue226() +72: [11:06:00] ----------------------------------------- 72: -72: [02:19:04] ----------------------------------------- 68: Test 68: 68: badWedgeError.sdf @@ -19002,98 +19067,69 @@ 68: 68: MulticenterSgroup.mrv 68: -72: [02:19:04] Finished: testSuppliersEmptyFile() -72: [02:19:04] ----------------------------------------- -72: -72: [02:19:04] ----------------------------------------- -72: [02:19:04] Finished: testCisTrans() -72: [02:19:04] ----------------------------------------- +68: [11:06:00] Can't kekulize mol. Unkekulized atoms: 6 7 8 9 10 +68: [11:06:00] Can't kekulize mol. Unkekulized atoms: 6 7 8 9 10 +72: [11:06:00] ----------------------------------------- +72: [11:06:00] Finished: testTDTSupplier1() +72: [11:06:00] ----------------------------------------- 72: -72: [02:19:04] ----------------------------------------- -73: [02:19:04] -73: ----------------------------------------- -73: [02:19:04] Finished: testDetermineFormat() -73: [02:19:04] ----------------------------------------- -73: -73: [02:19:04] -73: ----------------------------------------- -72: [02:19:04] Finished: testStereoRound() -72: [02:19:04] ----------------------------------------- +72: [11:06:00] ----------------------------------------- +72: [11:06:00] Finished: testTDTSupplier2() +72: [11:06:00] ----------------------------------------- 72: -72: [02:19:04] ----------------------------------------- -72: [02:19:04] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -72: [02:19:04] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -68: [02:19:04] Can't kekulize mol. Unkekulized atoms: 6 7 8 9 10 -68: [02:19:04] Can't kekulize mol. Unkekulized atoms: 6 7 8 9 10 -72: [02:19:04] Finished: testIssue226() -72: [02:19:04] ----------------------------------------- +72: [11:06:00] ----------------------------------------- +72: [11:06:00] Finished: testTDTSupplier3() +72: [11:06:00] ----------------------------------------- 72: -72: [02:19:04] ----------------------------------------- -72: [02:19:04] Finished: testTDTSupplier1() -72: [02:19:04] ----------------------------------------- +72: [11:06:00] ----------------------------------------- +72: [11:06:00] Finished: testSDSupplierFromText() +72: [11:06:00] ----------------------------------------- 72: -72: [02:19:04] ----------------------------------------- -72: [02:19:04] Finished: testTDTSupplier2() -72: [02:19:04] ----------------------------------------- +72: [11:06:00] ----------------------------------------- +72: [11:06:00] ERROR: Problems encountered parsing data fields +72: [11:06:00] ERROR: moving to the beginning of the next molecule +72: [11:06:00] ERROR: Problems encountered parsing data fields +72: [11:06:00] ERROR: moving to the beginning of the next molecule +72: [11:06:00] Spurious data before the first property will be ignored +72: [11:06:00] Property will be truncated after the first blank line +72: [11:06:00] Property will be truncated after the first blank line +72: [11:06:00] Property will be truncated after the first blank line +72: [11:06:00] Finished: testSDSupplierStrLax1() +72: [11:06:00] ----------------------------------------- 72: -72: [02:19:04] ----------------------------------------- -72: [02:19:04] Finished: testTDTSupplier3() -72: [02:19:04] ----------------------------------------- +72: [11:06:00] ----------------------------------------- +72: [11:06:00] ERROR: Problems encountered parsing data fields +72: [11:06:00] ERROR: moving to the beginning of the next molecule +72: [11:06:00] Property will be truncated after the first blank line +72: [11:06:00] Finished: testSDSupplierStrLax2() +72: [11:06:00] ----------------------------------------- 72: -72: [02:19:04] ----------------------------------------- -72: [02:19:04] Finished: testSDSupplierFromText() -72: [02:19:04] ----------------------------------------- +72: [11:06:00] ----------------------------------------- +72: [11:06:00] ERROR: Problems encountered parsing data fields +72: [11:06:00] ERROR: moving to the beginning of the next molecule +72: [11:06:00] ERROR: Problems encountered parsing data fields +72: [11:06:00] ERROR: moving to the beginning of the next molecule +72: [11:06:00] Spurious data before the first property will be ignored +72: [11:06:00] Property will be truncated after the first blank line +72: [11:06:00] Property will be truncated after the first blank line +72: [11:06:00] Property will be truncated after the first blank line +72: [11:06:00] Finished: testSDSupplierFromTextStrLax1() +72: [11:06:00] ----------------------------------------- 72: -72: [02:19:04] ----------------------------------------- -72: [02:19:04] ERROR: Problems encountered parsing data fields -72: [02:19:04] ERROR: moving to the beginning of the next molecule -72: [02:19:04] ERROR: Problems encountered parsing data fields -72: [02:19:04] ERROR: moving to the beginning of the next molecule -72: [02:19:04] Spurious data before the first property will be ignored -72: [02:19:04] Property will be truncated after the first blank line -72: [02:19:04] Property will be truncated after the first blank line -72: [02:19:04] Property will be truncated after the first blank line -72: [02:19:04] Finished: testSDSupplierStrLax1() -72: [02:19:04] ----------------------------------------- +72: [11:06:00] ----------------------------------------- +72: [11:06:00] ERROR: Problems encountered parsing data fields +72: [11:06:00] ERROR: moving to the beginning of the next molecule +72: [11:06:00] Property will be truncated after the first blank line +72: [11:06:00] Finished: testSDSupplierFromTextStrLax2() +72: [11:06:00] ----------------------------------------- 72: -72: [02:19:04] ----------------------------------------- -72: [02:19:04] ERROR: Problems encountered parsing data fields -72: [02:19:04] ERROR: moving to the beginning of the next molecule -72: [02:19:04] Property will be truncated after the first blank line -72: [02:19:04] Finished: testSDSupplierStrLax2() -72: [02:19:04] ----------------------------------------- +72: [11:06:00] ----------------------------------------- +72: [11:06:00] Finished: testIssue265() +72: [11:06:00] ----------------------------------------- 72: -72: [02:19:04] ----------------------------------------- -72: [02:19:04] ERROR: Problems encountered parsing data fields -72: [02:19:04] ERROR: moving to the beginning of the next molecule -72: [02:19:04] ERROR: Problems encountered parsing data fields -72: [02:19:04] ERROR: moving to the beginning of the next molecule -72: [02:19:04] Spurious data before the first property will be ignored -72: [02:19:04] Property will be truncated after the first blank line -72: [02:19:04] Property will be truncated after the first blank line -72: [02:19:04] Property will be truncated after the first blank line -72: [02:19:04] Finished: testSDSupplierFromTextStrLax1() -72: [02:19:04] ----------------------------------------- -72: -72: [02:19:04] ----------------------------------------- -72: [02:19:04] ERROR: Problems encountered parsing data fields -72: [02:19:04] ERROR: moving to the beginning of the next molecule -72: [02:19:04] Property will be truncated after the first blank line -72: [02:19:04] Finished: testSDSupplierFromTextStrLax2() -72: [02:19:04] ----------------------------------------- -72: -72: [02:19:04] ----------------------------------------- -72: [02:19:04] Finished: testIssue265() -72: [02:19:04] ----------------------------------------- -72: -72: [02:19:04] ----------------------------------------- -72: [02:19:04] ERROR: End of data field name not found -72: [02:19:04] ERROR: moving to the beginning of the next molecule -72: [02:19:04] Explicit valence for atom # 0 F, 2, is greater than permitted -72: [02:19:04] ERROR: Could not sanitize molecule ending on line 16 -72: [02:19:04] ERROR: Explicit valence for atom # 0 F, 2, is greater than permitted -72: [02:19:04] ERROR: Atom line too short: ' 1 2 1 0 0 0 0' on line 12 -72: [02:19:04] ERROR: moving to the beginning of the next molecule +72: [11:06:00] ----------------------------------------- +72: [11:06:00] ERROR: End of data field name not found +72: [11:06:00] ERROR: moving to the beginning of the next molecule 68: Test 68: 68: GenericSgroup.mrv @@ -19126,7 +19162,7 @@ 68: 68: MarvinBadMissingMolID.mrv 68: -68: [02:19:04] +68: [11:06:00] 68: 68: **** 68: Test Assert @@ -19137,19 +19173,30 @@ 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# 0x0000AAAADA97AC5C in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/MarvinParse/testMrvToMol -68: 3# 0x0000AAAADA985D5C in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/MarvinParse/testMrvToMol -68: 4# 0x0000AAAADA974918 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/MarvinParse/testMrvToMol -68: 5# 0x0000FFFFB39F229C in /lib/aarch64-linux-gnu/libc.so.6 +68: 2# 0x0000AAAAE6B4AC5C in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/MarvinParse/testMrvToMol +68: 3# 0x0000AAAAE6B55D5C in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/MarvinParse/testMrvToMol +68: 4# 0x0000AAAAE6B44918 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/MarvinParse/testMrvToMol +68: 5# 0x0000FFFF9480229C in /lib/aarch64-linux-gnu/libc.so.6 68: 6# __libc_start_main in /lib/aarch64-linux-gnu/libc.so.6 -68: 7# 0x0000AAAADA974B70 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/MarvinParse/testMrvToMol +68: 7# 0x0000AAAAE6B44B70 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/MarvinParse/testMrvToMol 68: ---------- 68: **** 68: +72: [11:06:00] Explicit valence for atom # 0 F, 2, is greater than permitted 68: Test 68: 68: MarvinBadMissingAtomID.mrv 68: +72: [11:06:00] ERROR: Could not sanitize molecule ending on line 16 +72: [11:06:00] ERROR: Explicit valence for atom # 0 F, 2, is greater than permitted +72: [11:06:00] ERROR: Atom line too short: ' 1 2 1 0 0 0 0' on line 12 +72: [11:06:00] ERROR: moving to the beginning of the next molecule +72: [11:06:00] ERROR: Bond line too short: 'M END' on line 18 +72: [11:06:00] ERROR: moving to the beginning of the next molecule +72: [11:06:00] Finished: testSDErrorHandling() +72: [11:06:00] ----------------------------------------- +72: +72: [11:06:00] ----------------------------------------- 68: Expected id, elementType for an atom definition in MRV file 68: Test 68: @@ -19166,9 +19213,7 @@ 68: MarvinBadStereoGroupsAbs.mrv 68: 68: Unrecognized group definition -72: [02:19:04] ERROR: Bond line too short: 'M END' on line 18 -72: [02:19:04] ERROR: moving to the beginning of the next molecule -72: [02:19:04] Finished: testSDErrorHandling() +72: [11:06:00] Finished: testIssue381() 68: Test 68: 68: MarvinBadElementType.mrv @@ -19186,19 +19231,14 @@ 68: MarvinBadMissingBondOrder.mrv 68: 68: bond must have one of: order, queryType, or convention in MRV File -73: [02:19:04] Finished: testSdf() -73: [02:19:04] ----------------------------------------- -73: -73: [02:19:04] -73: ----------------------------------------- 68: Test 68: 68: MarvinBadMissingSruMolID.mrv 68: 68: Expected a molID in MRV file -72: [02:19:04] ----------------------------------------- +72: [11:06:00] ----------------------------------------- 72: -72: [02:19:04] ----------------------------------------- +72: [11:06:00] ----------------------------------------- 68: Test 68: 68: MarvinBadMissingSruID.mrv @@ -19263,6 +19303,18 @@ 68: MarvinBadSupAttachAtom.mrv 68: 68: Atom specification for an AttachmentPoint definition must be in the parent's atom array in MRV file +72: [11:06:00] Finished: testSetStreamIndices() +72: [11:06:00] ----------------------------------------- +72: +72: [11:06:00] ----------------------------------------- +73: [11:06:00] Finished: testMae() +73: [11:06:00] ----------------------------------------- +73: +73: [11:06:00] +73: ----------------------------------------- +73: [11:06:00] Finished: testTdt() +73: [11:06:00] ----------------------------------------- +73: 68: Test 68: 68: MarvinBadSupAttachAtom.mrv @@ -19277,135 +19329,83 @@ 68: 68: MarvinBadSupMissingAttachBond.mrv 68: + 62/238 Test #73: testGeneralFileReader .................. Passed 0.09 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 +72: [11:06:00] Finished: testMixIterAndRandom() +72: [11:06:00] ----------------------------------------- +72: +72: [11:06:00] ----------------------------------------- +72: build: +72: [11:06:00] Finished: testRemoveHs() +72: [11:06:00] ----------------------------------------- +72: +72: [11:06:00] ----------------------------------------- 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 -72: [02:19:04] Finished: testIssue381() -72: [02:19:04] ----------------------------------------- -72: -72: [02:19:04] ----------------------------------------- -73: [02:19:04] Finished: testSmi() -73: [02:19:04] ----------------------------------------- -73: -73: [02:19:04] -73: ----------------------------------------- -72: [02:19:04] Finished: testSetStreamIndices() -72: [02:19:04] ----------------------------------------- -72: -72: [02:19:04] ----------------------------------------- -72: [02:19:04] Finished: testMixIterAndRandom() -72: [02:19:04] ----------------------------------------- -72: -72: [02:19:04] ----------------------------------------- -72: build: -72: [02:19:04] Finished: testRemoveHs() -72: [02:19:04] ----------------------------------------- +72: [11:06:00] Finished: testGetItemText() +72: [11:06:00] ----------------------------------------- 72: -72: [02:19:04] ----------------------------------------- -29: Checking against /build/reproducible-path/rdkit-202503.1/Code/ForceField/MMFF/test_data/MMFF94_reference.log... -72: [02:19:04] Finished: testGetItemText() -72: [02:19:04] ----------------------------------------- -72: -72: [02:19:04] ----------------------------------------- -73: [02:19:04] Finished: testMae() -73: [02:19:04] ----------------------------------------- -73: -73: [02:19:04] -73: ----------------------------------------- -73: [02:19:04] Finished: testTdt() -73: [02:19:04] ----------------------------------------- -73: -72: [02:19:04] Finished: testForwardSDSupplier() -72: [02:19:04] ----------------------------------------- +72: [11:06:00] ----------------------------------------- +72: [11:06:00] Finished: testForwardSDSupplier() +72: [11:06:00] ----------------------------------------- 72: -72: [02:19:04] ----------------------------------------- -72: [02:19:04] Finished: testMissingCRSDSupplier() -72: [02:19:04] ----------------------------------------- +72: [11:06:00] ----------------------------------------- +72: [11:06:00] Finished: testMissingCRSDSupplier() +72: [11:06:00] ----------------------------------------- 72: -72: [02:19:04] ----------------------------------------- -72: [02:19:04] Finished: testIssue3482695() -72: [02:19:04] ----------------------------------------- +72: [11:06:00] ----------------------------------------- +72: [11:06:00] Finished: testIssue3482695() +72: [11:06:00] ----------------------------------------- 72: -72: [02:19:04] ----------------------------------------- - 62/238 Test #73: testGeneralFileReader .................. Passed 0.07 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 -72: [02:19:04] ERROR: Cannot convert 'foo' to unsigned int on line 557 -72: [02:19:04] ERROR: moving to the beginning of the next molecule -72: [02:19:04] Finished: testIssue3525673() -72: [02:19:04] ----------------------------------------- +72: [11:06:00] ----------------------------------------- +72: [11:06:00] ERROR: Cannot convert 'foo' to unsigned int on line 557 +72: [11:06:00] ERROR: moving to the beginning of the next molecule +72: [11:06:00] Finished: testIssue3525673() +72: [11:06:00] ----------------------------------------- 72: -72: [02:19:04] ----------------------------------------- -72: [02:19:04] Finished: testBlankLinesInProps() -72: [02:19:04] ----------------------------------------- +72: [11:06:00] ----------------------------------------- +72: [11:06:00] Finished: testBlankLinesInProps() +72: [11:06:00] ----------------------------------------- 72: -72: [02:19:04] ----------------------------------------- -72: [02:19:04] Finished: testSkipLines() -72: [02:19:04] ----------------------------------------- +72: [11:06:00] ----------------------------------------- +72: [11:06:00] Finished: testSkipLines() +72: [11:06:00] ----------------------------------------- 72: -72: [02:19:04] ----------------------------------------- -72: [02:19:04] Finished: testGitHub23() -72: [02:19:04] ----------------------------------------- +72: [11:06:00] ----------------------------------------- +72: [11:06:00] Finished: testGitHub23() +72: [11:06:00] ----------------------------------------- 72: -72: [02:19:04] ----------------------------------------- -72: [02:19:04] Finished: testGitHub88() -72: [02:19:04] ----------------------------------------- +72: [11:06:00] ----------------------------------------- +72: [11:06:00] Finished: testGitHub88() +72: [11:06:00] ----------------------------------------- 72: -72: [02:19:04] ----------------------------------------- -74: [02:19:04] +72: [11:06:00] ----------------------------------------- +74: [11:06:00] 74: ----------------------------------------- -72: [02:19:04] Finished: testGitHub2285() -72: [02:19:04] ----------------------------------------- -72: -72: [02:19:04] ----------------------------------------- -72: [02:19:04] SMILES Parse Error: unclosed ring for input: 'c1ccccc' -72: [02:19:04] ERROR: Smiles parse error on line 1 -72: [02:19:04] ERROR: Cannot create molecule from : 'c1ccccc' -72: [02:19:04] SMILES Parse Error: extra open parentheses while parsing: C(C -72: [02:19:04] SMILES Parse Error: check for mistakes around position 2: -72: [02:19:04] C(C -72: [02:19:04] ~^ -72: [02:19:04] SMILES Parse Error: Failed parsing SMILES 'C(C' for input: 'C(C' -72: [02:19:04] ERROR: Smiles parse error on line 3 -72: [02:19:04] ERROR: Cannot create molecule from : 'C(C' -72: [02:19:04] Explicit valence for atom # 1 C, 5, is greater than permitted -72: [02:19:04] ERROR: Could not sanitize molecule on line 5 -72: [02:19:04] ERROR: Explicit valence for atom # 1 C, 5, is greater than permitted -72: [02:19:04] Explicit valence for atom # 1 F, 2, is greater than permitted -72: [02:19:04] ERROR: Could not sanitize molecule ending on line 21 -72: [02:19:04] ERROR: Explicit valence for atom # 1 F, 2, is greater than permitted -72: [02:19:04] Explicit valence for atom # 1 F, 2, is greater than permitted -72: [02:19:04] ERROR: Could not sanitize molecule ending on line 21 -72: [02:19:04] ERROR: Explicit valence for atom # 1 F, 2, is greater than permitted -72: [02:19:04] Explicit valence for atom # 1 F, 2, is greater than permitted -72: [02:19:04] ERROR: Could not sanitize molecule ending on line 21 -72: [02:19:04] ERROR: Explicit valence for atom # 1 F, 2, is greater than permitted -72: [02:19:04] ERROR: Atom line too short: ' -9.6' on line 28 -72: [02:19:04] ERROR: moving to the beginning of the next molecule -72: [02:19:04] Explicit valence for atom # 1 F, 2, is greater than permitted -72: [02:19:04] ERROR: Could not sanitize molecule ending on line 21 -72: [02:19:04] ERROR: Explicit valence for atom # 1 F, 2, is greater than permitted -72: [02:19:04] ERROR: Atom line too short: ' -9.6' on line 28 -72: [02:19:04] ERROR: moving to the beginning of the next molecule -72: [02:19:04] Finished: testGitHub2479() -72: [02:19:04] ----------------------------------------- -72: -72: [02:19:04] ----------------------------------------- -72: [02:19:04] Ignoring invalid chirality label: '7_S_8_9_6_10' -72: [02:19:04] Finished: testGitHub2881() -72: [02:19:04] ----------------------------------------- -72: -72: [02:19:04] ----------------------------------------- -72: [02:19:04] Finished: testGitHub3517() -72: [02:19:04] ----------------------------------------- +72: [11:06:00] Finished: testGitHub2285() +72: [11:06:00] ----------------------------------------- 72: +72: [11:06:00] ----------------------------------------- +72: [11:06:00] SMILES Parse Error: unclosed ring for input: 'c1ccccc' +72: [11:06:00] ERROR: Smiles parse error on line 1 +72: [11:06:00] ERROR: Cannot create molecule from : 'c1ccccc' +72: [11:06:00] SMILES Parse Error: extra open parentheses while parsing: C(C +72: [11:06:00] SMILES Parse Error: check for mistakes around position 2: +72: [11:06:00] C(C +72: [11:06:00] ~^ +72: [11:06:00] SMILES Parse Error: Failed parsing SMILES 'C(C' for input: 'C(C' +72: [11:06:00] ERROR: Smiles parse error on line 3 +72: [11:06:00] ERROR: Cannot create molecule from : 'C(C' +72: [11:06:00] Explicit valence for atom # 1 C, 5, is greater than permitted 68: Test 68: 68: marvin03.mrv @@ -19470,21 +19470,50 @@ 68: 68: BMS-986142_atrop5.mrv 68: -68: [02:19:04] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored -68: [02:19:04] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored -70: [02:19:04] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -70: [02:19:04] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. - 63/238 Test #72: testMolSupplier ........................ Passed 0.28 sec +68: [11:06:00] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored +68: [11:06:00] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored +72: [11:06:00] ERROR: Could not sanitize molecule on line 5 +72: [11:06:00] ERROR: Explicit valence for atom # 1 C, 5, is greater than permitted +72: [11:06:00] Explicit valence for atom # 1 F, 2, is greater than permitted +72: [11:06:00] ERROR: Could not sanitize molecule ending on line 21 +72: [11:06:00] ERROR: Explicit valence for atom # 1 F, 2, is greater than permitted +72: [11:06:00] Explicit valence for atom # 1 F, 2, is greater than permitted +72: [11:06:00] ERROR: Could not sanitize molecule ending on line 21 +72: [11:06:00] ERROR: Explicit valence for atom # 1 F, 2, is greater than permitted +72: [11:06:00] Explicit valence for atom # 1 F, 2, is greater than permitted +72: [11:06:00] ERROR: Could not sanitize molecule ending on line 21 +72: [11:06:00] ERROR: Explicit valence for atom # 1 F, 2, is greater than permitted +72: [11:06:00] ERROR: Atom line too short: ' -9.6' on line 28 +72: [11:06:00] ERROR: moving to the beginning of the next molecule +72: [11:06:00] Explicit valence for atom # 1 F, 2, is greater than permitted +72: [11:06:00] ERROR: Could not sanitize molecule ending on line 21 +72: [11:06:00] ERROR: Explicit valence for atom # 1 F, 2, is greater than permitted +72: [11:06:00] ERROR: Atom line too short: ' -9.6' on line 28 +72: [11:06:00] ERROR: moving to the beginning of the next molecule +72: [11:06:00] Finished: testGitHub2479() +72: [11:06:00] ----------------------------------------- +72: +72: [11:06:00] ----------------------------------------- +72: [11:06:00] Ignoring invalid chirality label: '7_S_8_9_6_10' +72: [11:06:00] Finished: testGitHub2881() +72: [11:06:00] ----------------------------------------- +72: +72: [11:06:00] ----------------------------------------- +72: [11:06:00] Finished: testGitHub3517() +72: [11:06:00] ----------------------------------------- +72: + 63/238 Test #72: testMolSupplier ........................ Passed 0.25 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 -29: All 191 tests passed -70: Atropisomers- 1 hits 3 misses -70: Final results: -70: Found atropisomers in TestMultInSDF.sdf - 1 hits 4 misses +67: ..... +67: ---------------------------------------------------------------------- +67: Ran 19 tests in 0.274s +67: +67: OK 68: Test 68: 68: BMS-986142_atrop6.mrv @@ -19497,20 +19526,36 @@ 68: 68: BMS-986142_atrop8.mrv 68: -68: [02:19:04] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored -68: [02:19:04] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored - 64/238 Test #70: testAtropisomers ....................... Passed 0.32 sec -test 76 - Start 76: testTplParser - -76: Test command: /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/testTplParser -76: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers -76: Test timeout computed to be: 1500 +68: [11:06:00] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored +68: [11:06:00] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored 68: Test 68: 68: BMS-986142_atropBad2.mrv 68: -68: [02:19:04] The bonds on one end of an atropisomer are both UP or both DOWN - atoms are: 7 29 +68: [11:06:00] The bonds on one end of an atropisomer are both UP or both DOWN - atoms are: 7 29 +60: Test +60: +60: AtropCanon1.cxsmi +60: +60: Test +60: +60: AtropCanon2.cxsmi +60: +60: Test +60: +60: AtropCanon3.cxsmi +60: +60: Test +60: +60: BMS-986142_3d_chiral.cxsmi +60: +60: Test +60: +60: BMS-986142_3d.cxsmi +60: +60: =============================================================================== +60: All tests passed (2496 assertions in 31 test cases) +60: 68: Test 68: 68: JDQ443_3d.mrv @@ -19531,14 +19576,14 @@ 68: 68: JDQ443_atropBad1.mrv 68: - 65/238 Test #76: testTplParser .......................... Passed 0.03 sec -test 77 - Start 77: testMol2ToMol +68: [11:06:00] The 2 defining bonds for an atropisomer are co-planar - atoms are: 17 21 + 64/238 Test #60: cxsmilesTest ........................... Passed 0.64 sec +test 76 + Start 76: testTplParser -77: Test command: /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/testMol2ToMol -77: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers -77: Test timeout computed to be: 1500 -68: [02:19:04] The 2 defining bonds for an atropisomer are co-planar - atoms are: 17 21 +76: Test command: /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/testTplParser +76: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers +76: Test timeout computed to be: 1500 68: Test 68: 68: RP-6306_atrop1.mrv @@ -19559,27 +19604,21 @@ 68: 68: RP-6306_atrop5.mrv 68: -68: [02:19:04] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 2 ignored -68: [02:19:04] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 2 ignored +68: [11:06:00] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 2 ignored +68: [11:06:00] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 2 ignored 68: Test 68: 68: RP-6306_atropBad1.mrv 68: -68: [02:19:04] The bonds on one end of an atropisomer are both UP or both DOWN - atoms are: 2 8 +68: [11:06:00] 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: [02:19:04] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 2 ignored -68: [02:19:04] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 2 ignored -68: [02:19:04] The 2 defining bonds for an atropisomer are co-planar - atoms are: 2 8 - 66/238 Test #77: testMol2ToMol .......................... Passed 0.05 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: [11:06:00] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 2 ignored +68: [11:06:00] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 2 ignored +68: [11:06:00] The 2 defining bonds for an atropisomer are co-planar - atoms are: 2 8 +29: Checking against /build/reproducible-path/rdkit-202503.1/Code/ForceField/MMFF/test_data/MMFF94_reference.log... 68: Test 68: 68: RP-6306_3d.mrv @@ -19604,50 +19643,32 @@ 68: 68: Sotorasib_atrop5.mrv 68: -68: [02:19:04] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored -68: [02:19:04] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored + 65/238 Test #67: pyDepictor ............................. Passed 0.51 sec + 66/238 Test #76: testTplParser .......................... Passed 0.03 sec +68: [11:06:00] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored +68: [11:06:00] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored +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 +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: Sotorasib_atropBad1.mrv 68: -68: [02:19:04] The 2 defining bonds for an atropisomer are co-planar - atoms are: 7 20 +68: [11:06:00] The 2 defining bonds for an atropisomer are co-planar - atoms are: 7 20 68: Test 68: 68: Sotorasib_atropBad2.mrv 68: -68: [02:19:04] The bonds on one end of an atropisomer are both UP or both DOWN - atoms are: 7 20 -29: -29: Computing MMFF94 energies for /build/reproducible-path/rdkit-202503.1/Code/ForceField/MMFF/test_data/MMFF94_hypervalent.sdf... -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: - 67/238 Test #60: cxsmilesTest ........................... Passed 0.80 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: [11:06:00] The bonds on one end of an atropisomer are both UP or both DOWN - atoms are: 7 20 68: Test 68: 68: Sotorasib_3d.mrv @@ -19668,7 +19689,7 @@ 68: 68: ZM374979_atropBad1.mrv 68: -68: [02:19:04] The 2 defining bonds for an atropisomer are co-planar - atoms are: 0 31 +68: [11:06:00] The 2 defining bonds for an atropisomer are co-planar - atoms are: 0 31 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 @@ -20653,20 +20674,7 @@ 78: CONECT 27 28 28 29 78: END 78: - 68/238 Test #78: testSequence ........................... Passed 0.04 sec - 69/238 Test #79: testExtendedStereoParsing .............. Passed 0.02 sec -test 80 - Start 80: fileParsersCatchTest - -80: Test command: /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -80: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers -80: Test timeout computed to be: 1500 -test 81 - Start 81: testPropertyLists - -81: Test command: /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/testPropertyLists -81: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers -81: Test timeout computed to be: 1500 + 67/238 Test #78: testSequence ........................... Passed 0.03 sec 68: Test 68: 68: mrtx1719_3d.mrv @@ -20687,99 +20695,27 @@ 68: 68: mrtx1719_atropBad1.mrv 68: -68: [02:19:04] The 2 defining bonds for an atropisomer are co-planar - atoms are: 15 16 -81: Randomness seeded to: 3101903430 -81: =============================================================================== -81: All tests passed (95 assertions in 4 test cases) -81: - 70/238 Test #81: testPropertyLists ...................... Passed 0.03 sec -test 82 - Start 82: XYZFileParserCatchTest +68: [11:06:00] The 2 defining bonds for an atropisomer are co-planar - atoms are: 15 16 +test 79 + Start 79: testExtendedStereoParsing -82: Test command: /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/XYZFileParserCatchTest -82: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers -82: Test timeout computed to be: 1500 -80: Randomness seeded to: 2078383001 -80: [02:19:04] SGroup SAP line too short: 'M SAP 1 1 8' on line 29 -80: [02:19:04] SGroup SAP line too short: 'M SAP 1 1 8' on line 28 -80: [02:19:04] Could not infer missing lvIdx on malformed SAP line for SGroup 1 -80: [02:19:04] SGroup 1 is invalid and will be ignored -80: [02:19:04] SGroup SAP line too short: 'M SAP 1 1 8' on line 28 -80: [02:19:04] Could not infer missing lvIdx on malformed SAP line for SGroup 1 -80: [02:19:04] SGroup 1 is invalid and will be ignored -80: [02:19:04] SGroup SAP line too short: 'M SAP 1 1 8' on line 35 -80: [02:19:04] SGroup SAP line too short: 'M SAP 2 1 12' on line 39 -80: [02:19:04] SGroup SAP line too short: 'M SAP 1 1 8' on line 34 -80: [02:19:04] SGroup SAP line too short: 'M SAP 2 1 12' on line 38 -80: [02:19:04] Could not infer missing lvIdx on malformed SAP line for SGroup 1 -80: [02:19:04] SGroup 1 is invalid and will be ignored -80: [02:19:04] SGroup SAP line too short: 'M SAP 1 1 8' on line 34 -80: [02:19:04] SGroup SAP line too short: 'M SAP 2 1 12' on line 39 -80: [02:19:04] Could not infer missing lvIdx on malformed SAP line for SGroup 1 -80: [02:19:04] SGroup 1 is invalid and will be ignored -80: [02:19:04] SGroup 3 referenced on line 40 not found. -80: [02:19:04] -80: -80: **** -80: Pre-condition Violation -80: no bonds -80: Violation occurred on line 181 in file ./Code/GraphMol/SubstanceGroup.cpp -80: Failed Expression: !d_bonds.empty() -80: ---------- -80: Stacktrace: -80: 0# Invar::Invariant::toString[abi:cxx11]() const in /build/reproducible-path/rdkit-202503.1/obj-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::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# 0x0000FFFFB8FCEDE8 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# 0x0000AAAAB8979C7C in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -80: 8# 0x0000AAAAB89EEAAC in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -80: 9# 0x0000AAAAB89EF460 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -80: 10# 0x0000AAAAB89EF894 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -80: 11# 0x0000AAAAB89C3D38 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -80: 12# 0x0000AAAAB89C4284 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -80: 13# 0x0000AAAAB893C1B0 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -80: 14# 0x0000FFFFB868229C in /lib/aarch64-linux-gnu/libc.so.6 -80: 15# __libc_start_main in /lib/aarch64-linux-gnu/libc.so.6 -80: 16# 0x0000AAAAB893C270 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -80: ---------- -80: **** -80: -80: [02:19:04] SGroup 3 referenced on line 40 not found. -80: [02:19:04] -80: -80: **** -82: Randomness seeded to: 2663924635 -82: =============================================================================== -82: All tests passed (100 assertions in 2 test cases) -82: -80: Pre-condition Violation -80: no bonds -80: Violation occurred on line 181 in file ./Code/GraphMol/SubstanceGroup.cpp -80: Failed Expression: !d_bonds.empty() -80: ---------- -80: Stacktrace: -80: 0# Invar::Invariant::toString[abi:cxx11]() const in /build/reproducible-path/rdkit-202503.1/obj-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::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# 0x0000FFFFB8FCEDE8 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# 0x0000AAAAB8979CFC in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -80: 8# 0x0000AAAAB89EEAAC in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -80: 9# 0x0000AAAAB89EF460 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -80: 10# 0x0000AAAAB89EF894 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -80: 11# 0x0000AAAAB89C3D38 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -80: 12# 0x0000AAAAB89C4284 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -80: 13# 0x0000AAAAB893C1B0 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -80: 14# 0x0000FFFFB868229C in /lib/aarch64-linux-gnu/libc.so.6 -80: 15# __libc_start_main in /lib/aarch64-linux-gnu/libc.so.6 -80: 16# 0x0000AAAAB893C270 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -80: ---------- - 71/238 Test #82: XYZFileParserCatchTest ................. Passed 0.02 sec +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 + 68/238 Test #77: testMol2ToMol .......................... Passed 0.04 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 + 69/238 Test #79: testExtendedStereoParsing .............. Passed 0.02 sec +test 81 + Start 81: testPropertyLists + +81: Test command: /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/testPropertyLists +81: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers +81: Test timeout computed to be: 1500 68: Test 68: 68: FalseAtropisomer.mrv @@ -20836,23 +20772,112 @@ 68: 68: BMS-986142_atrop5.mrv 68: -68: [02:19:04] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored -68: [02:19:04] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored -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 +68: [11:06:00] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored +68: [11:06:00] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored +80: Randomness seeded to: 3888399991 +80: [11:06:00] SGroup SAP line too short: 'M SAP 1 1 8' on line 29 +80: [11:06:00] SGroup SAP line too short: 'M SAP 1 1 8' on line 28 +80: [11:06:00] Could not infer missing lvIdx on malformed SAP line for SGroup 1 +80: [11:06:00] SGroup 1 is invalid and will be ignored +80: [11:06:00] SGroup SAP line too short: 'M SAP 1 1 8' on line 28 +80: [11:06:00] Could not infer missing lvIdx on malformed SAP line for SGroup 1 +80: [11:06:00] SGroup 1 is invalid and will be ignored +80: [11:06:00] SGroup SAP line too short: 'M SAP 1 1 8' on line 35 +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: [11:06:00] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored +80: [11:06:00] SGroup SAP line too short: 'M SAP 2 1 12' on line 39 +68: [11:06:00] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored +80: [11:06:00] SGroup SAP line too short: 'M SAP 1 1 8' on line 34 +80: [11:06:00] SGroup SAP line too short: 'M SAP 2 1 12' on line 38 +80: [11:06:00] Could not infer missing lvIdx on malformed SAP line for SGroup 1 +80: [11:06:00] SGroup 1 is invalid and will be ignored +80: [11:06:00] SGroup SAP line too short: 'M SAP 1 1 8' on line 34 +80: [11:06:00] SGroup SAP line too short: 'M SAP 2 1 12' on line 39 +80: [11:06:00] Could not infer missing lvIdx on malformed SAP line for SGroup 1 +80: [11:06:00] SGroup 1 is invalid and will be ignored +80: [11:06:00] SGroup 3 referenced on line 40 not found. +80: [11:06:00] +80: +80: **** +68: Test +68: +68: BMS-986142_atropBad2.mrv +68: +68: [11:06:00] The bonds on one end of an atropisomer are both UP or both DOWN - atoms are: 7 29 +80: Pre-condition Violation +80: no bonds +80: Violation occurred on line 181 in file ./Code/GraphMol/SubstanceGroup.cpp +80: Failed Expression: !d_bonds.empty() +80: ---------- +80: Stacktrace: +80: 0# Invar::Invariant::toString[abi:cxx11]() const in /build/reproducible-path/rdkit-202503.1/obj-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::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# 0x0000FFFF8EEBEDE8 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# 0x0000AAAAC7509C7C in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +80: 8# 0x0000AAAAC757EAAC in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +80: 9# 0x0000AAAAC757F460 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +80: 10# 0x0000AAAAC757F894 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +80: 11# 0x0000AAAAC7553D38 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +80: 12# 0x0000AAAAC7554284 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +80: 13# 0x0000AAAAC74CC1B0 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +80: 14# 0x0000FFFF8E57229C in /lib/aarch64-linux-gnu/libc.so.6 +80: 15# __libc_start_main in /lib/aarch64-linux-gnu/libc.so.6 +80: 16# 0x0000AAAAC74CC270 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +80: ---------- +80: **** +80: +80: [11:06:00] SGroup 3 referenced on line 40 not found. +80: [11:06:00] +80: +80: **** +80: Pre-condition Violation +80: no bonds +80: Violation occurred on line 181 in file ./Code/GraphMol/SubstanceGroup.cpp +80: Failed Expression: !d_bonds.empty() +80: ---------- +80: Stacktrace: +80: 0# Invar::Invariant::toString[abi:cxx11]() const in /build/reproducible-path/rdkit-202503.1/obj-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::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# 0x0000FFFF8EEBEDE8 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# 0x0000AAAAC7509CFC in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +80: 8# 0x0000AAAAC757EAAC in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +80: 9# 0x0000AAAAC757F460 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +80: 10# 0x0000AAAAC757F894 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +80: 11# 0x0000AAAAC7553D38 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +80: 12# 0x0000AAAAC7554284 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +80: 13# 0x0000AAAAC74CC1B0 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +80: 14# 0x0000FFFF8E57229C in /lib/aarch64-linux-gnu/libc.so.6 +80: 15# __libc_start_main in /lib/aarch64-linux-gnu/libc.so.6 +80: 16# 0x0000AAAAC74CC270 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +80: ---------- 80: **** 80: -80: [02:19:04] no bonds -80: [02:19:04] SGroup 1 is invalid and will be ignored -80: [02:19:04] SGroup line too short: 'M SBV 1 6' on line 42 -80: [02:19:04] SGroup 1 is invalid and will be ignored -80: [02:19:04] SGroup line too short: 'M SBL 2 3 9 10' on line 46 -80: [02:19:04] SGroup 2 is invalid and will be ignored -80: [02:19:04] +80: [11:06:00] no bonds +80: [11:06:00] SGroup 1 is invalid and will be ignored +80: [11:06:00] SGroup line too short: 'M SBV 1 6' on line 42 +80: [11:06:00] SGroup 1 is invalid and will be ignored +80: [11:06:00] SGroup line too short: 'M SBL 2 3 9 10' on line 46 +80: [11:06:00] SGroup 2 is invalid and will be ignored +80: [11:06:00] 80: 80: **** 80: Pre-condition Violation @@ -20866,23 +20891,23 @@ 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# 0x0000FFFFB8FCED50 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu//lib/libRDKitFileParsers.so.1 +80: 5# 0x0000FFFF8EEBED50 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# 0x0000AAAAB897A6A4 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -80: 9# 0x0000AAAAB89EEAAC in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -80: 10# 0x0000AAAAB89EF460 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -80: 11# 0x0000AAAAB89EF894 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -80: 12# 0x0000AAAAB89C3D38 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -80: 13# 0x0000AAAAB89C4284 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -80: 14# 0x0000AAAAB893C1B0 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -80: 15# 0x0000FFFFB868229C in /lib/aarch64-linux-gnu/libc.so.6 +80: 8# 0x0000AAAAC750A6A4 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +80: 9# 0x0000AAAAC757EAAC in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +80: 10# 0x0000AAAAC757F460 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +80: 11# 0x0000AAAAC757F894 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +80: 12# 0x0000AAAAC7553D38 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +80: 13# 0x0000AAAAC7554284 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +80: 14# 0x0000AAAAC74CC1B0 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +80: 15# 0x0000FFFF8E57229C in /lib/aarch64-linux-gnu/libc.so.6 80: 16# __libc_start_main in /lib/aarch64-linux-gnu/libc.so.6 -80: 17# 0x0000AAAAB893C270 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +80: 17# 0x0000AAAAC74CC270 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest 80: ---------- 80: **** 80: -80: [02:19:04] +80: [11:06:00] 80: 80: **** 80: Pre-condition Violation @@ -20896,24 +20921,24 @@ 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# 0x0000FFFFB8FCED50 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu//lib/libRDKitFileParsers.so.1 +80: 5# 0x0000FFFF8EEBED50 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# 0x0000AAAAB897A724 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -80: 9# 0x0000AAAAB89EEAAC in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -80: 10# 0x0000AAAAB89EF460 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -80: 11# 0x0000AAAAB89EF894 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -80: 12# 0x0000AAAAB89C3D38 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -80: 13# 0x0000AAAAB89C4284 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -80: 14# 0x0000AAAAB893C1B0 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -80: 15# 0x0000FFFFB868229C in /lib/aarch64-linux-gnu/libc.so.6 +80: 8# 0x0000AAAAC750A724 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +80: 9# 0x0000AAAAC757EAAC in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +80: 10# 0x0000AAAAC757F460 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +80: 11# 0x0000AAAAC757F894 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +80: 12# 0x0000AAAAC7553D38 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +80: 13# 0x0000AAAAC7554284 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +80: 14# 0x0000AAAAC74CC1B0 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +80: 15# 0x0000FFFF8E57229C in /lib/aarch64-linux-gnu/libc.so.6 80: 16# __libc_start_main in /lib/aarch64-linux-gnu/libc.so.6 -80: 17# 0x0000AAAAB893C270 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +80: 17# 0x0000AAAAC74CC270 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest 80: ---------- 80: **** 80: -80: [02:19:04] bookmark not found -80: [02:19:04] +80: [11:06:00] bookmark not found +80: [11:06:00] 80: 80: **** 80: Pre-condition Violation @@ -20927,25 +20952,25 @@ 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# 0x0000FFFFB8FCEDE8 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu//lib/libRDKitFileParsers.so.1 +80: 5# 0x0000FFFF8EEBEDE8 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# 0x0000AAAAB897A724 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -80: 9# 0x0000AAAAB89EEAAC in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -80: 10# 0x0000AAAAB89EF460 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -80: 11# 0x0000AAAAB89EF894 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -80: 12# 0x0000AAAAB89C3D38 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -80: 13# 0x0000AAAAB89C4284 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -80: 14# 0x0000AAAAB893C1B0 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -80: 15# 0x0000FFFFB868229C in /lib/aarch64-linux-gnu/libc.so.6 +80: 8# 0x0000AAAAC750A724 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +80: 9# 0x0000AAAAC757EAAC in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +80: 10# 0x0000AAAAC757F460 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +80: 11# 0x0000AAAAC757F894 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +80: 12# 0x0000AAAAC7553D38 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +80: 13# 0x0000AAAAC7554284 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +80: 14# 0x0000AAAAC74CC1B0 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +80: 15# 0x0000FFFF8E57229C in /lib/aarch64-linux-gnu/libc.so.6 80: 16# __libc_start_main in /lib/aarch64-linux-gnu/libc.so.6 -80: 17# 0x0000AAAAB893C270 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +80: 17# 0x0000AAAAC74CC270 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest 80: ---------- 80: **** 80: -80: [02:19:04] bond is not part of the SubstanceGroup -80: [02:19:04] SGroup 2 is invalid and will be ignored -80: [02:19:04] +80: [11:06:00] bond is not part of the SubstanceGroup +80: [11:06:00] SGroup 2 is invalid and will be ignored +80: [11:06:00] 80: 80: **** 80: Pre-condition Violation @@ -20959,23 +20984,23 @@ 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# 0x0000FFFFB8FCED50 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu//lib/libRDKitFileParsers.so.1 +80: 5# 0x0000FFFF8EEBED50 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# 0x0000AAAAB897AA14 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -80: 9# 0x0000AAAAB89EEAAC in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -80: 10# 0x0000AAAAB89EF460 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -80: 11# 0x0000AAAAB89EF894 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -80: 12# 0x0000AAAAB89C3D38 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -80: 13# 0x0000AAAAB89C4284 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -80: 14# 0x0000AAAAB893C1B0 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -80: 15# 0x0000FFFFB868229C in /lib/aarch64-linux-gnu/libc.so.6 +80: 8# 0x0000AAAAC750AA14 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +80: 9# 0x0000AAAAC757EAAC in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +80: 10# 0x0000AAAAC757F460 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +80: 11# 0x0000AAAAC757F894 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +80: 12# 0x0000AAAAC7553D38 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +80: 13# 0x0000AAAAC7554284 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +80: 14# 0x0000AAAAC74CC1B0 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +80: 15# 0x0000FFFF8E57229C in /lib/aarch64-linux-gnu/libc.so.6 80: 16# __libc_start_main in /lib/aarch64-linux-gnu/libc.so.6 -80: 17# 0x0000AAAAB893C270 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +80: 17# 0x0000AAAAC74CC270 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest 80: ---------- 80: **** 80: -80: [02:19:04] +80: [11:06:00] 80: 80: **** 80: Pre-condition Violation @@ -20989,27 +21014,27 @@ 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# 0x0000FFFFB8FCED50 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu//lib/libRDKitFileParsers.so.1 +80: 5# 0x0000FFFF8EEBED50 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# 0x0000AAAAB897AA94 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -80: 9# 0x0000AAAAB89EEAAC in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -80: 10# 0x0000AAAAB89EF460 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -80: 11# 0x0000AAAAB89EF894 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -80: 12# 0x0000AAAAB89C3D38 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -80: 13# 0x0000AAAAB89C4284 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -80: 14# 0x0000AAAAB893C1B0 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -80: 15# 0x0000FFFFB868229C in /lib/aarch64-linux-gnu/libc.so.6 +80: 8# 0x0000AAAAC750AA94 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +80: 9# 0x0000AAAAC757EAAC in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +80: 10# 0x0000AAAAC757F460 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +80: 11# 0x0000AAAAC757F894 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +80: 12# 0x0000AAAAC7553D38 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +80: 13# 0x0000AAAAC7554284 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +80: 14# 0x0000AAAAC74CC1B0 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +80: 15# 0x0000FFFF8E57229C in /lib/aarch64-linux-gnu/libc.so.6 80: 16# __libc_start_main in /lib/aarch64-linux-gnu/libc.so.6 -80: 17# 0x0000AAAAB893C270 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +80: 17# 0x0000AAAAC74CC270 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest 80: ---------- 80: **** 80: -80: [02:19:04] bookmark not found -80: [02:19:04] Neither beginning nor ending atoms of bond 9 is in this SubstanceGroup. -80: [02:19:04] SGroup 2 is invalid and will be ignored -80: [02:19:04] WARNING: final character of V3000 array is not ')' -80: [02:19:04] +80: [11:06:00] bookmark not found +80: [11:06:00] Neither beginning nor ending atoms of bond 9 is in this SubstanceGroup. +80: [11:06:00] SGroup 2 is invalid and will be ignored +80: [11:06:00] WARNING: final character of V3000 array is not ')' +80: [11:06:00] 80: 80: **** 80: Pre-condition Violation @@ -21027,21 +21052,21 @@ 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# 0x0000AAAAB8978698 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -80: 10# 0x0000AAAAB89EEAAC in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -80: 11# 0x0000AAAAB89EF460 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -80: 12# 0x0000AAAAB89EF894 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -80: 13# 0x0000AAAAB89C3D38 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -80: 14# 0x0000AAAAB89C4284 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -80: 15# 0x0000AAAAB893C1B0 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -80: 16# 0x0000FFFFB868229C in /lib/aarch64-linux-gnu/libc.so.6 +80: 9# 0x0000AAAAC7508698 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +80: 10# 0x0000AAAAC757EAAC in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +80: 11# 0x0000AAAAC757F460 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +80: 12# 0x0000AAAAC757F894 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +80: 13# 0x0000AAAAC7553D38 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +80: 14# 0x0000AAAAC7554284 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +80: 15# 0x0000AAAAC74CC1B0 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +80: 16# 0x0000FFFF8E57229C in /lib/aarch64-linux-gnu/libc.so.6 80: 17# __libc_start_main in /lib/aarch64-linux-gnu/libc.so.6 -80: 18# 0x0000AAAAB893C270 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +80: 18# 0x0000AAAAC74CC270 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest 80: ---------- 80: **** 80: -80: [02:19:04] WARNING: final character of V3000 array is not ')' -80: [02:19:04] +80: [11:06:00] WARNING: final character of V3000 array is not ')' +80: [11:06:00] 80: 80: **** 80: Pre-condition Violation @@ -21059,23 +21084,23 @@ 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# 0x0000AAAAB8978714 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -80: 10# 0x0000AAAAB89EEAAC in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -80: 11# 0x0000AAAAB89EF460 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -80: 12# 0x0000AAAAB89EF894 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -80: 13# 0x0000AAAAB89C3D38 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -80: 14# 0x0000AAAAB89C4284 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -80: 15# 0x0000AAAAB893C1B0 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -80: 16# 0x0000FFFFB868229C in /lib/aarch64-linux-gnu/libc.so.6 +80: 9# 0x0000AAAAC7508714 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +80: 10# 0x0000AAAAC757EAAC in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +80: 11# 0x0000AAAAC757F460 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +80: 12# 0x0000AAAAC757F894 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +80: 13# 0x0000AAAAC7553D38 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +80: 14# 0x0000AAAAC7554284 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +80: 15# 0x0000AAAAC74CC1B0 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +80: 16# 0x0000FFFF8E57229C in /lib/aarch64-linux-gnu/libc.so.6 80: 17# __libc_start_main in /lib/aarch64-linux-gnu/libc.so.6 -80: 18# 0x0000AAAAB893C270 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +80: 18# 0x0000AAAAC74CC270 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest 80: ---------- 80: **** 80: -80: [02:19:04] bookmark not found -80: [02:19:04] SGroup 1 is invalid and will be ignored -80: [02:19:04] WARNING: final character of V3000 array is not ')' -80: [02:19:04] +80: [11:06:00] bookmark not found +80: [11:06:00] SGroup 1 is invalid and will be ignored +80: [11:06:00] WARNING: final character of V3000 array is not ')' +80: [11:06:00] 80: 80: **** 80: Pre-condition Violation @@ -21093,21 +21118,21 @@ 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# 0x0000AAAAB89789E8 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -80: 10# 0x0000AAAAB89EEAAC in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -80: 11# 0x0000AAAAB89EF460 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -80: 12# 0x0000AAAAB89EF894 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -80: 13# 0x0000AAAAB89C3D38 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -80: 14# 0x0000AAAAB89C4284 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -80: 15# 0x0000AAAAB893C1B0 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -80: 16# 0x0000FFFFB868229C in /lib/aarch64-linux-gnu/libc.so.6 +80: 9# 0x0000AAAAC75089E8 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +80: 10# 0x0000AAAAC757EAAC in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +80: 11# 0x0000AAAAC757F460 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +80: 12# 0x0000AAAAC757F894 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +80: 13# 0x0000AAAAC7553D38 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +80: 14# 0x0000AAAAC7554284 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +80: 15# 0x0000AAAAC74CC1B0 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +80: 16# 0x0000FFFF8E57229C in /lib/aarch64-linux-gnu/libc.so.6 80: 17# __libc_start_main in /lib/aarch64-linux-gnu/libc.so.6 -80: 18# 0x0000AAAAB893C270 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +80: 18# 0x0000AAAAC74CC270 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest 80: ---------- 80: **** 80: -80: [02:19:04] WARNING: final character of V3000 array is not ')' -80: [02:19:04] +80: [11:06:00] WARNING: final character of V3000 array is not ')' +80: [11:06:00] 80: 80: **** 80: Pre-condition Violation @@ -21125,22 +21150,22 @@ 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# 0x0000AAAAB8978A64 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -80: 10# 0x0000AAAAB89EEAAC in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -80: 11# 0x0000AAAAB89EF460 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -80: 12# 0x0000AAAAB89EF894 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -80: 13# 0x0000AAAAB89C3D38 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -80: 14# 0x0000AAAAB89C4284 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -80: 15# 0x0000AAAAB893C1B0 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -80: 16# 0x0000FFFFB868229C in /lib/aarch64-linux-gnu/libc.so.6 +80: 9# 0x0000AAAAC7508A64 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +80: 10# 0x0000AAAAC757EAAC in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +80: 11# 0x0000AAAAC757F460 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +80: 12# 0x0000AAAAC757F894 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +80: 13# 0x0000AAAAC7553D38 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +80: 14# 0x0000AAAAC7554284 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +80: 15# 0x0000AAAAC74CC1B0 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +80: 16# 0x0000FFFF8E57229C in /lib/aarch64-linux-gnu/libc.so.6 80: 17# __libc_start_main in /lib/aarch64-linux-gnu/libc.so.6 -80: 18# 0x0000AAAAB893C270 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +80: 18# 0x0000AAAAC74CC270 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest 80: ---------- 80: **** 80: -80: [02:19:04] bookmark not found -80: [02:19:04] SGroup 1 is invalid and will be ignored -80: [02:19:04] +80: [11:06:00] bookmark not found +80: [11:06:00] SGroup 1 is invalid and will be ignored +80: [11:06:00] 80: 80: **** 80: Pre-condition Violation @@ -21158,41 +21183,22 @@ 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# 0x0000AAAAB8978D38 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -80: 10# 0x0000AAAAB89EEAAC in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -80: 11# 0x0000AAAAB89EF460 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -80: 12# 0x0000AAAAB89EF894 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -80: 13# 0x0000AAAAB89C3D38 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -80: 14# 0x0000AAAAB89C4284 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -80: 15# 0x0000AAAAB893C1B0 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -80: 16# 0x0000FFFFB868229C in /lib/aarch64-linux-gnu/libc.so.6 +80: 9# 0x0000AAAAC7508D38 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +80: 10# 0x0000AAAAC757EAAC in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +80: 11# 0x0000AAAAC757F460 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +80: 12# 0x0000AAAAC757F894 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +80: 13# 0x0000AAAAC7553D38 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +80: 14# 0x0000AAAAC7554284 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +80: 15# 0x0000AAAAC74CC1B0 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +80: 16# 0x0000FFFF8E57229C in /lib/aarch64-linux-gnu/libc.so.6 80: 17# __libc_start_main in /lib/aarch64-linux-gnu/libc.so.6 -80: 18# 0x0000AAAAB893C270 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +80: 18# 0x0000AAAAC74CC270 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest 80: ---------- 80: **** 80: -80: [02:19:04] +80: [11:06:00] 80: 80: **** -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: [02:19:04] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored -68: [02:19:04] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored -68: Test -68: -68: BMS-986142_atropBad2.mrv -68: -68: [02:19:04] The bonds on one end of an atropisomer are both UP or both DOWN - atoms are: 7 29 80: Pre-condition Violation 80: bookmark not found 80: Violation occurred on line 267 in file ./Code/GraphMol/ROMol.cpp @@ -21208,22 +21214,22 @@ 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# 0x0000AAAAB8978DB4 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -80: 10# 0x0000AAAAB89EEAAC in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -80: 11# 0x0000AAAAB89EF460 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -80: 12# 0x0000AAAAB89EF894 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -80: 13# 0x0000AAAAB89C3D38 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -80: 14# 0x0000AAAAB89C4284 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -80: 15# 0x0000AAAAB893C1B0 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -80: 16# 0x0000FFFFB868229C in /lib/aarch64-linux-gnu/libc.so.6 +80: 9# 0x0000AAAAC7508DB4 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +80: 10# 0x0000AAAAC757EAAC in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +80: 11# 0x0000AAAAC757F460 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +80: 12# 0x0000AAAAC757F894 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +80: 13# 0x0000AAAAC7553D38 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +80: 14# 0x0000AAAAC7554284 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +80: 15# 0x0000AAAAC74CC1B0 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +80: 16# 0x0000FFFF8E57229C in /lib/aarch64-linux-gnu/libc.so.6 80: 17# __libc_start_main in /lib/aarch64-linux-gnu/libc.so.6 -80: 18# 0x0000AAAAB893C270 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +80: 18# 0x0000AAAAC74CC270 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest 80: ---------- 80: **** 80: -80: [02:19:04] bookmark not found -80: [02:19:04] SGroup 2 is invalid and will be ignored -80: [02:19:04] +80: [11:06:00] bookmark not found +80: [11:06:00] SGroup 2 is invalid and will be ignored +80: [11:06:00] 80: 80: **** 80: Pre-condition Violation @@ -21241,20 +21247,24 @@ 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# 0x0000AAAAB8979088 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -80: 10# 0x0000AAAAB89EEAAC in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -80: 11# 0x0000AAAAB89EF460 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -80: 12# 0x0000AAAAB89EF894 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -80: 13# 0x0000AAAAB89C3D38 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -80: 14# 0x0000AAAAB89C4284 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -80: 15# 0x0000AAAAB893C1B0 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -80: 16# 0x0000FFFFB868229C in /lib/aarch64-linux-gnu/libc.so.6 +80: 9# 0x0000AAAAC7509088 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +80: 10# 0x0000AAAAC757EAAC in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +80: 11# 0x0000AAAAC757F460 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +80: 12# 0x0000AAAAC757F894 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +80: 13# 0x0000AAAAC7553D38 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +80: 14# 0x0000AAAAC7554284 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +80: 15# 0x0000AAAAC74CC1B0 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +80: 16# 0x0000FFFF8E57229C in /lib/aarch64-linux-gnu/libc.so.6 80: 17# __libc_start_main in /lib/aarch64-linux-gnu/libc.so.6 -80: 18# 0x0000AAAAB893C270 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +80: 18# 0x0000AAAAC74CC270 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest 80: ---------- +81: Randomness seeded to: 2755845742 +81: =============================================================================== +81: All tests passed (95 assertions in 4 test cases) +81: 80: **** 80: -80: [02:19:04] +80: [11:06:00] 80: 80: **** 80: Pre-condition Violation @@ -21272,24 +21282,31 @@ 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# 0x0000AAAAB8979104 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -80: 10# 0x0000AAAAB89EEAAC in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -80: 11# 0x0000AAAAB89EF460 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -80: 12# 0x0000AAAAB89EF894 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -80: 13# 0x0000AAAAB89C3D38 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -80: 14# 0x0000AAAAB89C4284 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -80: 15# 0x0000AAAAB893C1B0 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -80: 16# 0x0000FFFFB868229C in /lib/aarch64-linux-gnu/libc.so.6 +80: 9# 0x0000AAAAC7509104 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +80: 10# 0x0000AAAAC757EAAC in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +80: 11# 0x0000AAAAC757F460 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +80: 12# 0x0000AAAAC757F894 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +80: 13# 0x0000AAAAC7553D38 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +80: 14# 0x0000AAAAC7554284 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +80: 15# 0x0000AAAAC74CC1B0 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +80: 16# 0x0000FFFF8E57229C in /lib/aarch64-linux-gnu/libc.so.6 80: 17# __libc_start_main in /lib/aarch64-linux-gnu/libc.so.6 -80: 18# 0x0000AAAAB893C270 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +80: 18# 0x0000AAAAC74CC270 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest 80: ---------- 80: **** 80: -80: [02:19:04] bookmark not found -80: [02:19:04] SGroup 2 is invalid and will be ignored -80: [02:19:04] Explicit valence for atom # 2 O, 3, is greater than permitted -80: [02:19:04] Explicit valence for atom # 1 O, 3, is greater than permitted -80: [02:19:04] Explicit valence for atom # 1 C, 5, is greater than permitted +80: [11:06:00] bookmark not found +80: [11:06:00] SGroup 2 is invalid and will be ignored +80: [11:06:00] Explicit valence for atom # 2 O, 3, is greater than permitted +80: [11:06:00] Explicit valence for atom # 1 O, 3, is greater than permitted +80: [11:06:00] Explicit valence for atom # 1 C, 5, is greater than permitted + 70/238 Test #81: testPropertyLists ...................... Passed 0.04 sec +test 82 + Start 82: XYZFileParserCatchTest + +82: Test command: /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/XYZFileParserCatchTest +82: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers +82: Test timeout computed to be: 1500 68: Test 68: 68: JDQ443_3d.mrv @@ -21310,8 +21327,8 @@ 68: 68: JDQ443_atropBad1.mrv 68: -68: [02:19:04] The 2 defining bonds for an atropisomer are co-planar - atoms are: 17 21 -80: [02:19:04] sanitize [02:19:04] UNK: [02:19:04] Warning: molecule is tagged as 3D, but all Z coords are zero and 2D stereo markers have been found, marking the mol as 2D. +68: [11:06:00] The 2 defining bonds for an atropisomer are co-planar - atoms are: 17 21 +80: [11:06:00] sanitize [11:06:00] UNK: [11:06:00] Warning: molecule is tagged as 3D, but all Z coords are zero and 2D stereo markers have been found, marking the mol as 2D. 68: Test 68: 68: RP-6306_atrop1.mrv @@ -21332,47 +21349,25 @@ 68: 68: RP-6306_atrop5.mrv 68: -68: [02:19:04] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 2 ignored -68: [02:19:04] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 2 ignored +68: [11:06:00] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 2 ignored +68: [11:06:00] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 2 ignored 68: Test 68: 68: RP-6306_atropBad1.mrv 68: -68: [02:19:04] The bonds on one end of an atropisomer are both UP or both DOWN - atoms are: 2 8 -80: [02:19:04] skipping block at line 7: 'BEGIN ATOM' +68: [11:06:00] The bonds on one end of an atropisomer are both UP or both DOWN - atoms are: 2 8 +80: [11:06:00] 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: 68: Test 68: 68: RP-6306_atropBad2.mrv 68: -68: [02:19:04] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 2 ignored -68: [02:19:04] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 2 ignored -68: [02:19:04] The 2 defining bonds for an atropisomer are co-planar - atoms are: 2 8 -75: [02:19:04] Warning: molecule is tagged as 3D, but all Z coords are zero and 2D stereo markers have been found, marking the mol as 2D. -80: ATOM 1 CHLO CHL 0 0.000 0.000 0.000 1.00 0.00 CL -80: END -80: -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 -80: [02:19:04] +68: [11:06:00] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 2 ignored +68: [11:06:00] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 2 ignored +68: [11:06:00] The 2 defining bonds for an atropisomer are co-planar - atoms are: 2 8 +80: [11:06:00] 80: 80: **** 80: Pre-condition Violation @@ -21384,21 +21379,21 @@ 80: 0# Invar::Invariant::toString[abi:cxx11]() const in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu//lib/libRDKitRDGeneral.so.1 80: 1# Invar::operator<<(std::ostream&, Invar::Invariant const&) in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu//lib/libRDKitRDGeneral.so.1 80: 2# RDKit::v2::FileParsers::SDMolSupplier::next() in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu//lib/libRDKitFileParsers.so.1 -80: 3# 0x0000AAAAB89ADBC0 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -80: 4# 0x0000AAAAB896B084 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -80: 5# 0x0000AAAAB89EEAAC in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -80: 6# 0x0000AAAAB89EF460 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -80: 7# 0x0000AAAAB89EF894 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -80: 8# 0x0000AAAAB89C3D38 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -80: 9# 0x0000AAAAB89C4284 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -80: 10# 0x0000AAAAB893C1B0 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -80: 11# 0x0000FFFFB868229C in /lib/aarch64-linux-gnu/libc.so.6 +80: 3# 0x0000AAAAC753DBC0 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +80: 4# 0x0000AAAAC74FB084 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +80: 5# 0x0000AAAAC757EAAC in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +80: 6# 0x0000AAAAC757F460 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +80: 7# 0x0000AAAAC757F894 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +80: 8# 0x0000AAAAC7553D38 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +80: 9# 0x0000AAAAC7554284 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +80: 10# 0x0000AAAAC74CC1B0 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +80: 11# 0x0000FFFF8E57229C in /lib/aarch64-linux-gnu/libc.so.6 80: 12# __libc_start_main in /lib/aarch64-linux-gnu/libc.so.6 -80: 13# 0x0000AAAAB893C270 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +80: 13# 0x0000AAAAC74CC270 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest 80: ---------- 80: **** 80: -80: [02:19:04] +80: [11:06:00] 80: 80: **** 80: Pre-condition Violation @@ -21410,21 +21405,21 @@ 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# 0x0000AAAAB89ADBC0 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -80: 4# 0x0000AAAAB896B1F4 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -80: 5# 0x0000AAAAB89EEAAC in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -80: 6# 0x0000AAAAB89EF460 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -80: 7# 0x0000AAAAB89EF894 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -80: 8# 0x0000AAAAB89C3D38 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -80: 9# 0x0000AAAAB89C4284 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -80: 10# 0x0000AAAAB893C1B0 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -80: 11# 0x0000FFFFB868229C in /lib/aarch64-linux-gnu/libc.so.6 +80: 3# 0x0000AAAAC753DBC0 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +80: 4# 0x0000AAAAC74FB1F4 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +80: 5# 0x0000AAAAC757EAAC in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +80: 6# 0x0000AAAAC757F460 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +80: 7# 0x0000AAAAC757F894 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +80: 8# 0x0000AAAAC7553D38 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +80: 9# 0x0000AAAAC7554284 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +80: 10# 0x0000AAAAC74CC1B0 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +80: 11# 0x0000FFFF8E57229C in /lib/aarch64-linux-gnu/libc.so.6 80: 12# __libc_start_main in /lib/aarch64-linux-gnu/libc.so.6 -80: 13# 0x0000AAAAB893C270 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +80: 13# 0x0000AAAAC74CC270 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest 80: ---------- 80: **** 80: -80: [02:19:04] +80: [11:06:00] 80: 80: **** 80: Pre-condition Violation @@ -21436,21 +21431,21 @@ 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# 0x0000AAAAB89ADBC0 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -80: 4# 0x0000AAAAB896B528 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -80: 5# 0x0000AAAAB89EEAAC in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -80: 6# 0x0000AAAAB89EF460 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -80: 7# 0x0000AAAAB89EF894 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -80: 8# 0x0000AAAAB89C3D38 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -80: 9# 0x0000AAAAB89C4284 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -80: 10# 0x0000AAAAB893C1B0 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -80: 11# 0x0000FFFFB868229C in /lib/aarch64-linux-gnu/libc.so.6 +80: 3# 0x0000AAAAC753DBC0 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +80: 4# 0x0000AAAAC74FB528 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +80: 5# 0x0000AAAAC757EAAC in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +80: 6# 0x0000AAAAC757F460 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +80: 7# 0x0000AAAAC757F894 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +80: 8# 0x0000AAAAC7553D38 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +80: 9# 0x0000AAAAC7554284 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +80: 10# 0x0000AAAAC74CC1B0 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +80: 11# 0x0000FFFF8E57229C in /lib/aarch64-linux-gnu/libc.so.6 80: 12# __libc_start_main in /lib/aarch64-linux-gnu/libc.so.6 -80: 13# 0x0000AAAAB893C270 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +80: 13# 0x0000AAAAC74CC270 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest 80: ---------- 80: **** 80: -80: [02:19:04] +80: [11:06:00] 80: 80: **** 80: Pre-condition Violation @@ -21462,23 +21457,21 @@ 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# 0x0000AAAAB89ADBC0 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -80: 4# 0x0000AAAAB896B7C4 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -80: 5# 0x0000AAAAB89EEAAC in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -80: 6# 0x0000AAAAB89EF460 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -80: 7# 0x0000AAAAB89EF894 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -80: 8# 0x0000AAAAB89C3D38 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -80: 9# 0x0000AAAAB89C4284 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -80: 10# 0x0000AAAAB893C1B0 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -80: 11# 0x0000FFFFB868229C in /lib/aarch64-linux-gnu/libc.so.6 +80: 3# 0x0000AAAAC753DBC0 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +80: 4# 0x0000AAAAC74FB7C4 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +80: 5# 0x0000AAAAC757EAAC in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +80: 6# 0x0000AAAAC757F460 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +80: 7# 0x0000AAAAC757F894 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +80: 8# 0x0000AAAAC7553D38 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +80: 9# 0x0000AAAAC7554284 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +80: 10# 0x0000AAAAC74CC1B0 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +80: 11# 0x0000FFFF8E57229C in /lib/aarch64-linux-gnu/libc.so.6 80: 12# __libc_start_main in /lib/aarch64-linux-gnu/libc.so.6 -80: 13# 0x0000AAAAB893C270 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +80: 13# 0x0000AAAAC74CC270 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest 80: ---------- 80: **** 80: -75: [02:19:04] bond with order 0 found on line 11. This is not part of the MDL specification. -75: [02:19:04] bond with order 0 found on line 16. This is not part of the MDL specification. -80: [02:19:04] +80: [11:06:00] 80: 80: **** 80: Pre-condition Violation @@ -21490,29 +21483,29 @@ 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# 0x0000AAAAB89ADBC0 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -80: 4# 0x0000AAAAB896B9BC in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -80: 5# 0x0000AAAAB89EEAAC in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -80: 6# 0x0000AAAAB89EF460 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -80: 7# 0x0000AAAAB89EF894 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -80: 8# 0x0000AAAAB89C3D38 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -80: 9# 0x0000AAAAB89C4284 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -80: 10# 0x0000AAAAB893C1B0 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -80: 11# 0x0000FFFFB868229C in /lib/aarch64-linux-gnu/libc.so.6 +80: 3# 0x0000AAAAC753DBC0 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +80: 4# 0x0000AAAAC74FB9BC in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +80: 5# 0x0000AAAAC757EAAC in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +80: 6# 0x0000AAAAC757F460 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +80: 7# 0x0000AAAAC757F894 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +80: 8# 0x0000AAAAC7553D38 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +80: 9# 0x0000AAAAC7554284 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +80: 10# 0x0000AAAAC74CC1B0 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +80: 11# 0x0000FFFF8E57229C in /lib/aarch64-linux-gnu/libc.so.6 80: 12# __libc_start_main in /lib/aarch64-linux-gnu/libc.so.6 -80: 13# 0x0000AAAAB893C270 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +80: 13# 0x0000AAAAC74CC270 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest 80: ---------- 80: **** 80: -80: [02:19:04] Found a SCD/SED line with missing/empty SDT specification at line 21 -80: [02:19:04] Found a SCD/SED line with missing/empty SDT specification at line 20 -80: [02:19:04] BEGIN SGROUP line not found on line 14 -80: [02:19:04] Unhandled CTAB feature: 'Unsupported SGroup type '' on line 18'. Molecule skipped. -80: [02:19:04] END SGROUP line not found on line 14 -80: [02:19:04] END SGROUP line not found on line 14 -80: [02:19:04] MRV_COORDINATE_BOND_TYPE SGroup with value 0 does not reference a query bond, ignoring. -80: [02:19:04] MRV_COORDINATE_BOND_TYPE SGroup with value 1 does not reference a query bond, ignoring. -80: [02:19:04] +80: [11:06:00] Found a SCD/SED line with missing/empty SDT specification at line 21 +80: [11:06:00] Found a SCD/SED line with missing/empty SDT specification at line 20 +80: [11:06:00] BEGIN SGROUP line not found on line 14 +80: [11:06:00] Unhandled CTAB feature: 'Unsupported SGroup type '' on line 18'. Molecule skipped. +80: [11:06:00] END SGROUP line not found on line 14 +80: [11:06:00] END SGROUP line not found on line 14 +80: [11:06:00] MRV_COORDINATE_BOND_TYPE SGroup with value 0 does not reference a query bond, ignoring. +80: [11:06:00] MRV_COORDINATE_BOND_TYPE SGroup with value 1 does not reference a query bond, ignoring. +80: [11:06:00] 80: 80: **** 80: Range Error @@ -21527,78 +21520,41 @@ 80: 3# RDKit::FileParserUtils::finishMolProcessing(RDKit::RWMol*, bool, RDKit::v2::FileParsers::MolFileParserParams const&) in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu//lib/libRDKitFileParsers.so.1 80: 4# RDKit::v2::FileParsers::MolFromMolDataStream(std::istream&, unsigned int&, RDKit::v2::FileParsers::MolFileParserParams const&) in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu//lib/libRDKitFileParsers.so.1 80: 5# RDKit::v2::FileParsers::MolFromMolBlock(std::__cxx11::basic_string, std::allocator > const&, RDKit::v2::FileParsers::MolFileParserParams const&) in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu//lib/libRDKitFileParsers.so.1 -80: 6# 0x0000AAAAB89AD834 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -80: 7# 0x0000AAAAB8970A10 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -80: 8# 0x0000AAAAB89EEAAC in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -80: 9# 0x0000AAAAB89EF460 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -80: 10# 0x0000AAAAB89EF894 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -80: 11# 0x0000AAAAB89C3D38 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -80: 12# 0x0000AAAAB89C4284 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -80: 13# 0x0000AAAAB893C1B0 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -80: 14# 0x0000FFFFB868229C in /lib/aarch64-linux-gnu/libc.so.6 +80: 6# 0x0000AAAAC753D834 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +80: 7# 0x0000AAAAC7500A10 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +80: 8# 0x0000AAAAC757EAAC in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +80: 9# 0x0000AAAAC757F460 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +80: 10# 0x0000AAAAC757F894 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +80: 11# 0x0000AAAAC7553D38 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +80: 12# 0x0000AAAAC7554284 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +80: 13# 0x0000AAAAC74CC1B0 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +80: 14# 0x0000FFFF8E57229C in /lib/aarch64-linux-gnu/libc.so.6 80: 15# __libc_start_main in /lib/aarch64-linux-gnu/libc.so.6 -80: 16# 0x0000AAAAB893C270 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +80: 16# 0x0000AAAAC74CC270 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest 80: ---------- 80: **** 80: -80: [02:19:04] molecule does not contain a bond matching the MRV_COORDINATE_BOND_TYPE SGroup for bond 99, ignoring. -80: [02:19:04] Multiple ATTCHPT values for atom 2 on line 9 -80: [02:19:04] Found a SCD/SED line with missing/empty SDT specification at line 12 -80: [02:19:04] SMARTS Parse Error: syntax error while parsing: [#6;R -80: [02:19:04] SMARTS Parse Error: Failed parsing SMARTS '[#6;R' for input: '[#6;R' -80: [02:19:04] SMARTS for SMARTSQ '[#6;R' could not be parsed or has no atoms. Ignoring it. -80: [02:19:04] Skipping empty SMARTS value for SMARTSQ. -80: [02:19:04] unrecognized QUERYOP '>' for SMARTSQ. Query ignored. -80: [02:19:04] Found a SCD/SED line with missing/empty SDT specification at line 12 -80: [02:19:04] Can't kekulize mol. Unkekulized atoms: 0 1 2 3 4 - 72/238 Test #75: testMolWriter .......................... Passed 0.24 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: [02:19:04] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -80: [02:19:04] WARNING: Skipping property bar because the value includes an illegal blank line -80: [02:19:04] WARNING: Skipping property baz because the value includes an illegal blank line -80: [02:19:04] WARNING: Skipping property bletch +80: [11:06:00] molecule does not contain a bond matching the MRV_COORDINATE_BOND_TYPE SGroup for bond 99, ignoring. +29: All 191 tests passed +80: [11:06:00] Multiple ATTCHPT values for atom 2 on line 9 +80: [11:06:00] Found a SCD/SED line with missing/empty SDT specification at line 12 +80: [11:06:00] SMARTS Parse Error: syntax error while parsing: [#6;R +80: [11:06:00] SMARTS Parse Error: Failed parsing SMARTS '[#6;R' for input: '[#6;R' +80: [11:06:00] SMARTS for SMARTSQ '[#6;R' could not be parsed or has no atoms. Ignoring it. +80: [11:06:00] Skipping empty SMARTS value for SMARTSQ. +80: [11:06:00] unrecognized QUERYOP '>' for SMARTSQ. Query ignored. +80: [11:06:00] Found a SCD/SED line with missing/empty SDT specification at line 12 +80: [11:06:00] Can't kekulize mol. Unkekulized atoms: 0 1 2 3 4 +80: [11:06:00] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +80: [11:06:00] WARNING: Skipping property bar because the value includes an illegal blank line +80: [11:06:00] WARNING: Skipping property baz because the value includes an illegal blank line +80: [11:06:00] WARNING: Skipping property bletch 80: nope because the name includes a newline -80: [02:19:04] WARNING: Skipping property bletch +80: [11:06:00] WARNING: Skipping property bletch 80: nope2 because the name includes a newline -80: [02:19:04] +80: [11:06:00] 80: 80: **** -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: [02:19:04] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored -68: [02:19:04] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored -68: Test -68: -68: Sotorasib_atropBad1.mrv -68: -68: [02:19:04] The 2 defining bonds for an atropisomer are co-planar - atoms are: 7 20 80: Post-condition Violation 80: Element 'QQQ' not found 80: Violation occurred on line 93 in file ./Code/GraphMol/PeriodicTable.h @@ -21608,26 +21564,26 @@ 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# 0x0000FFFFB8FB7F24 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu//lib/libRDKitFileParsers.so.1 -80: 4# 0x0000FFFFB8FC8190 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu//lib/libRDKitFileParsers.so.1 -80: 5# 0x0000FFFFB8FC8DCC in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu//lib/libRDKitFileParsers.so.1 +80: 3# 0x0000FFFF8EEA7F24 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu//lib/libRDKitFileParsers.so.1 +80: 4# 0x0000FFFF8EEB8190 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu//lib/libRDKitFileParsers.so.1 +80: 5# 0x0000FFFF8EEB8DCC 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# 0x0000AAAAB8944EF4 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -80: 10# 0x0000AAAAB89EEAAC in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -80: 11# 0x0000AAAAB89EF460 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -80: 12# 0x0000AAAAB89EF894 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -80: 13# 0x0000AAAAB89C3D38 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -80: 14# 0x0000AAAAB89C4284 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -80: 15# 0x0000AAAAB893C1B0 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -80: 16# 0x0000FFFFB868229C in /lib/aarch64-linux-gnu/libc.so.6 +80: 9# 0x0000AAAAC74D4EF4 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +80: 10# 0x0000AAAAC757EAAC in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +80: 11# 0x0000AAAAC757F460 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +80: 12# 0x0000AAAAC757F894 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +80: 13# 0x0000AAAAC7553D38 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +80: 14# 0x0000AAAAC7554284 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +80: 15# 0x0000AAAAC74CC1B0 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +80: 16# 0x0000FFFF8E57229C in /lib/aarch64-linux-gnu/libc.so.6 80: 17# __libc_start_main in /lib/aarch64-linux-gnu/libc.so.6 -80: 18# 0x0000AAAAB893C270 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +80: 18# 0x0000AAAAC74CC270 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest 80: ---------- 80: **** 80: -80: [02:19:04] +80: [11:06:00] 80: 80: **** 80: Post-condition Violation @@ -21639,26 +21595,26 @@ 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# 0x0000FFFFB8FB7F24 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu//lib/libRDKitFileParsers.so.1 -80: 4# 0x0000FFFFB8FC8190 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu//lib/libRDKitFileParsers.so.1 -80: 5# 0x0000FFFFB8FC8DCC in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu//lib/libRDKitFileParsers.so.1 +80: 3# 0x0000FFFF8EEA7F24 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu//lib/libRDKitFileParsers.so.1 +80: 4# 0x0000FFFF8EEB8190 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu//lib/libRDKitFileParsers.so.1 +80: 5# 0x0000FFFF8EEB8DCC 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# 0x0000AAAAB8944818 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -80: 10# 0x0000AAAAB89EEAAC in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -80: 11# 0x0000AAAAB89EF460 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -80: 12# 0x0000AAAAB89EF894 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -80: 13# 0x0000AAAAB89C3D38 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -80: 14# 0x0000AAAAB89C4284 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -80: 15# 0x0000AAAAB893C1B0 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -80: 16# 0x0000FFFFB868229C in /lib/aarch64-linux-gnu/libc.so.6 +80: 9# 0x0000AAAAC74D4818 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +80: 10# 0x0000AAAAC757EAAC in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +80: 11# 0x0000AAAAC757F460 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +80: 12# 0x0000AAAAC757F894 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +80: 13# 0x0000AAAAC7553D38 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +80: 14# 0x0000AAAAC7554284 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +80: 15# 0x0000AAAAC74CC1B0 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +80: 16# 0x0000FFFF8E57229C in /lib/aarch64-linux-gnu/libc.so.6 80: 17# __libc_start_main in /lib/aarch64-linux-gnu/libc.so.6 -80: 18# 0x0000AAAAB893C270 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +80: 18# 0x0000AAAAC74CC270 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest 80: ---------- 80: **** 80: -80: [02:19:04] +80: [11:06:00] 80: 80: **** 80: Post-condition Violation @@ -21670,28 +21626,58 @@ 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# 0x0000FFFFB8FB7F24 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu//lib/libRDKitFileParsers.so.1 -80: 4# 0x0000FFFFB8FC5B20 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu//lib/libRDKitFileParsers.so.1 -80: 5# 0x0000FFFFB8FC6A4C in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu//lib/libRDKitFileParsers.so.1 +80: 3# 0x0000FFFF8EEA7F24 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu//lib/libRDKitFileParsers.so.1 +80: 4# 0x0000FFFF8EEB5B20 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu//lib/libRDKitFileParsers.so.1 +80: 5# 0x0000FFFF8EEB6A4C 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# 0x0000AAAAB8944EB0 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -80: 10# 0x0000AAAAB89EEAAC in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -80: 11# 0x0000AAAAB89EF460 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -80: 12# 0x0000AAAAB89EF894 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -80: 13# 0x0000AAAAB89C3D38 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -80: 14# 0x0000AAAAB89C4284 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -80: 15# 0x0000AAAAB893C1B0 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -80: 16# 0x0000FFFFB868229C in /lib/aarch64-linux-gnu/libc.so.6 +80: 9# 0x0000AAAAC74D4EB0 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +80: 10# 0x0000AAAAC757EAAC in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +80: 11# 0x0000AAAAC757F460 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +80: 12# 0x0000AAAAC757F894 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +80: 13# 0x0000AAAAC7553D38 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +80: 14# 0x0000AAAAC7554284 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +80: 15# 0x0000AAAAC74CC1B0 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +80: 16# 0x0000FFFF8E57229C in /lib/aarch64-linux-gnu/libc.so.6 80: 17# __libc_start_main in /lib/aarch64-linux-gnu/libc.so.6 -80: 18# 0x0000AAAAB893C270 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +80: 18# 0x0000AAAAC74CC270 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest 80: ---------- +82: Randomness seeded to: 1419843174 +82: =============================================================================== +82: All tests passed (100 assertions in 2 test cases) +82: 80: **** 80: -80: [02:19:04] +80: [11:06:00] 80: 80: **** +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: [11:06:00] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored +68: [11:06:00] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored 80: Post-condition Violation 80: Element 'QQQ' not found 80: Violation occurred on line 93 in file ./Code/GraphMol/PeriodicTable.h @@ -21701,40 +21687,45 @@ 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# 0x0000FFFFB8FB7F24 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu//lib/libRDKitFileParsers.so.1 -80: 4# 0x0000FFFFB8FC5B20 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu//lib/libRDKitFileParsers.so.1 -80: 5# 0x0000FFFFB8FC6A4C in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu//lib/libRDKitFileParsers.so.1 +80: 3# 0x0000FFFF8EEA7F24 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu//lib/libRDKitFileParsers.so.1 +80: 4# 0x0000FFFF8EEB5B20 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu//lib/libRDKitFileParsers.so.1 +80: 5# 0x0000FFFF8EEB6A4C 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# 0x0000AAAAB8944BE8 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -80: 10# 0x0000AAAAB89EEAAC in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -80: 11# 0x0000AAAAB89EF460 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -80: 12# 0x0000AAAAB89EF894 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -80: 13# 0x0000AAAAB89C3D38 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -80: 14# 0x0000AAAAB89C4284 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -80: 15# 0x0000AAAAB893C1B0 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -80: 16# 0x0000FFFFB868229C in /lib/aarch64-linux-gnu/libc.so.6 +80: 9# 0x0000AAAAC74D4BE8 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +80: 10# 0x0000AAAAC757EAAC in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +80: 11# 0x0000AAAAC757F460 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +80: 12# 0x0000AAAAC757F894 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +80: 13# 0x0000AAAAC7553D38 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +80: 14# 0x0000AAAAC7554284 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +80: 15# 0x0000AAAAC74CC1B0 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +80: 16# 0x0000FFFF8E57229C in /lib/aarch64-linux-gnu/libc.so.6 80: 17# __libc_start_main in /lib/aarch64-linux-gnu/libc.so.6 -80: 18# 0x0000AAAAB893C270 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +80: 18# 0x0000AAAAC74CC270 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest 80: ---------- + 71/238 Test #82: XYZFileParserCatchTest ................. Passed 0.03 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 80: **** 80: -80: [02:19:04] atom 3 has a negative isotope value. line: 15 -83: Randomness seeded to: 248961083 -83: [02:19:04] Invalid or missing fragment id from CDXML fragment, assigning new one... -83: [02:19:04] Explicit valence for atom # 3 N, 4, is greater than permitted -83: [02:19:04] CDXMLParser: failed sanitizing skipping fragment 32 -83: [02:19:04] Bad bond in CDXML skipping fragment 58... -83: [02:19:04] Invalid or missing fragment id from CDXML fragment, assigning new one... -83: [02:19:04] Bad bond in CDXML skipping fragment 58... +80: [11:06:00] atom 3 has a negative isotope value. line: 15 +68: Test +68: +68: Sotorasib_atropBad1.mrv +68: +68: [11:06:00] The 2 defining bonds for an atropisomer are co-planar - atoms are: 7 20 68: Test 68: 68: Sotorasib_atropBad2.mrv 68: -68: [02:19:04] The bonds on one end of an atropisomer are both UP or both DOWN - atoms are: 7 20 -80: [02:19:04] Ignoring invalid chirality label: '2_bad_chirality' -80: [02:19:04] +68: [11:06:00] The bonds on one end of an atropisomer are both UP or both DOWN - atoms are: 7 20 +80: [11:06:00] Ignoring invalid chirality label: '2_bad_chirality' +80: [11:06:00] 80: 80: **** 80: Pre-condition Violation @@ -21747,16 +21738,16 @@ 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# 0x0000AAAAB8982054 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -80: 5# 0x0000AAAAB89EEAAC in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -80: 6# 0x0000AAAAB89EF460 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -80: 7# 0x0000AAAAB89EF894 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -80: 8# 0x0000AAAAB89C3D38 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -80: 9# 0x0000AAAAB89C4284 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -80: 10# 0x0000AAAAB893C1B0 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -80: 11# 0x0000FFFFB868229C in /lib/aarch64-linux-gnu/libc.so.6 +80: 4# 0x0000AAAAC7512054 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +80: 5# 0x0000AAAAC757EAAC in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +80: 6# 0x0000AAAAC757F460 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +80: 7# 0x0000AAAAC757F894 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +80: 8# 0x0000AAAAC7553D38 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +80: 9# 0x0000AAAAC7554284 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +80: 10# 0x0000AAAAC74CC1B0 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +80: 11# 0x0000FFFF8E57229C in /lib/aarch64-linux-gnu/libc.so.6 80: 12# __libc_start_main in /lib/aarch64-linux-gnu/libc.so.6 -80: 13# 0x0000AAAAB893C270 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +80: 13# 0x0000AAAAC74CC270 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest 80: ---------- 80: **** 80: @@ -21780,33 +21771,9 @@ 68: 68: ZM374979_atropBad1.mrv 68: -68: [02:19:04] The 2 defining bonds for an atropisomer are co-planar - atoms are: 0 31 -84: Randomness seeded to: 1321416827 -84: [02:19:04] Warning: ambiguous stereochemistry - opposing bonds have opposite wedging - at atom 2 ignored. -84: [02:19:04] Warning: ambiguous stereochemistry - opposing bonds have opposite wedging - at atom 2 ignored. -84: [02:19:04] Warning: ambiguous stereochemistry - opposing bonds have opposite wedging - at atom 2 ignored. -84: [02:19:04] Warning: ambiguous stereochemistry - opposing bonds have opposite wedging - at atom 2 ignored. -84: =============================================================================== -84: All tests passed (142 assertions in 6 test cases) -84: -83: [02:19:04] WARNING: not removing hydrogen atom without neighbors - 73/238 Test #84: molfileStereoCatchTest ................. Passed 0.03 sec -test 85 - Start 85: connectTheDotsTest - -85: Test command: /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/connectTheDotsTest -85: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers -85: Test timeout computed to be: 1500 -83: [02:19:04] WARNING: not removing hydrogen atom without neighbors -83: [02:19:04] WARNING: not removing hydrogen atom without neighbors -83: [02:19:04] WARNING: not removing hydrogen atom without neighbors -83: [02:19:04] WARNING: not removing hydrogen atom without neighbors -83: [02:19:04] WARNING: not removing hydrogen atom without neighbors -83: [02:19:04] WARNING: not removing hydrogen atom without neighbors -83: [02:19:04] WARNING: not removing hydrogen atom without neighbors -83: [02:19:04] WARNING: not removing hydrogen atom without neighbors -83: [02:19:04] WARNING: not removing hydrogen atom without neighbors -83: [02:19:04] CDXMLParser: Schema 80180 step 80181 ReactionStepAgents reaction fragment 64603 not found in document. +68: [11:06:00] The 2 defining bonds for an atropisomer are co-planar - atoms are: 0 31 +75: [11:06:00] Warning: molecule is tagged as 3D, but all Z coords are zero and 2D stereo markers have been found, marking the mol as 2D. +75: 0.40201265 0.40201265 68: Test 68: 68: mrtx1719_3d.mrv @@ -21827,56 +21794,43 @@ 68: 68: mrtx1719_atropBad1.mrv 68: -68: [02:19:04] The 2 defining bonds for an atropisomer are co-planar - atoms are: 15 16 -69: [02:19:04] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 1 ignored -69: [02:19:04] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 1 ignored -69: [02:19:04] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 1 ignored -69: [02:19:04] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 1 ignored -69: [02:19:04] 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: [02:19:04] -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# 0x0000FFFFB54A7F24 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu//lib/libRDKitFileParsers.so.1 -69: 4# 0x0000FFFFB54B5B20 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu//lib/libRDKitFileParsers.so.1 -69: 5# 0x0000FFFFB54B6A4C 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# 0x0000AAAAC289F77C in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersTest1 -69: 10# 0x0000AAAAC2914944 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersTest1 -69: 11# 0x0000AAAAC2885BF8 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersTest1 -69: 12# 0x0000FFFFB4B6229C in /lib/aarch64-linux-gnu/libc.so.6 -69: 13# __libc_start_main in /lib/aarch64-linux-gnu/libc.so.6 -69: 14# 0x0000AAAAC2885E30 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersTest1 -69: ---------- -69: **** -69: -85: Randomness seeded to: 3988678274 -85: =============================================================================== -85: All tests passed (8 assertions in 1 test case) -85: - 74/238 Test #85: connectTheDotsTest ..................... Passed 0.02 sec -test 86 - Start 86: v2MolSuppliers +68: [11:06:00] The 2 defining bonds for an atropisomer are co-planar - atoms are: 15 16 +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: [11:06:00] bond with order 0 found on line 11. This is not part of the MDL specification. +75: [11:06:00] bond with order 0 found on line 16. This is not part of the MDL specification. +83: Randomness seeded to: 4002855649 +83: [11:06:00] Invalid or missing fragment id from CDXML fragment, assigning new one... +83: [11:06:00] Explicit valence for atom # 3 N, 4, is greater than permitted +83: [11:06:00] CDXMLParser: failed sanitizing skipping fragment 32 +83: [11:06:00] Bad bond in CDXML skipping fragment 58... +83: [11:06:00] Invalid or missing fragment id from CDXML fragment, assigning new one... +83: [11:06:00] Bad bond in CDXML skipping fragment 58... + 72/238 Test #75: testMolWriter .......................... Passed 0.23 sec +test 84 + Start 84: molfileStereoCatchTest -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: [02:19:04] Can't kekulize mol. Unkekulized atoms: 0 1 2 3 4 -80: [02:19:04] 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.[02:19:04] Warning: molecule is tagged as 3D, but all Z coords are zero and 2D stereo markers have been found, marking the mol as 2D. -80: [02:19:04] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -80: [02:19:04] Warning: molecule is tagged as 3D, but all Z coords are zero and 2D stereo markers have been found, marking the mol as 2D. -80: [02:19:04] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +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: AlexRxn.mrv @@ -21917,25 +21871,20 @@ 68: 68: EmptyRxn.mrv 68: -68: [02:19:04] initialization failed -83: [02:19:04] Incomplete atom labelling, cannot make bond -83: [02:19:04] Incomplete atom labelling, cannot make bond -86: Randomness seeded to: 2271622850 -86: [02:19:04] Ignoring invalid chirality label: '12_R_1_3_4_5' -86: [02:19:04] Ignoring invalid chirality label: '12_ANR_1_3_4_15' -86: [02:19:04] Ignoring invalid chirality label: '2_S_1_3_4' -86: [02:19:04] Ignoring invalid chirality label: '2_ANS_1_3_4_5_2' -86: =============================================================================== -86: All tests passed (24 assertions in 6 test cases) -86: - 75/238 Test #86: v2MolSuppliers ......................... Passed 0.02 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 -83: [02:19:04] Incomplete atom labelling, cannot make bond +68: [11:06:00] initialization failed +80: [11:06:00] Can't kekulize mol. Unkekulized atoms: 0 1 2 3 4 +80: [11:06:00] 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.[11:06:00] 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: [11:06:00] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +80: [11:06:00] 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: [11:06:00] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +83: [11:06:00] WARNING: not removing hydrogen atom without neighbors +83: [11:06:00] WARNING: not removing hydrogen atom without neighbors +83: [11:06:00] WARNING: not removing hydrogen atom without neighbors +83: [11:06:00] WARNING: not removing hydrogen atom without neighbors +83: [11:06:00] WARNING: not removing hydrogen atom without neighbors +83: [11:06:00] WARNING: not removing hydrogen atom without neighbors +83: [11:06:00] WARNING: not removing hydrogen atom without neighbors +83: [11:06:00] WARNING: not removing hydrogen atom without neighbors 68: Test 68: 68: RxnNoCoords.mrv @@ -22024,22 +21973,107 @@ 68: 68: Smiles1 68: - 76/238 Test #68: testMrvToMol ........................... Passed 0.81 sec +83: [11:06:00] WARNING: not removing hydrogen atom without neighbors +83: [11:06:00] WARNING: not removing hydrogen atom without neighbors + 73/238 Test #68: testMrvToMol ........................... Passed 0.60 sec +test 85 + Start 85: connectTheDotsTest + +85: Test command: /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/connectTheDotsTest +85: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers +85: Test timeout computed to be: 1500 +83: [11:06:00] CDXMLParser: Schema 80180 step 80181 ReactionStepAgents reaction fragment 64603 not found in document. +83: [11:06:00] Incomplete atom labelling, cannot make bond +83: [11:06:00] Incomplete atom labelling, cannot make bond +29: +29: Computing MMFF94 energies for /build/reproducible-path/rdkit-202503.1/Code/ForceField/MMFF/test_data/MMFF94_hypervalent.sdf... +84: Randomness seeded to: 136644365 +84: [11:06:00] Warning: ambiguous stereochemistry - opposing bonds have opposite wedging - at atom 2 ignored. +84: [11:06:00] Warning: ambiguous stereochemistry - opposing bonds have opposite wedging - at atom 2 ignored. +84: [11:06:00] Warning: ambiguous stereochemistry - opposing bonds have opposite wedging - at atom 2 ignored. +84: [11:06:00] Warning: ambiguous stereochemistry - opposing bonds have opposite wedging - at atom 2 ignored. +84: =============================================================================== +84: All tests passed (142 assertions in 6 test cases) +84: + 74/238 Test #84: molfileStereoCatchTest ................. Passed 0.05 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 +85: Randomness seeded to: 3926191766 +85: =============================================================================== +85: All tests passed (8 assertions in 1 test case) +85: +83: [11:06:00] Incomplete atom labelling, cannot make bond + 75/238 Test #85: connectTheDotsTest ..................... Passed 0.02 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 +83: [11:06:00] Failed to parse XML fragment 5 node: n attribute: id: mydoghasfleas +83: [11:06:00] Failed to parse XML fragment 5 node: n attribute: id: mydoghasfleas +83: [11:06:00] Failed to parse XML fragment 5 node: b attribute: Order: slartibartfast +83: [11:06:00] Failed to parse XML fragment 5 node: b attribute: Order: 5 +83: [11:06:00] Invalid or missing fragment id from CDXML fragment, assigning new one... +83: =============================================================================== +83: All tests passed (263 assertions in 7 test cases) +83: + 76/238 Test #83: cdxmlParserCatchTest ................... Passed 0.12 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 -87: Randomness seeded to: 934819029 +69: [11:06:00] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 1 ignored +69: [11:06:00] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 1 ignored +69: [11:06:00] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 1 ignored +69: [11:06:00] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 1 ignored +69: [11:06:00] 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: [11:06:00] +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# 0x0000FFFFA2AA7F24 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu//lib/libRDKitFileParsers.so.1 +69: 4# 0x0000FFFFA2AB5B20 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu//lib/libRDKitFileParsers.so.1 +69: 5# 0x0000FFFFA2AB6A4C 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# 0x0000AAAACB00F77C in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersTest1 +69: 10# 0x0000AAAACB084944 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersTest1 +69: 11# 0x0000AAAACAFF5BF8 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersTest1 +69: 12# 0x0000FFFFA216229C in /lib/aarch64-linux-gnu/libc.so.6 +69: 13# __libc_start_main in /lib/aarch64-linux-gnu/libc.so.6 +69: 14# 0x0000AAAACAFF5E30 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersTest1 +69: ---------- +69: **** +69: +87: Randomness seeded to: 3153415610 87: =============================================================================== 87: All tests passed (6 assertions in 1 test case) 87: -83: [02:19:04] Failed to parse XML fragment 5 node: n attribute: id: mydoghasfleas -83: [02:19:04] Failed to parse XML fragment 5 node: n attribute: id: mydoghasfleas -83: [02:19:04] Failed to parse XML fragment 5 node: b attribute: Order: slartibartfast -83: [02:19:04] Failed to parse XML fragment 5 node: b attribute: Order: 5 -83: [02:19:04] Invalid or missing fragment id from CDXML fragment, assigning new one... +86: Randomness seeded to: 779421903 +86: [11:06:00] Ignoring invalid chirality label: '12_R_1_3_4_5' +88: Randomness seeded to: 1555163930 +88: =============================================================================== +88: All tests passed (26 assertions in 2 test cases) +88: +86: [11:06:00] Ignoring invalid chirality label: '12_ANR_1_3_4_15' +86: [11:06:00] Ignoring invalid chirality label: '2_S_1_3_4' 77/238 Test #87: v2FileParsersCatchTest ................. Passed 0.03 sec test 89 Start 89: multithreadedSupplierCatchTest @@ -22047,20 +22081,24 @@ 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 -83: =============================================================================== -83: All tests passed (263 assertions in 7 test cases) -83: - 78/238 Test #83: cdxmlParserCatchTest ................... Passed 0.17 sec + 78/238 Test #88: atropisomersCatch ...................... Passed 0.02 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 -88: Randomness seeded to: 853405273 -88: =============================================================================== -88: All tests passed (26 assertions in 2 test cases) -88: +86: [11:06:00] Ignoring invalid chirality label: '2_ANS_1_3_4_5_2' +86: =============================================================================== +86: All tests passed (24 assertions in 6 test cases) +86: + 79/238 Test #86: v2MolSuppliers ......................... Passed 0.05 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: ----------------- Test 1 90: Done 90: @@ -22085,27 +22123,20 @@ 90: ----------------- Testing serial numbers on recursive queries 90: Done 90: - 79/238 Test #88: atropisomersCatch ...................... Passed 0.03 sec -90: [02:19:04] ------------------------------------- -90: [02:19:04] Test multithreading +90: [11:06:00] ------------------------------------- +90: [11:06:00] Test multithreading 90: reading molecules -test 91 - Start 91: substructTestCatch - -91: Test command: /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/Substruct/substructTestCatch -91: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/Substruct -91: Test timeout computed to be: 1500 -69: [02:19:04] Warning: molecule is tagged as 3D, but all Z coords are zero and 2D stereo markers have been found, marking the mol as 2D. -69: [02:19:04] Warning: molecule is tagged as 3D, but all Z coords are zero and 2D stereo markers have been found, marking the mol as 2D. 90: hits: 1111110111111111111111011111100011011011111101010111011110111101111111111111111111111011111011111110 90: processing 90: launch :0 90: launch :1 90: launch :2 90: launch :3 +69: [11:06:01] Warning: molecule is tagged as 3D, but all Z coords are zero and 2D stereo markers have been found, marking the mol as 2D. +69: [11:06:01] Warning: molecule is tagged as 3D, but all Z coords are zero and 2D stereo markers have been found, marking the mol as 2D. 69: ---------------------------------- 69: ---------------------------------- -69: [02:19:04] +69: [11:06:01] 69: 69: **** 69: Pre-condition Violation @@ -22117,16 +22148,15 @@ 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# 0x0000AAAAC28AF23C in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersTest1 -69: 4# 0x0000AAAAC29149A4 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersTest1 -69: 5# 0x0000AAAAC2885BF8 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersTest1 -69: 6# 0x0000FFFFB4B6229C in /lib/aarch64-linux-gnu/libc.so.6 +69: 3# 0x0000AAAACB01F23C in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersTest1 +69: 4# 0x0000AAAACB0849A4 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersTest1 +69: 5# 0x0000AAAACAFF5BF8 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersTest1 +69: 6# 0x0000FFFFA216229C in /lib/aarch64-linux-gnu/libc.so.6 69: 7# __libc_start_main in /lib/aarch64-linux-gnu/libc.so.6 -69: 8# 0x0000AAAAC2885E30 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersTest1 +69: 8# 0x0000AAAACAFF5E30 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersTest1 69: ---------- 69: **** 69: -69: [02:19:04] WARNING: could not find number of expected rings. Switching to an approximate ring finding algorithm. 90: done 90: hits2: 1111110111111111111111011111100011011011111101010111011110111101111111111111111111111011111011111110 90: processing2 @@ -22134,6 +22164,7 @@ 90: launch2 :1 90: launch2 :2 90: launch2 :3 +69: [11:06:01] WARNING: could not find number of expected rings. Switching to an approximate ring finding algorithm. 90: done 90: preprocessing 3 90: hits3: 1110100011001000010011100110100011011000010101000100110010101111011100101000001111110000010100100110 @@ -22142,239 +22173,248 @@ 90: launch3 :1 90: launch3 :2 90: launch3 :3 -89: Randomness seeded to: 980233360 -89: [02:19:04] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [02:19:04] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [02:19:04] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [02:19:04] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [02:19:04] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [02:19:04] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [02:19:04] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [02:19:04] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [02:19:04] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [02:19:04] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [02:19:04] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [02:19:04] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [02:19:04] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [02:19:04] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [02:19:04] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [02:19:04] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [02:19:04] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [02:19:04] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [02:19:04] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [02:19:04] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [02:19:04] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [02:19:04] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [02:19:04] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [02:19:04] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [02:19:04] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [02:19:04] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [02:19:04] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [02:19:04] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [02:19:04] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [02:19:04] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [02:19:04] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [02:19:04] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [02:19:04] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [02:19:04] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [02:19:04] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [02:19:04] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [02:19:04] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [02:19:04] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [02:19:04] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [02:19:04] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [02:19:04] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [02:19:04] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [02:19:04] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [02:19:04] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [02:19:04] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [02:19:04] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [02:19:04] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [02:19:04] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [02:19:04] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [02:19:04] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [02:19:04] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [02:19:04] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [02:19:04] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [02:19:04] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [02:19:04] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [02:19:04] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [02:19:04] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [02:19:04] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [02:19:04] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [02:19:04] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [02:19:04] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [02:19:04] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [02:19:04] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [02:19:04] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [02:19:04] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [02:19:04] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [02:19:04] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [02:19:04] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [02:19:04] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [02:19:04] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [02:19:04] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [02:19:04] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [02:19:04] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [02:19:04] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [02:19:04] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [02:19:04] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [02:19:04] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [02:19:04] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [02:19:04] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [02:19:04] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [02:19:04] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [02:19:04] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [02:19:04] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [02:19:04] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [02:19:04] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [02:19:04] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [02:19:04] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [02:19:04] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [02:19:04] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [02:19:04] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [02:19:04] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [02:19:04] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [02:19:04] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [02:19:04] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [02:19:04] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [02:19:04] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [02:19:04] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [02:19:04] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [02:19:04] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [02:19:04] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [02:19:04] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [02:19:04] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [02:19:04] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [02:19:04] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [02:19:04] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [02:19:04] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [02:19:04] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [02:19:04] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [02:19:04] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [02:19:04] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [02:19:04] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [02:19:04] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [02:19:04] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [02:19:04] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [02:19:04] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [02:19:04] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [02:19:04] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [02:19:04] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [02:19:04] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [02:19:04] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [02:19:04] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [02:19:04] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [02:19:04] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [02:19:04] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [02:19:04] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [02:19:04] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [02:19:04] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [02:19:04] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [02:19:04] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [02:19:04] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [02:19:04] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [02:19:04] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [02:19:04] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [02:19:04] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [02:19:04] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [02:19:04] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [02:19:04] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [02:19:04] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [02:19:04] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [02:19:04] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [02:19:04] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [02:19:04] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [02:19:04] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [02:19:04] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [02:19:04] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [02:19:04] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [02:19:04] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [02:19:04] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [02:19:04] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [02:19:04] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [02:19:04] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [02:19:04] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [02:19:04] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [02:19:04] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [02:19:04] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [02:19:04] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [02:19:04] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [02:19:04] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [02:19:04] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [02:19:04] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [02:19:04] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [02:19:04] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [02:19:04] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [02:19:04] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [02:19:04] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [02:19:04] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [02:19:04] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [02:19:04] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [02:19:04] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [02:19:04] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [02:19:04] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [02:19:04] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [02:19:04] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [02:19:04] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [02:19:04] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [02:19:04] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [02:19:04] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [02:19:04] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [02:19:04] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [02:19:04] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [02:19:04] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [02:19:04] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [02:19:04] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [02:19:04] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [02:19:04] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [02:19:04] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [02:19:04] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [02:19:04] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [02:19:04] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [02:19:04] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [02:19:04] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [02:19:04] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [02:19:04] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [02:19:04] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: Randomness seeded to: 3451442757 +89: [11:06:01] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [11:06:01] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [11:06:01] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [11:06:01] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [11:06:01] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [11:06:01] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [11:06:01] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [11:06:01] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [11:06:01] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [11:06:01] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [11:06:01] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [11:06:01] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [11:06:01] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [11:06:01] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [11:06:01] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [11:06:01] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [11:06:01] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [11:06:01] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [11:06:01] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [11:06:01] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [11:06:01] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [11:06:01] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [11:06:01] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [11:06:01] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [11:06:01] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [11:06:01] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [11:06:01] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [11:06:01] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [11:06:01] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [11:06:01] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [11:06:01] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [11:06:01] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [11:06:01] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [11:06:01] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [11:06:01] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [11:06:01] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [11:06:01] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [11:06:01] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [11:06:01] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [11:06:01] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [11:06:01] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [11:06:01] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [11:06:01] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [11:06:01] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [11:06:01] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [11:06:01] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [11:06:01] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [11:06:01] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [11:06:01] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [11:06:01] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [11:06:01] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [11:06:01] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [11:06:01] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [11:06:01] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +91: Randomness seeded to: 1988857339 +91: =============================================================================== +91: All tests passed (242 assertions in 12 test cases) +91: +89: [11:06:01] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [11:06:01] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [11:06:01] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [11:06:01] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [11:06:01] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [11:06:01] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [11:06:01] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [11:06:01] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [11:06:01] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [11:06:01] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [11:06:01] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [11:06:01] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [11:06:01] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [11:06:01] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [11:06:01] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [11:06:01] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [11:06:01] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [11:06:01] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [11:06:01] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [11:06:01] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [11:06:01] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [11:06:01] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [11:06:01] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [11:06:01] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [11:06:01] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [11:06:01] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [11:06:01] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [11:06:01] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [11:06:01] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [11:06:01] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [11:06:01] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [11:06:01] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [11:06:01] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [11:06:01] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [11:06:01] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. + 80/238 Test #91: substructTestCatch ..................... Passed 0.20 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 90: done -89: [02:19:04] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [02:19:04] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [02:19:04] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [02:19:04] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [02:19:04] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [02:19:04] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [02:19:04] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -90: [02:19:04] done -90: [02:19:04] ------------------------------------- -90: [02:19:04] Test GitHub issue 15 -90: [02:19:04] done -90: [02:19:04] ------------------------------------- -90: [02:19:04] Test GitHub issue 409 -90: [02:19:04] done -90: [02:19:04] ------------------------------------- -90: [02:19:04] Test chiral matching -40: [02:19:04] done: 500000 -90: [02:19:04] done -90: [02:19:04] ------------------------------------- -90: [02:19:04] Test GitHub issue 688: partially specified chiral substructure queries don't work properly -40: [02:19:04] Done -90: [02:19:04] done -90: [02:19:04] ------------------------------------- -90: [02:19:04] Test dative-bond matching -90: [02:19:04] done -90: [02:19:04] ------------------------------------- -90: [02:19:04] Test cis/trans matching -90: [02:19:04] done -90: [02:19:04] ------------------------------------- -90: [02:19:04] Test cis/trans matching part 2 -90: [02:19:04] done -90: [02:19:04] ------------------------------------- -90: [02:19:04] Testing Github #1389: Substructure matching with chirality failure when query is built from SMARTS -90: [02:19:04] done -90: [02:19:04] ------------------------------------- -90: [02:19:04] Testing matching E/Z against Cis/Trans stereo bonds -90: [02:19:04] +90: [11:06:01] done +90: [11:06:01] ------------------------------------- +90: [11:06:01] Test GitHub issue 15 +90: [11:06:01] done +90: [11:06:01] ------------------------------------- +90: [11:06:01] Test GitHub issue 409 +90: [11:06:01] done +90: [11:06:01] ------------------------------------- +90: [11:06:01] Test chiral matching +90: [11:06:01] done +90: [11:06:01] ------------------------------------- +90: [11:06:01] Test GitHub issue 688: partially specified chiral substructure queries don't work properly +90: [11:06:01] done +90: [11:06:01] ------------------------------------- +90: [11:06:01] Test dative-bond matching +90: [11:06:01] done +90: [11:06:01] ------------------------------------- +90: [11:06:01] Test cis/trans matching +90: [11:06:01] done +90: [11:06:01] ------------------------------------- +90: [11:06:01] Test cis/trans matching part 2 +90: [11:06:01] done +90: [11:06:01] ------------------------------------- +90: [11:06:01] Testing Github #1389: Substructure matching with chirality failure when query is built from SMARTS +90: [11:06:01] done +89: [11:06:01] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [11:06:01] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [11:06:01] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [11:06:01] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [11:06:01] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [11:06:01] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [11:06:01] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [11:06:01] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [11:06:01] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [11:06:01] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [11:06:01] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [11:06:01] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [11:06:01] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [11:06:01] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [11:06:01] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [11:06:01] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [11:06:01] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [11:06:01] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [11:06:01] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [11:06:01] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [11:06:01] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [11:06:01] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [11:06:01] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [11:06:01] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [11:06:01] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [11:06:01] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [11:06:01] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [11:06:01] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [11:06:01] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [11:06:01] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [11:06:01] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [11:06:01] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [11:06:01] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [11:06:01] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [11:06:01] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [11:06:01] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [11:06:01] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [11:06:01] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [11:06:01] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [11:06:01] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [11:06:01] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [11:06:01] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [11:06:01] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [11:06:01] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [11:06:01] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [11:06:01] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [11:06:01] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [11:06:01] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [11:06:01] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [11:06:01] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [11:06:01] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [11:06:01] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [11:06:01] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [11:06:01] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [11:06:01] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [11:06:01] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [11:06:01] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [11:06:01] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [11:06:01] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [11:06:01] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [11:06:01] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [11:06:01] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [11:06:01] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [11:06:01] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [11:06:01] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [11:06:01] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [11:06:01] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [11:06:01] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [11:06:01] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [11:06:01] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [11:06:01] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [11:06:01] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [11:06:01] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [11:06:01] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [11:06:01] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +90: [11:06:01] ------------------------------------- +90: [11:06:01] Testing matching E/Z against Cis/Trans stereo bonds +89: [11:06:01] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [11:06:01] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [11:06:01] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [11:06:01] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [11:06:01] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [11:06:01] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [11:06:01] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [11:06:01] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [11:06:01] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [11:06:01] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [11:06:01] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [11:06:01] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [11:06:01] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [11:06:01] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [11:06:01] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [11:06:01] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [11:06:01] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [11:06:01] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [11:06:01] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [11:06:01] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [11:06:01] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [11:06:01] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [11:06:01] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [11:06:01] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [11:06:01] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [11:06:01] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [11:06:01] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [11:06:01] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [11:06:01] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [11:06:01] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [11:06:01] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [11:06:01] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [11:06:01] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [11:06:01] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [11:06:01] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [11:06:01] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [11:06:01] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +90: [11:06:01] 90: 90: **** 90: Pre-condition Violation @@ -22387,15 +22427,15 @@ 90: 1# Invar::operator<<(std::ostream&, Invar::Invariant const&) in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu//lib/libRDKitRDGeneral.so.1 90: 2# RDKit::detail::ScoreMatchesByDegreeOfCoreSubstitution::ScoreMatchesByDegreeOfCoreSubstitution(RDKit::ROMol const&, RDKit::ROMol const&, std::vector, std::allocator > >, std::allocator, std::allocator > > > > const&) in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu//lib/libRDKitSubstructMatch.so.1 90: 3# RDKit::getMostSubstitutedCoreMatch(RDKit::ROMol const&, RDKit::ROMol const&, std::vector, std::allocator > >, std::allocator, std::allocator > > > > const&) in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu//lib/libRDKitSubstructMatch.so.1 -90: 4# 0x0000AAAAE704AD50 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/Substruct/testSubstructMatch -90: 5# 0x0000AAAAE70399A8 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/Substruct/testSubstructMatch -90: 6# 0x0000FFFF80A2229C in /lib/aarch64-linux-gnu/libc.so.6 +90: 4# 0x0000AAAAB11BAD50 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/Substruct/testSubstructMatch +90: 5# 0x0000AAAAB11A99A8 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/Substruct/testSubstructMatch +90: 6# 0x0000FFFF9709229C in /lib/aarch64-linux-gnu/libc.so.6 90: 7# __libc_start_main in /lib/aarch64-linux-gnu/libc.so.6 -90: 8# 0x0000AAAAE7039BB0 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/Substruct/testSubstructMatch +90: 8# 0x0000AAAAB11A9BB0 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/Substruct/testSubstructMatch 90: ---------- 90: **** 90: -90: [02:19:04] +90: [11:06:01] 90: 90: **** 90: Pre-condition Violation @@ -22408,407 +22448,682 @@ 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# 0x0000AAAAE704B3A0 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/Substruct/testSubstructMatch -90: 5# 0x0000AAAAE70399A8 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/Substruct/testSubstructMatch -90: 6# 0x0000FFFF80A2229C in /lib/aarch64-linux-gnu/libc.so.6 +90: 4# 0x0000AAAAB11BB3A0 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/Substruct/testSubstructMatch +90: 5# 0x0000AAAAB11A99A8 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/Substruct/testSubstructMatch +90: 6# 0x0000FFFF9709229C in /lib/aarch64-linux-gnu/libc.so.6 90: 7# __libc_start_main in /lib/aarch64-linux-gnu/libc.so.6 -90: 8# 0x0000AAAAE7039BB0 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/Substruct/testSubstructMatch +90: 8# 0x0000AAAAB11A9BB0 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/Substruct/testSubstructMatch 90: ---------- 90: **** 90: -90: [02:19:04] ------------------------------------- -90: [02:19:04] Test substructure matching with a pathological case for symmetric SSSR -90: [02:19:04] ------------------------------------- -90: [02:19:04] Test isAtomTerminalRGroupOrQueryHydrogen - 80/238 Test #90: testSubstructMatch ..................... Passed 0.25 sec -test 92 - Start 92: testGenericGroups - -92: Test command: /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/GenericGroups/testGenericGroups -92: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/GenericGroups -92: Test timeout computed to be: 1500 -40: [02:19:04] Testing hanoi with a functor. -91: Randomness seeded to: 3352312939 -91: =============================================================================== -91: All tests passed (242 assertions in 12 test cases) -91: -40: [02:19:05] Done -40: [02:19:05] Testing basic partition refinement. -40: [02:19:05] Done -40: [02:19:05] Testing partition refinement with neighbors. -40: [02:19:05] Done -40: [02:19:05] testing canonicalization via tie breaking. -40: [02:19:05] Done -40: [02:19:05] testing canonicalization using the wrapper. - 81/238 Test #91: substructTestCatch ..................... Passed 0.25 sec +90: [11:06:01] ------------------------------------- +90: [11:06:01] Test substructure matching with a pathological case for symmetric SSSR +90: [11:06:01] ------------------------------------- +90: [11:06:01] Test isAtomTerminalRGroupOrQueryHydrogen + 81/238 Test #90: testSubstructMatch ..................... Passed 0.24 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 -40: [02:19:05] Done -40: [02:19:05] testing some specific ordering problems -40: [02:19:05] Finished -40: [02:19:05] testing chiral invariants. -40: [02:19:05] Finished -40: [02:19:05] testing unique ranks in w.r.t. renumbering. 93: smi: O=C1CNC(=O)CN1 93: 1: O=C1CNC(=O)CN1 93: 2: COOC -93: [02:19:05] SMARTS Parse Error: syntax error while parsing: [Q:1][C:2][C:3](=[O:4])[O:5] -93: [02:19:05] 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: [11:06:01] SMARTS Parse Error: syntax error while parsing: [Q:1][C:2][C:3](=[O:4])[O:5] +93: [11:06:01] 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 -40: [02:19:05] Finished -40: [02:19:05] testing mol fragments. -40: [02:19:05] Finished -40: [02:19:05] testing protein round-tripping. -93: [02:19:05] product atom-mapping number 1 found multiple times. -93: [02:19:05] mapped atoms in the reactants were not mapped in the products. +93: [11:06:01] product atom-mapping number 1 found multiple times. +93: [11:06:01] mapped atoms in the reactants were not mapped in the products. 93: unmapped numbers are: 4 -93: [02:19:05] atom 0 in product 0 has multiple charge specifications. +93: [11:06:01] atom 0 in product 0 has multiple charge specifications. 93: mass: 15.0001 93: Oc1ccccn1 93: Oc1ccc[nH]1 -93: [02:19:05] SMARTS Parse Error: syntax error while parsing: ([C:1](=O)O.[C:2] -93: [02:19:05] SMARTS Parse Error: Failed parsing SMARTS '([C:1](=O)O.[C:2]' for input: '([C:1](=O)O.[C:2]' -93: [02:19:05] SMARTS Parse Error: syntax error while parsing: ([C:2] -93: [02:19:05] SMARTS Parse Error: Failed parsing SMARTS '([C:2]' for input: '([C:2]' -93: [02:19:05] SMARTS Parse Error: syntax error while parsing: [C:1](=O)O).[C:2] -93: [02:19:05] SMARTS Parse Error: Failed parsing SMARTS '[C:1](=O)O).[C:2]' for input: '[C:1](=O)O).[C:2]' -93: [02:19:05] SMARTS Parse Error: syntax error while parsing: [C:2]) -93: [02:19:05] SMARTS Parse Error: Failed parsing SMARTS '[C:2])' for input: '[C:2])' -93: [02:19:05] SMILES Parse Error: syntax error while parsing: [Q:1][C:2][C:3](=[O:4])[O:5] -93: [02:19:05] SMILES Parse Error: check for mistakes around position 2: -93: [02:19:05] [Q:1][C:2][C:3](=[O:4])[O:5] -93: [02:19:05] ~^ -93: [02:19:05] 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: [02:19:05] reactant 2 has no mapped atoms. -93: [02:19:05] >> Atoms within one molecule have different RXN roles. -93: [02:19:05] >> Fragment 0 not included in the reaction, atoms do not have a correct RXN role. -93: [02:19:05] SMARTS Parse Error: syntax error while parsing: ([C:1][C:2] -93: [02:19:05] SMARTS Parse Error: Failed parsing SMARTS '([C:1][C:2]' for input: '([C:1][C:2]' -93: [02:19:05] SMARTS Parse Error: syntax error while parsing: ([C:2] -93: [02:19:05] SMARTS Parse Error: Failed parsing SMARTS '([C:2]' for input: '([C:2]' -93: [02:19:05] SMARTS Parse Error: syntax error while parsing: [C:1][C:2]) -93: [02:19:05] SMARTS Parse Error: Failed parsing SMARTS '[C:1][C:2])' for input: '[C:1][C:2])' -93: [02:19:05] SMARTS Parse Error: syntax error while parsing: [C:1]).[C:2] -93: [02:19:05] SMARTS Parse Error: Failed parsing SMARTS '[C:1]).[C:2]' for input: '[C:1]).[C:2]' -69: [02:19:05] SMARTS Parse Error: syntax error while parsing: MyDogHasFleas -69: [02:19:05] SMARTS Parse Error: Failed parsing SMARTS 'MyDogHasFleas' for input: 'MyDogHasFleas' -93: [02:19:05] reactant 0 has no mapped atoms. -93: [02:19:05] reactant 1 has no mapped atoms. -93: [02:19:05] reactant 3 has no mapped atoms. -93: [02:19:05] product atom-mapping number 2 found multiple times. -93: [02:19:05] product atom-mapping number 3 found multiple times. -93: [02:19:05] product atom-mapping number 4 found multiple times. -93: [02:19:05] product atom-mapping number 5 found multiple times. -93: [02:19:05] product atom-mapping number 6 found multiple times. -93: [02:19:05] product atom-mapping number 7 found multiple times. -93: [02:19:05] product atom-mapping number 8 found multiple times. -93: [02:19:05] product atom-mapping number 12 found multiple times. -93: [02:19:05] product atom-mapping number 9 found multiple times. -93: [02:19:05] product atom-mapping number 10 found multiple times. -93: [02:19:05] product atom-mapping number 11 found multiple times. -93: [02:19:05] reactant 0 has no mapped atoms. -93: [02:19:05] reactant 1 has no mapped atoms. -93: [02:19:05] reactant 3 has no mapped atoms. -93: [02:19:05] reactant atom-mapping number 19 found multiple times. -93: [02:19:05] reactant atom-mapping number 25 found multiple times. -93: [02:19:05] reactant atom-mapping number 20 found multiple times. -93: [02:19:05] reactant atom-mapping number 21 found multiple times. -93: [02:19:05] reactant atom-mapping number 22 found multiple times. -93: [02:19:05] reactant atom-mapping number 23 found multiple times. -93: [02:19:05] reactant atom-mapping number 24 found multiple times. -93: [02:19:05] product atom-mapping number 1 found multiple times. -93: [02:19:05] product atom-mapping number 1 found multiple times. -93: [02:19:05] product atom-mapping number 1 found multiple times. -93: [02:19:05] product atom-mapping number 1 found multiple times. -93: [02:19:05] product atom-mapping number 2 found multiple times. -93: [02:19:05] product atom-mapping number 1 found multiple times. -93: [02:19:05] product atom-mapping number 2 found multiple times. -93: [02:19:05] product atom-mapping number 1 found multiple times. -93: [02:19:05] product atom-mapping number 2 found multiple times. -93: [02:19:05] product atom-mapping number 1 found multiple times. -93: [02:19:05] product atom-mapping number 2 found multiple times. -93: [02:19:05] product atom-mapping number 1 found multiple times. +93: [11:06:01] SMARTS Parse Error: syntax error while parsing: ([C:1](=O)O.[C:2] +93: [11:06:01] SMARTS Parse Error: Failed parsing SMARTS '([C:1](=O)O.[C:2]' for input: '([C:1](=O)O.[C:2]' +93: [11:06:01] SMARTS Parse Error: syntax error while parsing: ([C:2] +93: [11:06:01] SMARTS Parse Error: Failed parsing SMARTS '([C:2]' for input: '([C:2]' +93: [11:06:01] SMARTS Parse Error: syntax error while parsing: [C:1](=O)O).[C:2] +93: [11:06:01] SMARTS Parse Error: Failed parsing SMARTS '[C:1](=O)O).[C:2]' for input: '[C:1](=O)O).[C:2]' +93: [11:06:01] SMARTS Parse Error: syntax error while parsing: [C:2]) +93: [11:06:01] SMARTS Parse Error: Failed parsing SMARTS '[C:2])' for input: '[C:2])' +93: [11:06:01] SMILES Parse Error: syntax error while parsing: [Q:1][C:2][C:3](=[O:4])[O:5] +93: [11:06:01] SMILES Parse Error: check for mistakes around position 2: +93: [11:06:01] [Q:1][C:2][C:3](=[O:4])[O:5] +93: [11:06:01] ~^ +93: [11:06:01] 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: [11:06:01] reactant 2 has no mapped atoms. +93: [11:06:01] >> Atoms within one molecule have different RXN roles. +93: [11:06:01] >> Fragment 0 not included in the reaction, atoms do not have a correct RXN role. +93: [11:06:01] SMARTS Parse Error: syntax error while parsing: ([C:1][C:2] +93: [11:06:01] SMARTS Parse Error: Failed parsing SMARTS '([C:1][C:2]' for input: '([C:1][C:2]' +93: [11:06:01] SMARTS Parse Error: syntax error while parsing: ([C:2] +93: [11:06:01] SMARTS Parse Error: Failed parsing SMARTS '([C:2]' for input: '([C:2]' +93: [11:06:01] SMARTS Parse Error: syntax error while parsing: [C:1][C:2]) +93: [11:06:01] SMARTS Parse Error: Failed parsing SMARTS '[C:1][C:2])' for input: '[C:1][C:2])' +93: [11:06:01] SMARTS Parse Error: syntax error while parsing: [C:1]).[C:2] +93: [11:06:01] SMARTS Parse Error: Failed parsing SMARTS '[C:1]).[C:2]' for input: '[C:1]).[C:2]' +93: [11:06:01] reactant 0 has no mapped atoms. +93: [11:06:01] reactant 1 has no mapped atoms. +93: [11:06:01] reactant 3 has no mapped atoms. +93: [11:06:01] product atom-mapping number 2 found multiple times. +93: [11:06:01] product atom-mapping number 3 found multiple times. +93: [11:06:01] product atom-mapping number 4 found multiple times. +93: [11:06:01] product atom-mapping number 5 found multiple times. +93: [11:06:01] product atom-mapping number 6 found multiple times. +93: [11:06:01] product atom-mapping number 7 found multiple times. +93: [11:06:01] product atom-mapping number 8 found multiple times. +93: [11:06:01] product atom-mapping number 12 found multiple times. +93: [11:06:01] product atom-mapping number 9 found multiple times. +93: [11:06:01] product atom-mapping number 10 found multiple times. +93: [11:06:01] product atom-mapping number 11 found multiple times. +93: [11:06:01] reactant 0 has no mapped atoms. +93: [11:06:01] reactant 1 has no mapped atoms. +93: [11:06:01] reactant 3 has no mapped atoms. +93: [11:06:01] reactant atom-mapping number 19 found multiple times. +93: [11:06:01] reactant atom-mapping number 25 found multiple times. +93: [11:06:01] reactant atom-mapping number 20 found multiple times. +93: [11:06:01] reactant atom-mapping number 21 found multiple times. +93: [11:06:01] reactant atom-mapping number 22 found multiple times. +93: [11:06:01] reactant atom-mapping number 23 found multiple times. +93: [11:06:01] reactant atom-mapping number 24 found multiple times. +93: [11:06:01] product atom-mapping number 1 found multiple times. +93: [11:06:01] product atom-mapping number 1 found multiple times. +93: [11:06:01] product atom-mapping number 1 found multiple times. +93: [11:06:01] product atom-mapping number 1 found multiple times. +93: [11:06:01] product atom-mapping number 2 found multiple times. +93: [11:06:01] product atom-mapping number 1 found multiple times. +93: [11:06:01] product atom-mapping number 2 found multiple times. +93: [11:06:01] product atom-mapping number 1 found multiple times. +93: [11:06:01] product atom-mapping number 2 found multiple times. +93: [11:06:01] product atom-mapping number 1 found multiple times. +93: [11:06:01] product atom-mapping number 2 found multiple times. +93: [11:06:01] product atom-mapping number 1 found multiple times. 93: F[C@@](Cl)(Br)ONO[C@](F)(Cl)Br -93: [02:19:05] product atom-mapping number 2 found multiple times. -93: [02:19:05] product atom-mapping number 1 found multiple times. -93: [02:19:05] product atom-mapping number 2 found multiple times. -93: [02:19:05] product atom-mapping number 1 found multiple times. +93: [11:06:01] product atom-mapping number 2 found multiple times. +93: [11:06:01] product atom-mapping number 1 found multiple times. +93: [11:06:01] product atom-mapping number 2 found multiple times. +93: [11:06:01] product atom-mapping number 1 found multiple times. 93: F[C@](Cl)(Br)ONO[C@](F)(Cl)Br -93: [02:19:05] product atom-mapping number 5 found multiple times. -93: [02:19:05] product atom-mapping number 2 found multiple times. -93: [02:19:05] product atom-mapping number 3 found multiple times. -93: [02:19:05] product atom-mapping number 1 found multiple times. -93: [02:19:05] product atom-mapping number 4 found multiple times. -93: [02:19:05] product atom-mapping number 5 found multiple times. -93: [02:19:05] product atom-mapping number 2 found multiple times. -93: [02:19:05] product atom-mapping number 3 found multiple times. -93: [02:19:05] product atom-mapping number 1 found multiple times. -93: [02:19:05] product atom-mapping number 4 found multiple times. +93: [11:06:01] product atom-mapping number 5 found multiple times. +93: [11:06:01] product atom-mapping number 2 found multiple times. +93: [11:06:01] product atom-mapping number 3 found multiple times. +93: [11:06:01] product atom-mapping number 1 found multiple times. +93: [11:06:01] product atom-mapping number 4 found multiple times. +93: [11:06:01] product atom-mapping number 5 found multiple times. +93: [11:06:01] product atom-mapping number 2 found multiple times. +93: [11:06:01] product atom-mapping number 3 found multiple times. +93: [11:06:01] product atom-mapping number 1 found multiple times. +93: [11:06:01] product atom-mapping number 4 found multiple times. 93: F[C@@](Cl)(Br)ONO[C@](F)(Cl)Br -93: [02:19:05] product atom-mapping number 5 found multiple times. -93: [02:19:05] product atom-mapping number 2 found multiple times. -93: [02:19:05] product atom-mapping number 3 found multiple times. -93: [02:19:05] product atom-mapping number 1 found multiple times. -93: [02:19:05] product atom-mapping number 4 found multiple times. -93: [02:19:05] product atom-mapping number 5 found multiple times. -93: [02:19:05] product atom-mapping number 2 found multiple times. -93: [02:19:05] product atom-mapping number 3 found multiple times. -93: [02:19:05] product atom-mapping number 1 found multiple times. -93: [02:19:05] product atom-mapping number 4 found multiple times. +93: [11:06:01] product atom-mapping number 5 found multiple times. +93: [11:06:01] product atom-mapping number 2 found multiple times. +93: [11:06:01] product atom-mapping number 3 found multiple times. +93: [11:06:01] product atom-mapping number 1 found multiple times. +93: [11:06:01] product atom-mapping number 4 found multiple times. +93: [11:06:01] product atom-mapping number 5 found multiple times. +93: [11:06:01] product atom-mapping number 2 found multiple times. +93: [11:06:01] product atom-mapping number 3 found multiple times. +93: [11:06:01] product atom-mapping number 1 found multiple times. +93: [11:06:01] product atom-mapping number 4 found multiple times. 93: F[C@](Cl)(Br)ONO[C@](F)(Cl)Br -93: [02:19:05] product atom-mapping number 2 found multiple times. -93: [02:19:05] product atom-mapping number 3 found multiple times. -93: [02:19:05] product atom-mapping number 1 found multiple times. -93: [02:19:05] product atom-mapping number 4 found multiple times. -93: [02:19:05] product atom-mapping number 2 found multiple times. -93: [02:19:05] product atom-mapping number 3 found multiple times. -93: [02:19:05] product atom-mapping number 1 found multiple times. -93: [02:19:05] product atom-mapping number 4 found multiple times. +93: [11:06:01] product atom-mapping number 2 found multiple times. +93: [11:06:01] product atom-mapping number 3 found multiple times. +93: [11:06:01] product atom-mapping number 1 found multiple times. +93: [11:06:01] product atom-mapping number 4 found multiple times. +93: [11:06:01] product atom-mapping number 2 found multiple times. +93: [11:06:01] product atom-mapping number 3 found multiple times. +93: [11:06:01] product atom-mapping number 1 found multiple times. +93: [11:06:01] product atom-mapping number 4 found multiple times. 93: F[C@@](Cl)(Br)O[C@](F)(Cl)Br -93: [02:19:05] product atom-mapping number 2 found multiple times. -93: [02:19:05] product atom-mapping number 3 found multiple times. -93: [02:19:05] product atom-mapping number 1 found multiple times. -93: [02:19:05] product atom-mapping number 4 found multiple times. -93: [02:19:05] product atom-mapping number 2 found multiple times. -93: [02:19:05] product atom-mapping number 3 found multiple times. -93: [02:19:05] product atom-mapping number 1 found multiple times. -93: [02:19:05] product atom-mapping number 4 found multiple times. +93: [11:06:01] product atom-mapping number 2 found multiple times. +93: [11:06:01] product atom-mapping number 3 found multiple times. +93: [11:06:01] product atom-mapping number 1 found multiple times. +93: [11:06:01] product atom-mapping number 4 found multiple times. +93: [11:06:01] product atom-mapping number 2 found multiple times. +93: [11:06:01] product atom-mapping number 3 found multiple times. +93: [11:06:01] product atom-mapping number 1 found multiple times. +93: [11:06:01] product atom-mapping number 4 found multiple times. 93: F[C@](Cl)(Br)O[C@](F)(Cl)Br -93: [02:19:05] product atom-mapping number 4 found multiple times. -93: [02:19:05] product atom-mapping number 3 found multiple times. -93: [02:19:05] product atom-mapping number 2 found multiple times. -93: [02:19:05] product atom-mapping number 1 found multiple times. -93: [02:19:05] product atom-mapping number 4 found multiple times. -93: [02:19:05] product atom-mapping number 3 found multiple times. -93: [02:19:05] product atom-mapping number 2 found multiple times. -93: [02:19:05] product atom-mapping number 1 found multiple times. -93: [02:19:05] product atom-mapping number 4 found multiple times. -93: [02:19:05] product atom-mapping number 3 found multiple times. -93: [02:19:05] product atom-mapping number 2 found multiple times. -93: [02:19:05] product atom-mapping number 1 found multiple times. -93: [02:19:05] product atom-mapping number 4 found multiple times. -93: [02:19:05] product atom-mapping number 3 found multiple times. -93: [02:19:05] product atom-mapping number 2 found multiple times. -93: [02:19:05] product atom-mapping number 1 found multiple times. -93: [02:19:05] product atom-mapping number 3 found multiple times. -93: [02:19:05] product atom-mapping number 2 found multiple times. -93: [02:19:05] product atom-mapping number 1 found multiple times. -93: [02:19:05] mapped atoms in the reactants were not mapped in the products. +93: [11:06:01] product atom-mapping number 4 found multiple times. +93: [11:06:01] product atom-mapping number 3 found multiple times. +93: [11:06:01] product atom-mapping number 2 found multiple times. +93: [11:06:01] product atom-mapping number 1 found multiple times. +93: [11:06:01] product atom-mapping number 4 found multiple times. +93: [11:06:01] product atom-mapping number 3 found multiple times. +93: [11:06:01] product atom-mapping number 2 found multiple times. +93: [11:06:01] product atom-mapping number 1 found multiple times. +93: [11:06:01] product atom-mapping number 4 found multiple times. +93: [11:06:01] product atom-mapping number 3 found multiple times. +93: [11:06:01] product atom-mapping number 2 found multiple times. +93: [11:06:01] product atom-mapping number 1 found multiple times. +93: [11:06:01] product atom-mapping number 4 found multiple times. +93: [11:06:01] product atom-mapping number 3 found multiple times. +93: [11:06:01] product atom-mapping number 2 found multiple times. +93: [11:06:01] product atom-mapping number 1 found multiple times. +93: [11:06:01] product atom-mapping number 3 found multiple times. +93: [11:06:01] product atom-mapping number 2 found multiple times. +93: [11:06:01] product atom-mapping number 1 found multiple times. +93: [11:06:01] mapped atoms in the reactants were not mapped in the products. 93: unmapped numbers are: 4 -93: [02:19:05] product atom-mapping number 3 found multiple times. -93: [02:19:05] product atom-mapping number 2 found multiple times. -93: [02:19:05] product atom-mapping number 1 found multiple times. -93: [02:19:05] mapped atoms in the reactants were not mapped in the products. +93: [11:06:01] product atom-mapping number 3 found multiple times. +93: [11:06:01] product atom-mapping number 2 found multiple times. +93: [11:06:01] product atom-mapping number 1 found multiple times. +93: [11:06:01] mapped atoms in the reactants were not mapped in the products. 93: unmapped numbers are: 4 -93: [02:19:05] product atom-mapping number 6 not found in reactants. -93: [02:19:05] product atom-mapping number 7 not found in reactants. -93: [02:19:05] product atom-mapping number 8 not found in reactants. -93: [02:19:05] product atom-mapping number 7 not found in reactants. -93: [02:19:05] product atom-mapping number 8 not found in reactants. -93: [02:19:05] product atom-mapping number 9 not found in reactants. -93: [02:19:05] product atom-mapping number 10 not found in reactants. -93: [02:19:05] mapped atoms in the reactants were not mapped in the products. +93: [11:06:01] product atom-mapping number 6 not found in reactants. +93: [11:06:01] product atom-mapping number 7 not found in reactants. +93: [11:06:01] product atom-mapping number 8 not found in reactants. +93: [11:06:01] product atom-mapping number 7 not found in reactants. +93: [11:06:01] product atom-mapping number 8 not found in reactants. +93: [11:06:01] product atom-mapping number 9 not found in reactants. +93: [11:06:01] product atom-mapping number 10 not found in reactants. +93: [11:06:01] mapped atoms in the reactants were not mapped in the products. 93: unmapped numbers are: 6 -93: [02:19:05] product atom-mapping number 7 not found in reactants. -93: [02:19:05] product atom-mapping number 8 not found in reactants. -93: [02:19:05] product atom-mapping number 9 not found in reactants. -93: [02:19:05] product atom-mapping number 10 not found in reactants. -93: [02:19:05] mapped atoms in the reactants were not mapped in the products. +93: [11:06:01] product atom-mapping number 7 not found in reactants. +93: [11:06:01] product atom-mapping number 8 not found in reactants. +93: [11:06:01] product atom-mapping number 9 not found in reactants. +93: [11:06:01] product atom-mapping number 10 not found in reactants. +93: [11:06:01] 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: [02:19:05] mapped atoms in the reactants were not mapped in the products. +93: [11:06:01] 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 -69: [02:19:05] Empty atom list: 'M ALS 1 0 F' on line 8. -93: [02:19:05] product atom-mapping number 17 not found in reactants. -93: [02:19:05] product atom-mapping number 18 not found in reactants. -93: [02:19:05] mapped atoms in the reactants were not mapped in the products. +69: [11:06:01] SMARTS Parse Error: syntax error while parsing: MyDogHasFleas +69: [11:06:01] SMARTS Parse Error: Failed parsing SMARTS 'MyDogHasFleas' for input: 'MyDogHasFleas' +93: [11:06:01] product atom-mapping number 17 not found in reactants. +93: [11:06:01] product atom-mapping number 18 not found in reactants. +93: [11:06:01] mapped atoms in the reactants were not mapped in the products. 93: unmapped numbers are: 12 -69: de_DE.UTF-8 -69: [02:19:05] ------------------------------------- -69: [02:19:05] Test multithreading Locale Switching -89: [02:19:05] Explicit valence for atom # 9 N, 5, is greater than permitted -93: [02:19:05] Reaction has explicit hydrogens, reactants will need explicit hydrogens (addHs) -93: [02:19:05] Reaction has explicit hydrogens, reactants will need explicit hydrogens (addHs) +40: [11:06:01] done: 500000 +40: [11:06:01] Done +93: [11:06:01] Reaction has explicit hydrogens, reactants will need explicit hydrogens (addHs) +93: [11:06:01] Reaction has explicit hydrogens, reactants will need explicit hydrogens (addHs) 93: -69: [02:19:05] Test multithreading (Done) -69: [02:19:05] ------------------------------------- -93: [02:19:05] Mismatched potential rlabels: 1 unmapped reactant dummy atom rlabels,0 unmappped product dummy atom rlabels +93: [11:06:01] Mismatched potential rlabels: 1 unmapped reactant dummy atom rlabels,0 unmappped product dummy atom rlabels 93: ------------- 93: CCOc1ccccc1 +69: [11:06:01] Empty atom list: 'M ALS 1 0 F' on line 8. +69: de_DE.UTF-8 +69: [11:06:01] ------------------------------------- +69: [11:06:01] Test multithreading Locale Switching +40: [11:06:01] Testing hanoi with a functor. +40: [11:06:01] Done +40: [11:06:01] Testing basic partition refinement. +40: [11:06:01] Done +40: [11:06:01] Testing partition refinement with neighbors. +40: [11:06:01] Done +40: [11:06:01] testing canonicalization via tie breaking. +40: [11:06:01] Done +40: [11:06:01] testing canonicalization using the wrapper. +69: [11:06:01] Test multithreading (Done) +69: [11:06:01] ------------------------------------- 69: *************************************** +40: [11:06:01] Done +40: [11:06:01] testing some specific ordering problems +40: [11:06:01] Finished +40: [11:06:01] testing chiral invariants. +40: [11:06:01] Finished +40: [11:06:01] testing unique ranks in w.r.t. renumbering. 69: *************************************** -69: [02:19:05] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -69: [02:19:05] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -69: [02:19:05] bond with order 0 found on line 7. This is not part of the MDL specification. -69: [02:19:05] Skipping unrecognized collection type at line 26: MDLV30/HILITE BONDS=(1 7) -69: [02:19:05] Skipping unrecognized collection type at line 27: MDLV30/HILITE ATOMS=(1 7) -69: [02:19:05] 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: [02:19:05] Explicit valence for atom # 3 Al, 6, is greater than permitted -69: generating smiles -69: smiles: c12n(C3OC(COP(OC4C(O)C(n5c(=O)[nH]c(=O)cc5)OC4COP(OC4C(O)C(n5c(=O)nc(N)cc5)OC4COP(OC4C(O)C(n5c6c(cc5)c(=O)[nH]c(N)n6)OC4COP(OC4C(O)C(n5c(=O)nc(N)cc5)OC4COP(OC4C(O)C(n5c6c(nc5)c(N)ncn6)OC4COP(OC4C(O)C(n5c6c(cc5)c(=O)[nH]c(N)n6)OC4COP(OC4C(O)C(n5c(=O)[nH]c(=O)cc5)OC4COP(OC4C(O)C(n5c(=O)nc(N)cc5)OC4COP(OC4C(O)C(n5c6c(nc5)c(N)ncn6)OC4COP(OC4C(O)C(n5c6c(nc5)c(N)ncn6)OC4CO)(=O)S)(=O)S)(=O)S)(S)=O)(S)=O)(=O)S)(=O)S)(S)=O)(=O)S)(S)=O)C(OP(S)(=O)OCC(COP(OC4C(O)C(n5c6c(cc5)c(=O)[nH]c(N)n6)OC4COP(OC4C(O)C(n5c(=O)[nH]c(=O)cc5)OC4COP(OC4C(O)C(n5c(=O)nc(N)cc5)OC4COP(OC4C(O)C(n5c6c(cc5)c(=O)[nH]c(N)n6)OC4COP(OC4C(O)C(n5c(=O)nc(N)cc5)OC4COP(OC4C(O)C(n5c6c(nc5)c(N)ncn6)OC4COP(OC4C(O)C(n5c6c(cc5)c(=O)[nH]c(N)n6)OC4COP(OC4C(O)C(n5c(=O)[nH]c(=O)cc5)OC4COP(OC4C(O)C(n5c(=O)nc(N)cc5)OC4COP(OC4C(O)C(n5c6c(nc5)c(N)ncn6)OC4COP(OC4C(O)C(n5c6c(nc5)c(N)ncn6)OC4CO)(=O)S)(=O)S)(=O)S)(S)=O)(S)=O)(=O)S)(=O)S)(S)=O)(=O)S)(S)=O)(S)=O)O)C3O)ccc1c(=O)[nH]c(N)n2 -69: converting back -69: check isomorphism -89: [02:19:05] Explicit valence for atom # 4 Al, 6, is greater than permitted -93: [02:19:05] reactant 0 has no mapped atoms. -93: [02:19:05] product 0 has no mapped atoms. -93: [02:19:05] WARNING: neither stereo atoms nor CIP codes found for double bond. Stereochemistry info will not be propagated to product. -89: [02:19:05] Explicit valence for atom # 10 Si, 6, is greater than permitted - 82/238 Test #93: testReaction ........................... Passed 0.30 sec +69: [11:06:01] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +69: [11:06:01] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +69: [11:06:01] bond with order 0 found on line 7. This is not part of the MDL specification. +40: [11:06:01] Finished +40: [11:06:01] testing mol fragments. +40: [11:06:01] Finished +40: [11:06:01] testing protein round-tripping. +69: [11:06:01] Skipping unrecognized collection type at line 26: MDLV30/HILITE BONDS=(1 7) +69: [11:06:01] Skipping unrecognized collection type at line 27: MDLV30/HILITE ATOMS=(1 7) +69: [11:06:01] Warning: molecule is tagged as 3D, but all Z coords are zero and 2D stereo markers have been found, marking the mol as 2D. +92: Randomness seeded to: 2231165339 +92: =============================================================================== +92: All tests passed (11480 assertions in 38 test cases) +92: + 82/238 Test #92: testGenericGroups ...................... Passed 0.27 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 -40: [02:19:05] Finished -40: [02:19:05] testing stability w.r.t. renumbering. -92: Randomness seeded to: 3758148695 -92: =============================================================================== -92: All tests passed (11480 assertions in 38 test cases) -92: - 83/238 Test #92: testGenericGroups ...................... Passed 0.34 sec +89: [11:06:01] Explicit valence for atom # 9 N, 5, is greater than permitted +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 +94: [11:06:01] ------------------------------------- +94: [11:06:01] Test Reaction StructuralFingerprint +94: [11:06:01] ------------------------------------- +94: [11:06:01] Test Reaction DifferenceFingerprint + 83/238 Test #94: testReactionFingerprints ............... Passed 0.04 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 -40: [02:19:05] Finished -40: [02:19:05] testing smiles round-tripping. -94: [02:19:05] ------------------------------------- -94: [02:19:05] Test Reaction StructuralFingerprint -94: [02:19:05] ------------------------------------- -94: [02:19:05] Test Reaction DifferenceFingerprint - 84/238 Test #94: testReactionFingerprints ............... Passed 0.05 sec +93: [11:06:01] reactant 0 has no mapped atoms. +93: [11:06:01] product 0 has no mapped atoms. +93: [11:06:01] WARNING: neither stereo atoms nor CIP codes found for double bond. Stereochemistry info will not be propagated to product. + 84/238 Test #93: testReaction ........................... Passed 0.29 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 -12: .................. -12: ---------------------------------------------------------------------- -12: Ran 18 tests in 1.983s -12: -12: OK +89: [11:06:01] Explicit valence for atom # 3 Al, 6, is greater than permitted +89: [11:06:01] Explicit valence for atom # 4 Al, 6, is greater than permitted +96: Randomness seeded to: 1026191933 +96: [11:06:01] atom 0 in product 0 has multiple charge specifications. +96: [11:06:01] Found a SCD/SED line with missing/empty SDT specification at line 34 +96: [11:06:01] Found a SCD/SED line with missing/empty SDT specification at line 36 +96: [11:06:01] Found a SCD/SED line with missing/empty SDT specification at line 38 +96: [11:06:01] Found a SCD/SED line with missing/empty SDT specification at line 40 +96: [11:06:01] Found a SCD/SED line with missing/empty SDT specification at line 42 +96: [11:06:01] Found a SCD/SED line with missing/empty SDT specification at line 87 +96: [11:06:01] Found a SCD/SED line with missing/empty SDT specification at line 89 +96: [11:06:01] Found a SCD/SED line with missing/empty SDT specification at line 91 +96: [11:06:01] Found a SCD/SED line with missing/empty SDT specification at line 93 +96: [11:06:01] Found a SCD/SED line with missing/empty SDT specification at line 95 +96: [11:06:01] mapped atoms in the reactants were not mapped in the products. +96: unmapped numbers are: 2 +89: [11:06:01] Explicit valence for atom # 10 Si, 6, is greater than permitted +96: [11:06:01] mapped atoms in the reactants were not mapped in the products. +96: unmapped numbers are: 2 +96: [11:06:01] SMARTS Parse Error: unclosed ring for input: 'CC1' +96: [11:06:01] SMILES Parse Error: unclosed ring for input: 'CC1' +96: [11:06:01] mapped atoms in the reactants were not mapped in the products. +96: unmapped numbers are: 2 +96: [11:06:01] product atom-mapping number 2 not found in reactants. +96: [11:06:01] mapped atoms in the reactants were not mapped in the products. +96: unmapped numbers are: 2 +96: [11:06:01] product atom-mapping number 2 not found in reactants. +96: [11:06:01] CX Extensions: Substance group hierarchy is not always preserved. +96: [11:06:01] CX Extensions: Substance group hierarchy is not always preserved. 95: 30000000 30000000 -40: [02:19:05] Finished -40: [02:19:05] testing github #1567: Non-canonical result from MolFragmentToSmiles() -40: [02:19:05] Finished - 85/238 Test #40: hanoiTest .............................. Passed 1.94 sec +96: [11:06:01] reactant 0 has no mapped atoms. +96: [11:06:01] product 0 has no mapped atoms. +96: [11:06:01] Can't kekulize mol. Unkekulized atoms: 0 1 2 3 4 +96: [11:06:01] Can't kekulize mol. Unkekulized atoms: 0 1 2 3 4 +96: [11:06:01] Explicit valence for atom # 1 O, 5, is greater than permitted +96: =============================================================================== +96: All tests passed (722 assertions in 30 test cases) +96: + 85/238 Test #96: rxnTestCatch ........................... Passed 0.15 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 - 86/238 Test #12: pyBV ................................... Passed 2.27 sec +40: [11:06:01] Finished +40: [11:06:01] testing stability w.r.t. renumbering. +40: [11:06:01] Finished +40: [11:06:01] testing smiles round-tripping. +89: [11:06:01] Explicit valence for atom # 2 O, 4, is greater than permitted +89: [11:06:01] Explicit valence for atom # 3 Be, 4, is greater than permitted +89: [11:06:01] Explicit valence for atom # 3 Al, 6, is greater than permitted +89: [11:06:01] Explicit valence for atom # 27 P, 6, is greater than permitted +12: .................. +12: ---------------------------------------------------------------------- +12: Ran 18 tests in 2.098s +12: +12: OK +40: [11:06:01] Finished +40: [11:06:01] testing github #1567: Non-canonical result from MolFragmentToSmiles() +40: [11:06:01] Finished + 86/238 Test #40: hanoiTest .............................. Passed 2.02 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: Randomness seeded to: 2887090253 -96: [02:19:05] atom 0 in product 0 has multiple charge specifications. -96: [02:19:05] Found a SCD/SED line with missing/empty SDT specification at line 34 -96: [02:19:05] Found a SCD/SED line with missing/empty SDT specification at line 36 -96: [02:19:05] Found a SCD/SED line with missing/empty SDT specification at line 38 -96: [02:19:05] Found a SCD/SED line with missing/empty SDT specification at line 40 -96: [02:19:05] Found a SCD/SED line with missing/empty SDT specification at line 42 -96: [02:19:05] Found a SCD/SED line with missing/empty SDT specification at line 87 -96: [02:19:05] Found a SCD/SED line with missing/empty SDT specification at line 89 -96: [02:19:05] Found a SCD/SED line with missing/empty SDT specification at line 91 -96: [02:19:05] Found a SCD/SED line with missing/empty SDT specification at line 93 -96: [02:19:05] Found a SCD/SED line with missing/empty SDT specification at line 95 -96: [02:19:05] mapped atoms in the reactants were not mapped in the products. -96: unmapped numbers are: 2 -96: [02:19:05] mapped atoms in the reactants were not mapped in the products. -96: unmapped numbers are: 2 -96: [02:19:05] SMARTS Parse Error: unclosed ring for input: 'CC1' -96: [02:19:05] SMILES Parse Error: unclosed ring for input: 'CC1' -96: [02:19:05] mapped atoms in the reactants were not mapped in the products. -96: unmapped numbers are: 2 -96: [02:19:05] product atom-mapping number 2 not found in reactants. -96: [02:19:05] mapped atoms in the reactants were not mapped in the products. -96: unmapped numbers are: 2 -96: [02:19:05] product atom-mapping number 2 not found in reactants. -96: [02:19:05] CX Extensions: Substance group hierarchy is not always preserved. -96: [02:19:05] CX Extensions: Substance group hierarchy is not always preserved. -96: [02:19:05] reactant 0 has no mapped atoms. -96: [02:19:05] product 0 has no mapped atoms. -96: [02:19:05] Can't kekulize mol. Unkekulized atoms: 0 1 2 3 4 -96: [02:19:05] Can't kekulize mol. Unkekulized atoms: 0 1 2 3 4 -96: [02:19:05] Explicit valence for atom # 1 O, 5, is greater than permitted -96: =============================================================================== -96: All tests passed (722 assertions in 30 test cases) -96: - 87/238 Test #96: rxnTestCatch ........................... Passed 0.11 sec + 87/238 Test #12: pyBV ................................... Passed 2.43 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 -89: [02:19:05] Explicit valence for atom # 2 O, 4, is greater than permitted -89: [02:19:05] Explicit valence for atom # 3 Be, 4, is greater than permitted -89: [02:19:05] Explicit valence for atom # 3 Al, 6, is greater than permitted -89: [02:19:05] Explicit valence for atom # 27 P, 6, is greater than permitted -29: Checking against /build/reproducible-path/rdkit-202503.1/Code/ForceField/MMFF/test_data/MMFF94_reference.log... -97: ...[02:19:05] +69: [11:06:01] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 1 ignored +69: [11:06:01] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 1 ignored +69: [11:06:01] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 1 ignored +69: [11:06:01] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 1 ignored +69: [11:06:01] 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: [11:06:01] +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# 0x0000FFFFA2AA7F24 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu//lib/libRDKitFileParsers.so.1 +69: 4# 0x0000FFFFA2AB5B20 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu//lib/libRDKitFileParsers.so.1 +69: 5# 0x0000FFFFA2AB6A4C 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# 0x0000AAAACB00F77C in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersTest1 +69: 10# 0x0000AAAACB084944 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersTest1 +69: 11# 0x0000AAAACAFF5C6C in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersTest1 +69: 12# 0x0000FFFFA216229C in /lib/aarch64-linux-gnu/libc.so.6 +69: 13# __libc_start_main in /lib/aarch64-linux-gnu/libc.so.6 +69: 14# 0x0000AAAACAFF5E30 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersTest1 +69: ---------- +69: **** +69: +98: [11:06:01] == testCartesianProduct +98: .[11:06:01] == testEnumerateLibrary +98: /build/reproducible-path/rdkit-202503.1/Code/GraphMol/ChemReactions/Wrap/testEnumerations.py:266: ResourceWarning: unclosed file <_io.BufferedReader name='/build/reproducible-path/rdkit-202503.1/Code/GraphMol/ChemReactions/testData/enumeration.pickle'> +98: open(os.path.join(self.dataDir, "enumeration.pickle"), 'rb').read()) +98: ResourceWarning: Enable tracemalloc to get the object allocation traceback +98: ..[11:06:02] == testRGroupState +98: .[11:06:02] == testRandomEnumerateAllBBsLibrary +98: ** [1, 1] +98: ** [0, 2] +98: ** [1, 0] +69: [11:06:02] 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: [11:06:02] Warning: molecule is tagged as 3D, but all Z coords are zero and 2D stereo markers have been found, marking the mol as 2D. +98: .[11:06:02] == testRandomEnumerateLibrary +98: .[11:06:02] == testRandomSample +98: .[11:06:02] == testRandomSampleAllBBs +98: .[11:06:02] deprecated -- please use MatchOnlyAtRgroupsAdjustParams instead +98: [11:06:02] deprecated -- please use MatchOnlyAtRgroupsAdjustParams instead +98: .[11:06:02] == testRemoveBadMatches +97: ...[11:06:02] +97: +97: **** +98: .[11:06:02] == testTimings +97: Pre-condition Violation +97: getNumImplicitHs() called without preceding call to calcImplicitValence() +97: Violation occurred on line 301 in file ./Code/GraphMol/Atom.cpp +97: Failed Expression: d_implicitValence > -1 +97: ---------- +97: Stacktrace: +97: 0# Invar::Invariant::toString[abi:cxx11]() const in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu//lib/libRDKitRDGeneral.so.1 +97: 1# Invar::operator<<(std::ostream&, Invar::Invariant const&) in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu//lib/libRDKitRDGeneral.so.1 +97: 2# RDKit::Atom::getNumImplicitHs() const in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu//lib/libRDKitGraphMol.so.1 +97: 3# RDKit::Atom::getTotalNumHs(bool) const in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu//lib/libRDKitGraphMol.so.1 +97: 4# Queries::EqualityQuery::Match(RDKit::Atom const*) const in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu//lib/libRDKitSmilesParse.so.1 +97: 5# Queries::AndQuery::Match(RDKit::Atom const*) const in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu//lib/libRDKitGraphMol.so.1 +97: 6# Queries::AndQuery::Match(RDKit::Atom const*) const in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu//lib/libRDKitGraphMol.so.1 +97: 7# Queries::OrQuery::Match(RDKit::Atom const*) const in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu//lib/libRDKitGraphMol.so.1 +97: 8# RDKit::atomCompat(RDKit::Atom const*, RDKit::Atom const*, RDKit::SubstructMatchParameters const&) in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu//lib/libRDKitSubstructMatch.so.1 +97: 9# boost::detail::VF2SubState const, RDKit::detail::AtomLabelFunctor, RDKit::detail::BondLabelFunctor, RDKit::MolMatchFinalCheckFunctor>::IsFeasiblePair(unsigned int, unsigned int) in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu//lib/libRDKitSubstructMatch.so.1 +97: 10# bool boost::detail::VF2SubState const, RDKit::detail::AtomLabelFunctor, RDKit::detail::BondLabelFunctor, RDKit::MolMatchFinalCheckFunctor>::MatchAll, std::allocator > >, std::allocator, std::allocator > > > > >(unsigned int*, unsigned int*, std::vector, std::allocator > >, std::allocator, std::allocator > > > >&, unsigned int) in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu//lib/libRDKitSubstructMatch.so.1 +97: 11# bool boost::vf2_all, RDKit::detail::AtomLabelFunctor, RDKit::detail::BondLabelFunctor, RDKit::MolMatchFinalCheckFunctor, std::vector, std::allocator > >, std::allocator, std::allocator > > > > >(boost::adjacency_list const&, boost::adjacency_list const&, RDKit::detail::AtomLabelFunctor&, RDKit::detail::BondLabelFunctor&, RDKit::MolMatchFinalCheckFunctor&, std::vector, std::allocator > >, std::allocator, std::allocator > > > >&, unsigned int) in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu//lib/libRDKitSubstructMatch.so.1 +97: 12# RDKit::detail::RecursiveMatcher(RDKit::ROMol const&, RDKit::ROMol const&, std::vector >&, std::map*, std::less, std::allocator*> > >&, RDKit::SubstructMatchParameters const&, std::vector >&) in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu//lib/libRDKitSubstructMatch.so.1 +97: 13# RDKit::detail::MatchSubqueries(RDKit::ROMol const&, Queries::Query*, RDKit::SubstructMatchParameters const&, std::map*, std::less, std::allocator*> > >&, std::vector >&) in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu//lib/libRDKitSubstructMatch.so.1 +97: 14# RDKit::detail::MatchSubqueries(RDKit::ROMol const&, Queries::Query*, RDKit::SubstructMatchParameters const&, std::map*, std::less, std::allocator*> > >&, std::vector >&) in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu//lib/libRDKitSubstructMatch.so.1 +97: 15# RDKit::detail::MatchSubqueries(RDKit::ROMol const&, Queries::Query*, RDKit::SubstructMatchParameters const&, std::map*, std::less, std::allocator*> > >&, std::vector >&) in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu//lib/libRDKitSubstructMatch.so.1 +97: 16# RDKit::detail::MatchSubqueries(RDKit::ROMol const&, Queries::Query*, RDKit::SubstructMatchParameters const&, std::map*, std::less, std::allocator*> > >&, std::vector >&) in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu//lib/libRDKitSubstructMatch.so.1 +97: 17# RDKit::SubstructMatch(RDKit::ROMol const&, RDKit::ROMol const&, RDKit::SubstructMatchParameters const&) in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu//lib/libRDKitSubstructMatch.so.1 +97: 18# RDKit::ReactionRunnerUtils::getReactantMatchesToTemplate(RDKit::ROMol const&, RDKit::ROMol const&, unsigned int, RDKit::SubstructMatchParameters const&) in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu//lib/libRDKitChemReactions.so.1 +97: 19# RDKit::ReactionRunnerUtils::getReactantMatches(std::vector, std::allocator > > const&, RDKit::ChemicalReaction const&, std::vector, std::allocator > >, std::allocator, std::allocator > > > >, std::allocator, std::allocator > >, std::allocator, std::allocator > > > > > >&, unsigned int, unsigned int) in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu//lib/libRDKitChemReactions.so.1 +97: 20# RDKit::run_Reactants(RDKit::ChemicalReaction const&, std::vector, std::allocator > > const&, unsigned int) in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu//lib/libRDKitChemReactions.so.1 +97: 21# RDKit::ChemicalReaction::runReactants(std::vector, std::allocator > >, unsigned int) const in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu//lib/libRDKitChemReactions.so.1 +97: 22# _object* RDKit::RunReactants(RDKit::ChemicalReaction*, boost::python::tuple, unsigned int) in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdChemReactions.so +97: 23# boost::python::objects::caller_py_function_impl > >::operator()(_object*, _object*) in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdChemReactions.so +97: 24# boost::python::objects::function::call(_object*, _object*) const in /lib/aarch64-linux-gnu/libboost_python313.so.1.83.0 +97: 25# 0x0000FFFFA3D72680 in /lib/aarch64-linux-gnu/libboost_python313.so.1.83.0 +97: 26# boost::python::detail::exception_handler::operator()(boost::function0 const&) const in /lib/aarch64-linux-gnu/libboost_python313.so.1.83.0 +97: 27# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdSLNParse.so +97: 28# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdDepictor.so +97: 29# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdChemReactions.so +97: 30# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdChemReactions.so +97: 31# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdMolChemicalFeatures.so +97: 32# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdmolfiles.so +97: 33# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdmolfiles.so +97: 34# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdCIPLabeler.so +97: 35# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so +97: 36# 0x0000FFFFA232C320 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so +97: 37# 0x0000FFFFA232C2B8 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so +97: 38# 0x0000FFFFA232C248 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so +97: 39# 0x0000FFFFA232C1E0 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so +97: 40# 0x0000FFFFA232C178 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# 0x0000FFFFA3D6F25C in /lib/aarch64-linux-gnu/libboost_python313.so.1.83.0 +97: 47# _PyObject_MakeTpCall in /usr/bin/python3 +97: 48# _PyEval_EvalFrameDefault in /usr/bin/python3 +97: 49# 0x000000000053D3B0 in /usr/bin/python3 +97: 50# _PyEval_EvalFrameDefault in /usr/bin/python3 +97: 51# 0x000000000061C8E0 in /usr/bin/python3 +97: 52# 0x00000000005A787C in /usr/bin/python3 +97: 53# _PyObject_MakeTpCall in /usr/bin/python3 +97: 54# _PyEval_EvalFrameDefault in /usr/bin/python3 +97: 55# 0x000000000053D3B0 in /usr/bin/python3 +97: 56# _PyEval_EvalFrameDefault in /usr/bin/python3 +97: 57# 0x000000000061C8E0 in /usr/bin/python3 +97: 58# 0x00000000005A787C in /usr/bin/python3 +97: 59# _PyObject_MakeTpCall in /usr/bin/python3 +97: 60# _PyEval_EvalFrameDefault in /usr/bin/python3 +97: 61# 0x000000000053D3B0 in /usr/bin/python3 +97: 62# _PyEval_EvalFrameDefault in /usr/bin/python3 +97: 63# 0x000000000061C8E0 in /usr/bin/python3 +97: 64# 0x00000000005A787C in /usr/bin/python3 +97: 65# _PyObject_MakeTpCall in /usr/bin/python3 +97: 66# _PyEval_EvalFrameDefault in /usr/bin/python3 +97: 67# 0x000000000050B150 in /usr/bin/python3 +97: 68# _PyObject_MakeTpCall in /usr/bin/python3 +97: 69# _PyEval_EvalFrameDefault in /usr/bin/python3 +97: 70# PyEval_EvalCode in /usr/bin/python3 +97: 71# 0x000000000064023C in /usr/bin/python3 +97: 72# 0x000000000063BC30 in /usr/bin/python3 +97: 73# 0x000000000065F810 in /usr/bin/python3 +97: 74# 0x000000000065F0B4 in /usr/bin/python3 +97: 75# 0x000000000065EE50 in /usr/bin/python3 +97: 76# Py_RunMain in /usr/bin/python3 +97: 77# Py_BytesMain in /usr/bin/python3 +97: 78# 0x0000FFFFA48A229C 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: [11:06:02] 97: 97: **** -99: .[02:19:05] reactant 0 has no mapped atoms. -99: [02:19:05] product 0 has no mapped atoms. -99: [02:19:05] reactant 0 has no mapped atoms. -99: [02:19:05] product 0 has no mapped atoms. -99: .[02:19:05] reactant 0 has no mapped atoms. -99: [02:19:05] reactant 1 has no mapped atoms. -99: [02:19:05] product 0 has no mapped atoms. -99: [02:19:05] reactant 0 has no mapped atoms. -99: [02:19:05] reactant 1 has no mapped atoms. -99: [02:19:05] product 0 has no mapped atoms. -99: [02:19:05] reactant 0 has no mapped atoms. -99: [02:19:05] reactant 1 has no mapped atoms. -99: [02:19:05] product 0 has no mapped atoms. -99: [02:19:05] reactant 0 has no mapped atoms. -99: [02:19:05] reactant 1 has no mapped atoms. -99: [02:19:05] product 0 has no mapped atoms. -99: [02:19:05] reactant 0 has no mapped atoms. -99: [02:19:05] reactant 1 has no mapped atoms. -99: [02:19:05] product 0 has no mapped atoms. -99: [02:19:05] reactant 0 has no mapped atoms. -99: [02:19:05] reactant 1 has no mapped atoms. -99: [02:19:05] product 0 has no mapped atoms. -99: [02:19:05] reactant 0 has no mapped atoms. -99: [02:19:05] reactant 1 has no mapped atoms. -99: [02:19:05] product 0 has no mapped atoms. -99: [02:19:05] reactant 0 has no mapped atoms. -99: [02:19:05] reactant 1 has no mapped atoms. -99: [02:19:05] product 0 has no mapped atoms. -99: [02:19:05] reactant 0 has no mapped atoms. -99: [02:19:05] reactant 1 has no mapped atoms. -99: [02:19:05] product 0 has no mapped atoms. -99: [02:19:05] reactant 0 has no mapped atoms. -99: [02:19:05] reactant 1 has no mapped atoms. -99: [02:19:05] product 0 has no mapped atoms. -99: [02:19:05] reactant 0 has no mapped atoms. -99: [02:19:05] reactant 1 has no mapped atoms. -99: [02:19:05] product 0 has no mapped atoms. -99: [02:19:05] reactant 0 has no mapped atoms. -99: [02:19:05] reactant 1 has no mapped atoms. -99: [02:19:05] product 0 has no mapped atoms. -99: [02:19:05] reactant 0 has no mapped atoms. -99: [02:19:05] reactant 1 has no mapped atoms. -99: [02:19:05] product 0 has no mapped atoms. -99: [02:19:05] reactant 0 has no mapped atoms. -99: [02:19:05] reactant 1 has no mapped atoms. -99: [02:19:05] product 0 has no mapped atoms. +97: Pre-condition Violation +97: getNumImplicitHs() called without preceding call to calcImplicitValence() +97: Violation occurred on line 301 in file ./Code/GraphMol/Atom.cpp +97: Failed Expression: d_implicitValence > -1 +97: ---------- +97: Stacktrace: +97: 0# Invar::Invariant::toString[abi:cxx11]() const in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu//lib/libRDKitRDGeneral.so.1 +97: 1# Invar::operator<<(std::ostream&, Invar::Invariant const&) in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu//lib/libRDKitRDGeneral.so.1 +97: 2# RDKit::Atom::getNumImplicitHs() const in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu//lib/libRDKitGraphMol.so.1 +97: 3# RDKit::Atom::getTotalNumHs(bool) const in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu//lib/libRDKitGraphMol.so.1 +97: 4# Queries::EqualityQuery::Match(RDKit::Atom const*) const in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu//lib/libRDKitSmilesParse.so.1 +97: 5# Queries::AndQuery::Match(RDKit::Atom const*) const in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu//lib/libRDKitGraphMol.so.1 +97: 6# Queries::AndQuery::Match(RDKit::Atom const*) const in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu//lib/libRDKitGraphMol.so.1 +97: 7# Queries::OrQuery::Match(RDKit::Atom const*) const in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu//lib/libRDKitGraphMol.so.1 +97: 8# RDKit::atomCompat(RDKit::Atom const*, RDKit::Atom const*, RDKit::SubstructMatchParameters const&) in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu//lib/libRDKitSubstructMatch.so.1 +97: 9# boost::detail::VF2SubState const, RDKit::detail::AtomLabelFunctor, RDKit::detail::BondLabelFunctor, RDKit::MolMatchFinalCheckFunctor>::IsFeasiblePair(unsigned int, unsigned int) in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu//lib/libRDKitSubstructMatch.so.1 +97: 10# bool boost::detail::VF2SubState const, RDKit::detail::AtomLabelFunctor, RDKit::detail::BondLabelFunctor, RDKit::MolMatchFinalCheckFunctor>::MatchAll, std::allocator > >, std::allocator, std::allocator > > > > >(unsigned int*, unsigned int*, std::vector, std::allocator > >, std::allocator, std::allocator > > > >&, unsigned int) in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu//lib/libRDKitSubstructMatch.so.1 +97: 11# bool boost::vf2_all, RDKit::detail::AtomLabelFunctor, RDKit::detail::BondLabelFunctor, RDKit::MolMatchFinalCheckFunctor, std::vector, std::allocator > >, std::allocator, std::allocator > > > > >(boost::adjacency_list const&, boost::adjacency_list const&, RDKit::detail::AtomLabelFunctor&, RDKit::detail::BondLabelFunctor&, RDKit::MolMatchFinalCheckFunctor&, std::vector, std::allocator > >, std::allocator, std::allocator > > > >&, unsigned int) in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu//lib/libRDKitSubstructMatch.so.1 +97: 12# RDKit::detail::RecursiveMatcher(RDKit::ROMol const&, RDKit::ROMol const&, std::vector >&, std::map*, std::less, std::allocator*> > >&, RDKit::SubstructMatchParameters const&, std::vector >&) in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu//lib/libRDKitSubstructMatch.so.1 +97: 13# RDKit::detail::MatchSubqueries(RDKit::ROMol const&, Queries::Query*, RDKit::SubstructMatchParameters const&, std::map*, std::less, std::allocator*> > >&, std::vector >&) in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu//lib/libRDKitSubstructMatch.so.1 +97: 14# RDKit::detail::MatchSubqueries(RDKit::ROMol const&, Queries::Query*, RDKit::SubstructMatchParameters const&, std::map*, std::less, std::allocator*> > >&, std::vector >&) in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu//lib/libRDKitSubstructMatch.so.1 +97: 15# RDKit::detail::MatchSubqueries(RDKit::ROMol const&, Queries::Query*, RDKit::SubstructMatchParameters const&, std::map*, std::less, std::allocator*> > >&, std::vector >&) in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu//lib/libRDKitSubstructMatch.so.1 +97: 16# RDKit::detail::MatchSubqueries(RDKit::ROMol const&, Queries::Query*, RDKit::SubstructMatchParameters const&, std::map*, std::less, std::allocator*> > >&, std::vector >&) in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu//lib/libRDKitSubstructMatch.so.1 +97: 17# RDKit::SubstructMatch(RDKit::ROMol const&, RDKit::ROMol const&, RDKit::SubstructMatchParameters const&) in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu//lib/libRDKitSubstructMatch.so.1 +97: 18# RDKit::ReactionRunnerUtils::getReactantMatchesToTemplate(RDKit::ROMol const&, RDKit::ROMol const&, unsigned int, RDKit::SubstructMatchParameters const&) in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu//lib/libRDKitChemReactions.so.1 +97: 19# RDKit::ReactionRunnerUtils::getReactantMatches(std::vector, std::allocator > > const&, RDKit::ChemicalReaction const&, std::vector, std::allocator > >, std::allocator, std::allocator > > > >, std::allocator, std::allocator > >, std::allocator, std::allocator > > > > > >&, unsigned int, unsigned int) in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu//lib/libRDKitChemReactions.so.1 +97: 20# RDKit::run_Reactants(RDKit::ChemicalReaction const&, std::vector, std::allocator > > const&, unsigned int) in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu//lib/libRDKitChemReactions.so.1 +97: 21# RDKit::ChemicalReaction::runReactants(std::vector, std::allocator > >, unsigned int) const in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu//lib/libRDKitChemReactions.so.1 +97: 22# _object* RDKit::RunReactants(RDKit::ChemicalReaction*, boost::python::tuple, unsigned int) in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdChemReactions.so +97: 23# boost::python::objects::caller_py_function_impl > >::operator()(_object*, _object*) in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdChemReactions.so +97: 24# boost::python::objects::function::call(_object*, _object*) const in /lib/aarch64-linux-gnu/libboost_python313.so.1.83.0 +97: 25# 0x0000FFFFA3D72680 in /lib/aarch64-linux-gnu/libboost_python313.so.1.83.0 +97: 26# boost::python::detail::exception_handler::operator()(boost::function0 const&) const in /lib/aarch64-linux-gnu/libboost_python313.so.1.83.0 +97: 27# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdSLNParse.so +97: 28# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdDepictor.so +97: 29# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdChemReactions.so +97: 30# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdChemReactions.so +97: 31# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdMolChemicalFeatures.so +97: 32# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdmolfiles.so +97: 33# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdmolfiles.so +97: 34# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdCIPLabeler.so +97: 35# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so +97: 36# 0x0000FFFFA232C320 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so +97: 37# 0x0000FFFFA232C2B8 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so +97: 38# 0x0000FFFFA232C248 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so +97: 39# 0x0000FFFFA232C1E0 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so +97: 40# 0x0000FFFFA232C178 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# 0x0000FFFFA3D6F25C in /lib/aarch64-linux-gnu/libboost_python313.so.1.83.0 +97: 47# _PyObject_MakeTpCall in /usr/bin/python3 +97: 48# _PyEval_EvalFrameDefault in /usr/bin/python3 +97: 49# 0x000000000053D3B0 in /usr/bin/python3 +97: 50# _PyEval_EvalFrameDefault in /usr/bin/python3 +97: 51# 0x000000000061C8E0 in /usr/bin/python3 +97: 52# 0x00000000005A787C in /usr/bin/python3 +97: 53# _PyObject_MakeTpCall in /usr/bin/python3 +97: 54# _PyEval_EvalFrameDefault in /usr/bin/python3 +97: 55# 0x000000000053D3B0 in /usr/bin/python3 +97: 56# _PyEval_EvalFrameDefault in /usr/bin/python3 +97: 57# 0x000000000061C8E0 in /usr/bin/python3 +97: 58# 0x00000000005A787C in /usr/bin/python3 +97: 59# _PyObject_MakeTpCall in /usr/bin/python3 +97: 60# _PyEval_EvalFrameDefault in /usr/bin/python3 +97: 61# 0x000000000053D3B0 in /usr/bin/python3 +97: 62# _PyEval_EvalFrameDefault in /usr/bin/python3 +97: 63# 0x000000000061C8E0 in /usr/bin/python3 +97: 64# 0x00000000005A787C in /usr/bin/python3 +97: 65# _PyObject_MakeTpCall in /usr/bin/python3 +97: 66# _PyEval_EvalFrameDefault in /usr/bin/python3 +97: 67# 0x000000000050B150 in /usr/bin/python3 +97: 68# _PyObject_MakeTpCall in /usr/bin/python3 +97: 69# _PyEval_EvalFrameDefault in /usr/bin/python3 +97: 70# PyEval_EvalCode in /usr/bin/python3 +97: 71# 0x000000000064023C in /usr/bin/python3 +97: 72# 0x000000000063BC30 in /usr/bin/python3 +97: 73# 0x000000000065F810 in /usr/bin/python3 +97: 74# 0x000000000065F0B4 in /usr/bin/python3 +97: 75# 0x000000000065EE50 in /usr/bin/python3 +97: 76# Py_RunMain in /usr/bin/python3 +97: 77# Py_BytesMain in /usr/bin/python3 +97: 78# 0x0000FFFFA48A229C 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: ---------- +69: ---------------------------------- +69: ---------------------------------- +69: [11:06:02] +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# 0x0000AAAACB01F23C in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersTest1 +69: 4# 0x0000AAAACB0849A4 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersTest1 +69: 5# 0x0000AAAACAFF5C6C in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersTest1 +69: 6# 0x0000FFFFA216229C in /lib/aarch64-linux-gnu/libc.so.6 +69: 7# __libc_start_main in /lib/aarch64-linux-gnu/libc.so.6 +69: 8# 0x0000AAAACAFF5E30 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersTest1 +69: ---------- +69: **** +69: +69: [11:06:02] WARNING: could not find number of expected rings. Switching to an approximate ring finding algorithm. +97: **** +97: +97: .........[11:06:02] stereo atoms in input cannot be mapped to output (atoms are no longer bonded) +97: [11:06:02] stereo atoms in input cannot be mapped to output (atoms are no longer bonded) +97: [11:06:02] stereo atoms in input cannot be mapped to output (atoms are no longer bonded) +97: [11:06:02] stereo atoms in input cannot be mapped to output (atoms are no longer bonded) +97: .[11:06:02] product atom-mapping number 1 found multiple times. +97: [11:06:02] product atom-mapping number 1 found multiple times. +89: [11:06:02] Explicit valence for atom # 9 N, 5, is greater than permitted +97: ................[11:06:02] mapped atoms in the reactants were not mapped in the products. +97: unmapped numbers are: 3 +97: [11:06:02] mapped atoms in the reactants were not mapped in the products. +97: unmapped numbers are: 3 +97: .:488: RuntimeWarning: to-Python converter for boost::shared_ptr already registered; second conversion method ignored. +97: [11:06:02] mapped atoms in the reactants were not mapped in the products. +97: unmapped numbers are: 3 +97: ..[11:06:02] reactant 2 has no mapped atoms. +97: [11:06:02] reactant 2 has no mapped atoms. +97: [11:06:02] product 1 has no mapped atoms. +97: ........[11:06:02] SMARTS Parse Error: syntax error while parsing: [C:1](=[O:2])Q +97: [11:06:02] SMARTS Parse Error: Failed parsing SMARTS '[C:1](=[O:2])Q' for input: '[C:1](=[O:2])Q' +97: [11:06:02] SMARTS Parse Error: syntax error while parsing: [C:1](=[O:2])[N:3]Q +97: [11:06:02] SMARTS Parse Error: Failed parsing SMARTS '[C:1](=[O:2])[N:3]Q' for input: '[C:1](=[O:2])[N:3]Q' +97: .[11:06:02] reactant atom-mapping number 1 found multiple times. +97: [11:06:02] product atom-mapping number 2 not found in reactants. +97: [11:06:02] mapped atoms in the reactants were not mapped in the products. +97: unmapped numbers are: 4 +97: [11:06:02] product atom-mapping number 5 not found in reactants. +99: .[11:06:02] reactant 0 has no mapped atoms. +99: [11:06:02] product 0 has no mapped atoms. +99: [11:06:02] reactant 0 has no mapped atoms. +99: [11:06:02] product 0 has no mapped atoms. +99: .[11:06:02] reactant 0 has no mapped atoms. +99: [11:06:02] reactant 1 has no mapped atoms. +99: [11:06:02] product 0 has no mapped atoms. +99: [11:06:02] reactant 0 has no mapped atoms. +99: [11:06:02] reactant 1 has no mapped atoms. +99: [11:06:02] product 0 has no mapped atoms. +99: [11:06:02] reactant 0 has no mapped atoms. +99: [11:06:02] reactant 1 has no mapped atoms. +99: [11:06:02] product 0 has no mapped atoms. +99: [11:06:02] reactant 0 has no mapped atoms. +99: [11:06:02] reactant 1 has no mapped atoms. +99: [11:06:02] product 0 has no mapped atoms. +99: [11:06:02] reactant 0 has no mapped atoms. +99: [11:06:02] reactant 1 has no mapped atoms. +99: [11:06:02] product 0 has no mapped atoms. +99: [11:06:02] reactant 0 has no mapped atoms. +99: [11:06:02] reactant 1 has no mapped atoms. +99: [11:06:02] product 0 has no mapped atoms. +99: [11:06:02] reactant 0 has no mapped atoms. +99: [11:06:02] reactant 1 has no mapped atoms. +99: [11:06:02] product 0 has no mapped atoms. +99: [11:06:02] reactant 0 has no mapped atoms. +99: [11:06:02] reactant 1 has no mapped atoms. +99: [11:06:02] product 0 has no mapped atoms. +99: [11:06:02] reactant 0 has no mapped atoms. +99: [11:06:02] reactant 1 has no mapped atoms. +99: [11:06:02] product 0 has no mapped atoms. +99: [11:06:02] reactant 0 has no mapped atoms. +99: [11:06:02] reactant 1 has no mapped atoms. +99: [11:06:02] product 0 has no mapped atoms. +99: [11:06:02] reactant 0 has no mapped atoms. +99: [11:06:02] reactant 1 has no mapped atoms. +99: [11:06:02] product 0 has no mapped atoms. +99: [11:06:02] reactant 0 has no mapped atoms. +99: [11:06:02] reactant 1 has no mapped atoms. +99: [11:06:02] product 0 has no mapped atoms. +99: [11:06:02] reactant 0 has no mapped atoms. +99: [11:06:02] reactant 1 has no mapped atoms. +99: [11:06:02] product 0 has no mapped atoms. +99: [11:06:02] reactant 0 has no mapped atoms. +99: [11:06:02] reactant 1 has no mapped atoms. +99: [11:06:02] product 0 has no mapped atoms. 99: () 99: ******************************************** 99: $RXN @@ -23172,16 +23487,19 @@ 99: 1 2 1 0 99: M ISO 2 1 1 2 2 99: M END -99: [02:19:05] reactant 0 has no mapped atoms. -99: [02:19:05] reactant 1 has no mapped atoms. -99: [02:19:05] product 0 has no mapped atoms. -99: [02:19:05] Could not find RLabel mapping for atom: 0 in template: 1 -99: [02:19:05] reactant 1 has no mapped atoms. -99: [02:19:05] reactant 1 has no mapped atoms. -99: [02:19:05] reactant 1 has no mapped atoms. +99: [11:06:02] reactant 0 has no mapped atoms. +99: [11:06:02] reactant 1 has no mapped atoms. +99: [11:06:02] product 0 has no mapped atoms. +99: [11:06:02] Could not find RLabel mapping for atom: 0 in template: 1 +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 +99: [11:06:02] reactant 1 has no mapped atoms. +99: [11:06:02] reactant 1 has no mapped atoms. +99: [11:06:02] reactant 1 has no mapped atoms. 99: .. 99: ---------------------------------------------------------------------- -99: Ran 4 tests in 0.014s +99: Ran 4 tests in 0.034s 99: 99: OK 99: @@ -23238,304 +23556,107 @@ 99: M END 99: 99: $RXN Failed -97: Pre-condition Violation -97: getNumImplicitHs() called without preceding call to calcImplicitValence() -97: Violation occurred on line 301 in file ./Code/GraphMol/Atom.cpp -97: Failed Expression: d_implicitValence > -1 -97: ---------- -97: Stacktrace: -97: 0# Invar::Invariant::toString[abi:cxx11]() const in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu//lib/libRDKitRDGeneral.so.1 -97: 1# Invar::operator<<(std::ostream&, Invar::Invariant const&) in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu//lib/libRDKitRDGeneral.so.1 -97: 2# RDKit::Atom::getNumImplicitHs() const in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu//lib/libRDKitGraphMol.so.1 -97: 3# RDKit::Atom::getTotalNumHs(bool) const in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu//lib/libRDKitGraphMol.so.1 -97: 4# Queries::EqualityQuery::Match(RDKit::Atom const*) const in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu//lib/libRDKitSmilesParse.so.1 -97: 5# Queries::AndQuery::Match(RDKit::Atom const*) const in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu//lib/libRDKitGraphMol.so.1 -97: 6# Queries::AndQuery::Match(RDKit::Atom const*) const in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu//lib/libRDKitGraphMol.so.1 -97: 7# Queries::OrQuery::Match(RDKit::Atom const*) const in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu//lib/libRDKitGraphMol.so.1 -97: 8# RDKit::atomCompat(RDKit::Atom const*, RDKit::Atom const*, RDKit::SubstructMatchParameters const&) in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu//lib/libRDKitSubstructMatch.so.1 -97: 9# boost::detail::VF2SubState const, RDKit::detail::AtomLabelFunctor, RDKit::detail::BondLabelFunctor, RDKit::MolMatchFinalCheckFunctor>::IsFeasiblePair(unsigned int, unsigned int) in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu//lib/libRDKitSubstructMatch.so.1 -97: 10# bool boost::detail::VF2SubState const, RDKit::detail::AtomLabelFunctor, RDKit::detail::BondLabelFunctor, RDKit::MolMatchFinalCheckFunctor>::MatchAll, std::allocator > >, std::allocator, std::allocator > > > > >(unsigned int*, unsigned int*, std::vector, std::allocator > >, std::allocator, std::allocator > > > >&, unsigned int) in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu//lib/libRDKitSubstructMatch.so.1 -97: 11# bool boost::vf2_all, RDKit::detail::AtomLabelFunctor, RDKit::detail::BondLabelFunctor, RDKit::MolMatchFinalCheckFunctor, std::vector, std::allocator > >, std::allocator, std::allocator > > > > >(boost::adjacency_list const&, boost::adjacency_list const&, RDKit::detail::AtomLabelFunctor&, RDKit::detail::BondLabelFunctor&, RDKit::MolMatchFinalCheckFunctor&, std::vector, std::allocator > >, std::allocator, std::allocator > > > >&, unsigned int) in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu//lib/libRDKitSubstructMatch.so.1 -97: 12# RDKit::detail::RecursiveMatcher(RDKit::ROMol const&, RDKit::ROMol const&, std::vector >&, std::map*, std::less, std::allocator*> > >&, RDKit::SubstructMatchParameters const&, std::vector >&) in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu//lib/libRDKitSubstructMatch.so.1 -97: 13# RDKit::detail::MatchSubqueries(RDKit::ROMol const&, Queries::Query*, RDKit::SubstructMatchParameters const&, std::map*, std::less, std::allocator*> > >&, std::vector >&) in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu//lib/libRDKitSubstructMatch.so.1 -97: 14# RDKit::detail::MatchSubqueries(RDKit::ROMol const&, Queries::Query*, RDKit::SubstructMatchParameters const&, std::map*, std::less, std::allocator*> > >&, std::vector >&) in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu//lib/libRDKitSubstructMatch.so.1 -97: 15# RDKit::detail::MatchSubqueries(RDKit::ROMol const&, Queries::Query*, RDKit::SubstructMatchParameters const&, std::map*, std::less, std::allocator*> > >&, std::vector >&) in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu//lib/libRDKitSubstructMatch.so.1 -97: 16# RDKit::detail::MatchSubqueries(RDKit::ROMol const&, Queries::Query*, RDKit::SubstructMatchParameters const&, std::map*, std::less, std::allocator*> > >&, std::vector >&) in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu//lib/libRDKitSubstructMatch.so.1 -97: 17# RDKit::SubstructMatch(RDKit::ROMol const&, RDKit::ROMol const&, RDKit::SubstructMatchParameters const&) in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu//lib/libRDKitSubstructMatch.so.1 -97: 18# RDKit::ReactionRunnerUtils::getReactantMatchesToTemplate(RDKit::ROMol const&, RDKit::ROMol const&, unsigned int, RDKit::SubstructMatchParameters const&) in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu//lib/libRDKitChemReactions.so.1 -97: 19# RDKit::ReactionRunnerUtils::getReactantMatches(std::vector, std::allocator > > const&, RDKit::ChemicalReaction const&, std::vector, std::allocator > >, std::allocator, std::allocator > > > >, std::allocator, std::allocator > >, std::allocator, std::allocator > > > > > >&, unsigned int, unsigned int) in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu//lib/libRDKitChemReactions.so.1 -97: 20# RDKit::run_Reactants(RDKit::ChemicalReaction const&, std::vector, std::allocator > > const&, unsigned int) in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu//lib/libRDKitChemReactions.so.1 -97: 21# RDKit::ChemicalReaction::runReactants(std::vector, std::allocator > >, unsigned int) const in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu//lib/libRDKitChemReactions.so.1 -97: 22# _object* RDKit::RunReactants(RDKit::ChemicalReaction*, boost::python::tuple, unsigned int) in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdChemReactions.so -97: 23# boost::python::objects::caller_py_function_impl > >::operator()(_object*, _object*) in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdChemReactions.so -97: 24# boost::python::objects::function::call(_object*, _object*) const in /lib/aarch64-linux-gnu/libboost_python313.so.1.83.0 -97: 25# 0x0000FFFF8B5C2680 in /lib/aarch64-linux-gnu/libboost_python313.so.1.83.0 -97: 26# boost::python::detail::exception_handler::operator()(boost::function0 const&) const in /lib/aarch64-linux-gnu/libboost_python313.so.1.83.0 -97: 27# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdSLNParse.so -97: 28# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdDepictor.so -97: 29# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdChemReactions.so -97: 30# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdChemReactions.so -97: 31# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdMolChemicalFeatures.so -97: 32# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdmolfiles.so -97: 33# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdmolfiles.so -97: 34# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdCIPLabeler.so -97: 35# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so -97: 36# 0x0000FFFF89B7C320 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so -97: 37# 0x0000FFFF89B7C2B8 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so -97: 38# 0x0000FFFF89B7C248 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so -97: 39# 0x0000FFFF89B7C1E0 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so -97: 40# 0x0000FFFF89B7C178 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# 0x0000FFFF8B5BF25C in /lib/aarch64-linux-gnu/libboost_python313.so.1.83.0 -97: 47# _PyObject_MakeTpCall in /usr/bin/python3 -97: 48# _PyEval_EvalFrameDefault in /usr/bin/python3 -97: 49# 0x000000000053D3B0 in /usr/bin/python3 -97: 50# _PyEval_EvalFrameDefault in /usr/bin/python3 -97: 51# 0x000000000061C8E0 in /usr/bin/python3 -97: 52# 0x00000000005A787C in /usr/bin/python3 -97: 53# _PyObject_MakeTpCall in /usr/bin/python3 -97: 54# _PyEval_EvalFrameDefault in /usr/bin/python3 -97: 55# 0x000000000053D3B0 in /usr/bin/python3 -97: 56# _PyEval_EvalFrameDefault in /usr/bin/python3 -97: 57# 0x000000000061C8E0 in /usr/bin/python3 -97: 58# 0x00000000005A787C in /usr/bin/python3 -97: 59# _PyObject_MakeTpCall in /usr/bin/python3 -97: 60# _PyEval_EvalFrameDefault in /usr/bin/python3 -97: 61# 0x000000000053D3B0 in /usr/bin/python3 -97: 62# _PyEval_EvalFrameDefault in /usr/bin/python3 -97: 63# 0x000000000061C8E0 in /usr/bin/python3 -97: 64# 0x00000000005A787C in /usr/bin/python3 -97: 65# _PyObject_MakeTpCall in /usr/bin/python3 -97: 66# _PyEval_EvalFrameDefault in /usr/bin/python3 -97: 67# 0x000000000050B150 in /usr/bin/python3 -97: 68# _PyObject_MakeTpCall in /usr/bin/python3 -97: 69# _PyEval_EvalFrameDefault in /usr/bin/python3 -97: 70# PyEval_EvalCode in /usr/bin/python3 -97: 71# 0x000000000064023C in /usr/bin/python3 -97: 72# 0x000000000063BC30 in /usr/bin/python3 -97: 73# 0x000000000065F810 in /usr/bin/python3 -97: 74# 0x000000000065F0B4 in /usr/bin/python3 -97: 75# 0x000000000065EE50 in /usr/bin/python3 -97: 76# Py_RunMain in /usr/bin/python3 -97: 77# Py_BytesMain in /usr/bin/python3 -97: 78# 0x0000FFFF8C0F229C 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: [02:19:05] -97: -97: **** -97: Pre-condition Violation -97: getNumImplicitHs() called without preceding call to calcImplicitValence() -97: Violation occurred on line 301 in file ./Code/GraphMol/Atom.cpp -97: Failed Expression: d_implicitValence > -1 -97: ---------- -97: Stacktrace: -97: 0# Invar::Invariant::toString[abi:cxx11]() const in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu//lib/libRDKitRDGeneral.so.1 -97: 1# Invar::operator<<(std::ostream&, Invar::Invariant const&) in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu//lib/libRDKitRDGeneral.so.1 -97: 2# RDKit::Atom::getNumImplicitHs() const in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu//lib/libRDKitGraphMol.so.1 -97: 3# RDKit::Atom::getTotalNumHs(bool) const in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu//lib/libRDKitGraphMol.so.1 -97: 4# Queries::EqualityQuery::Match(RDKit::Atom const*) const in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu//lib/libRDKitSmilesParse.so.1 -97: 5# Queries::AndQuery::Match(RDKit::Atom const*) const in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu//lib/libRDKitGraphMol.so.1 -97: 6# Queries::AndQuery::Match(RDKit::Atom const*) const in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu//lib/libRDKitGraphMol.so.1 -97: 7# Queries::OrQuery::Match(RDKit::Atom const*) const in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu//lib/libRDKitGraphMol.so.1 -97: 8# RDKit::atomCompat(RDKit::Atom const*, RDKit::Atom const*, RDKit::SubstructMatchParameters const&) in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu//lib/libRDKitSubstructMatch.so.1 -97: 9# boost::detail::VF2SubState const, RDKit::detail::AtomLabelFunctor, RDKit::detail::BondLabelFunctor, RDKit::MolMatchFinalCheckFunctor>::IsFeasiblePair(unsigned int, unsigned int) in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu//lib/libRDKitSubstructMatch.so.1 -97: 10# bool boost::detail::VF2SubState const, RDKit::detail::AtomLabelFunctor, RDKit::detail::BondLabelFunctor, RDKit::MolMatchFinalCheckFunctor>::MatchAll, std::allocator > >, std::allocator, std::allocator > > > > >(unsigned int*, unsigned int*, std::vector, std::allocator > >, std::allocator, std::allocator > > > >&, unsigned int) in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu//lib/libRDKitSubstructMatch.so.1 -97: 11# bool boost::vf2_all, RDKit::detail::AtomLabelFunctor, RDKit::detail::BondLabelFunctor, RDKit::MolMatchFinalCheckFunctor, std::vector, std::allocator > >, std::allocator, std::allocator > > > > >(boost::adjacency_list const&, boost::adjacency_list const&, RDKit::detail::AtomLabelFunctor&, RDKit::detail::BondLabelFunctor&, RDKit::MolMatchFinalCheckFunctor&, std::vector, std::allocator > >, std::allocator, std::allocator > > > >&, unsigned int) in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu//lib/libRDKitSubstructMatch.so.1 -97: 12# RDKit::detail::RecursiveMatcher(RDKit::ROMol const&, RDKit::ROMol const&, std::vector >&, std::map*, std::less, std::allocator*> > >&, RDKit::SubstructMatchParameters const&, std::vector >&) in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu//lib/libRDKitSubstructMatch.so.1 -97: 13# RDKit::detail::MatchSubqueries(RDKit::ROMol const&, Queries::Query*, RDKit::SubstructMatchParameters const&, std::map*, std::less, std::allocator*> > >&, std::vector >&) in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu//lib/libRDKitSubstructMatch.so.1 -97: 14# RDKit::detail::MatchSubqueries(RDKit::ROMol const&, Queries::Query*, RDKit::SubstructMatchParameters const&, std::map*, std::less, std::allocator*> > >&, std::vector >&) in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu//lib/libRDKitSubstructMatch.so.1 -97: 15# RDKit::detail::MatchSubqueries(RDKit::ROMol const&, Queries::Query*, RDKit::SubstructMatchParameters const&, std::map*, std::less, std::allocator*> > >&, std::vector >&) in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu//lib/libRDKitSubstructMatch.so.1 -97: 16# RDKit::detail::MatchSubqueries(RDKit::ROMol const&, Queries::Query*, RDKit::SubstructMatchParameters const&, std::map*, std::less, std::allocator*> > >&, std::vector >&) in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu//lib/libRDKitSubstructMatch.so.1 -97: 17# RDKit::SubstructMatch(RDKit::ROMol const&, RDKit::ROMol const&, RDKit::SubstructMatchParameters const&) in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu//lib/libRDKitSubstructMatch.so.1 -97: 18# RDKit::ReactionRunnerUtils::getReactantMatchesToTemplate(RDKit::ROMol const&, RDKit::ROMol const&, unsigned int, RDKit::SubstructMatchParameters const&) in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu//lib/libRDKitChemReactions.so.1 -97: 19# RDKit::ReactionRunnerUtils::getReactantMatches(std::vector, std::allocator > > const&, RDKit::ChemicalReaction const&, std::vector, std::allocator > >, std::allocator, std::allocator > > > >, std::allocator, std::allocator > >, std::allocator, std::allocator > > > > > >&, unsigned int, unsigned int) in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu//lib/libRDKitChemReactions.so.1 -97: 20# RDKit::run_Reactants(RDKit::ChemicalReaction const&, std::vector, std::allocator > > const&, unsigned int) in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu//lib/libRDKitChemReactions.so.1 -97: 21# RDKit::ChemicalReaction::runReactants(std::vector, std::allocator > >, unsigned int) const in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu//lib/libRDKitChemReactions.so.1 -97: 22# _object* RDKit::RunReactants(RDKit::ChemicalReaction*, boost::python::tuple, unsigned int) in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdChemReactions.so -97: 23# boost::python::objects::caller_py_function_impl > >::operator()(_object*, _object*) in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdChemReactions.so -97: 24# boost::python::objects::function::call(_object*, _object*) const in /lib/aarch64-linux-gnu/libboost_python313.so.1.83.0 -97: 25# 0x0000FFFF8B5C2680 in /lib/aarch64-linux-gnu/libboost_python313.so.1.83.0 -97: 26# boost::python::detail::exception_handler::operator()(boost::function0 const&) const in /lib/aarch64-linux-gnu/libboost_python313.so.1.83.0 -97: 27# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdSLNParse.so -97: 28# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdDepictor.so -97: 29# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdChemReactions.so -97: 30# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdChemReactions.so -97: 31# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdMolChemicalFeatures.so -97: 32# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdmolfiles.so -97: 33# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdmolfiles.so -97: 34# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdCIPLabeler.so -97: 35# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so -97: 36# 0x0000FFFF89B7C320 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so -97: 37# 0x0000FFFF89B7C2B8 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so -97: 38# 0x0000FFFF89B7C248 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so -97: 39# 0x0000FFFF89B7C1E0 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so -97: 40# 0x0000FFFF89B7C178 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# 0x0000FFFF8B5BF25C in /lib/aarch64-linux-gnu/libboost_python313.so.1.83.0 -97: 47# _PyObject_MakeTpCall in /usr/bin/python3 -97: 48# _PyEval_EvalFrameDefault in /usr/bin/python3 -97: 49# 0x000000000053D3B0 in /usr/bin/python3 -97: 50# _PyEval_EvalFrameDefault in /usr/bin/python3 -97: 51# 0x000000000061C8E0 in /usr/bin/python3 -97: 52# 0x00000000005A787C in /usr/bin/python3 -97: 53# _PyObject_MakeTpCall in /usr/bin/python3 -97: 54# _PyEval_EvalFrameDefault in /usr/bin/python3 -97: 55# 0x000000000053D3B0 in /usr/bin/python3 -97: 56# _PyEval_EvalFrameDefault in /usr/bin/python3 -97: 57# 0x000000000061C8E0 in /usr/bin/python3 -97: 58# 0x00000000005A787C in /usr/bin/python3 -97: 59# _PyObject_MakeTpCall in /usr/bin/python3 -97: 60# _PyEval_EvalFrameDefault in /usr/bin/python3 -97: 61# 0x000000000053D3B0 in /usr/bin/python3 -97: 62# _PyEval_EvalFrameDefault in /usr/bin/python3 -97: 63# 0x000000000061C8E0 in /usr/bin/python3 -97: 64# 0x00000000005A787C in /usr/bin/python3 -97: 65# _PyObject_MakeTpCall in /usr/bin/python3 -97: 66# _PyEval_EvalFrameDefault in /usr/bin/python3 -97: 67# 0x000000000050B150 in /usr/bin/python3 -97: 68# _PyObject_MakeTpCall in /usr/bin/python3 -97: 69# _PyEval_EvalFrameDefault in /usr/bin/python3 -97: 70# PyEval_EvalCode in /usr/bin/python3 -97: 71# 0x000000000064023C in /usr/bin/python3 -97: 72# 0x000000000063BC30 in /usr/bin/python3 -97: 73# 0x000000000065F810 in /usr/bin/python3 -97: 74# 0x000000000065F0B4 in /usr/bin/python3 -97: 75# 0x000000000065EE50 in /usr/bin/python3 -97: 76# Py_RunMain in /usr/bin/python3 -97: 77# Py_BytesMain in /usr/bin/python3 -97: 78# 0x0000FFFF8C0F229C 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: -29: All 191 tests passed -98: [02:19:05] == testCartesianProduct -98: .[02:19:05] == testEnumerateLibrary -97: .........[02:19:05] stereo atoms in input cannot be mapped to output (atoms are no longer bonded) -97: [02:19:05] stereo atoms in input cannot be mapped to output (atoms are no longer bonded) -97: [02:19:05] stereo atoms in input cannot be mapped to output (atoms are no longer bonded) -97: [02:19:05] stereo atoms in input cannot be mapped to output (atoms are no longer bonded) -97: .[02:19:05] product atom-mapping number 1 found multiple times. -97: [02:19:05] product atom-mapping number 1 found multiple times. -98: /build/reproducible-path/rdkit-202503.1/Code/GraphMol/ChemReactions/Wrap/testEnumerations.py:266: ResourceWarning: unclosed file <_io.BufferedReader name='/build/reproducible-path/rdkit-202503.1/Code/GraphMol/ChemReactions/testData/enumeration.pickle'> -98: open(os.path.join(self.dataDir, "enumeration.pickle"), 'rb').read()) -98: ResourceWarning: Enable tracemalloc to get the object allocation traceback -97: ................[02:19:05] mapped atoms in the reactants were not mapped in the products. -97: unmapped numbers are: 3 -97: [02:19:05] mapped atoms in the reactants were not mapped in the products. -97: unmapped numbers are: 3 -97: .:488: RuntimeWarning: to-Python converter for boost::shared_ptr already registered; second conversion method ignored. -97: [02:19:05] mapped atoms in the reactants were not mapped in the products. -97: unmapped numbers are: 3 -97: ..[02:19:05] reactant 2 has no mapped atoms. -97: [02:19:05] reactant 2 has no mapped atoms. -97: [02:19:05] product 1 has no mapped atoms. -98: ..[02:19:05] == testRGroupState -97: ........[02:19:05] SMARTS Parse Error: syntax error while parsing: [C:1](=[O:2])Q -97: [02:19:05] SMARTS Parse Error: Failed parsing SMARTS '[C:1](=[O:2])Q' for input: '[C:1](=[O:2])Q' -97: [02:19:05] SMARTS Parse Error: syntax error while parsing: [C:1](=[O:2])[N:3]Q -97: [02:19:05] SMARTS Parse Error: Failed parsing SMARTS '[C:1](=[O:2])[N:3]Q' for input: '[C:1](=[O:2])[N:3]Q' -97: .[02:19:05] reactant atom-mapping number 1 found multiple times. -97: [02:19:05] product atom-mapping number 2 not found in reactants. -97: [02:19:05] mapped atoms in the reactants were not mapped in the products. -97: unmapped numbers are: 4 -97: [02:19:05] product atom-mapping number 5 not found in reactants. -98: .[02:19:05] == testRandomEnumerateAllBBsLibrary -98: ** [1, 1] -98: ** [0, 2] -98: ** [1, 0] - 88/238 Test #99: pyChemReactionSanitize ................. Passed 0.28 sec +97: [11:06:02] Found a SCD/SED line with missing/empty SDT specification at line 34 +97: [11:06:02] Found a SCD/SED line with missing/empty SDT specification at line 36 +97: [11:06:02] Found a SCD/SED line with missing/empty SDT specification at line 38 +97: [11:06:02] Found a SCD/SED line with missing/empty SDT specification at line 40 +97: [11:06:02] Found a SCD/SED line with missing/empty SDT specification at line 42 +97: [11:06:02] Found a SCD/SED line with missing/empty SDT specification at line 87 +97: [11:06:02] Found a SCD/SED line with missing/empty SDT specification at line 89 +97: [11:06:02] Found a SCD/SED line with missing/empty SDT specification at line 91 +97: [11:06:02] Found a SCD/SED line with missing/empty SDT specification at line 93 +97: [11:06:02] Found a SCD/SED line with missing/empty SDT specification at line 95 +89: [11:06:02] Explicit valence for atom # 3 Al, 6, is greater than permitted +97: ..[11:06:02] SMARTS Parse Error: syntax error while parsing: boromicacid +97: [11:06:02] SMARTS Parse Error: Failed parsing SMARTS 'boromicacid' for input: 'boromicacid' +69: [11:06:02] SMARTS Parse Error: syntax error while parsing: MyDogHasFleas +69: [11:06:02] SMARTS Parse Error: Failed parsing SMARTS 'MyDogHasFleas' for input: 'MyDogHasFleas' + 88/238 Test #42: resMolSupplierTest ..................... Passed 2.45 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 -98: .[02:19:05] == testRandomEnumerateLibrary -98: .[02:19:05] == testRandomSample -98: .[02:19:05] == testRandomSampleAllBBs -98: .[02:19:05] deprecated -- please use MatchOnlyAtRgroupsAdjustParams instead -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 -98: [02:19:05] deprecated -- please use MatchOnlyAtRgroupsAdjustParams instead +97: [11:06:02] SMARTS Parse Error: syntax error while parsing: carboxylicacid,acidchlroide +97: [11:06:02] SMARTS Parse Error: Failed parsing SMARTS 'carboxylicacid,acidchlroide' for input: 'carboxylicacid,acidchlroide' +97: [11:06:02] SMARTS Parse Error: syntax error while parsing: carboxyliccaid,acidchloride +97: [11:06:02] SMARTS Parse Error: Failed parsing SMARTS 'carboxyliccaid,acidchloride' for input: 'carboxyliccaid,acidchloride' +97: [11:06:02] reaction has no reactants +97: [11:06:02] reaction has no products +97: [11:06:02] initialization failed +97: [11:06:02] reaction has no reactants +97: [11:06:02] reaction has no products +97: .[11:06:02] SMARTS Parse Error: syntax error while parsing: boromicacid +97: [11:06:02] SMARTS Parse Error: Failed parsing SMARTS 'boromicacid' for input: 'boromicacid' +97: [11:06:02] SMARTS Parse Error: syntax error while parsing: carboxylicacid,acidchlroide +97: [11:06:02] SMARTS Parse Error: Failed parsing SMARTS 'carboxylicacid,acidchlroide' for input: 'carboxylicacid,acidchlroide' +97: [11:06:02] SMARTS Parse Error: syntax error while parsing: carboxyliccaid,acidchloride +97: [11:06:02] SMARTS Parse Error: Failed parsing SMARTS 'carboxyliccaid,acidchloride' for input: 'carboxyliccaid,acidchloride' +97: [11:06:02] reaction has no reactants +97: [11:06:02] reaction has no products +97: [11:06:02] initialization failed +97: [11:06:02] reaction has no reactants +97: [11:06:02] reaction has no products 100: 1 smi: CC 100: 1 smi: CC 100: 2 smi: CCO[C@H](N)P 100: 2 smi: CC -100: replaceSub smi1:CCP(CC)[C@@H](N)O -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 -98: .[02:19:05] == testRemoveBadMatches -98: .[02:19:05] == testTimings -97: [02:19:05] Found a SCD/SED line with missing/empty SDT specification at line 34 -97: [02:19:05] Found a SCD/SED line with missing/empty SDT specification at line 36 -97: [02:19:05] Found a SCD/SED line with missing/empty SDT specification at line 38 -97: [02:19:05] Found a SCD/SED line with missing/empty SDT specification at line 40 -97: [02:19:05] Found a SCD/SED line with missing/empty SDT specification at line 42 -97: [02:19:05] Found a SCD/SED line with missing/empty SDT specification at line 87 -97: [02:19:05] Found a SCD/SED line with missing/empty SDT specification at line 89 -97: [02:19:05] Found a SCD/SED line with missing/empty SDT specification at line 91 -97: [02:19:05] Found a SCD/SED line with missing/empty SDT specification at line 93 -97: [02:19:05] Found a SCD/SED line with missing/empty SDT specification at line 95 -97: ..[02:19:05] SMARTS Parse Error: syntax error while parsing: boromicacid -97: [02:19:05] SMARTS Parse Error: Failed parsing SMARTS 'boromicacid' for input: 'boromicacid' -100: [02:19:05] SMARTS Parse Error: syntax error while parsing: bar -100: [02:19:05] SMARTS Parse Error: Failed parsing SMARTS 'bar' for input: 'bar' -97: [02:19:05] SMARTS Parse Error: syntax error while parsing: carboxylicacid,acidchlroide -97: [02:19:05] SMARTS Parse Error: Failed parsing SMARTS 'carboxylicacid,acidchlroide' for input: 'carboxylicacid,acidchlroide' -97: [02:19:05] SMARTS Parse Error: syntax error while parsing: carboxyliccaid,acidchloride -97: [02:19:05] SMARTS Parse Error: Failed parsing SMARTS 'carboxyliccaid,acidchloride' for input: 'carboxyliccaid,acidchloride' -97: [02:19:05] reaction has no reactants -97: [02:19:05] reaction has no products -97: [02:19:05] initialization failed -97: [02:19:05] reaction has no reactants -97: [02:19:05] reaction has no products -97: .[02:19:05] SMARTS Parse Error: syntax error while parsing: boromicacid -97: [02:19:05] SMARTS Parse Error: Failed parsing SMARTS 'boromicacid' for input: 'boromicacid' -29: -29: Computing MMFF94 energies for /build/reproducible-path/rdkit-202503.1/Code/ForceField/MMFF/test_data/MMFF94_dative.smi... -97: [02:19:05] SMARTS Parse Error: syntax error while parsing: carboxylicacid,acidchlroide -97: [02:19:05] SMARTS Parse Error: Failed parsing SMARTS 'carboxylicacid,acidchlroide' for input: 'carboxylicacid,acidchlroide' -97: [02:19:05] SMARTS Parse Error: syntax error while parsing: carboxyliccaid,acidchloride -97: [02:19:05] SMARTS Parse Error: Failed parsing SMARTS 'carboxyliccaid,acidchloride' for input: 'carboxyliccaid,acidchloride' -97: [02:19:05] reaction has no reactants -97: [02:19:05] reaction has no products -97: [02:19:05] initialization failed -97: [02:19:05] reaction has no reactants -97: [02:19:05] reaction has no products 97: . 97: ---------------------------------------------------------------------- -97: Ran 54 tests in 0.143s +97: Ran 54 tests in 0.190s 97: 97: OK +100: replaceSub smi1:CCP(CC)[C@@H](N)O +100: replaceSub smi1:CCNCC 97: ******************************************** 97: /build/reproducible-path/rdkit-202503.1/Code/GraphMol/ChemReactions/testData/AmideBond.rxn -97: - 89/238 Test #100: testChemTransforms ..................... Passed 0.05 sec +97: +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: [11:06:02] SMARTS Parse Error: syntax error while parsing: bar +100: [11:06:02] SMARTS Parse Error: Failed parsing SMARTS 'bar' for input: 'bar' +69: [11:06:02] Empty atom list: 'M ALS 1 0 F' on line 8. + 89/238 Test #69: fileParsersTest1 ....................... Passed 1.97 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 -101: Randomness seeded to: 1078159912 -101: [02:19:05] Incomplete atom labelling, cannot make bond -101: [02:19:05] +89: [11:06:02] Explicit valence for atom # 4 Al, 6, is greater than permitted + 90/238 Test #100: testChemTransforms ..................... Passed 0.05 sec +test 102 + Start 102: tautomerQueryTestCatch + +102: Test command: /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/TautomerQuery/tautomerQueryTestCatch +102: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/TautomerQuery +102: Test timeout computed to be: 1500 + 91/238 Test #99: pyChemReactionSanitize ................. Passed 0.46 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 + 92/238 Test #97: pyChemReactions ........................ Passed 0.66 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 +104: ----------------------- +104: Subgraph retrieval +104: Finished +104: ----------------------- +104: testSubgraphs2a +104: Finished +104: ----------------------- +104: testSubgraphs2 +101: Randomness seeded to: 2779488181 +101: [11:06:02] Incomplete atom labelling, cannot make bond +101: [11:06:02] 101: 101: **** 101: Invariant Violation @@ -23548,28 +23669,22 @@ 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# 0x0000AAAAB99772AC in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/ChemTransforms/chemTransformsTestCatch -101: 5# 0x0000AAAAB99C52CC in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/ChemTransforms/chemTransformsTestCatch -101: 6# 0x0000AAAAB99C5C80 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/ChemTransforms/chemTransformsTestCatch -101: 7# 0x0000AAAAB99C60B4 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/ChemTransforms/chemTransformsTestCatch -101: 8# 0x0000AAAAB999A638 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/ChemTransforms/chemTransformsTestCatch -101: 9# 0x0000AAAAB999AB84 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/ChemTransforms/chemTransformsTestCatch -101: 10# 0x0000AAAAB996C550 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/ChemTransforms/chemTransformsTestCatch -101: 11# 0x0000FFFF8E27229C in /lib/aarch64-linux-gnu/libc.so.6 +101: 4# 0x0000AAAAB70C72AC in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/ChemTransforms/chemTransformsTestCatch +101: 5# 0x0000AAAAB71152CC in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/ChemTransforms/chemTransformsTestCatch +101: 6# 0x0000AAAAB7115C80 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/ChemTransforms/chemTransformsTestCatch +101: 7# 0x0000AAAAB71160B4 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/ChemTransforms/chemTransformsTestCatch +101: 8# 0x0000AAAAB70EA638 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/ChemTransforms/chemTransformsTestCatch +101: 9# 0x0000AAAAB70EAB84 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/ChemTransforms/chemTransformsTestCatch +101: 10# 0x0000AAAAB70BC550 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/ChemTransforms/chemTransformsTestCatch +101: 11# 0x0000FFFFBE55229C in /lib/aarch64-linux-gnu/libc.so.6 101: 12# __libc_start_main in /lib/aarch64-linux-gnu/libc.so.6 -101: 13# 0x0000AAAAB996C630 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/ChemTransforms/chemTransformsTestCatch +101: 13# 0x0000AAAAB70BC630 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/ChemTransforms/chemTransformsTestCatch 101: ---------- 101: **** 101: - 90/238 Test #97: pyChemReactions ........................ Passed 0.45 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: [02:19:05] Incomplete atom labelling, cannot make bond -101: [02:19:05] +89: [11:06:02] Explicit valence for atom # 10 Si, 6, is greater than permitted +101: [11:06:02] Incomplete atom labelling, cannot make bond +101: [11:06:02] 101: 101: **** 101: Invariant Violation @@ -23582,21 +23697,21 @@ 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# 0x0000AAAAB99772AC in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/ChemTransforms/chemTransformsTestCatch -101: 5# 0x0000AAAAB99C52CC in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/ChemTransforms/chemTransformsTestCatch -101: 6# 0x0000AAAAB99C5C80 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/ChemTransforms/chemTransformsTestCatch -101: 7# 0x0000AAAAB99C60B4 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/ChemTransforms/chemTransformsTestCatch -101: 8# 0x0000AAAAB999A638 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/ChemTransforms/chemTransformsTestCatch -101: 9# 0x0000AAAAB999AB84 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/ChemTransforms/chemTransformsTestCatch -101: 10# 0x0000AAAAB996C550 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/ChemTransforms/chemTransformsTestCatch -101: 11# 0x0000FFFF8E27229C in /lib/aarch64-linux-gnu/libc.so.6 +101: 4# 0x0000AAAAB70C72AC in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/ChemTransforms/chemTransformsTestCatch +101: 5# 0x0000AAAAB71152CC in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/ChemTransforms/chemTransformsTestCatch +101: 6# 0x0000AAAAB7115C80 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/ChemTransforms/chemTransformsTestCatch +101: 7# 0x0000AAAAB71160B4 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/ChemTransforms/chemTransformsTestCatch +101: 8# 0x0000AAAAB70EA638 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/ChemTransforms/chemTransformsTestCatch +101: 9# 0x0000AAAAB70EAB84 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/ChemTransforms/chemTransformsTestCatch +101: 10# 0x0000AAAAB70BC550 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/ChemTransforms/chemTransformsTestCatch +101: 11# 0x0000FFFFBE55229C in /lib/aarch64-linux-gnu/libc.so.6 101: 12# __libc_start_main in /lib/aarch64-linux-gnu/libc.so.6 -101: 13# 0x0000AAAAB996C630 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/ChemTransforms/chemTransformsTestCatch +101: 13# 0x0000AAAAB70BC630 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/ChemTransforms/chemTransformsTestCatch 101: ---------- 101: **** 101: -101: [02:19:05] Incomplete atom labelling, cannot make bond -101: [02:19:05] +101: [11:06:02] Incomplete atom labelling, cannot make bond +101: [11:06:02] 101: 101: **** 101: Invariant Violation @@ -23609,23 +23724,23 @@ 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# 0x0000AAAAB99772AC in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/ChemTransforms/chemTransformsTestCatch -101: 5# 0x0000AAAAB99C52CC in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/ChemTransforms/chemTransformsTestCatch -101: 6# 0x0000AAAAB99C5C80 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/ChemTransforms/chemTransformsTestCatch -101: 7# 0x0000AAAAB99C60B4 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/ChemTransforms/chemTransformsTestCatch -101: 8# 0x0000AAAAB999A638 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/ChemTransforms/chemTransformsTestCatch -101: 9# 0x0000AAAAB999AB84 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/ChemTransforms/chemTransformsTestCatch -101: 10# 0x0000AAAAB996C550 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/ChemTransforms/chemTransformsTestCatch -101: 11# 0x0000FFFF8E27229C in /lib/aarch64-linux-gnu/libc.so.6 +101: 4# 0x0000AAAAB70C72AC in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/ChemTransforms/chemTransformsTestCatch +101: 5# 0x0000AAAAB71152CC in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/ChemTransforms/chemTransformsTestCatch +101: 6# 0x0000AAAAB7115C80 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/ChemTransforms/chemTransformsTestCatch +101: 7# 0x0000AAAAB71160B4 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/ChemTransforms/chemTransformsTestCatch +101: 8# 0x0000AAAAB70EA638 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/ChemTransforms/chemTransformsTestCatch +101: 9# 0x0000AAAAB70EAB84 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/ChemTransforms/chemTransformsTestCatch +101: 10# 0x0000AAAAB70BC550 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/ChemTransforms/chemTransformsTestCatch +101: 11# 0x0000FFFFBE55229C in /lib/aarch64-linux-gnu/libc.so.6 101: 12# __libc_start_main in /lib/aarch64-linux-gnu/libc.so.6 -101: 13# 0x0000AAAAB996C630 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/ChemTransforms/chemTransformsTestCatch +101: 13# 0x0000AAAAB70BC630 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/ChemTransforms/chemTransformsTestCatch 101: ---------- 101: **** 101: -101: [02:19:05] Incomplete atom labelling, cannot make bond -101: [02:19:05] Incomplete atom labelling, cannot make bond -101: [02:19:05] Incomplete atom labelling, cannot make bond -101: [02:19:05] +101: [11:06:02] Incomplete atom labelling, cannot make bond +101: [11:06:02] Incomplete atom labelling, cannot make bond +101: [11:06:02] Incomplete atom labelling, cannot make bond +101: [11:06:02] 101: 101: **** 101: Invariant Violation @@ -23638,21 +23753,21 @@ 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# 0x0000AAAAB99772AC in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/ChemTransforms/chemTransformsTestCatch -101: 5# 0x0000AAAAB99C52CC in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/ChemTransforms/chemTransformsTestCatch -101: 6# 0x0000AAAAB99C5C80 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/ChemTransforms/chemTransformsTestCatch -101: 7# 0x0000AAAAB99C60B4 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/ChemTransforms/chemTransformsTestCatch -101: 8# 0x0000AAAAB999A638 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/ChemTransforms/chemTransformsTestCatch -101: 9# 0x0000AAAAB999AB84 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/ChemTransforms/chemTransformsTestCatch -101: 10# 0x0000AAAAB996C550 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/ChemTransforms/chemTransformsTestCatch -101: 11# 0x0000FFFF8E27229C in /lib/aarch64-linux-gnu/libc.so.6 +101: 4# 0x0000AAAAB70C72AC in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/ChemTransforms/chemTransformsTestCatch +101: 5# 0x0000AAAAB71152CC in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/ChemTransforms/chemTransformsTestCatch +101: 6# 0x0000AAAAB7115C80 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/ChemTransforms/chemTransformsTestCatch +101: 7# 0x0000AAAAB71160B4 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/ChemTransforms/chemTransformsTestCatch +101: 8# 0x0000AAAAB70EA638 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/ChemTransforms/chemTransformsTestCatch +101: 9# 0x0000AAAAB70EAB84 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/ChemTransforms/chemTransformsTestCatch +101: 10# 0x0000AAAAB70BC550 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/ChemTransforms/chemTransformsTestCatch +101: 11# 0x0000FFFFBE55229C in /lib/aarch64-linux-gnu/libc.so.6 101: 12# __libc_start_main in /lib/aarch64-linux-gnu/libc.so.6 -101: 13# 0x0000AAAAB996C630 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/ChemTransforms/chemTransformsTestCatch +101: 13# 0x0000AAAAB70BC630 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/ChemTransforms/chemTransformsTestCatch 101: ---------- 101: **** 101: -101: [02:19:05] Incomplete atom labelling, cannot make bond -101: [02:19:05] +101: [11:06:02] Incomplete atom labelling, cannot make bond +101: [11:06:02] 101: 101: **** 101: Invariant Violation @@ -23665,20 +23780,20 @@ 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# 0x0000AAAAB99772AC in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/ChemTransforms/chemTransformsTestCatch -101: 5# 0x0000AAAAB99C52CC in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/ChemTransforms/chemTransformsTestCatch -101: 6# 0x0000AAAAB99C5C80 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/ChemTransforms/chemTransformsTestCatch -101: 7# 0x0000AAAAB99C60B4 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/ChemTransforms/chemTransformsTestCatch -101: 8# 0x0000AAAAB999A638 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/ChemTransforms/chemTransformsTestCatch -101: 9# 0x0000AAAAB999AB84 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/ChemTransforms/chemTransformsTestCatch -101: 10# 0x0000AAAAB996C550 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/ChemTransforms/chemTransformsTestCatch -101: 11# 0x0000FFFF8E27229C in /lib/aarch64-linux-gnu/libc.so.6 +101: 4# 0x0000AAAAB70C72AC in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/ChemTransforms/chemTransformsTestCatch +101: 5# 0x0000AAAAB71152CC in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/ChemTransforms/chemTransformsTestCatch +101: 6# 0x0000AAAAB7115C80 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/ChemTransforms/chemTransformsTestCatch +101: 7# 0x0000AAAAB71160B4 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/ChemTransforms/chemTransformsTestCatch +101: 8# 0x0000AAAAB70EA638 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/ChemTransforms/chemTransformsTestCatch +101: 9# 0x0000AAAAB70EAB84 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/ChemTransforms/chemTransformsTestCatch +101: 10# 0x0000AAAAB70BC550 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/ChemTransforms/chemTransformsTestCatch +101: 11# 0x0000FFFFBE55229C in /lib/aarch64-linux-gnu/libc.so.6 101: 12# __libc_start_main in /lib/aarch64-linux-gnu/libc.so.6 -101: 13# 0x0000AAAAB996C630 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/ChemTransforms/chemTransformsTestCatch +101: 13# 0x0000AAAAB70BC630 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/ChemTransforms/chemTransformsTestCatch 101: ---------- 101: **** 101: -101: [02:19:05] +101: [11:06:02] 101: 101: **** 101: Invariant Violation @@ -23692,92 +23807,29 @@ 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# 0x0000AAAAB996D6DC in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/ChemTransforms/chemTransformsTestCatch -101: 6# 0x0000AAAAB99C52CC in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/ChemTransforms/chemTransformsTestCatch -101: 7# 0x0000AAAAB99C5C80 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/ChemTransforms/chemTransformsTestCatch -101: 8# 0x0000AAAAB99C60B4 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/ChemTransforms/chemTransformsTestCatch -101: 9# 0x0000AAAAB999A638 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/ChemTransforms/chemTransformsTestCatch -101: 10# 0x0000AAAAB999AB84 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/ChemTransforms/chemTransformsTestCatch -101: 11# 0x0000AAAAB996C550 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/ChemTransforms/chemTransformsTestCatch -101: 12# 0x0000FFFF8E27229C in /lib/aarch64-linux-gnu/libc.so.6 +101: 5# 0x0000AAAAB70BD6DC in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/ChemTransforms/chemTransformsTestCatch +101: 6# 0x0000AAAAB71152CC in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/ChemTransforms/chemTransformsTestCatch +101: 7# 0x0000AAAAB7115C80 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/ChemTransforms/chemTransformsTestCatch +101: 8# 0x0000AAAAB71160B4 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/ChemTransforms/chemTransformsTestCatch +101: 9# 0x0000AAAAB70EA638 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/ChemTransforms/chemTransformsTestCatch +101: 10# 0x0000AAAAB70EAB84 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/ChemTransforms/chemTransformsTestCatch +101: 11# 0x0000AAAAB70BC550 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/ChemTransforms/chemTransformsTestCatch +101: 12# 0x0000FFFFBE55229C in /lib/aarch64-linux-gnu/libc.so.6 101: 13# __libc_start_main in /lib/aarch64-linux-gnu/libc.so.6 -101: 14# 0x0000AAAAB996C630 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/ChemTransforms/chemTransformsTestCatch +101: 14# 0x0000AAAAB70BC630 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: -89: [02:19:05] Explicit valence for atom # 9 N, 5, is greater than permitted - 91/238 Test #101: chemTransformsTestCatch ................ Passed 0.10 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: [02:19:05] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 1 ignored -69: [02:19:05] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 1 ignored -69: [02:19:05] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 1 ignored -69: [02:19:05] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 1 ignored -69: [02:19:05] 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: [02:19:05] -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# 0x0000FFFFB54A7F24 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu//lib/libRDKitFileParsers.so.1 -69: 4# 0x0000FFFFB54B5B20 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu//lib/libRDKitFileParsers.so.1 -69: 5# 0x0000FFFFB54B6A4C 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# 0x0000AAAAC289F77C in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersTest1 -69: 10# 0x0000AAAAC2914944 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersTest1 -69: 11# 0x0000AAAAC2885C6C in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersTest1 -69: 12# 0x0000FFFFB4B6229C in /lib/aarch64-linux-gnu/libc.so.6 -69: 13# __libc_start_main in /lib/aarch64-linux-gnu/libc.so.6 -69: 14# 0x0000AAAAC2885E30 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersTest1 -69: ---------- -69: **** -69: -102: Randomness seeded to: 585952823 -102: =============================================================================== -102: All tests passed (93 assertions in 13 test cases) -102: - 92/238 Test #102: tautomerQueryTestCatch ................. Passed 0.15 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: [02:19:06] Explicit valence for atom # 3 Al, 6, is greater than permitted -104: ----------------------- -104: Subgraph retrieval -104: Finished -104: ----------------------- -104: testSubgraphs2a -104: Finished -104: ----------------------- -104: testSubgraphs2 - 93/238 Test #42: resMolSupplierTest ..................... Passed 2.56 sec + 93/238 Test #101: chemTransformsTestCatch ................ Passed 0.07 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 104: Finished 104: ----------------------- 104: Path retrieval @@ -23790,6 +23842,9 @@ 104: Finished 104: ----------------------- 104: testUniqueSubgraphs2 +29: Checking against /build/reproducible-path/rdkit-202503.1/Code/ForceField/MMFF/test_data/MMFF94_reference.log... +105: ----------------------- +105: Test1: pathToSubmol 105: Finished 105: ----------------------- 105: Test2: Atom Environments @@ -23803,15 +23858,14 @@ 105: ----------------------- 105: Testing github Issue103: more stereochemistry and pathToSubmol (path needs to be in sorted order) 105: Finished -89: [02:19:06] Explicit valence for atom # 4 Al, 6, is greater than permitted - 94/238 Test #105: testSubgraphs2 ......................... Passed 0.02 sec + 94/238 Test #105: testSubgraphs2 ......................... Passed 0.03 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 -106: Randomness seeded to: 2714473220 +106: Randomness seeded to: 2429964011 106: --------- 106: =============================================================================== 106: All tests passed (11 assertions in 1 test case) @@ -23823,9 +23877,32 @@ 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 -89: [02:19:06] Explicit valence for atom # 10 Si, 6, is greater than permitted -69: [02:19:06] 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: [02:19:06] 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: 949635044 +102: =============================================================================== +102: All tests passed (93 assertions in 13 test cases) +102: + 96/238 Test #102: tautomerQueryTestCatch ................. Passed 0.12 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 +29: All 191 tests passed +104: Finished +104: ----------------------- +104: testRootedSubgraphs +104: Finished +104: ----------------------- +104: testRootedPaths +104: Finished + 97/238 Test #104: testSubgraphs1 ......................... Passed 0.16 sec +test 109 + Start 109: testFragCatalog + +109: Test command: /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FragCatalog/testFragCatalog +109: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FragCatalog +109: Test timeout computed to be: 1500 107: Warning: molecule failed filter 107: Warning: molecule failed filter: reason hzone_phenol_A(479) 107: v = { @@ -23914,87 +23991,29 @@ 107: 10,15}, 107: 11,16}, 107: } -104: Finished -104: ----------------------- -104: testRootedSubgraphs -104: Finished -104: ----------------------- -104: testRootedPaths -104: Finished - 96/238 Test #104: testSubgraphs1 ......................... Passed 0.16 sec -test 108 - Start 108: pyFilterCatalog - -108: Test command: /usr/bin/python3 "/build/reproducible-path/rdkit-202503.1/Code/GraphMol/FilterCatalog/Wrap/rough_test.py" -108: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FilterCatalog/Wrap -108: Test timeout computed to be: 1500 -69: ---------------------------------- -69: ---------------------------------- -69: [02:19:06] -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# 0x0000AAAAC28AF23C in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersTest1 -69: 4# 0x0000AAAAC29149A4 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersTest1 -69: 5# 0x0000AAAAC2885C6C in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersTest1 -69: 6# 0x0000FFFFB4B6229C in /lib/aarch64-linux-gnu/libc.so.6 -69: 7# __libc_start_main in /lib/aarch64-linux-gnu/libc.so.6 -69: 8# 0x0000AAAAC2885E30 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersTest1 -69: ---------- -69: **** -69: -69: [02:19:06] WARNING: could not find number of expected rings. Switching to an approximate ring finding algorithm. +109: 21 103: ..... 103: ---------------------------------------------------------------------- -103: Ran 5 tests in 0.031s +103: Ran 5 tests in 0.025s 103: 103: OK - 97/238 Test #107: filterCatalogTest ...................... Passed 0.16 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: . -98: ---------------------------------------------------------------------- -98: Ran 11 tests in 0.561s -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 0.033854007720947266 seconds -98: Skipped 10000000 in 0.26155924797058105 seconds -98: Skipped 10000000 in 0.1133580207824707 seconds -109: 21 -89: [02:19:06] Explicit valence for atom # 2 O, 4, is greater than permitted -89: [02:19:06] Explicit valence for atom # 3 Al, 6, is greater than permitted -89: [02:19:06] Explicit valence for atom # 3 Be, 4, is greater than permitted - 98/238 Test #103: pyTautomerQuery ........................ Passed 0.40 sec +89: [11:06:02] Explicit valence for atom # 2 O, 4, is greater than permitted +89: [11:06:02] Explicit valence for atom # 3 Al, 6, is greater than permitted[11:06:02] Explicit valence for atom # 3 Be, 4, is greater than permitted +89: +89: [11:06:02] Explicit valence for atom # 27 P, 6, is greater than permitted + 98/238 Test #103: pyTautomerQuery ........................ Passed 0.25 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 -89: [02:19:06] Explicit valence for atom # 27 P, 6, is greater than permitted - 99/238 Test #98: pyChemReactionEnumerations ............. Passed 0.92 sec +29: +29: Computing MMFF94 energies for /build/reproducible-path/rdkit-202503.1/Code/ForceField/MMFF/test_data/MMFF94_dative.smi... +89: =============================================================================== +89: All tests passed (21562 assertions in 3 test cases) +89: + 99/238 Test #89: multithreadedSupplierCatchTest ......... Passed 1.63 sec test 111 Start 111: testDescriptors @@ -24002,171 +24021,65 @@ 111: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/Descriptors 111: Test timeout computed to be: 1500 108: :488: RuntimeWarning: to-Python converter for boost::shared_ptr already registered; second conversion method ignored. -111: [02:19:06] ------------------------------------- -111: [02:19:06] Test Crippen parameter acquisition. -111: [02:19:06] done -111: [02:19:06] ------------------------------------- -111: [02:19:06] Test Crippen calculation. -89: =============================================================================== -89: All tests passed (21562 assertions in 3 test cases) -89: -100/238 Test #89: multithreadedSupplierCatchTest ......... Passed 1.64 sec +111: [11:06:02] ------------------------------------- +111: [11:06:02] Test Crippen parameter acquisition. +111: [11:06:02] done +111: [11:06:02] ------------------------------------- +111: [11:06:02] Test Crippen calculation. +111: [11:06:02] done +111: [11:06:02] ------------------------------------- +111: [11:06:02] Test Issue262: problems with Crippen calculation from pickles. +111: [11:06:02] done +111: [11:06:02] ------------------------------------- +111: [11:06:02] Test AMW calculation. +111: [11:06:02] done +111: [11:06:02] ------------------------------------- +111: [11:06:02] Test Exact MW calculation. +111: [11:06:02] done +111: [11:06:02] ------------------------------------- +111: [11:06:02] Test Labute ASA descriptors. +111: [11:06:02] done +111: [11:06:02] ------------------------------------- +111: [11:06:02] Test TPSA descriptors. +111: [11:06:02] done +111: [11:06:02] ------------------------------------- +111: [11:06:02] Test Lipinski parameters. +100/238 Test #107: filterCatalogTest ...................... Passed 0.26 sec test 112 Start 112: testAUTOCORR2D 112: Test command: /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/Descriptors/testAUTOCORR2D 112: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/Descriptors 112: Test timeout computed to be: 1500 -111: [02:19:06] done -111: [02:19:06] ------------------------------------- -111: [02:19:06] Test Issue262: problems with Crippen calculation from pickles. -111: [02:19:06] done -111: [02:19:06] ------------------------------------- -111: [02:19:06] Test AMW calculation. -111: [02:19:06] done -111: [02:19:06] ------------------------------------- -111: [02:19:06] Test Exact MW calculation. -111: [02:19:06] done -111: [02:19:06] ------------------------------------- -111: [02:19:06] Test Labute ASA descriptors. -111: [02:19:06] done -111: [02:19:06] ------------------------------------- -111: [02:19:06] Test TPSA descriptors. -69: [02:19:06] SMARTS Parse Error: syntax error while parsing: MyDogHasFleas -69: [02:19:06] SMARTS Parse Error: Failed parsing SMARTS 'MyDogHasFleas' for input: 'MyDogHasFleas' -112: [02:19:06] ---------------------------- +112: [11:06:02] ---------------------------- 112: start test autocorr2D -69: [02:19:06] Empty atom list: 'M ALS 1 0 F' on line 8. -111: [02:19:06] done -111: [02:19:06] ------------------------------------- -111: [02:19:06] Test Lipinski parameters. -101/238 Test #69: fileParsersTest1 ....................... Passed 2.36 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 -102/238 Test #113: testATF ................................ Passed 0.01 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: [02:19:06] ------------------------------------- -114: [02:19:06] Basic BCUT tests. -114: [02:19:06] done -114: [02:19:06] ------------------------------------- -114: [02:19:06] Larger BCUT tests. -110: ......... -110: ---------------------------------------------------------------------- -110: Ran 9 tests in 0.037s -110: -110: OK -111: [02:19:06] done -111: [02:19:06] ------------------------------------- -111: [02:19:06] Test VSA descriptors. -111: [02:19:06] done -111: [02:19:06] ------------------------------------- -111: [02:19:06] Test molecular formula calculation. -111: [02:19:06] done -111: [02:19:06] ------------------------------------- -111: [02:19:06] Test Issue 3415534. -111: [02:19:06] done -111: [02:19:06] ------------------------------------- -111: [02:19:06] Test Issue3433771: Bad definition for Crippen atom type O11. -111: [02:19:06] done -111: [02:19:06] ------------------------------------- -111: [02:19:06] Test multithreading +111: [11:06:02] done +111: [11:06:02] ------------------------------------- +111: [11:06:02] Test VSA descriptors. +111: [11:06:02] done +111: [11:06:02] ------------------------------------- +111: [11:06:02] Test molecular formula calculation. +111: [11:06:02] done +111: [11:06:02] ------------------------------------- +111: [11:06:02] Test Issue 3415534. +111: [11:06:02] done +111: [11:06:02] ------------------------------------- +111: [11:06:02] Test Issue3433771: Bad definition for Crippen atom type O11. +111: [11:06:02] done +111: [11:06:02] ------------------------------------- +111: [11:06:02] Test multithreading 111: reading molecules 111: processing 111: launch :0 111: launch :1 111: launch :2 111: launch :3 -103/238 Test #110: pyFragCatalog .......................... Passed 0.25 sec -test 115 - Start 115: testEEM - -115: Test command: /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/Descriptors/testEEM -115: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/Descriptors -115: Test timeout computed to be: 1500 -115: =>start test EEM -115: [02:19:06] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: 0 -115: [02:19:06] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [02:19:06] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [02:19:06] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [02:19:06] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [02:19:06] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [02:19:06] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [02:19:06] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [02:19:06] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [02:19:06] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [02:19:06] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [02:19:06] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [02:19:06] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [02:19:06] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [02:19:06] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [02:19:06] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [02:19:06] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [02:19:06] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [02:19:06] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [02:19:06] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [02:19:06] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [02:19:06] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [02:19:06] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [02:19:06] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [02:19:06] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [02:19:06] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [02:19:06] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [02:19:06] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [02:19:06] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [02:19:06] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [02:19:06] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [02:19:06] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [02:19:06] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [02:19:06] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [02:19:06] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [02:19:06] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [02:19:06] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [02:19:06] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [02:19:06] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [02:19:06] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [02:19:06] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [02:19:06] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [02:19:06] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [02:19:06] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [02:19:06] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [02:19:06] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [02:19:06] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [02:19:06] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [02:19:06] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [02:19:06] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [02:19:06] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [02:19:06] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [02:19:06] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [02:19:06] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [02:19:06] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [02:19:06] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [02:19:06] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [02:19:06] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [02:19:06] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [02:19:06] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [02:19:06] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [02:19:06] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [02:19:06] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [02:19:06] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [02:19:06] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [02:19:06] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [02:19:06] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [02:19:06] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [02:19:06] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [02:19:06] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [02:19:06] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [02:19:06] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -109: [02:19:06] +110: ......... +110: ---------------------------------------------------------------------- +110: Ran 9 tests in 0.067s +110: +110: OK +109: [11:06:02] 109: 109: **** 109: Invariant Violation @@ -24177,20 +24090,19 @@ 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# 0x0000FFFFBC571948 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu//lib/libRDKitFragCatalog.so.1 +109: 2# 0x0000FFFF80FD1948 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# 0x0000AAAAD3047B08 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FragCatalog/testFragCatalog -109: 5# 0x0000AAAAD3044960 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FragCatalog/testFragCatalog -109: 6# 0x0000FFFFBBB3229C in /lib/aarch64-linux-gnu/libc.so.6 +109: 4# 0x0000AAAACA367B08 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FragCatalog/testFragCatalog +109: 5# 0x0000AAAACA364960 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FragCatalog/testFragCatalog +109: 6# 0x0000FFFF8059229C in /lib/aarch64-linux-gnu/libc.so.6 109: 7# __libc_start_main in /lib/aarch64-linux-gnu/libc.so.6 -109: 8# 0x0000AAAAD3044B30 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FragCatalog/testFragCatalog +109: 8# 0x0000AAAACA364B30 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FragCatalog/testFragCatalog 109: ---------- 109: **** 109: -109: [02:19:06] +109: [11:06:02] 109: 109: **** -115: [02:19:06] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 109: Invariant Violation 109: nonsense no new line 109: Violation occurred on line 52 in file ./Code/GraphMol/FragCatalog/FragCatalogUtils.cpp @@ -24199,17 +24111,17 @@ 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# 0x0000FFFFBC571948 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu//lib/libRDKitFragCatalog.so.1 +109: 2# 0x0000FFFF80FD1948 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# 0x0000AAAAD3047B08 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FragCatalog/testFragCatalog -109: 5# 0x0000AAAAD3044960 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FragCatalog/testFragCatalog -109: 6# 0x0000FFFFBBB3229C in /lib/aarch64-linux-gnu/libc.so.6 +109: 4# 0x0000AAAACA367B08 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FragCatalog/testFragCatalog +109: 5# 0x0000AAAACA364960 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FragCatalog/testFragCatalog +109: 6# 0x0000FFFF8059229C in /lib/aarch64-linux-gnu/libc.so.6 109: 7# __libc_start_main in /lib/aarch64-linux-gnu/libc.so.6 -109: 8# 0x0000AAAAD3044B30 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FragCatalog/testFragCatalog +109: 8# 0x0000AAAACA364B30 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FragCatalog/testFragCatalog 109: ---------- 109: **** 109: -109: [02:19:06] +109: [11:06:02] 109: 109: **** 109: Invariant Violation @@ -24220,433 +24132,808 @@ 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# 0x0000FFFFBC571948 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu//lib/libRDKitFragCatalog.so.1 +109: 2# 0x0000FFFF80FD1948 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# 0x0000AAAAD3047B08 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FragCatalog/testFragCatalog -109: 5# 0x0000AAAAD3044960 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FragCatalog/testFragCatalog -109: 6# 0x0000FFFFBBB3229C in /lib/aarch64-linux-gnu/libc.so.6 +109: 4# 0x0000AAAACA367B08 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FragCatalog/testFragCatalog +109: 5# 0x0000AAAACA364960 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FragCatalog/testFragCatalog +109: 6# 0x0000FFFF8059229C in /lib/aarch64-linux-gnu/libc.so.6 109: 7# __libc_start_main in /lib/aarch64-linux-gnu/libc.so.6 -109: 8# 0x0000AAAAD3044B30 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FragCatalog/testFragCatalog +109: 8# 0x0000AAAACA364B30 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FragCatalog/testFragCatalog 109: ---------- 109: **** 109: -115: [02:19:06] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -104/238 Test #109: testFragCatalog ........................ Passed 0.44 sec +101/238 Test #109: testFragCatalog ........................ Passed 0.41 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 +102/238 Test #113: testATF ................................ Passed 0.02 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: [11:06:02] ------------------------------------- +114: [11:06:02] Basic BCUT tests. +114: [11:06:02] done +114: [11:06:02] ------------------------------------- +114: [11:06:02] Larger BCUT tests. +103/238 Test #110: pyFragCatalog .......................... Passed 0.42 sec +test 115 + Start 115: testEEM + +115: Test command: /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/Descriptors/testEEM +115: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/Descriptors +115: Test timeout computed to be: 1500 +98: . +98: ---------------------------------------------------------------------- +98: Ran 11 tests in 1.007s +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 0.0653073787689209 seconds +98: Skipped 10000000 in 0.5098130702972412 seconds +98: Skipped 10000000 in 0.1644582748413086 seconds +115: =>start test EEM +115: [11:06:02] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: 0 +115: [11:06:02] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [11:06:02] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [11:06:02] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [11:06:02] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [11:06:02] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [11:06:02] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [11:06:02] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [11:06:02] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [11:06:02] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [11:06:02] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [11:06:02] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [11:06:02] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [11:06:02] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [11:06:02] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [11:06:02] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [11:06:02] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [11:06:02] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [11:06:02] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [11:06:02] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [11:06:02] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [11:06:02] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [11:06:02] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [11:06:02] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [11:06:02] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [11:06:02] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [11:06:02] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [11:06:02] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [11:06:02] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [11:06:02] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [11:06:02] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [11:06:02] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [11:06:02] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [11:06:02] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [11:06:02] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [11:06:02] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [11:06:02] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [11:06:02] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [11:06:03] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [11:06:03] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [11:06:03] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [11:06:03] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [11:06:03] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [11:06:03] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [11:06:03] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [11:06:03] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [11:06:03] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [11:06:03] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [11:06:03] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [11:06:03] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [11:06:03] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [11:06:03] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [11:06:03] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [11:06:03] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [11:06:03] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [11:06:03] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [11:06:03] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [11:06:03] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +112: [11:06:03] done +115: [11:06:03] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +112: [11:06:03] ------------------------------------- +112: [11:06:03] Test Github #3806: NaNs from AUTOCORR2D descriptor +112: [11:06:03] done +115: [11:06:03] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [11:06:03] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [11:06:03] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [11:06:03] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [11:06:03] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [11:06:03] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [11:06:03] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [11:06:03] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [11:06:03] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [11:06:03] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [11:06:03] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +104/238 Test #112: testAUTOCORR2D ......................... Passed 0.41 sec +115: [11:06:03] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. test 116 Start 116: testPBF 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: [02:19:06] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [02:19:06] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [02:19:06] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [02:19:06] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [02:19:06] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [02:19:06] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [02:19:06] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -116: [02:19:06] ------------------------------------- -116: [02:19:06] Basic PBF tests. -115: [02:19:06] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [02:19:06] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [02:19:06] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [02:19:06] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [02:19:06] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [02:19:06] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [02:19:06] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [02:19:06] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [02:19:06] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [02:19:06] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [02:19:06] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [02:19:06] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [02:19:06] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [02:19:06] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [02:19:06] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [02:19:06] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [02:19:06] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [02:19:06] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [02:19:06] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [02:19:06] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [11:06:03] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [11:06:03] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [11:06:03] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [11:06:03] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [11:06:03] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [11:06:03] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [11:06:03] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [11:06:03] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [11:06:03] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [11:06:03] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [11:06:03] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [11:06:03] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [11:06:03] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [11:06:03] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [11:06:03] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [11:06:03] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [11:06:03] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [11:06:03] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [11:06:03] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [11:06:03] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [11:06:03] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [11:06:03] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [11:06:03] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [11:06:03] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [11:06:03] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [11:06:03] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [11:06:03] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [11:06:03] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [11:06:03] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [11:06:03] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 115: 100 -115: [02:19:06] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [02:19:06] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [02:19:06] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [02:19:06] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [02:19:06] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [02:19:06] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [02:19:06] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [02:19:06] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [02:19:06] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [02:19:06] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [02:19:06] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [02:19:06] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [02:19:06] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [02:19:06] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [02:19:06] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [02:19:06] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [02:19:06] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [02:19:06] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [02:19:06] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [02:19:06] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [02:19:06] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [02:19:06] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [02:19:06] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [02:19:06] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [02:19:06] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [02:19:06] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [02:19:06] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [02:19:06] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [02:19:06] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [02:19:06] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [02:19:06] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -112: [02:19:06] done -115: [02:19:06] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -112: [02:19:06] ------------------------------------- -112: [02:19:06] Test Github #3806: NaNs from AUTOCORR2D descriptor -112: [02:19:06] done -115: [02:19:06] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [02:19:06] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -105/238 Test #112: testAUTOCORR2D ......................... Passed 0.41 sec -115: [02:19:06] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [11:06:03] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [11:06:03] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [11:06:03] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [11:06:03] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [11:06:03] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +105/238 Test #98: pyChemReactionEnumerations ............. Passed 1.30 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: [02:19:06] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [02:19:06] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [02:19:06] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [02:19:06] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [02:19:06] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [02:19:06] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [02:19:06] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [02:19:06] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [02:19:06] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [02:19:06] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [02:19:06] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [02:19:06] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [02:19:06] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [02:19:06] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [02:19:06] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [02:19:06] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [02:19:06] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [02:19:06] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [02:19:06] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [02:19:06] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [02:19:06] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [02:19:06] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [02:19:06] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [02:19:06] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [02:19:06] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [02:19:06] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [02:19:06] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [02:19:06] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [02:19:06] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [02:19:06] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [02:19:06] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [02:19:06] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [02:19:06] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [02:19:06] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [02:19:06] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [02:19:06] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [02:19:06] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [02:19:06] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [02:19:06] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -108: .............[02:19:06] SMILES Parse Error: syntax error while parsing: --- -108: [02:19:06] SMILES Parse Error: check for mistakes around position 1: -108: [02:19:06] --- -108: [02:19:06] ^ -108: [02:19:06] SMILES Parse Error: Failed parsing SMILES '---' for input: '---' -108: [02:19:06] dasfsadf -108: [02:19:06] SMILES Parse Error: syntax error while parsing: --- -108: [02:19:06] SMILES Parse Error: check for mistakes around position 1: -108: [02:19:06] --- -108: [02:19:06] ^ -108: [02:19:06] SMILES Parse Error: Failed parsing SMILES '---' for input: '---' -108: [02:19:06] dasfsadf -108: [02:19:06] SMILES Parse Error: syntax error while parsing: --- -108: [02:19:06] SMILES Parse Error: check for mistakes around position 1: -108: [02:19:06] --- -108: [02:19:06] ^ -108: [02:19:06] SMILES Parse Error: Failed parsing SMILES '---' for input: '---' -108: [02:19:06] dasfsadf -108: [02:19:06] SMILES Parse Error: syntax error while parsing: --- -108: [02:19:06] SMILES Parse Error: check for mistakes around position 1: -108: [02:19:06] --- -108: [02:19:06] ^ -108: [02:19:06] SMILES Parse Error: Failed parsing SMILES '---' for input: '---' -108: [02:19:06] dasfsadf -108: [02:19:06] SMILES Parse Error: syntax error while parsing: --- -108: [02:19:06] SMILES Parse Error: check for mistakes around position 1: -108: [02:19:06] --- -108: [02:19:06] ^ -108: [02:19:06] SMILES Parse Error: Failed parsing SMILES '---' for input: '---' -108: [02:19:06] dasfsadf -108: [02:19:06] SMILES Parse Error: syntax error while parsing: --- -108: [02:19:06] SMILES Parse Error: check for mistakes around position 1: -108: [02:19:06] --- -108: [02:19:06] ^ -108: [02:19:06] SMILES Parse Error: Failed parsing SMILES '---' for input: '---' -108: [02:19:06] dasfsadf -108: [02:19:06] SMILES Parse Error: syntax error while parsing: --- -108: [02:19:06] SMILES Parse Error: check for mistakes around position 1: -108: [02:19:06] --- -108: [02:19:06] ^ -108: [02:19:06] SMILES Parse Error: Failed parsing SMILES '---' for input: '---' -108: [02:19:06] dasfsadf -108: [02:19:06] SMILES Parse Error: syntax error while parsing: --- -108: [02:19:06] SMILES Parse Error: check for mistakes around position 1: -108: [02:19:06] --- -108: [02:19:06] ^ -108: [02:19:06] SMILES Parse Error: Failed parsing SMILES '---' for input: '---' -108: [02:19:06] dasfsadf -108: [02:19:06] SMILES Parse Error: syntax error while parsing: --- -108: [02:19:06] SMILES Parse Error: check for mistakes around position 1: -108: [02:19:06] --- -108: [02:19:06] ^ -108: [02:19:06] SMILES Parse Error: Failed parsing SMILES '---' for input: '---' -108: [02:19:06] dasfsadf -108: [02:19:06] SMILES Parse Error: syntax error while parsing: --- -108: [02:19:06] SMILES Parse Error: check for mistakes around position 1: -108: [02:19:06] --- -108: [02:19:06] ^ -108: [02:19:06] SMILES Parse Error: Failed parsing SMILES '---' for input: '---' -108: [02:19:06] dasfsadf -115: [02:19:06] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -108: [02:19:06] SMILES Parse Error: syntax error while parsing: --- -115: [02:19:06] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -108: [02:19:06] SMILES Parse Error: check for mistakes around position 1: -108: [02:19:06] --- -108: [02:19:06] ^ -108: [02:19:06] SMILES Parse Error: Failed parsing SMILES '---' for input: '---' -108: [02:19:06] dasfsadf -115: [02:19:06] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -108: [02:19:06] SMILES Parse Error: syntax error while parsing: --- -108: [02:19:06] SMILES Parse Error: check for mistakes around position 1: -108: [02:19:06] --- -108: [02:19:06] ^ -108: [02:19:06] SMILES Parse Error: Failed parsing SMILES '---' for input: '---' -108: [02:19:06] dasfsadf -108: [02:19:06] SMILES Parse Error: syntax error while parsing: --- -108: [02:19:06] SMILES Parse Error: check for mistakes around position 1: -108: [02:19:06] --- -108: [02:19:06] ^ -108: [02:19:06] SMILES Parse Error: Failed parsing SMILES '---' for input: '---' -108: [02:19:06] dasfsadf -108: [02:19:06] SMILES Parse Error: syntax error while parsing: --- -108: [02:19:06] SMILES Parse Error: check for mistakes around position 1: -108: [02:19:06] --- -108: [02:19:06] ^ -108: [02:19:06] SMILES Parse Error: Failed parsing SMILES '---' for input: '---' -108: [02:19:06] dasfsadf -108: [02:19:06] SMILES Parse Error: syntax error while parsing: --- -108: [02:19:06] SMILES Parse Error: check for mistakes around position 1: -108: [02:19:06] --- -108: [02:19:06] ^ -108: [02:19:06] SMILES Parse Error: Failed parsing SMILES '---' for input: '---' -108: [02:19:06] dasfsadf -108: [02:19:06] SMILES Parse Error: syntax error while parsing: --- -108: [02:19:06] SMILES Parse Error: check for mistakes around position 1: -108: [02:19:06] --- -108: [02:19:06] ^ -108: [02:19:06] SMILES Parse Error: Failed parsing SMILES '---' for input: '---' -108: [02:19:06] dasfsadf -108: [02:19:06] SMILES Parse Error: syntax error while parsing: --- -108: [02:19:06] SMILES Parse Error: check for mistakes around position 1: -108: [02:19:06] --- -108: [02:19:06] ^ -108: [02:19:06] SMILES Parse Error: Failed parsing SMILES '---' for input: '---' -108: [02:19:06] dasfsadf -108: [02:19:06] SMILES Parse Error: syntax error while parsing: --- -108: [02:19:06] SMILES Parse Error: check for mistakes around position 1: -108: [02:19:06] --- -108: [02:19:06] ^ -108: [02:19:06] SMILES Parse Error: Failed parsing SMILES '---' for input: '---' -108: [02:19:06] dasfsadf -108: [02:19:06] SMILES Parse Error: syntax error while parsing: --- -108: [02:19:06] SMILES Parse Error: check for mistakes around position 1: -108: [02:19:06] --- -108: [02:19:06] ^ -108: [02:19:06] SMILES Parse Error: Failed parsing SMILES '---' for input: '---' -108: [02:19:06] dasfsadf -115: [02:19:06] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -108: [02:19:06] SMILES Parse Error: syntax error while parsing: --- -108: [02:19:06] SMILES Parse Error: check for mistakes around position 1: -108: [02:19:06] --- -108: [02:19:06] ^ -108: [02:19:06] SMILES Parse Error: Failed parsing SMILES '---' for input: '---' -108: [02:19:06] dasfsadf -108: [02:19:06] SMILES Parse Error: syntax error while parsing: --- -108: [02:19:06] SMILES Parse Error: check for mistakes around position 1: -108: [02:19:06] --- -108: [02:19:06] ^ -108: [02:19:06] SMILES Parse Error: Failed parsing SMILES '---' for input: '---' -108: [02:19:06] dasfsadf -108: [02:19:06] SMILES Parse Error: syntax error while parsing: --- -108: [02:19:06] SMILES Parse Error: check for mistakes around position 1: -108: [02:19:06] --- -108: [02:19:06] ^ -108: [02:19:06] SMILES Parse Error: Failed parsing SMILES '---' for input: '---' -108: [02:19:06] dasfsadf -108: [02:19:06] SMILES Parse Error: syntax error while parsing: --- -108: [02:19:06] SMILES Parse Error: check for mistakes around position 1: -108: [02:19:06] --- -108: [02:19:06] ^ -108: [02:19:06] SMILES Parse Error: Failed parsing SMILES '---' for input: '---' -108: [02:19:06] dasfsadf -108: [02:19:06] SMILES Parse Error: syntax error while parsing: --- -108: [02:19:06] SMILES Parse Error: check for mistakes around position 1: -108: [02:19:06] --- -108: [02:19:06] ^ -108: [02:19:06] SMILES Parse Error: Failed parsing SMILES '---' for input: '---' -108: [02:19:06] dasfsadf -108: [02:19:06] SMILES Parse Error: syntax error while parsing: --- -108: [02:19:06] SMILES Parse Error: check for mistakes around position 1: -108: [02:19:06] --- -108: [02:19:06] ^ -108: [02:19:06] SMILES Parse Error: Failed parsing SMILES '---' for input: '---' -108: [02:19:06] dasfsadf -108: [02:19:06] SMILES Parse Error: syntax error while parsing: --- -108: [02:19:06] SMILES Parse Error: check for mistakes around position 1: -108: [02:19:06] --- -108: [02:19:06] ^ -108: [02:19:06] SMILES Parse Error: Failed parsing SMILES '---' for input: '---' -108: [02:19:06] dasfsadf -115: [02:19:06] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -108: [02:19:06] SMILES Parse Error: syntax error while parsing: --- -108: [02:19:06] SMILES Parse Error: check for mistakes around position 1: -108: [02:19:06] --- -108: [02:19:06] ^ -108: [02:19:06] SMILES Parse Error: Failed parsing SMILES '---' for input: '---' -108: [02:19:06] dasfsadf -115: [02:19:06] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -108: [02:19:06] SMILES Parse Error: syntax error while parsing: --- -108: [02:19:06] SMILES Parse Error: check for mistakes around position 1: -108: [02:19:06] --- -108: [02:19:06] ^ -108: [02:19:06] SMILES Parse Error: Failed parsing SMILES '---' for input: '---' -108: [02:19:06] dasfsadf -108: [02:19:06] SMILES Parse Error: syntax error while parsing: --- -108: [02:19:06] SMILES Parse Error: check for mistakes around position 1: -108: [02:19:06] --- -108: [02:19:06] ^ -108: [02:19:06] SMILES Parse Error: Failed parsing SMILES '---' for input: '---' -108: [02:19:06] dasfsadf -108: [02:19:06] SMILES Parse Error: syntax error while parsing: --- -108: [02:19:06] SMILES Parse Error: check for mistakes around position 1: -108: [02:19:06] --- -108: [02:19:06] ^ -108: [02:19:06] SMILES Parse Error: Failed parsing SMILES '---' for input: '---' -108: [02:19:06] dasfsadf -115: [02:19:06] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [02:19:06] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [02:19:06] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [02:19:06] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [02:19:06] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [02:19:06] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [02:19:06] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [02:19:06] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [02:19:06] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [02:19:06] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [02:19:06] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [02:19:06] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [02:19:06] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [02:19:06] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [02:19:06] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [02:19:06] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [02:19:06] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [02:19:06] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [02:19:06] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [02:19:06] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [11:06:03] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [11:06:03] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [11:06:03] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [11:06:03] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [11:06:03] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [11:06:03] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [11:06:03] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [11:06:03] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [11:06:03] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [11:06:03] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [11:06:03] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [11:06:03] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [11:06:03] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [11:06:03] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [11:06:03] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [11:06:03] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [11:06:03] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [11:06:03] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [11:06:03] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +116: [11:06:03] ------------------------------------- +116: [11:06:03] Basic PBF tests. +115: [11:06:03] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [11:06:03] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [11:06:03] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [11:06:03] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [11:06:03] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [11:06:03] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [11:06:03] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [11:06:03] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [11:06:03] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [11:06:03] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [11:06:03] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [11:06:03] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [11:06:03] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [11:06:03] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [11:06:03] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [11:06:03] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [11:06:03] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [11:06:03] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [11:06:03] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [11:06:03] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [11:06:03] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [11:06:03] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [11:06:03] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [11:06:03] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [11:06:03] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [11:06:03] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [11:06:03] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [11:06:03] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [11:06:03] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [11:06:03] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [11:06:03] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [11:06:03] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [11:06:03] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [11:06:03] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [11:06:03] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [11:06:03] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [11:06:03] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [11:06:03] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [11:06:03] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [11:06:03] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [11:06:03] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [11:06:03] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [11:06:03] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [11:06:03] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [11:06:03] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [11:06:03] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [11:06:03] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [11:06:03] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [11:06:03] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [11:06:03] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [11:06:03] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [11:06:03] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [11:06:03] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [11:06:03] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [11:06:03] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [11:06:03] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [11:06:03] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [11:06:03] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [11:06:03] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [11:06:03] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [11:06:03] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [11:06:03] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [11:06:03] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [11:06:03] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [11:06:03] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [11:06:03] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [11:06:03] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [11:06:03] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [11:06:03] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [11:06:03] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [11:06:03] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [11:06:03] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [11:06:03] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [11:06:03] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [11:06:03] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [11:06:03] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 115: 200 -115: [02:19:06] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [02:19:06] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [02:19:06] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [02:19:06] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [02:19:06] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [02:19:06] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [02:19:06] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [02:19:06] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [02:19:06] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [02:19:06] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [02:19:06] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [02:19:06] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [02:19:06] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [02:19:06] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -108: .[02:19:06] SMILES Parse Error: syntax error while parsing: mydoghasfleas -108: [02:19:06] SMILES Parse Error: check for mistakes around position 1: -108: [02:19:06] mydoghasfleas -108: [02:19:06] ^ -108: [02:19:06] SMILES Parse Error: Failed parsing SMILES 'mydoghasfleas' for input: 'mydoghasfleas' -116: [02:19:06] done -116: [02:19:06] ------------------------------------- -116: [02:19:06] PBF edge cases. -115: [02:19:06] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -116: [02:19:06] done -115: [02:19:06] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -106/238 Test #116: testPBF ................................ Passed 0.21 sec +115: [11:06:03] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [11:06:03] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [11:06:03] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [11:06:03] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [11:06:03] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [11:06:03] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [11:06:03] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [11:06:03] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [11:06:03] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [11:06:03] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [11:06:03] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [11:06:03] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [11:06:03] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [11:06:03] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [11:06:03] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [11:06:03] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [11:06:03] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [11:06:03] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [11:06:03] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [11:06:03] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [11:06:03] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [11:06:03] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [11:06:03] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [11:06:03] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [11:06:03] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [11:06:03] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [11:06:03] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [11:06:03] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [11:06:03] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [11:06:03] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [11:06:03] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [11:06:03] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [11:06:03] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [11:06:03] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [11:06:03] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [11:06:03] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [11:06:03] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [11:06:03] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [11:06:03] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [11:06:03] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [11:06:03] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [11:06:03] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [11:06:03] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [11:06:03] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [11:06:03] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [11:06:03] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [11:06:03] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [11:06:03] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [11:06:03] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [11:06:03] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [11:06:03] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [11:06:03] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [11:06:03] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [11:06:03] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [11:06:03] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [11:06:03] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [11:06:03] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [11:06:03] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [11:06:03] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [11:06:03] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [11:06:03] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [11:06:03] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [11:06:03] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [11:06:03] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [11:06:03] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [11:06:03] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [11:06:03] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [11:06:03] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [11:06:03] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [11:06:03] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [11:06:03] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [11:06:03] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [11:06:03] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [11:06:03] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [11:06:03] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [11:06:03] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [11:06:03] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [11:06:03] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [11:06:03] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [11:06:03] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [11:06:03] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [11:06:03] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [11:06:03] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [11:06:03] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [11:06:03] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [11:06:03] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [11:06:03] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [11:06:03] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [11:06:03] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [11:06:03] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [11:06:03] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [11:06:03] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [11:06:03] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [11:06:03] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [11:06:03] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [11:06:03] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [11:06:03] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +114: [11:06:03] ------------------------------------- +114: [11:06:03] Test empty molecule BCUT. +115: [11:06:03] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [11:06:03] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [11:06:03] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: 300 +115: [11:06:03] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +106/238 Test #114: testBCUT ............................... Passed 0.34 sec +115: [11:06:03] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 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: [02:19:06] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [02:19:06] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [02:19:06] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [02:19:06] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [02:19:06] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [02:19:06] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [02:19:06] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [02:19:06] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [02:19:06] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [02:19:06] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [02:19:06] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [02:19:06] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [02:19:06] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [02:19:06] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [02:19:06] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [02:19:06] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [02:19:06] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [02:19:06] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [02:19:06] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [02:19:06] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [02:19:06] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [02:19:06] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [02:19:06] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [02:19:06] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [02:19:06] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [02:19:06] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [02:19:06] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [02:19:06] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [02:19:06] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [02:19:06] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [02:19:06] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [02:19:06] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [02:19:06] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [02:19:06] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [02:19:06] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [02:19:06] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [02:19:06] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [02:19:06] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [02:19:06] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [02:19:06] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [02:19:06] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [02:19:06] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [02:19:06] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [02:19:06] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [02:19:06] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [02:19:06] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [02:19:06] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [02:19:06] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [02:19:06] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [02:19:06] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [02:19:06] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [02:19:06] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [11:06:03] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [11:06:03] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [11:06:03] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [11:06:03] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [11:06:03] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [11:06:03] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [11:06:03] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [11:06:03] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [11:06:03] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [11:06:03] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [11:06:03] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [11:06:03] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [11:06:03] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [11:06:03] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [11:06:03] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [11:06:03] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [11:06:03] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [11:06:03] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [11:06:03] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [11:06:03] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [11:06:03] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [11:06:03] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [11:06:03] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [11:06:03] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [11:06:03] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [11:06:03] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [11:06:03] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [11:06:03] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [11:06:03] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [11:06:03] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [11:06:03] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [11:06:03] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [11:06:03] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [11:06:03] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [11:06:03] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [11:06:03] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [11:06:03] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [11:06:03] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [11:06:03] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [11:06:03] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [11:06:03] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [11:06:03] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [11:06:03] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [11:06:03] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [11:06:03] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [11:06:03] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [11:06:03] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [11:06:03] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [11:06:03] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [11:06:03] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [11:06:03] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [11:06:03] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [11:06:03] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [11:06:03] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [11:06:03] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [11:06:03] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [11:06:03] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [11:06:03] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [11:06:03] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [11:06:03] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [11:06:03] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [11:06:03] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [11:06:03] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [11:06:03] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [11:06:03] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [11:06:03] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [11:06:03] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [11:06:03] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [11:06:03] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [11:06:03] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [11:06:03] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [11:06:03] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [11:06:03] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [11:06:03] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [11:06:03] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [11:06:03] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [11:06:03] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +116: [11:06:03] done +116: [11:06:03] ------------------------------------- +116: [11:06:03] PBF edge cases. +116: [11:06:03] done +115: [11:06:03] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [11:06:03] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [11:06:03] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [11:06:03] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [11:06:03] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [11:06:03] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +107/238 Test #116: testPBF ................................ Passed 0.24 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 +108: .............[11:06:03] SMILES Parse Error: syntax error while parsing: --- +108: [11:06:03] SMILES Parse Error: check for mistakes around position 1: +108: [11:06:03] --- +108: [11:06:03] ^ +108: [11:06:03] SMILES Parse Error: Failed parsing SMILES '---' for input: '---' +108: [11:06:03] dasfsadf +108: [11:06:03] SMILES Parse Error: syntax error while parsing: --- +108: [11:06:03] SMILES Parse Error: check for mistakes around position 1: +108: [11:06:03] --- +108: [11:06:03] ^ +108: [11:06:03] SMILES Parse Error: Failed parsing SMILES '---' for input: '---' +108: [11:06:03] dasfsadf +108: [11:06:03] SMILES Parse Error: syntax error while parsing: --- +108: [11:06:03] SMILES Parse Error: check for mistakes around position 1: +108: [11:06:03] --- +108: [11:06:03] ^ +108: [11:06:03] SMILES Parse Error: Failed parsing SMILES '---' for input: '---' +108: [11:06:03] dasfsadf +108: [11:06:03] SMILES Parse Error: syntax error while parsing: --- +108: [11:06:03] SMILES Parse Error: check for mistakes around position 1: +108: [11:06:03] --- +108: [11:06:03] ^ +108: [11:06:03] SMILES Parse Error: Failed parsing SMILES '---' for input: '---' +108: [11:06:03] dasfsadf +108: [11:06:03] SMILES Parse Error: syntax error while parsing: --- +108: [11:06:03] SMILES Parse Error: check for mistakes around position 1: +108: [11:06:03] --- +108: [11:06:03] ^ +108: [11:06:03] SMILES Parse Error: Failed parsing SMILES '---' for input: '---' +108: [11:06:03] dasfsadf +108: [11:06:03] SMILES Parse Error: syntax error while parsing: --- +108: [11:06:03] SMILES Parse Error: check for mistakes around position 1: +108: [11:06:03] --- +108: [11:06:03] ^ +108: [11:06:03] SMILES Parse Error: Failed parsing SMILES '---' for input: '---' +108: [11:06:03] dasfsadf +108: [11:06:03] SMILES Parse Error: syntax error while parsing: --- +108: [11:06:03] SMILES Parse Error: check for mistakes around position 1: +108: [11:06:03] --- +108: [11:06:03] ^ +108: [11:06:03] SMILES Parse Error: Failed parsing SMILES '---' for input: '---' +108: [11:06:03] dasfsadf +108: [11:06:03] SMILES Parse Error: syntax error while parsing: --- +108: [11:06:03] SMILES Parse Error: check for mistakes around position 1: +108: [11:06:03] --- +108: [11:06:03] ^ +108: [11:06:03] SMILES Parse Error: Failed parsing SMILES '---' for input: '---' +108: [11:06:03] dasfsadf +108: [11:06:03] SMILES Parse Error: syntax error while parsing: --- +108: [11:06:03] SMILES Parse Error: check for mistakes around position 1: +108: [11:06:03] --- +108: [11:06:03] ^ +108: [11:06:03] SMILES Parse Error: Failed parsing SMILES '---' for input: '---' +108: [11:06:03] dasfsadf +108: [11:06:03] SMILES Parse Error: syntax error while parsing: --- +108: [11:06:03] SMILES Parse Error: check for mistakes around position 1: +108: [11:06:03] --- +108: [11:06:03] ^ +108: [11:06:03] SMILES Parse Error: Failed parsing SMILES '---' for input: '---' +108: [11:06:03] dasfsadf +108: [11:06:03] SMILES Parse Error: syntax error while parsing: --- +108: [11:06:03] SMILES Parse Error: check for mistakes around position 1: +108: [11:06:03] --- +108: [11:06:03] ^ +108: [11:06:03] SMILES Parse Error: Failed parsing SMILES '---' for input: '---' +108: [11:06:03] dasfsadf +108: [11:06:03] SMILES Parse Error: syntax error while parsing: --- +108: [11:06:03] SMILES Parse Error: check for mistakes around position 1: +108: [11:06:03] --- +108: [11:06:03] ^ +108: [11:06:03] SMILES Parse Error: Failed parsing SMILES '---' for input: '---' +108: [11:06:03] dasfsadf +108: [11:06:03] SMILES Parse Error: syntax error while parsing: --- +108: [11:06:03] SMILES Parse Error: check for mistakes around position 1: +108: [11:06:03] --- +108: [11:06:03] ^ +108: [11:06:03] SMILES Parse Error: Failed parsing SMILES '---' for input: '---' +108: [11:06:03] dasfsadf +108: [11:06:03] SMILES Parse Error: syntax error while parsing: --- +108: [11:06:03] SMILES Parse Error: check for mistakes around position 1: +108: [11:06:03] --- +108: [11:06:03] ^ +108: [11:06:03] SMILES Parse Error: Failed parsing SMILES '---' for input: '---' +108: [11:06:03] dasfsadf +115: [11:06:03] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [11:06:03] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [11:06:03] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [11:06:03] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [11:06:03] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [11:06:03] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [11:06:03] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [11:06:03] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [11:06:03] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [11:06:03] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [11:06:03] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [11:06:03] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [11:06:03] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [11:06:03] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [11:06:03] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: 400 +115: [11:06:03] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [11:06:03] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [11:06:03] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +108: [11:06:03] SMILES Parse Error: syntax error while parsing: --- +108: [11:06:03] SMILES Parse Error: check for mistakes around position 1: +108: [11:06:03] --- +108: [11:06:03] ^ +108: [11:06:03] SMILES Parse Error: Failed parsing SMILES '---' for input: '---' +108: [11:06:03] dasfsadf +108: [11:06:03] SMILES Parse Error: syntax error while parsing: --- +108: [11:06:03] SMILES Parse Error: check for mistakes around position 1: +108: [11:06:03] --- +108: [11:06:03] ^ +108: [11:06:03] SMILES Parse Error: Failed parsing SMILES '---' for input: '---' +108: [11:06:03] dasfsadf +108: [11:06:03] SMILES Parse Error: syntax error while parsing: --- +108: [11:06:03] SMILES Parse Error: check for mistakes around position 1: +108: [11:06:03] --- +108: [11:06:03] ^ +108: [11:06:03] SMILES Parse Error: Failed parsing SMILES '---' for input: '---' +108: [11:06:03] dasfsadf +108: [11:06:03] SMILES Parse Error: syntax error while parsing: --- +108: [11:06:03] SMILES Parse Error: check for mistakes around position 1: +108: [11:06:03] --- +108: [11:06:03] ^ +108: [11:06:03] SMILES Parse Error: Failed parsing SMILES '---' for input: '---' +108: [11:06:03] dasfsadf +108: [11:06:03] SMILES Parse Error: syntax error while parsing: --- +108: [11:06:03] SMILES Parse Error: check for mistakes around position 1: +108: [11:06:03] --- +108: [11:06:03] ^ +108: [11:06:03] SMILES Parse Error: Failed parsing SMILES '---' for input: '---' +108: [11:06:03] dasfsadf +108: [11:06:03] SMILES Parse Error: syntax error while parsing: --- +108: [11:06:03] SMILES Parse Error: check for mistakes around position 1: +108: [11:06:03] --- +108: [11:06:03] ^ +108: [11:06:03] SMILES Parse Error: Failed parsing SMILES '---' for input: '---' +108: [11:06:03] dasfsadf +108: [11:06:03] SMILES Parse Error: syntax error while parsing: --- +108: [11:06:03] SMILES Parse Error: check for mistakes around position 1: +108: [11:06:03] --- +108: [11:06:03] ^ +108: [11:06:03] SMILES Parse Error: Failed parsing SMILES '---' for input: '---' +108: [11:06:03] dasfsadf +108: [11:06:03] SMILES Parse Error: syntax error while parsing: --- +108: [11:06:03] SMILES Parse Error: check for mistakes around position 1: +108: [11:06:03] --- +108: [11:06:03] ^ +108: [11:06:03] SMILES Parse Error: Failed parsing SMILES '---' for input: '---' +108: [11:06:03] dasfsadf +108: [11:06:03] SMILES Parse Error: syntax error while parsing: --- +108: [11:06:03] SMILES Parse Error: check for mistakes around position 1: +108: [11:06:03] --- +108: [11:06:03] ^ +108: [11:06:03] SMILES Parse Error: Failed parsing SMILES '---' for input: '---' +108: [11:06:03] dasfsadf +108: [11:06:03] SMILES Parse Error: syntax error while parsing: --- +108: [11:06:03] SMILES Parse Error: check for mistakes around position 1: +108: [11:06:03] --- +108: [11:06:03] ^ +108: [11:06:03] SMILES Parse Error: Failed parsing SMILES '---' for input: '---' +108: [11:06:03] dasfsadf +108: [11:06:03] SMILES Parse Error: syntax error while parsing: --- +108: [11:06:03] SMILES Parse Error: check for mistakes around position 1: +108: [11:06:03] --- +108: [11:06:03] ^ +108: [11:06:03] SMILES Parse Error: Failed parsing SMILES '---' for input: '---' +108: [11:06:03] dasfsadf +115: [11:06:03] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [11:06:03] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +108: [11:06:03] SMILES Parse Error: syntax error while parsing: --- +108: [11:06:03] SMILES Parse Error: check for mistakes around position 1: +108: [11:06:03] --- +108: [11:06:03] ^ +108: [11:06:03] SMILES Parse Error: Failed parsing SMILES '---' for input: '---' +108: [11:06:03] dasfsadf +115: [11:06:03] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [11:06:03] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [11:06:03] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [11:06:03] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [11:06:03] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [11:06:03] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [11:06:03] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [11:06:03] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +108: [11:06:03] SMILES Parse Error: syntax error while parsing: --- +108: [11:06:03] SMILES Parse Error: check for mistakes around position 1: +108: [11:06:03] --- +108: [11:06:03] ^ +108: [11:06:03] SMILES Parse Error: Failed parsing SMILES '---' for input: '---' +108: [11:06:03] dasfsadf +108: [11:06:03] SMILES Parse Error: syntax error while parsing: --- +108: [11:06:03] SMILES Parse Error: check for mistakes around position 1: +108: [11:06:03] --- +108: [11:06:03] ^ +108: [11:06:03] SMILES Parse Error: Failed parsing SMILES '---' for input: '---' +108: [11:06:03] dasfsadf +108: [11:06:03] SMILES Parse Error: syntax error while parsing: --- +108: [11:06:03] SMILES Parse Error: check for mistakes around position 1: +108: [11:06:03] --- +108: [11:06:03] ^ +108: [11:06:03] SMILES Parse Error: Failed parsing SMILES '---' for input: '---' +108: [11:06:03] dasfsadf +108: [11:06:03] SMILES Parse Error: syntax error while parsing: --- +108: [11:06:03] SMILES Parse Error: check for mistakes around position 1: +108: [11:06:03] --- +108: [11:06:03] ^ +108: [11:06:03] SMILES Parse Error: Failed parsing SMILES '---' for input: '---' +108: [11:06:03] dasfsadf +115: [11:06:03] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [11:06:03] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [11:06:03] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [11:06:03] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [11:06:03] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [11:06:03] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [11:06:03] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [11:06:03] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [11:06:03] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [11:06:03] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [11:06:03] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [11:06:03] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [11:06:03] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [11:06:03] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [11:06:03] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [11:06:03] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [11:06:03] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [11:06:03] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [11:06:03] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [11:06:03] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [11:06:03] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [11:06:03] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [11:06:03] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [11:06:03] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [11:06:03] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [11:06:03] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [11:06:03] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [11:06:03] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [11:06:03] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [11:06:03] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [11:06:03] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [11:06:03] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [11:06:03] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [11:06:03] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [11:06:03] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [11:06:03] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [11:06:03] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [11:06:03] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [11:06:03] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [11:06:03] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [11:06:03] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [11:06:03] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [11:06:03] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [11:06:03] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [11:06:03] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [11:06:03] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [11:06:03] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [11:06:03] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [11:06:03] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [11:06:03] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [11:06:03] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [11:06:03] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [11:06:03] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [11:06:03] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [11:06:03] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [11:06:03] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [11:06:03] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [11:06:03] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [11:06:03] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [11:06:03] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [11:06:03] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [11:06:03] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [11:06:03] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [11:06:03] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [11:06:03] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [11:06:03] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [11:06:03] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [11:06:03] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [11:06:03] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [11:06:03] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [11:06:03] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [11:06:03] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [11:06:03] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [11:06:03] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [11:06:03] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [11:06:03] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [11:06:03] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [11:06:03] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [11:06:03] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [11:06:03] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [11:06:03] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [11:06:03] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [11:06:03] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [11:06:03] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [11:06:03] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [11:06:03] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: Elapsed time: 0.40885 s +115: Errors:0 +115: [11:06:03] test on : 500 molecules done +108/238 Test #115: testEEM ................................ Passed 0.43 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: .[11:06:03] SMILES Parse Error: syntax error while parsing: mydoghasfleas +108: [11:06:03] SMILES Parse Error: check for mistakes around position 1: +108: [11:06:03] mydoghasfleas +108: [11:06:03] ^ +108: [11:06:03] SMILES Parse Error: Failed parsing SMILES 'mydoghasfleas' for input: 'mydoghasfleas' +120: [11:06:03] ------------------------------------- +120: [11:06:03] Basic PMI tests. +117: =>start test rdf custom +117: [11:06:03] test on : 365 molecules done 108: ....... 108: ---------------------------------------------------------------------- -108: Ran 21 tests in 0.598s +108: Ran 21 tests in 0.935s 108: 108: OK 108: (Five aromatic carbons And (Not any of Five aromatic carbons)) @@ -24668,310 +24955,54 @@ 108: 1 108: 2 108: running -115: [02:19:06] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [02:19:06] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [02:19:06] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [02:19:06] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [02:19:06] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [02:19:06] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [02:19:06] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [02:19:06] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [02:19:06] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [02:19:06] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [02:19:06] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [02:19:06] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [02:19:06] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [02:19:06] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [02:19:06] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [02:19:06] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [02:19:06] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [02:19:06] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [02:19:06] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [02:19:06] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [02:19:06] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [02:19:06] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [02:19:06] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [02:19:06] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [02:19:06] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [02:19:06] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [02:19:06] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [02:19:06] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [02:19:06] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -114: [02:19:07] ------------------------------------- -114: [02:19:07] Test empty molecule BCUT. -107/238 Test #108: pyFilterCatalog ........................ Passed 0.84 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: [02:19:07] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [02:19:07] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [02:19:07] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: 300 -115: [02:19:07] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [02:19:07] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [02:19:07] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [02:19:07] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [02:19:07] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [02:19:07] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -108/238 Test #114: testBCUT ............................... Passed 0.58 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: [02:19:07] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [02:19:07] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [02:19:07] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [02:19:07] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [02:19:07] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [02:19:07] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [02:19:07] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [02:19:07] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [02:19:07] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [02:19:07] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -120: [02:19:07] ------------------------------------- -120: [02:19:07] Basic PMI tests. -115: [02:19:07] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [02:19:07] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [02:19:07] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [02:19:07] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [02:19:07] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [02:19:07] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [02:19:07] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [02:19:07] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [02:19:07] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [02:19:07] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [02:19:07] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [02:19:07] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [02:19:07] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [02:19:07] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [02:19:07] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [02:19:07] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [02:19:07] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [02:19:07] 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: [02:19:07] test on : 365 molecules done -115: [02:19:07] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [02:19:07] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [02:19:07] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [02:19:07] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [02:19:07] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [02:19:07] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [02:19:07] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [02:19:07] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [02:19:07] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [02:19:07] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [02:19:07] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [02:19:07] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [02:19:07] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [02:19:07] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [02:19:07] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [02:19:07] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [02:19:07] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [02:19:07] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [02:19:07] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [02:19:07] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [02:19:07] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [02:19:07] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [02:19:07] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [02:19:07] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [02:19:07] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [02:19:07] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [02:19:07] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [02:19:07] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [02:19:07] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [02:19:07] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [02:19:07] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [02:19:07] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [02:19:07] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [02:19:07] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [02:19:07] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [02:19:07] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [02:19:07] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [02:19:07] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [02:19:07] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [02:19:07] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [02:19:07] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [02:19:07] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [02:19:07] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [02:19:07] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [02:19:07] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [02:19:07] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [02:19:07] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [02:19:07] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [02:19:07] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [02:19:07] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [02:19:07] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [02:19:07] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [02:19:07] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [02:19:07] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [02:19:07] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [02:19:07] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [02:19:07] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [02:19:07] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [02:19:07] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [02:19:07] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [02:19:07] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [02:19:07] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [02:19:07] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [02:19:07] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [02:19:07] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [02:19:07] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: 400 -115: [02:19:07] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [02:19:07] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [02:19:07] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [02:19:07] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [02:19:07] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [02:19:07] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [02:19:07] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [02:19:07] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [02:19:07] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [02:19:07] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [02:19:07] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [02:19:07] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [02:19:07] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [02:19:07] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [02:19:07] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [02:19:07] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [02:19:07] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +120: [11:06:03] done +120: [11:06:03] ------------------------------------- +120: [11:06:03] More PMI/NPR tests. +120: [11:06:03] done +120: [11:06:03] ------------------------------------- +120: [11:06:03] Basic NPR tests. 118: =>start test rdf -115: [02:19:07] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -118: [02:19:07] test on : 365 molecules done -115: [02:19:07] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -109/238 Test #118: testRDF ................................ Passed 0.30 sec +118: [11:06:03] test on : 365 molecules done +109/238 Test #118: testRDF ................................ Passed 0.39 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 -115: [02:19:07] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [02:19:07] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [02:19:07] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [02:19:07] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [02:19:07] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [02:19:07] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [02:19:07] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [02:19:07] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [02:19:07] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [02:19:07] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [02:19:07] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [02:19:07] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [02:19:07] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [02:19:07] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [02:19:07] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [02:19:07] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [02:19:07] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [02:19:07] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [02:19:07] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [02:19:07] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [02:19:07] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [02:19:07] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [02:19:07] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [02:19:07] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [02:19:07] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [02:19:07] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [02:19:07] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [02:19:07] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [02:19:07] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [02:19:07] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [02:19:07] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [02:19:07] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [02:19:07] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [02:19:07] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [02:19:07] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [02:19:07] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [02:19:07] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [02:19:07] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [02:19:07] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [02:19:07] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [02:19:07] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [02:19:07] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [02:19:07] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [02:19:07] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [02:19:07] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [02:19:07] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [02:19:07] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [02:19:07] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [02:19:07] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [02:19:07] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [02:19:07] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [02:19:07] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [02:19:07] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [02:19:07] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [02:19:07] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [02:19:07] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [02:19:07] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [02:19:07] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [02:19:07] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [02:19:07] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [02:19:07] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [02:19:07] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [02:19:07] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [02:19:07] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [02:19:07] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [02:19:07] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -120: [02:19:07] done -120: [02:19:07] ------------------------------------- -120: [02:19:07] More PMI/NPR tests. -120: [02:19:07] done -120: [02:19:07] ------------------------------------- -120: [02:19:07] Basic NPR tests. -115: [02:19:07] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [02:19:07] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [02:19:07] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [02:19:07] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [02:19:07] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [02:19:07] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [02:19:07] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [02:19:07] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [02:19:07] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [02:19:07] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [02:19:07] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [02:19:07] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [02:19:07] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [02:19:07] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: Elapsed time: 0.753044 s -115: Errors:0 -115: [02:19:07] test on : 500 molecules done -110/238 Test #115: testEEM ................................ Passed 0.77 sec +110/238 Test #108: pyFilterCatalog ........................ Passed 1.26 sec test 122 Start 122: testGETAWAY 122: Test command: /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/Descriptors/testGETAWAY 122: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/Descriptors 122: Test timeout computed to be: 1500 -120: [02:19:07] done -120: [02:19:07] ------------------------------------- -120: [02:19:07] PMI edge cases. -120: [02:19:07] done -120: [02:19:07] ------------------------------------- -120: [02:19:07] NPR edge cases. -120: [02:19:07] done -120: [02:19:07] ------------------------------------- -120: [02:19:07] 3D descriptors. -120: [02:19:07] done -120: [02:19:07] ------------------------------------- -120: [02:19:07] 3D descriptor edge cases. -120: [02:19:07] done -120: [02:19:07] ------------------------------------- -120: [02:19:07] Inertial shape factor. -120: [02:19:07] done -111/238 Test #120: test3D ................................. Passed 0.50 sec +120: [11:06:03] done +120: [11:06:03] ------------------------------------- +120: [11:06:03] PMI edge cases. +120: [11:06:03] done +120: [11:06:03] ------------------------------------- +120: [11:06:03] NPR edge cases. +120: [11:06:03] done +120: [11:06:03] ------------------------------------- +120: [11:06:03] 3D descriptors. +120: [11:06:03] done +120: [11:06:03] ------------------------------------- +120: [11:06:03] 3D descriptor edge cases. +120: [11:06:03] done +120: [11:06:03] ------------------------------------- +120: [11:06:03] Inertial shape factor. +120: [11:06:03] done +111/238 Test #120: test3D ................................. Passed 0.27 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 -121: =>start test WHIM -121: [02:19:07] test on : 365 molecules done -112/238 Test #121: testWHIM ............................... Passed 0.35 sec +123: =>start test autocorr3D +123: [11:06:03] test on : 365 molecules done +112/238 Test #123: testAUTOCORR3D ......................... Passed 0.21 sec test 124 Start 124: testCoulombMat @@ -24980,63 +25011,172 @@ 124: Test timeout computed to be: 1500 124: ===================== Testing CoulombMat ======================= 124: CM test 1 mat Done -113/238 Test #124: testCoulombMat ......................... Passed 0.05 sec +113/238 Test #124: testCoulombMat ......................... Passed 0.02 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: 2153395763 +125: Randomness seeded to: 827492867 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 +121: =>start test WHIM +121: [11:06:03] test on : 365 molecules done 125: Warning: Atom Count for residue ASN157A does not match expected count -125: Warning: Atom Count for residue GLU5A does not match expected count -117: =>start test morse custom -117: [02:19:07] test on : 365 molecules done -119: =>start test MORSE -119: =>read file -119: [02:19:07] test on : 365 molecules done -114/238 Test #119: testMORSE .............................. Passed 0.82 sec +114/238 Test #121: testWHIM ............................... Passed 0.36 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 -123: =>start test autocorr3D -123: [02:19:07] test on : 365 molecules done -115/238 Test #123: testAUTOCORR3D ......................... Passed 0.35 sec +125: Warning: Atom Count for residue GLU5A does not match expected count +119: =>start test MORSE +119: =>read file +119: [11:06:04] test on : 365 molecules done +115/238 Test #119: testMORSE .............................. Passed 0.80 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 +117: =>start test morse custom +117: [11:06:04] test on : 365 molecules done 125: Warning: Atom Count for residue ASN39A does not match expected count -117: =>start test AUTOCORR3D custom -117: [02:19:07] test on : 365 molecules done 125: Warning: Atom Count for residue GLU53A does not match expected count -125: Warning: Atom Count for residue ARG64A does not match expected count 127: ........ 127: ---------------------------------------------------------------------- -127: Ran 8 tests in 0.096s +127: Ran 8 tests in 0.099s 127: 127: OK -117: =>start test 2 WHIM custom -117: [02:19:08] test on : 365 molecules done -116/238 Test #127: pyMolDescriptors3D ..................... Passed 0.33 sec +125: Warning: Atom Count for residue ARG64A does not match expected count +126: [11:06:04] DEPRECATION WARNING: please use AtomPairGenerator +126: [11:06:04] DEPRECATION WARNING: please use AtomPairGenerator +126: [11:06:04] DEPRECATION WARNING: please use AtomPairGenerator +126: [11:06:04] DEPRECATION WARNING: please use AtomPairGenerator +126: [11:06:04] DEPRECATION WARNING: please use AtomPairGenerator +126: [11:06:04] DEPRECATION WARNING: please use AtomPairGenerator +126: [11:06:04] DEPRECATION WARNING: please use AtomPairGenerator +126: [11:06:04] DEPRECATION WARNING: please use AtomPairGenerator +126: [11:06:04] DEPRECATION WARNING: please use AtomPairGenerator +126: [11:06:04] DEPRECATION WARNING: please use AtomPairGenerator +126: [11:06:04] DEPRECATION WARNING: please use AtomPairGenerator +126: [11:06:04] DEPRECATION WARNING: please use AtomPairGenerator +126: [11:06:04] DEPRECATION WARNING: please use TopologicalTorsionGenerator +126: [11:06:04] DEPRECATION WARNING: please use TopologicalTorsionGenerator +126: [11:06:04] DEPRECATION WARNING: please use TopologicalTorsionGenerator +126: [11:06:04] DEPRECATION WARNING: please use TopologicalTorsionGenerator +126: [11:06:04] DEPRECATION WARNING: please use TopologicalTorsionGenerator +126: [11:06:04] DEPRECATION WARNING: please use TopologicalTorsionGenerator +126: [11:06:04] DEPRECATION WARNING: please use TopologicalTorsionGenerator +126: [11:06:04] DEPRECATION WARNING: please use TopologicalTorsionGenerator +126: [11:06:04] DEPRECATION WARNING: please use TopologicalTorsionGenerator +126: [11:06:04] DEPRECATION WARNING: please use TopologicalTorsionGenerator +126: [11:06:04] DEPRECATION WARNING: please use TopologicalTorsionGenerator +126: [11:06:04] DEPRECATION WARNING: please use TopologicalTorsionGenerator +116/238 Test #127: pyMolDescriptors3D ..................... Passed 0.37 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 -125: Warning: Atom Count for residue LYS80A does not match expected count +126: ..[11:06:04] DEPRECATION WARNING: please use AtomPairGenerator +126: [11:06:04] DEPRECATION WARNING: please use AtomPairGenerator +126: [11:06:04] DEPRECATION WARNING: please use AtomPairGenerator +126: [11:06:04] DEPRECATION WARNING: please use AtomPairGenerator +126: [11:06:04] DEPRECATION WARNING: please use AtomPairGenerator +126: [11:06:04] DEPRECATION WARNING: please use AtomPairGenerator +126: .[11:06:04] DEPRECATION WARNING: please use AtomPairGenerator +126: [11:06:04] DEPRECATION WARNING: please use AtomPairGenerator +126: [11:06:04] DEPRECATION WARNING: please use AtomPairGenerator +126: ..[11:06:04] +126: +126: **** +126: Pre-condition Violation +126: Number of atom props not equal to number of atoms +126: Violation occurred on line 89 in file ./Code/GraphMol/Descriptors/BCUT.cpp +126: Failed Expression: atom_props.size() == num_atoms +126: ---------- +126: Stacktrace: +126: 0# Invar::Invariant::toString[abi:cxx11]() const in /build/reproducible-path/rdkit-202503.1/obj-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# 0x0000FFFF8A96D0B8 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdMolDescriptors.so +126: 4# 0x0000FFFF8A982370 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# 0x0000FFFF8E832680 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 +126: 10# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdChemReactions.so +126: 11# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdChemReactions.so +126: 12# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdMolChemicalFeatures.so +126: 13# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdmolfiles.so +126: 14# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202503.1/obj-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# 0x0000FFFF8CDBC320 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so +126: 18# 0x0000FFFF8CDBC2B8 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so +126: 19# 0x0000FFFF8CDBC248 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so +126: 20# 0x0000FFFF8CDBC1E0 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so +126: 21# 0x0000FFFF8CDBC178 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# 0x0000FFFF8E82F25C in /lib/aarch64-linux-gnu/libboost_python313.so.1.83.0 +126: 28# _PyObject_MakeTpCall in /usr/bin/python3 +126: 29# _PyEval_EvalFrameDefault in /usr/bin/python3 +126: 30# 0x000000000053D3B0 in /usr/bin/python3 +126: 31# _PyEval_EvalFrameDefault in /usr/bin/python3 +126: 32# 0x000000000061C8E0 in /usr/bin/python3 +126: 33# 0x00000000005A787C in /usr/bin/python3 +126: 34# _PyObject_MakeTpCall in /usr/bin/python3 +126: 35# _PyEval_EvalFrameDefault in /usr/bin/python3 +126: 36# 0x000000000053D3B0 in /usr/bin/python3 +126: 37# _PyEval_EvalFrameDefault in /usr/bin/python3 +126: 38# 0x000000000061C8E0 in /usr/bin/python3 +126: 39# 0x00000000005A787C in /usr/bin/python3 +126: 40# _PyObject_MakeTpCall in /usr/bin/python3 +126: 41# _PyEval_EvalFrameDefault in /usr/bin/python3 +126: 42# 0x000000000053D3B0 in /usr/bin/python3 +126: 43# _PyEval_EvalFrameDefault in /usr/bin/python3 +126: 44# 0x000000000061C8E0 in /usr/bin/python3 +126: 45# 0x00000000005A787C in /usr/bin/python3 +126: 46# _PyObject_MakeTpCall in /usr/bin/python3 +126: 47# _PyEval_EvalFrameDefault in /usr/bin/python3 +126: 48# 0x000000000050B030 in /usr/bin/python3 +126: 49# _PyObject_MakeTpCall in /usr/bin/python3 +126: 50# _PyEval_EvalFrameDefault in /usr/bin/python3 +126: 51# PyEval_EvalCode in /usr/bin/python3 +126: 52# 0x000000000064023C in /usr/bin/python3 +126: 53# 0x000000000063BC30 in /usr/bin/python3 +126: 54# 0x000000000065F810 in /usr/bin/python3 +126: 55# 0x000000000065F0B4 in /usr/bin/python3 +126: 56# 0x000000000065EE50 in /usr/bin/python3 +126: 57# Py_RunMain in /usr/bin/python3 +126: 58# Py_BytesMain in /usr/bin/python3 +126: 59# 0x0000FFFF8F13229C 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: +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 128: 128: 128: @@ -25520,743 +25660,630 @@ 128: 128: ------------------- 128: -128: [02:19:08] ------------------------------------- -128: [02:19:08] Test Morgan Fingerprints. -128: [02:19:08] done -128: [02:19:08] ------------------------------------- -128: [02:19:08] Test Morgan Fingerprints using fromAtoms argument. -128: [02:19:08] done -128: [02:19:08] ------------------------------------- -128: [02:19:08] Test Morgan Fingerprints as bit vects. -128: [02:19:08] done -128: [02:19:08] ------------------------------------- -128: [02:19:08] Test Morgan Fingerprints with feature invariants. -128: [02:19:08] done -128: [02:19:08] ------------------------------------- -128: [02:19:08] Test additional Morgan fingerprints options. -128: [02:19:08] done -128: [02:19:08] ------------------------------------- -128: [02:19:08] Test Atom Codes. -128: [02:19:08] done -128: [02:19:08] ------------------------------------- -128: [02:19:08] Test Atom Pairs. -128: [02:19:08] DEPRECATION WARNING: please use AtomPairGenerator -128: [02:19:08] DEPRECATION WARNING: please use AtomPairGenerator -128: [02:19:08] done -128: [02:19:08] ------------------------------------- -128: [02:19:08] Test Atom Pairs part 2. -128: [02:19:08] DEPRECATION WARNING: please use AtomPairGenerator -128: [02:19:08] DEPRECATION WARNING: please use AtomPairGenerator -128: [02:19:08] done -128: [02:19:08] ------------------------------------- -128: [02:19:08] Test Topological Torsions. -128: [02:19:08] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [02:19:08] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [02:19:08] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [02:19:08] done -128: [02:19:08] ------------------------------------- -128: [02:19:08] Test Bulk Topological Torsions. -128: [02:19:08] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [02:19:08] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [02:19:08] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [02:19:08] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [02:19:08] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [02:19:08] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [02:19:08] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [02:19:08] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [02:19:08] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [02:19:08] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [02:19:08] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [02:19:08] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [02:19:08] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [02:19:08] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [02:19:08] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [02:19:08] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [02:19:08] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [02:19:08] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [02:19:08] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [02:19:08] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [02:19:08] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [02:19:08] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [02:19:08] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [02:19:08] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [02:19:08] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [02:19:08] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [02:19:08] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [02:19:08] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [02:19:08] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [02:19:08] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [02:19:08] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [02:19:08] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [02:19:08] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [02:19:08] DEPRECATION WARNING: please use TopologicalTorsionGenerator -111: [02:19:08] done -111: [02:19:08] ------------------------------------- -111: [02:19:08] Test Issue252: Bad definitions for Crippen atom types. -128: [02:19:08] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [02:19:08] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [02:19:08] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [02:19:08] DEPRECATION WARNING: please use TopologicalTorsionGenerator -111: [02:19:08] done -128: [02:19:08] DEPRECATION WARNING: please use TopologicalTorsionGenerator -111: [02:19:08] ------------------------------------- -111: [02:19:08] Test calculation of ChiVs. -128: [02:19:08] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [02:19:08] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [02:19:08] DEPRECATION WARNING: please use TopologicalTorsionGenerator -111: [02:19:08] done -111: [02:19:08] ------------------------------------- -111: [02:19:08] Test calculation of ChiNs. -128: [02:19:08] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [02:19:08] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [02:19:08] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [02:19:08] DEPRECATION WARNING: please use TopologicalTorsionGenerator -111: [02:19:08] done -111: [02:19:08] ------------------------------------- -111: [02:19:08] Test calculation of HallKierAlpha. -128: [02:19:08] DEPRECATION WARNING: please use TopologicalTorsionGenerator -111: [02:19:08] done -111: [02:19:08] ------------------------------------- -111: [02:19:08] Test calculation of Kappa1. -111: [02:19:08] done -128: [02:19:08] DEPRECATION WARNING: please use TopologicalTorsionGenerator -111: [02:19:08] ------------------------------------- -111: [02:19:08] Test calculation of Kappa2. -111: [02:19:08] done -111: [02:19:08] ------------------------------------- -111: [02:19:08] Test calculation of Kappa3. -128: [02:19:08] DEPRECATION WARNING: please use TopologicalTorsionGenerator -111: [02:19:08] done -111: [02:19:08] ------------------------------------- -111: [02:19:08] Test Crippen atom type calculations. -128: [02:19:08] DEPRECATION WARNING: please use TopologicalTorsionGenerator -111: [02:19:08] done -111: [02:19:08] ------------------------------------- -111: [02:19:08] Test ring descriptors -128: [02:19:08] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [02:19:08] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [02:19:08] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [02:19:08] DEPRECATION WARNING: please use TopologicalTorsionGenerator -111: [02:19:08] done -111: [02:19:08] ------------------------------------- -111: [02:19:08] Test other count descriptors. -111: [02:19:08] done -111: [02:19:08] ------------------------------------- -111: [02:19:08] Test MQN -128: [02:19:08] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [02:19:08] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [02:19:08] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [02:19:08] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [02:19:08] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [02:19:08] DEPRECATION WARNING: please use TopologicalTorsionGenerator -126: [02:19:08] DEPRECATION WARNING: please use AtomPairGenerator -126: [02:19:08] DEPRECATION WARNING: please use AtomPairGenerator -126: [02:19:08] DEPRECATION WARNING: please use AtomPairGenerator -126: [02:19:08] DEPRECATION WARNING: please use AtomPairGenerator -126: [02:19:08] DEPRECATION WARNING: please use AtomPairGenerator -128: [02:19:08] DEPRECATION WARNING: please use TopologicalTorsionGenerator -126: [02:19:08] DEPRECATION WARNING: please use AtomPairGenerator -126: [02:19:08] DEPRECATION WARNING: please use AtomPairGenerator -111: [02:19:08] done -111: [02:19:08] ------------------------------------- -126: [02:19:08] DEPRECATION WARNING: please use AtomPairGenerator -126: [02:19:08] DEPRECATION WARNING: please use AtomPairGenerator -126: [02:19:08] DEPRECATION WARNING: please use AtomPairGenerator -126: [02:19:08] DEPRECATION WARNING: please use AtomPairGenerator -126: [02:19:08] DEPRECATION WARNING: please use AtomPairGenerator -126: [02:19:08] DEPRECATION WARNING: please use TopologicalTorsionGenerator -126: [02:19:08] DEPRECATION WARNING: please use TopologicalTorsionGenerator -111: [02:19:08] Test GitHub Issue 56. -111: [02:19:08] WARNING: not removing hydrogen atom without neighbors -126: [02:19:08] DEPRECATION WARNING: please use TopologicalTorsionGenerator -111: [02:19:08] WARNING: not removing hydrogen atom without neighbors -126: [02:19:08] DEPRECATION WARNING: please use TopologicalTorsionGenerator -111: [02:19:08] WARNING: not removing hydrogen atom without neighbors -126: [02:19:08] DEPRECATION WARNING: please use TopologicalTorsionGenerator -126: [02:19:08] DEPRECATION WARNING: please use TopologicalTorsionGenerator -126: [02:19:08] DEPRECATION WARNING: please use TopologicalTorsionGenerator -111: [02:19:08] WARNING: not removing hydrogen atom without neighbors -111: [02:19:08] done -111: [02:19:08] ------------------------------------- -111: [02:19:08] Test Github92: Bad Crippen atom type for pyrrole H. -111: [02:19:08] done -128: [02:19:08] DEPRECATION WARNING: please use TopologicalTorsionGenerator -111: [02:19:08] ------------------------------------- -111: [02:19:08] Test Github362: order dependence in Kier-Hall descriptors. -128: [02:19:08] DEPRECATION WARNING: please use TopologicalTorsionGenerator -111: [02:19:08] done -111: [02:19:08] ------------------------------------- -111: [02:19:08] Test calculation of spiro and bridgehead counts. -128: [02:19:08] DEPRECATION WARNING: please use TopologicalTorsionGenerator -111: [02:19:08] done -111: [02:19:08] ------------------------------------- -111: [02:19:08] Test Github694: ExactMolWt ignoring the mass of the electron -111: [02:19:08] done -111: [02:19:08] ------------------------------------- -111: [02:19:08] Testing Properties and KitchenSink -111: [02:19:08] ---Caught keyerror (bad property name)--- -111: [02:19:08] ------------------------------------- -111: [02:19:08] Test USR Descriptor -111: [02:19:08] done -111: [02:19:08] ------------------------------------- -111: [02:19:08] Test Github #1702: AUTOCORR2D.h not installed unless RDK_BUILD_DESCRIPTORS3D but is required -111: [02:19:08] done -111: [02:19:08] ------------------------------------- -111: [02:19:08] Test Github #1973: support P and S terms for TPSA calculation -111: [02:19:08] done -111: [02:19:08] ------------------------------------- -111: [02:19:08] Test Github #2948: Empty molecule has non-zero LabuteASA -111: [02:19:08] done -128: [02:19:08] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [02:19:08] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [02:19:08] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [02:19:08] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [02:19:08] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [02:19:08] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [02:19:08] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [02:19:08] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [02:19:08] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [02:19:08] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [02:19:08] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [02:19:08] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [02:19:08] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [02:19:08] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [02:19:08] DEPRECATION WARNING: please use TopologicalTorsionGenerator -126: [02:19:08] DEPRECATION WARNING: please use TopologicalTorsionGenerator -126: [02:19:08] DEPRECATION WARNING: please use TopologicalTorsionGenerator -126: [02:19:08] DEPRECATION WARNING: please use TopologicalTorsionGenerator -126: [02:19:08] DEPRECATION WARNING: please use TopologicalTorsionGenerator -126: [02:19:08] DEPRECATION WARNING: please use TopologicalTorsionGenerator -126: ..[02:19:08] DEPRECATION WARNING: please use AtomPairGenerator -126: [02:19:08] DEPRECATION WARNING: please use AtomPairGenerator -126: [02:19:08] DEPRECATION WARNING: please use AtomPairGenerator -126: [02:19:08] DEPRECATION WARNING: please use AtomPairGenerator -126: [02:19:08] DEPRECATION WARNING: please use AtomPairGenerator -126: [02:19:08] DEPRECATION WARNING: please use AtomPairGenerator -126: .[02:19:08] DEPRECATION WARNING: please use AtomPairGenerator -126: [02:19:08] DEPRECATION WARNING: please use AtomPairGenerator -126: [02:19:08] DEPRECATION WARNING: please use AtomPairGenerator -126: ..[02:19:08] -126: -126: **** -128: [02:19:08] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [02:19:08] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [02:19:08] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [02:19:08] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [02:19:08] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [02:19:08] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [02:19:08] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [02:19:08] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [02:19:08] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [02:19:08] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [02:19:08] DEPRECATION WARNING: please use TopologicalTorsionGenerator -117/238 Test #111: testDescriptors ........................ Passed 1.92 sec +111: [11:06:04] done +111: [11:06:04] ------------------------------------- +111: [11:06:04] Test Issue252: Bad definitions for Crippen atom types. +111: [11:06:04] done +111: [11:06:04] ------------------------------------- +111: [11:06:04] Test calculation of ChiVs. +111: [11:06:04] done +111: [11:06:04] ------------------------------------- +111: [11:06:04] Test calculation of ChiNs. +111: [11:06:04] done +111: [11:06:04] ------------------------------------- +111: [11:06:04] Test calculation of HallKierAlpha. +111: [11:06:04] done +111: [11:06:04] ------------------------------------- +111: [11:06:04] Test calculation of Kappa1. +128: [11:06:04] ------------------------------------- +128: [11:06:04] Test Morgan Fingerprints. +128: [11:06:04] done +128: [11:06:04] ------------------------------------- +128: [11:06:04] Test Morgan Fingerprints using fromAtoms argument. +128: [11:06:04] done +128: [11:06:04] ------------------------------------- +128: [11:06:04] Test Morgan Fingerprints as bit vects. +128: [11:06:04] done +128: [11:06:04] ------------------------------------- +128: [11:06:04] Test Morgan Fingerprints with feature invariants. +128: [11:06:04] done +128: [11:06:04] ------------------------------------- +128: [11:06:04] Test additional Morgan fingerprints options. +128: [11:06:04] done +128: [11:06:04] ------------------------------------- +128: [11:06:04] Test Atom Codes. +128: [11:06:04] done +128: [11:06:04] ------------------------------------- +128: [11:06:04] Test Atom Pairs. +128: [11:06:04] DEPRECATION WARNING: please use AtomPairGenerator +128: [11:06:04] DEPRECATION WARNING: please use AtomPairGenerator +128: [11:06:04] done +128: [11:06:04] ------------------------------------- +128: [11:06:04] Test Atom Pairs part 2. +128: [11:06:04] DEPRECATION WARNING: please use AtomPairGenerator +128: [11:06:04] DEPRECATION WARNING: please use AtomPairGenerator +128: [11:06:04] done +128: [11:06:04] ------------------------------------- +128: [11:06:04] Test Topological Torsions. +128: [11:06:04] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [11:06:04] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [11:06:04] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [11:06:04] done +128: [11:06:04] ------------------------------------- +128: [11:06:04] Test Bulk Topological Torsions. +128: [11:06:04] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [11:06:04] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [11:06:04] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [11:06:04] DEPRECATION WARNING: please use TopologicalTorsionGenerator +111: [11:06:04] done +111: [11:06:04] ------------------------------------- +111: [11:06:04] Test calculation of Kappa2. +128: [11:06:04] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [11:06:04] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [11:06:04] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [11:06:04] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [11:06:04] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [11:06:04] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [11:06:04] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [11:06:04] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [11:06:04] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [11:06:04] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [11:06:04] DEPRECATION WARNING: please use TopologicalTorsionGenerator +111: [11:06:04] done +111: [11:06:04] ------------------------------------- +111: [11:06:04] Test calculation of Kappa3. +111: [11:06:04] done +111: [11:06:04] ------------------------------------- +111: [11:06:04] Test Crippen atom type calculations. +111: [11:06:04] done +111: [11:06:04] ------------------------------------- +111: [11:06:04] Test ring descriptors +111: [11:06:04] done +111: [11:06:04] ------------------------------------- +111: [11:06:04] Test other count descriptors. +111: [11:06:04] done +111: [11:06:04] ------------------------------------- +111: [11:06:04] Test MQN +128: [11:06:04] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [11:06:04] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [11:06:04] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [11:06:04] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [11:06:04] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [11:06:04] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [11:06:04] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [11:06:04] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [11:06:04] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [11:06:04] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [11:06:04] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [11:06:04] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [11:06:04] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [11:06:04] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [11:06:04] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [11:06:04] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [11:06:04] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [11:06:04] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [11:06:04] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [11:06:04] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [11:06:04] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [11:06:04] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [11:06:04] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [11:06:04] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [11:06:04] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [11:06:04] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [11:06:04] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [11:06:04] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [11:06:04] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [11:06:04] DEPRECATION WARNING: please use TopologicalTorsionGenerator +111: [11:06:04] done +111: [11:06:04] ------------------------------------- +111: [11:06:04] Test GitHub Issue 56. +111: [11:06:04] WARNING: not removing hydrogen atom without neighbors +111: [11:06:04] WARNING: not removing hydrogen atom without neighbors +111: [11:06:04] WARNING: not removing hydrogen atom without neighbors +111: [11:06:04] WARNING: not removing hydrogen atom without neighbors +111: [11:06:04] done +111: [11:06:04] ------------------------------------- +111: [11:06:04] Test Github92: Bad Crippen atom type for pyrrole H. +111: [11:06:04] done +111: [11:06:04] ------------------------------------- +111: [11:06:04] Test Github362: order dependence in Kier-Hall descriptors. +111: [11:06:04] done +111: [11:06:04] ------------------------------------- +111: [11:06:04] Test calculation of spiro and bridgehead counts. +111: [11:06:04] done +111: [11:06:04] ------------------------------------- +111: [11:06:04] Test Github694: ExactMolWt ignoring the mass of the electron +111: [11:06:04] done +111: [11:06:04] ------------------------------------- +111: [11:06:04] Testing Properties and KitchenSink +111: [11:06:04] ---Caught keyerror (bad property name)--- +111: [11:06:04] ------------------------------------- +111: [11:06:04] Test USR Descriptor +111: [11:06:04] done +111: [11:06:04] ------------------------------------- +111: [11:06:04] Test Github #1702: AUTOCORR2D.h not installed unless RDK_BUILD_DESCRIPTORS3D but is required +111: [11:06:04] done +111: [11:06:04] ------------------------------------- +111: [11:06:04] Test Github #1973: support P and S terms for TPSA calculation +128: [11:06:04] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [11:06:04] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [11:06:04] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [11:06:04] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [11:06:04] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [11:06:04] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [11:06:04] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [11:06:04] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [11:06:04] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [11:06:04] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [11:06:04] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [11:06:04] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [11:06:04] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [11:06:04] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [11:06:04] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [11:06:04] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [11:06:04] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [11:06:04] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [11:06:04] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [11:06:04] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [11:06:04] DEPRECATION WARNING: please use TopologicalTorsionGenerator +111: [11:06:04] done +111: [11:06:04] ------------------------------------- +111: [11:06:04] Test Github #2948: Empty molecule has non-zero LabuteASA +111: [11:06:04] done +128: [11:06:04] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [11:06:04] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [11:06:04] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [11:06:04] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [11:06:04] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [11:06:04] DEPRECATION WARNING: please use TopologicalTorsionGenerator +126: Warning: Atom Count for residue GLU5A does not match expected count +128: [11:06:04] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [11:06:04] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [11:06:04] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [11:06:04] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [11:06:04] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [11:06:04] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [11:06:04] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [11:06:04] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [11:06:04] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [11:06:04] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [11:06:04] DEPRECATION WARNING: please use TopologicalTorsionGenerator +117: =>start test AUTOCORR3D custom +128: [11:06:04] DEPRECATION WARNING: please use TopologicalTorsionGenerator +117: [11:06:04] test on : 365 molecules done +128: [11:06:04] DEPRECATION WARNING: please use TopologicalTorsionGenerator +117/238 Test #111: testDescriptors ........................ Passed 1.97 sec +128: [11:06:04] DEPRECATION WARNING: please use TopologicalTorsionGenerator 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: [02:19:08] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [02:19:08] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [02:19:08] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [02:19:08] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [02:19:08] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [02:19:08] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [02:19:08] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [02:19:08] DEPRECATION WARNING: please use TopologicalTorsionGenerator -126: Pre-condition Violation -126: Number of atom props not equal to number of atoms -126: Violation occurred on line 89 in file ./Code/GraphMol/Descriptors/BCUT.cpp -126: Failed Expression: atom_props.size() == num_atoms -126: ---------- -126: Stacktrace: -126: 0# Invar::Invariant::toString[abi:cxx11]() const in /build/reproducible-path/rdkit-202503.1/obj-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# 0x0000FFFFBA04D0B8 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdMolDescriptors.so -126: 4# 0x0000FFFFBA062370 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# 0x0000FFFFBDF12680 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 -126: 10# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdChemReactions.so -126: 11# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdChemReactions.so -126: 12# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdMolChemicalFeatures.so -126: 13# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdmolfiles.so -126: 14# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202503.1/obj-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# 0x0000FFFFBC49C320 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so -126: 18# 0x0000FFFFBC49C2B8 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so -126: 19# 0x0000FFFFBC49C248 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so -126: 20# 0x0000FFFFBC49C1E0 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so -126: 21# 0x0000FFFFBC49C178 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# 0x0000FFFFBDF0F25C in /lib/aarch64-linux-gnu/libboost_python313.so.1.83.0 -126: 28# _PyObject_MakeTpCall in /usr/bin/python3 -126: 29# _PyEval_EvalFrameDefault in /usr/bin/python3 -126: 30# 0x000000000053D3B0 in /usr/bin/python3 -126: 31# _PyEval_EvalFrameDefault in /usr/bin/python3 -126: 32# 0x000000000061C8E0 in /usr/bin/python3 -126: 33# 0x00000000005A787C in /usr/bin/python3 -126: 34# _PyObject_MakeTpCall in /usr/bin/python3 -126: 35# _PyEval_EvalFrameDefault in /usr/bin/python3 -126: 36# 0x000000000053D3B0 in /usr/bin/python3 -126: 37# _PyEval_EvalFrameDefault in /usr/bin/python3 -126: 38# 0x000000000061C8E0 in /usr/bin/python3 -126: 39# 0x00000000005A787C in /usr/bin/python3 -126: 40# _PyObject_MakeTpCall in /usr/bin/python3 -126: 41# _PyEval_EvalFrameDefault in /usr/bin/python3 -126: 42# 0x000000000053D3B0 in /usr/bin/python3 -126: 43# _PyEval_EvalFrameDefault in /usr/bin/python3 -126: 44# 0x000000000061C8E0 in /usr/bin/python3 -126: 45# 0x00000000005A787C in /usr/bin/python3 -126: 46# _PyObject_MakeTpCall in /usr/bin/python3 -126: 47# _PyEval_EvalFrameDefault in /usr/bin/python3 -126: 48# 0x000000000050B030 in /usr/bin/python3 -126: 49# _PyObject_MakeTpCall in /usr/bin/python3 -126: 50# _PyEval_EvalFrameDefault in /usr/bin/python3 -126: 51# PyEval_EvalCode in /usr/bin/python3 -126: 52# 0x000000000064023C in /usr/bin/python3 -126: 53# 0x000000000063BC30 in /usr/bin/python3 -126: 54# 0x000000000065F810 in /usr/bin/python3 -126: 55# 0x000000000065F0B4 in /usr/bin/python3 -126: 56# 0x000000000065EE50 in /usr/bin/python3 -126: 57# Py_RunMain in /usr/bin/python3 -126: 58# Py_BytesMain in /usr/bin/python3 -126: 59# 0x0000FFFFBE81229C 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: [02:19:08] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [02:19:08] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [02:19:08] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [02:19:08] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [02:19:08] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [02:19:08] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [02:19:08] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [02:19:08] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [02:19:08] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [02:19:08] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [02:19:08] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [02:19:08] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [02:19:08] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [02:19:08] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [02:19:08] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [02:19:08] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [02:19:08] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [02:19:08] DEPRECATION WARNING: please use TopologicalTorsionGenerator -129: [02:19:08] ------------------------------------- -129: [02:19:08] Test MHFP fingerprint encoder initialization -128: [02:19:08] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [02:19:08] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [02:19:08] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [02:19:08] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [02:19:08] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [02:19:08] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [02:19:08] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [02:19:08] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [02:19:08] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [02:19:08] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [02:19:08] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [02:19:08] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [02:19:08] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [02:19:08] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [02:19:08] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [02:19:08] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [02:19:08] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [02:19:08] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [02:19:08] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [02:19:08] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [02:19:08] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [02:19:08] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [02:19:08] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [02:19:08] DEPRECATION WARNING: please use TopologicalTorsionGenerator -126: ...Warning: Atom Count for residue GLU5A does not match expected count -129: [02:19:08] done -129: [02:19:08] ------------------------------------- -129: [02:19:08] Test MHFP shingling creation -128: [02:19:08] DEPRECATION WARNING: please use TopologicalTorsionGenerator -126: Warning: Atom Count for residue ASN39A does not match expected count -128: [02:19:08] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [02:19:08] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [02:19:08] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [02:19:08] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [02:19:08] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [02:19:08] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [02:19:08] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [02:19:08] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [02:19:08] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [02:19:08] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [02:19:08] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [02:19:08] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [02:19:08] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [02:19:08] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [02:19:08] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [02:19:08] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [02:19:08] DEPRECATION WARNING: please use TopologicalTorsionGenerator -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 -129: [02:19:08] done -129: [02:19:08] ------------------------------------- -129: [02:19:08] Test MHFP hashing of string and uint arrays -129: [02:19:08] done -129: [02:19:08] ------------------------------------- -129: [02:19:08] Test SECFP fingerprint functionality -128: [02:19:08] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [02:19:08] DEPRECATION WARNING: please use TopologicalTorsionGenerator -126: Warning: Atom Count for residue GLU150A does not match expected count -128: [02:19:08] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [02:19:08] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [02:19:08] DEPRECATION WARNING: please use TopologicalTorsionGenerator -129: [02:19:08] done -126: Warning: Atom Count for residue ASN157A does not match expected count -128: [02:19:08] DEPRECATION WARNING: please use TopologicalTorsionGenerator -118/238 Test #129: testMHFPFingerprint .................... Passed 0.04 sec +128: [11:06:04] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [11:06:04] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [11:06:04] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [11:06:04] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [11:06:04] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [11:06:04] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [11:06:04] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [11:06:04] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [11:06:04] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [11:06:04] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [11:06:04] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [11:06:04] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [11:06:04] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [11:06:04] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [11:06:04] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [11:06:04] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [11:06:04] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [11:06:04] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [11:06:04] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [11:06:04] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [11:06:04] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [11:06:04] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [11:06:04] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [11:06:04] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [11:06:04] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [11:06:04] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [11:06:04] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [11:06:04] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [11:06:04] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [11:06:04] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [11:06:04] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [11:06:04] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [11:06:04] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [11:06:04] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [11:06:04] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [11:06:04] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [11:06:04] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [11:06:04] DEPRECATION WARNING: please use TopologicalTorsionGenerator +129: [11:06:04] ------------------------------------- +129: [11:06:04] Test MHFP fingerprint encoder initialization +128: [11:06:04] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [11:06:04] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [11:06:04] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [11:06:04] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [11:06:04] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [11:06:04] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [11:06:04] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [11:06:04] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [11:06:04] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [11:06:04] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [11:06:04] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [11:06:04] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [11:06:04] DEPRECATION WARNING: please use TopologicalTorsionGenerator +125: Warning: Atom Count for residue LYS80A does not match expected count +128: [11:06:04] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [11:06:04] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [11:06:04] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [11:06:04] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [11:06:04] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [11:06:04] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [11:06:04] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [11:06:04] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [11:06:04] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [11:06:04] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [11:06:04] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [11:06:04] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [11:06:04] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [11:06:04] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [11:06:04] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [11:06:04] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [11:06:04] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [11:06:04] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [11:06:04] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [11:06:04] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [11:06:04] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [11:06:04] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [11:06:04] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [11:06:04] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [11:06:04] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [11:06:04] DEPRECATION WARNING: please use TopologicalTorsionGenerator +129: [11:06:04] done +129: [11:06:04] ------------------------------------- +129: [11:06:04] Test MHFP shingling creation +128: [11:06:04] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [11:06:04] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [11:06:04] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [11:06:04] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [11:06:04] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [11:06:04] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [11:06:04] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [11:06:04] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [11:06:04] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [11:06:04] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [11:06:04] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [11:06:04] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [11:06:04] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [11:06:04] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [11:06:04] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [11:06:04] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [11:06:04] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [11:06:04] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [11:06:04] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [11:06:04] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [11:06:04] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [11:06:04] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [11:06:04] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [11:06:04] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [11:06:04] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [11:06:04] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [11:06:04] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [11:06:04] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [11:06:04] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [11:06:04] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [11:06:04] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [11:06:04] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [11:06:04] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [11:06:04] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [11:06:04] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [11:06:04] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [11:06:04] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [11:06:04] done +128: [11:06:04] ------------------------------------- +128: [11:06:04] Test Hashed Atom Pairs. +128: [11:06:04] DEPRECATION WARNING: please use AtomPairGenerator +128: [11:06:04] DEPRECATION WARNING: please use AtomPairGenerator +128: [11:06:04] DEPRECATION WARNING: please use AtomPairGenerator +128: [11:06:04] DEPRECATION WARNING: please use AtomPairGenerator +128: [11:06:04] DEPRECATION WARNING: please use AtomPairGenerator +128: [11:06:04] DEPRECATION WARNING: please use AtomPairGenerator +128: [11:06:04] done +128: [11:06:04] ------------------------------------- +128: [11:06:04] Test Hashed torsions. +129: [11:06:04] done +129: [11:06:04] ------------------------------------- +129: [11:06:04] Test MHFP hashing of string and uint arrays +129: [11:06:04] done +129: [11:06:04] ------------------------------------- +129: [11:06:04] Test SECFP fingerprint functionality +128: [11:06:04] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [11:06:04] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [11:06:04] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [11:06:04] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [11:06:04] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [11:06:04] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [11:06:04] done +128: [11:06:04] ------------------------------------- +128: [11:06:04] Test Rooted Atom Pairs. +128: [11:06:04] DEPRECATION WARNING: please use AtomPairGenerator +128: [11:06:04] DEPRECATION WARNING: please use AtomPairGenerator +128: [11:06:04] done +128: [11:06:04] ------------------------------------- +128: [11:06:04] Test ignoring atoms in Atom Pairs. +128: [11:06:04] DEPRECATION WARNING: please use AtomPairGenerator +128: [11:06:04] DEPRECATION WARNING: please use AtomPairGenerator +128: [11:06:04] DEPRECATION WARNING: please use AtomPairGenerator +128: [11:06:04] DEPRECATION WARNING: please use AtomPairGenerator +128: [11:06:04] DEPRECATION WARNING: please use AtomPairGenerator +128: [11:06:04] done +128: [11:06:04] ------------------------------------- +128: [11:06:04] Test Rooted Topological Torsions. +128: [11:06:04] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [11:06:04] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [11:06:04] done +128: [11:06:04] ------------------------------------- +128: [11:06:04] Test ignoring atoms in Topological Torsions. +128: [11:06:04] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [11:06:04] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [11:06:04] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [11:06:04] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [11:06:04] done +128: [11:06:04] ------------------------------------- +128: [11:06:04] Test atom info from morgan fingerprints. +128: [11:06:04] done +128: [11:06:04] ------------------------------------- +128: [11:06:04] Test atom info from morgan fingerprints including Info Redundant Environments. +128: [11:06:04] done +128: [11:06:04] ------------------------------------- +128: [11:06:04] ------------------------------------- +128: [11:06:04] DEPRECATION WARNING: please use AtomPairGenerator +128: [11:06:04] DEPRECATION WARNING: please use AtomPairGenerator +128: [11:06:04] DEPRECATION WARNING: please use AtomPairGenerator +128: [11:06:04] DEPRECATION WARNING: please use AtomPairGenerator +128: [11:06:04] DEPRECATION WARNING: please use AtomPairGenerator +128: [11:06:04] DEPRECATION WARNING: please use AtomPairGenerator +128: [11:06:04] DEPRECATION WARNING: please use AtomPairGenerator +128: [11:06:04] DEPRECATION WARNING: please use AtomPairGenerator +128: [11:06:04] DEPRECATION WARNING: please use AtomPairGenerator +128: [11:06:04] DEPRECATION WARNING: please use AtomPairGenerator +128: [11:06:04] DEPRECATION WARNING: please use AtomPairGenerator +128: [11:06:04] DEPRECATION WARNING: please use AtomPairGenerator +128: [11:06:04] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [11:06:04] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [11:06:04] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [11:06:04] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [11:06:04] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [11:06:04] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [11:06:04] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [11:06:04] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [11:06:04] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [11:06:04] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [11:06:04] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [11:06:04] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [11:06:04] ------------------------------------- +128: [11:06:04] ------------------------------------- +128: [11:06:04] ------------------------------------- +128: [11:06:04] ------------------------------------- +128: [11:06:04] Test Atom Pairs including info about chirality. +128: [11:06:04] DEPRECATION WARNING: please use AtomPairGenerator +128: [11:06:04] DEPRECATION WARNING: please use AtomPairGenerator +128: [11:06:04] DEPRECATION WARNING: please use AtomPairGenerator +128: [11:06:04] DEPRECATION WARNING: please use AtomPairGenerator +128: [11:06:04] DEPRECATION WARNING: please use AtomPairGenerator +128: [11:06:04] DEPRECATION WARNING: please use AtomPairGenerator +128: [11:06:04] DEPRECATION WARNING: please use AtomPairGenerator +128: [11:06:04] DEPRECATION WARNING: please use AtomPairGenerator +128: [11:06:04] DEPRECATION WARNING: please use AtomPairGenerator +128: [11:06:04] DEPRECATION WARNING: please use AtomPairGenerator +128: [11:06:04] DEPRECATION WARNING: please use AtomPairGenerator +128: [11:06:04] DEPRECATION WARNING: please use AtomPairGenerator +128: [11:06:04] done +128: [11:06:04] ------------------------------------- +128: [11:06:04] Test Topological Torsions including info about chirality. +128: [11:06:04] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [11:06:04] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [11:06:04] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [11:06:04] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [11:06:04] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [11:06:04] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [11:06:04] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [11:06:04] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [11:06:04] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [11:06:04] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [11:06:04] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [11:06:04] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [11:06:04] done +128: [11:06:04] ------------------------------------- +128: [11:06:04] Test GitHub Issue 25: fingerprint backwards compatibility. +128: [11:06:04] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [11:06:04] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [11:06:04] DEPRECATION WARNING: please use AtomPairGenerator +128: [11:06:04] DEPRECATION WARNING: please use AtomPairGenerator +128: [11:06:04] done +128: [11:06:04] ------------------------------------- +128: [11:06:04] Test GitHub Issue 151: PatternFingerprint problems +129: [11:06:04] done +118/238 Test #129: testMHFPFingerprint .................... Passed 0.06 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: [02:19:08] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [02:19:08] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [02:19:08] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [02:19:08] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [02:19:08] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [02:19:08] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [02:19:08] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [02:19:08] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [02:19:08] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [02:19:08] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [02:19:08] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [02:19:08] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [02:19:08] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [02:19:08] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [02:19:08] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [02:19:08] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [02:19:08] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [02:19:08] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [02:19:08] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [02:19:08] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [02:19:08] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [02:19:08] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [02:19:08] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [02:19:08] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [02:19:08] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [02:19:08] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [02:19:08] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [02:19:08] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [02:19:08] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [02:19:08] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [02:19:08] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [02:19:08] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [02:19:08] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [02:19:08] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [02:19:08] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [02:19:08] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [02:19:08] done -128: [02:19:08] ------------------------------------- -128: [02:19:08] Test Hashed Atom Pairs. -128: [02:19:08] DEPRECATION WARNING: please use AtomPairGenerator -128: [02:19:08] DEPRECATION WARNING: please use AtomPairGenerator -128: [02:19:08] DEPRECATION WARNING: please use AtomPairGenerator -128: [02:19:08] DEPRECATION WARNING: please use AtomPairGenerator -128: [02:19:08] DEPRECATION WARNING: please use AtomPairGenerator -128: [02:19:08] DEPRECATION WARNING: please use AtomPairGenerator -128: [02:19:08] done -128: [02:19:08] ------------------------------------- -128: [02:19:08] Test Hashed torsions. -128: [02:19:08] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [02:19:08] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [02:19:08] DEPRECATION WARNING: please use TopologicalTorsionGenerator -130: [02:19:08] ------------------------------------- -128: [02:19:08] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [02:19:08] DEPRECATION WARNING: please use TopologicalTorsionGenerator -130: [02:19:08] Test atom-pair fp generator -128: [02:19:08] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [02:19:08] done -128: [02:19:08] ------------------------------------- -128: [02:19:08] Test Rooted Atom Pairs. -128: [02:19:08] DEPRECATION WARNING: please use AtomPairGenerator -128: [02:19:08] DEPRECATION WARNING: please use AtomPairGenerator -128: [02:19:08] done -128: [02:19:08] ------------------------------------- -128: [02:19:08] Test ignoring atoms in Atom Pairs. -128: [02:19:08] DEPRECATION WARNING: please use AtomPairGenerator -128: [02:19:08] DEPRECATION WARNING: please use AtomPairGenerator -128: [02:19:08] DEPRECATION WARNING: please use AtomPairGenerator -128: [02:19:08] DEPRECATION WARNING: please use AtomPairGenerator -128: [02:19:08] DEPRECATION WARNING: please use AtomPairGenerator -128: [02:19:08] done -128: [02:19:08] ------------------------------------- -128: [02:19:08] Test Rooted Topological Torsions. -128: [02:19:08] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [02:19:08] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [02:19:08] done -128: [02:19:08] ------------------------------------- -128: [02:19:08] Test ignoring atoms in Topological Torsions. -128: [02:19:08] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [02:19:08] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [02:19:08] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [02:19:08] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [02:19:08] done -128: [02:19:08] ------------------------------------- -128: [02:19:08] Test atom info from morgan fingerprints. -128: [02:19:08] done -128: [02:19:08] ------------------------------------- -128: [02:19:08] Test atom info from morgan fingerprints including Info Redundant Environments. -128: [02:19:08] done -128: [02:19:08] ------------------------------------- -128: [02:19:08] ------------------------------------- -128: [02:19:08] DEPRECATION WARNING: please use AtomPairGenerator -128: [02:19:08] DEPRECATION WARNING: please use AtomPairGenerator -128: [02:19:08] DEPRECATION WARNING: please use AtomPairGenerator -128: [02:19:08] DEPRECATION WARNING: please use AtomPairGenerator -128: [02:19:08] DEPRECATION WARNING: please use AtomPairGenerator -128: [02:19:08] DEPRECATION WARNING: please use AtomPairGenerator -128: [02:19:08] DEPRECATION WARNING: please use AtomPairGenerator -130: [02:19:08] done -128: [02:19:08] DEPRECATION WARNING: please use AtomPairGenerator -130: [02:19:08] ------------------------------------- -130: [02:19:08] Test atom-pair fp generator with different arguments -130: [02:19:08] done -130: [02:19:08] ------------------------------------- -130: [02:19:08] Test compatibility between atom pair implementation for FingerprintGenerator and old atom pairs implementation -130: [02:19:08] DEPRECATION WARNING: please use AtomPairGenerator -130: [02:19:08] DEPRECATION WARNING: please use AtomPairGenerator -130: [02:19:08] DEPRECATION WARNING: please use AtomPairGenerator -130: [02:19:08] DEPRECATION WARNING: please use AtomPairGenerator -130: [02:19:08] DEPRECATION WARNING: please use AtomPairGenerator -130: [02:19:08] DEPRECATION WARNING: please use AtomPairGenerator -130: [02:19:08] DEPRECATION WARNING: please use AtomPairGenerator -130: [02:19:08] DEPRECATION WARNING: please use AtomPairGenerator -128: [02:19:08] DEPRECATION WARNING: please use AtomPairGenerator -128: [02:19:08] DEPRECATION WARNING: please use AtomPairGenerator -128: [02:19:08] DEPRECATION WARNING: please use AtomPairGenerator -128: [02:19:08] DEPRECATION WARNING: please use AtomPairGenerator -128: [02:19:08] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [02:19:08] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [02:19:08] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [02:19:08] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [02:19:08] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [02:19:08] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [02:19:08] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [02:19:08] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [02:19:08] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [02:19:08] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [02:19:08] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [02:19:08] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [02:19:08] ------------------------------------- -117: =>start test 1 WHIM custom -117: [02:19:08] test on : 365 molecules done -128: [02:19:08] ------------------------------------- -128: [02:19:08] ------------------------------------- -130: [02:19:08] DEPRECATION WARNING: please use AtomPairGenerator -128: [02:19:08] ------------------------------------- -128: [02:19:08] Test Atom Pairs including info about chirality. -128: [02:19:08] DEPRECATION WARNING: please use AtomPairGenerator -128: [02:19:08] DEPRECATION WARNING: please use AtomPairGenerator -128: [02:19:08] DEPRECATION WARNING: please use AtomPairGenerator -128: [02:19:08] DEPRECATION WARNING: please use AtomPairGenerator -128: [02:19:08] DEPRECATION WARNING: please use AtomPairGenerator -128: [02:19:08] DEPRECATION WARNING: please use AtomPairGenerator -128: [02:19:08] DEPRECATION WARNING: please use AtomPairGenerator -128: [02:19:08] DEPRECATION WARNING: please use AtomPairGenerator -128: [02:19:08] DEPRECATION WARNING: please use AtomPairGenerator -128: [02:19:08] DEPRECATION WARNING: please use AtomPairGenerator -128: [02:19:08] DEPRECATION WARNING: please use AtomPairGenerator -128: [02:19:08] DEPRECATION WARNING: please use AtomPairGenerator -128: [02:19:08] done -128: [02:19:08] ------------------------------------- -128: [02:19:08] Test Topological Torsions including info about chirality. -128: [02:19:08] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [02:19:08] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [02:19:08] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [02:19:08] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [02:19:08] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [02:19:08] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [02:19:08] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [02:19:08] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [02:19:08] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [02:19:08] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [02:19:08] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [02:19:08] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [02:19:08] done -130: [02:19:08] DEPRECATION WARNING: please use AtomPairGenerator -128: [02:19:08] ------------------------------------- -128: [02:19:08] Test GitHub Issue 25: fingerprint backwards compatibility. -128: [02:19:08] DEPRECATION WARNING: please use TopologicalTorsionGenerator -130: [02:19:08] done -130: [02:19:08] ------------------------------------- -130: [02:19:08] Test atom-pair additional output -130: [02:19:08] done -130: [02:19:08] ------------------------------------- -130: [02:19:08] Test Folded Atom Pairs. -128: [02:19:08] DEPRECATION WARNING: please use TopologicalTorsionGenerator -130: [02:19:08] done -128: [02:19:08] DEPRECATION WARNING: please use AtomPairGenerator -128: [02:19:08] DEPRECATION WARNING: please use AtomPairGenerator -128: [02:19:08] done -128: [02:19:08] ------------------------------------- -128: [02:19:08] Test GitHub Issue 151: PatternFingerprint problems -130: [02:19:08] ------------------------------------- -130: [02:19:08] Test Rooted Atom Pairs. -130: [02:19:08] done -130: [02:19:08] ------------------------------------- -130: [02:19:08] Test ignoring atoms in Atom Pairs. -130: [02:19:08] done -130: [02:19:08] ------------------------------------- -130: [02:19:08] Test Atom Pairs including info about chirality. -130: [02:19:08] done -130: [02:19:08] ------------------------------------- -130: [02:19:08] Test Morgan Fingerprints. -130: [02:19:08] done -130: [02:19:08] ------------------------------------- -130: [02:19:08] Test morgan fp generator -128: [02:19:08] done -128: [02:19:08] ------------------------------------- -128: [02:19:08] Test 3D atom pairs. -128: [02:19:08] DEPRECATION WARNING: please use AtomPairGenerator -128: [02:19:08] DEPRECATION WARNING: please use AtomPairGenerator -128: [02:19:08] DEPRECATION WARNING: please use AtomPairGenerator -128: [02:19:08] DEPRECATION WARNING: please use AtomPairGenerator -128: [02:19:08] DEPRECATION WARNING: please use AtomPairGenerator -128: [02:19:08] done -128: [02:19:08] ------------------------------------- -128: [02:19:08] Test GitHub Issue 195: GenMACCSKeys() raises an exception with an empty molecule -128: [02:19:08] done -128: [02:19:08] ------------------------------------- -128: [02:19:08] Test multithreading with the pattern FP +128: [11:06:04] done +128: [11:06:04] ------------------------------------- +128: [11:06:04] Test 3D atom pairs. +128: [11:06:04] DEPRECATION WARNING: please use AtomPairGenerator +128: [11:06:04] DEPRECATION WARNING: please use AtomPairGenerator +128: [11:06:04] DEPRECATION WARNING: please use AtomPairGenerator +128: [11:06:04] DEPRECATION WARNING: please use AtomPairGenerator +128: [11:06:04] DEPRECATION WARNING: please use AtomPairGenerator +128: [11:06:04] done +128: [11:06:04] ------------------------------------- +128: [11:06:04] Test GitHub Issue 195: GenMACCSKeys() raises an exception with an empty molecule +128: [11:06:04] done +128: [11:06:04] ------------------------------------- +128: [11:06:04] Test multithreading with the pattern FP 128: reading molecules -130: [02:19:08] done -130: [02:19:08] ------------------------------------- -130: [02:19:08] Test Morgan Fingerprints using fromAtoms argument. -130: [02:19:08] done -130: [02:19:08] ------------------------------------- -130: [02:19:08] Test Morgan Fingerprints as bit vects. -130: [02:19:08] done -130: [02:19:08] ------------------------------------- -130: [02:19:08] Test Morgan Fingerprints with feature invariants. -130: [02:19:08] done -130: [02:19:08] ------------------------------------- -130: [02:19:08] Test additional Morgan fingerprints options. -130: [02:19:08] done -130: [02:19:08] ------------------------------------- -130: [02:19:08] Test GitHub Issue 695: Include cis/trans stereochemistry when useChirality=true with the morgan fingerprints -130: [02:19:08] done -130: [02:19:08] ------------------------------------- -130: [02:19:08] Single atoms setting radius 1 bits in Morgan fingerprints -130: [02:19:08] done -130: [02:19:08] ------------------------------------- -130: [02:19:08] Test different invariant generator combinations -130: [02:19:08] done -130: [02:19:08] ------------------------------------- -130: [02:19:08] Test invariant overriding -130: [02:19:08] done -130: [02:19:08] ------------------------------------- -130: [02:19:08] Test RDKit fp generator -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 +130: [11:06:04] ------------------------------------- +130: [11:06:04] Test atom-pair fp generator +130: [11:06:04] done +130: [11:06:04] ------------------------------------- +130: [11:06:04] Test atom-pair fp generator with different arguments +130: [11:06:04] done +130: [11:06:04] ------------------------------------- +130: [11:06:04] Test compatibility between atom pair implementation for FingerprintGenerator and old atom pairs implementation +130: [11:06:04] DEPRECATION WARNING: please use AtomPairGenerator +130: [11:06:04] DEPRECATION WARNING: please use AtomPairGenerator +130: [11:06:04] DEPRECATION WARNING: please use AtomPairGenerator +130: [11:06:04] DEPRECATION WARNING: please use AtomPairGenerator +130: [11:06:04] DEPRECATION WARNING: please use AtomPairGenerator +130: [11:06:04] DEPRECATION WARNING: please use AtomPairGenerator +130: [11:06:04] DEPRECATION WARNING: please use AtomPairGenerator +130: [11:06:04] DEPRECATION WARNING: please use AtomPairGenerator +130: [11:06:04] DEPRECATION WARNING: please use AtomPairGenerator +130: [11:06:04] DEPRECATION WARNING: please use AtomPairGenerator +130: [11:06:04] done +130: [11:06:04] ------------------------------------- +130: [11:06:04] Test atom-pair additional output +130: [11:06:04] done +130: [11:06:04] ------------------------------------- +130: [11:06:04] Test Folded Atom Pairs. +130: [11:06:04] done +130: [11:06:04] ------------------------------------- +130: [11:06:04] Test Rooted Atom Pairs. +130: [11:06:04] done +130: [11:06:04] ------------------------------------- +130: [11:06:04] Test ignoring atoms in Atom Pairs. +130: [11:06:04] done +130: [11:06:04] ------------------------------------- +130: [11:06:04] Test Atom Pairs including info about chirality. +130: [11:06:04] done +130: [11:06:04] ------------------------------------- +130: [11:06:04] Test Morgan Fingerprints. +130: [11:06:04] done +130: [11:06:04] ------------------------------------- +130: [11:06:04] Test morgan fp generator +130: [11:06:04] done +130: [11:06:04] ------------------------------------- +130: [11:06:04] Test Morgan Fingerprints using fromAtoms argument. +130: [11:06:04] done +130: [11:06:04] ------------------------------------- +130: [11:06:04] Test Morgan Fingerprints as bit vects. +130: [11:06:04] done +130: [11:06:04] ------------------------------------- +130: [11:06:04] Test Morgan Fingerprints with feature invariants. +130: [11:06:04] done +130: [11:06:04] ------------------------------------- +130: [11:06:04] Test additional Morgan fingerprints options. +130: [11:06:04] done +130: [11:06:04] ------------------------------------- +130: [11:06:04] Test GitHub Issue 695: Include cis/trans stereochemistry when useChirality=true with the morgan fingerprints +130: [11:06:04] done +130: [11:06:04] ------------------------------------- +130: [11:06:04] Single atoms setting radius 1 bits in Morgan fingerprints +130: [11:06:04] done +130: [11:06:04] ------------------------------------- +130: [11:06:04] Test different invariant generator combinations +130: [11:06:04] done +130: [11:06:04] ------------------------------------- +130: [11:06:04] Test invariant overriding +130: [11:06:04] done +130: [11:06:04] ------------------------------------- +130: [11:06:04] Test RDKit fp generator 128: pass 2 128: launch :0 128: launch :1 +126: Warning: Atom Count for residue ASN39A does not match expected count 128: launch :2 128: launch :3 -130: [02:19:08] done -130: [02:19:08] ------------------------------------- -130: [02:19:08] Test unfolded version of RDKFP -130: [02:19:08] ------------------------------------- -130: [02:19:08] Test topological torsion fp generator -130: [02:19:08] DEPRECATION WARNING: please use TopologicalTorsionGenerator -130: [02:19:08] DEPRECATION WARNING: please use TopologicalTorsionGenerator -130: [02:19:08] DEPRECATION WARNING: please use TopologicalTorsionGenerator -130: [02:19:08] DEPRECATION WARNING: please use TopologicalTorsionGenerator -130: [02:19:08] DEPRECATION WARNING: please use TopologicalTorsionGenerator -130: [02:19:08] DEPRECATION WARNING: please use TopologicalTorsionGenerator -130: [02:19:08] DEPRECATION WARNING: please use TopologicalTorsionGenerator -130: [02:19:08] DEPRECATION WARNING: please use TopologicalTorsionGenerator -130: [02:19:08] DEPRECATION WARNING: please use TopologicalTorsionGenerator -126: Warning: Atom Count for residue ASN39A does not match expected count -130: [02:19:08] DEPRECATION WARNING: please use TopologicalTorsionGenerator -130: [02:19:08] done -130: [02:19:08] ------------------------------------- -130: [02:19:08] Test Topological Torsions. -130: [02:19:08] done -130: [02:19:08] ------------------------------------- -130: [02:19:08] Test Folded torsions. -130: [02:19:08] done -130: [02:19:08] ------------------------------------- -130: [02:19:08] Test Bulk Topological Torsions. -130: [02:19:08] done -130: [02:19:08] ------------------------------------- -130: [02:19:08] Test Rooted Topological Torsions. -130: [02:19:08] done -130: [02:19:08] ------------------------------------- -130: [02:19:08] Test ignoring atoms in Topological Torsions. -130: [02:19:08] done -130: [02:19:08] ------------------------------------- -130: [02:19:08] ------------------------------------- -130: [02:19:08] Test Topological Torsions including info about chirality. -130: [02:19:08] done -130: [02:19:08] ------------------------------------- -130: [02:19:08] Test GitHub Issue 25: fingerprint backwards compatibility. -130: [02:19:08] done -130: [02:19:08] ------------------------------------- -130: [02:19:08] Test GitHub Issue 334: explicit Hs in SMILES modifies atom pair (and topological torsion) FP. -130: [02:19:08] done -130: [02:19:08] ------------------------------------- -130: [02:19:08] Test GitHub Issue 811: rooted atom fingerprint non identical for the same molecules #811 -130: [02:19:08] done -130: [02:19:08] ------------------------------------- -130: [02:19:08] Test convenience and bulk fp calculation functions +117: =>start test 2 WHIM custom +117: [11:06:04] test on : 365 molecules done 126: Warning: Atom Count for residue GLU53A does not match expected count +130: [11:06:04] done +130: [11:06:04] ------------------------------------- +130: [11:06:04] Test unfolded version of RDKFP +130: [11:06:04] ------------------------------------- +130: [11:06:04] Test topological torsion fp generator +130: [11:06:04] DEPRECATION WARNING: please use TopologicalTorsionGenerator +130: [11:06:04] DEPRECATION WARNING: please use TopologicalTorsionGenerator +130: [11:06:04] DEPRECATION WARNING: please use TopologicalTorsionGenerator +130: [11:06:04] DEPRECATION WARNING: please use TopologicalTorsionGenerator +130: [11:06:04] DEPRECATION WARNING: please use TopologicalTorsionGenerator +130: [11:06:04] DEPRECATION WARNING: please use TopologicalTorsionGenerator +130: [11:06:04] DEPRECATION WARNING: please use TopologicalTorsionGenerator +130: [11:06:04] DEPRECATION WARNING: please use TopologicalTorsionGenerator +130: [11:06:04] DEPRECATION WARNING: please use TopologicalTorsionGenerator +130: [11:06:04] DEPRECATION WARNING: please use TopologicalTorsionGenerator +130: [11:06:04] done +130: [11:06:04] ------------------------------------- +130: [11:06:04] Test Topological Torsions. +130: [11:06:04] done +130: [11:06:04] ------------------------------------- +130: [11:06:04] Test Folded torsions. +130: [11:06:04] done +130: [11:06:04] ------------------------------------- +130: [11:06:04] Test Bulk Topological Torsions. 126: Warning: Atom Count for residue ARG64A does not match expected count +117: =>start test 1 WHIM custom +117: [11:06:04] test on : 365 molecules done +130: [11:06:04] done +130: [11:06:04] ------------------------------------- +130: [11:06:04] Test Rooted Topological Torsions. +130: [11:06:04] done +130: [11:06:04] ------------------------------------- +130: [11:06:04] Test ignoring atoms in Topological Torsions. +130: [11:06:04] done +130: [11:06:04] ------------------------------------- +130: [11:06:04] ------------------------------------- +130: [11:06:04] Test Topological Torsions including info about chirality. +130: [11:06:04] done +130: [11:06:04] ------------------------------------- +130: [11:06:04] Test GitHub Issue 25: fingerprint backwards compatibility. +130: [11:06:04] done +130: [11:06:04] ------------------------------------- +130: [11:06:04] Test GitHub Issue 334: explicit Hs in SMILES modifies atom pair (and topological torsion) FP. +130: [11:06:04] done +130: [11:06:04] ------------------------------------- +130: [11:06:04] Test GitHub Issue 811: rooted atom fingerprint non identical for the same molecules #811 +130: [11:06:04] done +130: [11:06:04] ------------------------------------- +130: [11:06:04] Test convenience and bulk fp calculation functions 29: Checking against /build/reproducible-path/rdkit-202503.1/Code/ForceField/MMFF/test_data/MMFF94_reference.log... -130: [02:19:08] done -130: [02:19:08] ------------------------------------- -130: [02:19:08] Test GitHub Issue #6958 -130: [02:19:08] DEPRECATION WARNING: please use AtomPairGenerator -119/238 Test #130: testFingerprintGenerators .............. Passed 0.47 sec +126: Warning: Atom Count for residue LYS80A does not match expected count +122: =>start test GETAWAY +122: [11:06:05] test on : 365 molecules done +119/238 Test #122: testGETAWAY ............................ Passed 1.46 sec test 131 Start 131: fpTestCatch 131: Test command: /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/Fingerprints/fpTestCatch 131: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/Fingerprints 131: Test timeout computed to be: 1500 -131: Randomness seeded to: 2401999466 +29: All 191 tests passed +131: Randomness seeded to: 858388234 131: =============================================================================== 131: All tests passed (188 assertions in 16 test cases) 131: -120/238 Test #131: fpTestCatch ............................ Passed 0.02 sec +120/238 Test #131: fpTestCatch ............................ Passed 0.06 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 -125: Warning: Atom Count for residue GLU150A does not match expected count -126: Warning: Atom Count for residue LYS80A does not match expected count -29: All 191 tests passed -125: Warning: Atom Count for residue ASN157A does not match expected count -132: Randomness seeded to: 2907613653 -132: =============================================================================== -132: All tests passed (2737 assertions in 7 test cases) -132: -121/238 Test #132: fpGenTestCatch ......................... Passed 0.08 sec +130: [11:06:05] done +130: [11:06:05] ------------------------------------- +130: [11:06:05] Test GitHub Issue #6958 +130: [11:06:05] DEPRECATION WARNING: please use AtomPairGenerator +121/238 Test #130: testFingerprintGenerators .............. Passed 0.58 sec test 133 Start 133: pyTestGenerator @@ -26265,57 +26292,52 @@ 133: 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.smi... -122: =>start test GETAWAY -122: [02:19:09] test on : 365 molecules done -122/238 Test #122: testGETAWAY ............................ Passed 1.68 sec +132: Randomness seeded to: 2830814687 +132: =============================================================================== +132: All tests passed (2737 assertions in 7 test cases) +132: +122/238 Test #132: fpGenTestCatch ......................... Passed 0.10 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 -74: [02:19:09] Finished: testSmiCorrectness() -74: [02:19:09] ----------------------------------------- -74: -74: [02:19:09] -74: ----------------------------------------- -133: .............. -133: ---------------------------------------------------------------------- -133: Ran 14 tests in 0.128s -133: -133: OK -74: [02:19:09] Property will be truncated after the first blank line -74: [02:19:09] Property will be truncated after the first blank line -74: [02:19:09] Spurious data before the first property will be ignored -74: [02:19:09] Property will be truncated after the first blank line +125: Warning: Atom Count for residue GLU150A does not match expected count +125: Warning: Atom Count for residue ASN157A does not match expected count 134: .. 134: ---------------------------------------------------------------------- -134: Ran 2 tests in 0.038s +134: Ran 2 tests in 0.020s 134: 134: OK -123/238 Test #134: pyTestMHFP ............................. Passed 0.41 sec +126: Warning: Atom Count for residue GLU150A does not match expected count +133: .............. +133: ---------------------------------------------------------------------- +133: Ran 14 tests in 0.114s +133: +133: OK +123/238 Test #134: pyTestMHFP ............................. Passed 0.27 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 -126: Warning: Atom Count for residue GLU150A does not match expected count -124/238 Test #135: testPartialCharges ..................... Passed 0.02 sec +126: Warning: Atom Count for residue ASN157A does not match expected count +124/238 Test #135: testPartialCharges ..................... Passed 0.04 sec test 136 Start 136: pyPartialCharges 136: Test command: /usr/bin/python3 "/build/reproducible-path/rdkit-202503.1/Code/GraphMol/PartialCharges/Wrap/testPartialCharges.py" 136: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/PartialCharges/Wrap 136: Test timeout computed to be: 1500 -125/238 Test #133: pyTestGenerator ........................ Passed 0.59 sec +125/238 Test #133: pyTestGenerator ........................ Passed 0.45 sec test 137 Start 137: testMolTransforms 137: Test command: /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/MolTransforms/testMolTransforms 137: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/MolTransforms 137: Test timeout computed to be: 1500 -126: Warning: Atom Count for residue ASN157A does not match expected count 137: *********************************************************** 137: Testing MolTransforms 137: --------------------------------- @@ -26353,7 +26375,7 @@ 138: Test command: /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/MolTransforms/molTransformsTestCatch 138: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/MolTransforms 138: Test timeout computed to be: 1500 -138: Randomness seeded to: 1288860319 +138: Randomness seeded to: 3757948881 138: =============================================================================== 138: All tests passed (4 assertions in 1 test case) 138: @@ -26364,80 +26386,79 @@ 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: [02:19:09] test on : 365 molecules done -128/238 Test #117: testRDFcustom .......................... Passed 2.85 sec +136: ....... +136: ---------------------------------------------------------------------- +136: Ran 7 tests in 0.058s +136: +136: OK +128/238 Test #136: pyPartialCharges ....................... Passed 0.28 sec test 140 Start 140: forceFieldHelpersCatch 140: Test command: /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/ForceFieldHelpers/forceFieldHelpersCatch 140: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/ForceFieldHelpers 140: Test timeout computed to be: 1500 -140: Randomness seeded to: 1775444587 +74: [11:06:05] Finished: testSmiCorrectness() +74: [11:06:05] ----------------------------------------- +74: +74: [11:06:05] +74: ----------------------------------------- +74: [11:06:05] Spurious data before the first property will be ignored +74: [11:06:05] Property will be truncated after the first blank line +74: [11:06:05] Property will be truncated after the first blank line +74: [11:06:05] Property will be truncated after the first blank line +140: Randomness seeded to: 489242305 140: =============================================================================== 140: All tests passed (17 assertions in 2 test cases) 140: -129/238 Test #140: forceFieldHelpersCatch ................. Passed 0.02 sec +129/238 Test #140: forceFieldHelpersCatch ................. Passed 0.03 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 -74: [02:19:09] Finished: testSDCorrectness() -74: [02:19:09] ----------------------------------------- -74: -130/238 Test #74: testMultithreadedMolSupplier ........... Passed 5.30 sec +141: [11:06:05] ------------------------------------- +141: [11:06:05] Test MMFF atom types. +141: [11:06:05] done +141: [11:06:05] ------------------------------------- +141: [11:06:05] Testing MMFF builder tools. +141: [11:06:05] done +141: [11:06:05] ------------------------------------- +141: [11:06:05] Testing MMFF builder+minimization. +117: =>start test GETAWAY custom +117: [11:06:05] test on : 365 molecules done +130/238 Test #117: testRDFcustom .......................... Passed 2.91 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: [02:19:09] ------------------------------------- -141: [02:19:09] Test MMFF atom types. -141: [02:19:09] done -141: [02:19:09] ------------------------------------- -141: [02:19:09] Testing MMFF builder tools. -142: [02:19:09] ------------------------------------- -142: [02:19:09] Test MMFF multithreading -141: [02:19:09] done -141: [02:19:09] ------------------------------------- -141: [02:19:09] Testing MMFF builder+minimization. -80: =============================================================================== -80: All tests passed (1596 assertions in 100 test cases) -80: -131/238 Test #80: fileParsersCatchTest ................... Passed 5.18 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 -143: [02:19:09] ------------------------------------- -143: [02:19:09] Test UFF atom labels. -143: [02:19:09] done -143: [02:19:09] ------------------------------------- -143: [02:19:09] Test UFF atom typer. -143: [02:19:09] done -143: [02:19:09] ------------------------------------- -143: [02:19:09] Testing UFF builder tools. -143: [02:19:09] done -143: [02:19:09] ------------------------------------- -143: [02:19:09] Testing UFF builder+minimization. +142: [11:06:05] ------------------------------------- +142: [11:06:05] Test MMFF multithreading +141: [11:06:05] done +141: [11:06:05] ------------------------------------- +141: [11:06:05] Testing Issue239. +141: [11:06:05] done +141: [11:06:06] ------------------------------------- +141: [11:06:06] Testing calcEnergy with passed coords. +141: [11:06:06] done +141: [11:06:06] ------------------------------------- +141: [11:06:06] Testing calcGrad. 142: processing 142: launch :0 142: launch :1 142: launch :2 142: launch :3 142: launch :4 -141: [02:19:09] done -141: [02:19:09] ------------------------------------- -141: [02:19:09] Testing Issue239. 142: launch :5 142: launch :6 142: launch :7 142: launch :8 +141: [11:06:06] done +141: [11:06:06] ------------------------------------- +141: [11:06:06] Testing Issue242. 142: launch :9 142: launch :10 142: launch :11 @@ -26453,528 +26474,636 @@ 142: launch :21 142: launch :22 142: launch :23 -141: [02:19:09] done -141: [02:19:09] ------------------------------------- -141: [02:19:09] Testing calcEnergy with passed coords. -141: [02:19:09] done -141: [02:19:09] ------------------------------------- -141: [02:19:09] Testing calcGrad. -141: [02:19:09] done -141: [02:19:09] ------------------------------------- -141: [02:19:09] Testing Issue242. -143: [02:19:09] done -143: [02:19:09] ------------------------------------- -143: [02:19:09] Testing UFF special cases. -143: [02:19:09] UFFTYPER: Unrecognized charge state for atom: 0 -143: [02:19:09] done -143: [02:19:09] ------------------------------------- -143: [02:19:09] Testing Issue239. -143: [02:19:09] done -143: [02:19:09] ------------------------------------- -143: [02:19:09] Testing calcEnergy with passed coords. -143: [02:19:09] done -143: [02:19:09] ------------------------------------- -143: [02:19:09] Testing calcGrad. -136: ....... -136: ---------------------------------------------------------------------- -136: Ran 7 tests in 0.112s -136: -136: OK -143: [02:19:09] done -143: [02:19:09] ------------------------------------- -143: [02:19:09] Testing SFIssue1653802. -143: [02:19:09] done -143: [02:19:09] ------------------------------------- -143: [02:19:09] Testing SFIssue2378119. -143: [02:19:09] done -143: [02:19:09] ------------------------------------- -143: [02:19:09] Test UFF force-field parameter getters. -143: [02:19:09] ------------------------------------- -143: [02:19:09] Testing handling missing parameters. -143: [02:19:09] UFFTYPER: Unrecognized hybridization for atom: 0 -143: [02:19:09] UFFTYPER: Unrecognized atom type: Cu+1 (0) -143: [02:19:09] UFFTYPER: Unrecognized hybridization for atom: 0 -143: [02:19:09] UFFTYPER: Unrecognized atom type: Cu+1 (0) -143: [02:19:09] done -143: [02:19:09] ------------------------------------- -143: [02:19:09] Testing SFIssue3009337. -141: [02:19:09] done -141: [02:19:09] ------------------------------------- -141: [02:19:09] Testing github 308: crash during MMFF parameterization . -143: [02:19:09] done -143: [02:19:09] ------------------------------------- -143: [02:19:09] Test UFF multithreading -141: [02:19:09] ------------------------------------- -141: [02:19:09] Testing SFIssue1653802. -143: generating reference data -141: [02:19:09] done -141: [02:19:09] ------------------------------------- -141: [02:19:09] Testing SFIssue2378119. -141: [02:19:09] done -141: [02:19:09] ------------------------------------- -141: [02:19:09] Test MMFF force-field parameter getters. -141: [02:19:09] ------------------------------------- -141: [02:19:09] Test MMFF multithreading +141: [11:06:06] done +141: [11:06:06] ------------------------------------- +141: [11:06:06] Testing github 308: crash during MMFF parameterization . +141: [11:06:06] ------------------------------------- +141: [11:06:06] Testing SFIssue1653802. +141: [11:06:06] done +141: [11:06:06] ------------------------------------- +141: [11:06:06] Testing SFIssue2378119. +141: [11:06:06] done +141: [11:06:06] ------------------------------------- +141: [11:06:06] Test MMFF force-field parameter getters. +141: [11:06:06] ------------------------------------- +141: [11:06:06] Test MMFF multithreading 141: generating reference data 139: ........ 139: ---------------------------------------------------------------------- -139: Ran 8 tests in 0.041s +139: Ran 8 tests in 0.061s 139: 139: OK -132/238 Test #136: pyPartialCharges ....................... Passed 0.45 sec +131/238 Test #139: pyMolTransforms ........................ Passed 0.48 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 +74: [11:06:06] Finished: testSDCorrectness() +74: [11:06:06] ----------------------------------------- +74: +132/238 Test #74: testMultithreadedMolSupplier ........... Passed 5.65 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 +143: [11:06:06] ------------------------------------- +143: [11:06:06] Test UFF atom labels. +142: done 144: ------------------------------------- 144: Test CrystalFF torsional term. -142: done -133/238 Test #139: pyMolTransforms ........................ Passed 0.40 sec +142: [11:06:06] done +143: [11:06:06] done +143: [11:06:06] ------------------------------------- +143: [11:06:06] Test UFF atom typer. +143: [11:06:06] done +143: [11:06:06] ------------------------------------- +143: [11:06:06] Testing UFF builder tools. +143: [11:06:06] done +143: [11:06:06] ------------------------------------- +143: [11:06:06] Testing UFF builder+minimization. +133/238 Test #142: testMMFFForceFieldHelpersMultiThread ... Passed 0.32 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 -142: [02:19:09] done -134/238 Test #144: testCrystalForceField .................. Passed 0.08 sec +141: processing +141: launch :0 +141: launch :1 +141: launch :[11:06:06] Rep: 0 Mol:0 +141: [11:06:06] Rep: 0 Mol:1 +141: 2 +141: launch :3 +141: [11:06:06] [11:06:06] Rep: 0 Mol:2 +141: [11:06:06] Rep: 0 Mol:4 +141: [11:06:06] Rep: 0 Mol:3 +141: Rep: 0 Mol:5 +141: [11:06:06] Rep: 0 Mol:9 +141: [11:06:06] Rep: 0 Mol:8 +141: [11:06:06] Rep: 0 Mol:12 +141: [11:06:06] Rep: 0 Mol:13 +141: [11:06:06] Rep: 0 Mol:16 +141: [11:06:06] Rep: 0 Mol:6 +141: [11:06:06] [11:06:06] Rep: 0 Mol:17 +141: Rep: 0 Mol:10 +141: [11:06:06] Rep: 0 Mol:7 +143: [11:06:06] done +143: [11:06:06] ------------------------------------- +143: [11:06:06] Testing UFF special cases. +141: [11:06:06] Rep: 0 Mol:20 +143: [11:06:06] UFFTYPER: Unrecognized charge state for atom: 0 +143: [11:06:06] done +143: [11:06:06] ------------------------------------- +143: [11:06:06] Testing Issue239. +134/238 Test #144: testCrystalForceField .................. Passed 0.15 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 -135/238 Test #142: testMMFFForceFieldHelpersMultiThread ... Passed 0.32 sec +141: [11:06:06] Rep: 0 Mol:24 +141: [11:06:06] Rep: 0 Mol:11 +141: [11:06:06] Rep: 0 Mol:15 +141: [11:06:06] Rep: 0 Mol:28 +143: [11:06:06] done +143: [11:06:06] ------------------------------------- +143: [11:06:06] Testing calcEnergy with passed coords. +141: [11:06:06] Rep: 0 Mol:19 +141: [11:06:06] Rep: 0 Mol:23 +141: [11:06:06] Rep: 0 Mol:27 +143: [11:06:06] done +143: [11:06:06] ------------------------------------- +143: [11:06:06] Testing calcGrad. +141: [11:06:06] Rep: 0 Mol:31 +141: [11:06:06] Rep: 0 Mol:21 +141: [11:06:06] Rep: 0 Mol:25 +143: [11:06:06] done +143: [11:06:06] ------------------------------------- +143: [11:06:06] Testing SFIssue1653802. +143: [11:06:06] done +143: [11:06:06] ------------------------------------- +143: [11:06:06] Testing SFIssue2378119. +143: [11:06:06] done +146: [11:06:06] ******************************************************** +146: [11:06:06] Testing DistGeomHelpers +146: [11:06:06] --------------------------------- +146: [11:06:06] test2 +146: +146: go +143: [11:06:06] ------------------------------------- +143: [11:06:06] Test UFF force-field parameter getters. +146: ------------------------------------- +146: +143: [11:06:06] ------------------------------------- +143: [11:06:06] Testing handling missing parameters. +143: [11:06:06] UFFTYPER: Unrecognized hybridization for atom: 0 +143: [11:06:06] UFFTYPER: Unrecognized atom type: Cu+1 (0) +143: [11:06:06] UFFTYPER: Unrecognized hybridization for atom: 0 +143: [11:06:06] UFFTYPER: Unrecognized atom type: Cu+1 (0) +143: [11:06:06] done +143: [11:06:06] ------------------------------------- +143: [11:06:06] Testing SFIssue3009337. +141: [11:06:06] Rep: 0 Mol:29 +143: [11:06:06] done +143: [11:06:06] ------------------------------------- +143: [11:06:06] Test UFF multithreading +141: [11:06:06] Rep: 0 Mol:14 +143: generating reference data +141: [11:06:06] Rep: 0 Mol:18 +141: [11:06:06] Rep: 0 Mol:22 +141: [11:06:06] Rep: 0 Mol:26 +141: [11:06:06] Rep: 0 Mol:30 +141: [11:06:06] Rep: 20 Mol:3 +141: [11:06:06] Rep: 20 Mol:7 +141: [11:06:06] Rep: 20 Mol:11 +141: [11:06:06] Rep: 20 Mol:15 +141: [11:06:06] Rep: 20 Mol:19 +141: [11:06:06] Rep: 20 Mol:23 +141: [11:06:06] Rep: 20 Mol:27 +141: [11:06:06] Rep: 20 Mol:31 +141: [11:06:06] Rep: 20 Mol:0 +141: [11:06:06] Rep: 20 Mol:4 +141: [11:06:06] Rep: 20 Mol:8 +141: [11:06:06] Rep: 20 Mol:12 +141: [11:06:06] Rep: 20 Mol:16 +141: [11:06:06] Rep: 20 Mol:20 +141: [11:06:06] Rep: 20 Mol:24 +141: [11:06:06] Rep: 20 Mol:28 +141: [11:06:06] Rep: 20 Mol:1 +141: [11:06:06] Rep: 20 Mol:5 +141: [11:06:06] Rep: 20 Mol:9 +141: [11:06:06] Rep: 20 Mol:13 +141: [11:06:06] Rep: 20 Mol:17 +141: [11:06:06] Rep: 20 Mol:21 +141: [11:06:06] Rep: 20 Mol:25 +141: [11:06:06] Rep: 20 Mol:29 +145: [11:06:06] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +145: [11:06:06] Molecule does not have explicit Hs. Consider calling AddHs() +145: [11:06:06] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +145: [11:06:06] Molecule does not have explicit Hs. Consider calling AddHs() +145: [11:06:06] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +145: [11:06:06] Molecule does not have explicit Hs. Consider calling AddHs() +145: [11:06:06] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +145: [11:06:06] Molecule does not have explicit Hs. Consider calling AddHs() +145: [11:06:06] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +145: [11:06:06] Molecule does not have explicit Hs. Consider calling AddHs() +145: ..[11:06:06] Molecule does not have explicit Hs. Consider calling AddHs() +145: [11:06:06] Molecule does not have explicit Hs. Consider calling AddHs() +145: .[11:06:06] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +145: [11:06:06] Molecule does not have explicit Hs. Consider calling AddHs() +80: =============================================================================== +80: All tests passed (1596 assertions in 100 test cases) +80: +135/238 Test #80: fileParsersCatchTest ................... Passed 5.95 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 -147: Randomness seeded to: 2196774687 -146: [02:19:10] ******************************************************** -146: [02:19:10] Testing DistGeomHelpers -146: [02:19:10] --------------------------------- -146: [02:19:10] test2 -146: -146: go -146: ------------------------------------- -146: -147: [02:19:10] [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: [02:19:10] [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: [02:19:10] [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: [02:19:10] [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: [02:19:10] [!#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: [02:19:10] [!#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: [02:19:10] [!#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: [02:19:10] [!#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: [02:19:10] [!#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: [02:19:10] [!#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: [02:19:10] [!#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: [02:19:10] [!#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: [02:19:10] [!#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: [02:19:10] [!#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: [02:19:10] [!#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: [02:19:10] [!#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: [02:19:10] [!#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: [02:19:10] [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: [02:19:10] [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: [02:19:10] [*: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: [02:19:10] [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: [02:19:10] [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: [02:19:10] [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: [02:19:10] [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: [02:19:10] [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: [02:19:10] [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: [02:19:10] [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: [02:19:10] [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: [02:19:10] [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: [02:19:10] [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: [02:19:10] [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: [02:19:10] [$([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: [02:19:10] [$(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: [02:19:10] [$(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: [02:19:10] [$(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: [02:19:10] [$(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: [02:19:10] [$(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: [02:19:10] [$(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: [02:19:10] [$(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: [02:19:10] [$(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: [02:19:10] [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: [02:19:10] [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: [02:19:10] [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: [02:19:10] [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: [02:19:10] [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: [02:19:10] 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: [02:19:10] [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: [02:19:10] [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: [02:19:10] [!#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: [02:19:10] [!#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: [02:19:10] [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: [02:19:10] [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: [02:19:10] [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: [02:19:10] [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: [02:19:10] [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: [02:19:10] [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: [02:19:10] [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: [02:19:10] [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: [02:19:10] [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: [02:19:10] [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: [02:19:10] [$([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: [02:19:10] [$([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: [02:19:10] [$(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: [02:19:10] [$(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: [02:19:10] [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: [02:19:10] [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: [02:19:10] 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: [02:19:10] 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: [02:19:10] [!#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: [02:19:10] [!#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: [02:19:10] [!#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: [02:19:10] [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: [02:19:10] [C:1][CX4;r{9-}:2]@;-[CX3;r{9-}:3]=[O:4]: 7 6 4 5, [(1 0), (1 0), (-1 1), (1 0), (1 0), (1 0)] -147: ----------- -147: [02:19:10] [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: [02:19:10] [$([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: [02:19:10] [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: [02:19:10] N[C;r{9-}:2](=[O:1])@;-[CH2;r{9-}:3][N:4]: 15 14 13 12, [(1 0), (-1 10), (1 0), (1 0), (1 0), (1 0)] -147: ----------- -147: ----------- -147: [02:19:10] [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: [02:19:10] [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: [02:19:10] [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: [02:19:10] [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: [02:19:10] [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: [02:19:10] [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: [02:19:10] [$(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: [02:19:10] [$(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: [02:19:10] [$(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: [02:19:10] [$(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: [02:19:10] [$(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: [02:19:10] [$(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: [02:19:10] [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: [02:19:10] [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: [02:19:10] [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: [02:19:10] [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: [02:19:10] [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: [02:19:10] [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)] -147: [02:19:10] UFFTYPER: Unrecognized atom type: Pt5+2 (1) -147: [02:19:10] UFFTYPER: Unrecognized charge state for atom: 1 -147: [02:19:10] UFFTYPER: Unrecognized charge state for atom: 1 +145: .[11:06:06] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +145: [11:06:06] Molecule does not have explicit Hs. Consider calling AddHs() 143: processing 143: launch :0 143: launch :1 -143: launch :2 -143: [02:19:10] Rep: 0 Mol:1 +143: launch :[11:06:06] Rep: 0 Mol:0 +143: 2 +143: [11:06:06] Rep: 0 Mol:1 +143: [11:06:06] Rep: 0 Mol:4 +143: [11:06:06] Rep: 0 Mol:5 +143: [11:06:06] Rep: 0 Mol:9 +143: [11:06:06] Rep: 0 Mol:2 +147: Randomness seeded to: 1407113199 +141: [11:06:06] Rep: 40 Mol:3 143: launch :3 -143: [02:19:10] Rep: 0 Mol:2 -143: [02:19:10] Rep: 0 Mol:0 -143: [02:19:10] Rep: 0 Mol:5 -143: [02:19:10] Rep: 0 Mol:9 -143: [02:19:10] Rep: 0 Mol:3 -147: [02:19:10] UFFTYPER: Unrecognized charge state for atom: 1 -143: [02:19:10] Rep: 0 Mol:13 -143: [02:19:10] Rep: 0 Mol:4 -143: [02:19:10] Rep: 0 Mol:17 -143: [02:19:10] Rep: 0 Mol:7 -143: [02:19:10] Rep: 0 Mol:11 -143: [02:19:10] Rep: 0 Mol:15 -145: [02:19:10] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -145: [02:19:10] Molecule does not have explicit Hs. Consider calling AddHs() -145: [02:19:10] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -143: [02:19:10] Rep: 0 Mol:6 -145: [02:19:10] Molecule does not have explicit Hs. Consider calling AddHs() -143: [02:19:10] Rep: 0 Mol:19 -145: [02:19:10] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -145: [02:19:10] Molecule does not have explicit Hs. Consider calling AddHs() -145: [02:19:10] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -145: [02:19:10] Molecule does not have explicit Hs. Consider calling AddHs() -145: [02:19:10] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -145: [02:19:10] Molecule does not have explicit Hs. Consider calling AddHs() -143: [02:19:10] Rep: 0 Mol:10 -143: [02:19:10] Rep: 0 Mol:23 -143: [02:19:10] Rep: 0 Mol:27 -145: ..[02:19:10] Molecule does not have explicit Hs. Consider calling AddHs() -145: [02:19:10] Molecule does not have explicit Hs. Consider calling AddHs() -145: .[02:19:10] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -145: [02:19:10] Molecule does not have explicit Hs. Consider calling AddHs() -143: [02:19:10] Rep: 0 Mol:31 -145: .[02:19:10] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -145: [02:19:10] Molecule does not have explicit Hs. Consider calling AddHs() -143: [02:19:10] Rep: 0 Mol:21 -143: [02:19:10] Rep: 0 Mol:8 -143: [02:19:10] Rep: 0 Mol:25 -143: [02:19:10] Rep: 0 Mol:29 -143: [02:19:10] Rep: 0 Mol:12 -143: [02:19:10] Rep: 0 Mol:16 -145: .[02:19:10] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -145: [02:19:10] Molecule does not have explicit Hs. Consider calling AddHs() -141: processing -141: launch :0 -141: launch :1 -141: launch :[02:19:10] Rep: 0 Mol:0 -141: [02:19:10] Rep: 0 Mol:1 -145: .[02:19:10] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -145: [02:19:10] Molecule does not have explicit Hs. Consider calling AddHs() -141: [02:19:10] Rep: 0 Mol:5 -141: [02:19:10] 2 -141: launch :3 -141: [02:19:10] Rep: 0 Mol:2 -141: Rep: 0 Mol:4 -143: [02:19:10] Rep: 0 Mol:14[02:19:10] Rep: 0 Mol:20 -143: -143: [02:19:10] Rep: 0 Mol:18 -141: [02:19:10] Rep: 0 Mol:3 -141: [02:19:10] Rep: 0 Mol:9 -145: .[02:19:10] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -145: [02:19:10] Molecule does not have explicit Hs. Consider calling AddHs() -145: .[02:19:10] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -145: [02:19:10] Molecule does not have explicit Hs. Consider calling AddHs() -145: .[02:19:10] UFFTYPER: Unrecognized hybridization for atom: 0 -145: [02:19:10] UFFTYPER: Unrecognized atom type: Cu+1 (0) -141: [02:19:10] Rep: 0 Mol:13 -145: .[02:19:10] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -143: [02:19:10] [02:19:10] Rep: 0 Mol:24 -143: Rep: 0 Mol:22 -145: [02:19:10] Molecule does not have explicit Hs. Consider calling AddHs() -145: [02:19:10] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -145: [02:19:10] Molecule does not have explicit Hs. Consider calling AddHs() -145: [02:19:10] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -145: [02:19:10] Molecule does not have explicit Hs. Consider calling AddHs() -145: [02:19:10] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -143: [02:19:10] Rep: 0 Mol:26 -145: [02:19:10] Molecule does not have explicit Hs. Consider calling AddHs() -143: [02:19:10] Rep: 0 Mol:28 -145: [02:19:10] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -145: [02:19:10] Molecule does not have explicit Hs. Consider calling AddHs() -145: .[02:19:10] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -145: [02:19:10] Molecule does not have explicit Hs. Consider calling AddHs() -141: [02:19:10] Rep: 0 Mol:8 -145: .[02:19:10] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -145: [02:19:10] Molecule does not have explicit Hs. Consider calling AddHs() -145: .[02:19:10] Molecule does not have explicit Hs. Consider calling AddHs() -145: [02:19:10] Molecule does not have explicit Hs. Consider calling AddHs() -145: ...[02:19:10] Molecule does not have explicit Hs. Consider calling AddHs() -145: [02:19:10] Molecule does not have explicit Hs. Consider calling AddHs() -141: [02:19:10] Rep: 0 Mol:12 -141: [02:19:10] Rep: 0 Mol:17 -141: [02:19:10] Rep: 0 Mol:6 -141: [02:19:10] Rep: 0 Mol:16 -143: [02:19:10] Rep: 0 Mol:30 -147: [02:19:10] UFFTYPER: Unrecognized charge state for atom: 5 -147: [02:19:10] UFFTYPER: Unrecognized charge state for atom: 5 -141: [02:19:10] Rep: 0 Mol:10 -145: [02:19:10] Molecule does not have explicit Hs. Consider calling AddHs() -141: [02:19:10] Rep: 0 Mol:20 -141: [02:19:10] Rep: 0 Mol:21 -147: [02:19:10] UFFTYPER: Unrecognized charge state for atom: 5 -141: [02:19:10] Rep: 0 Mol:24 +143: [11:06:06] Rep: 0 Mol:3 +143: [11:06:06] Rep: 0 Mol:13 +141: [11:06:06] Rep: 40 Mol:7 +141: [11:06:06] Rep: 40 Mol:11 +141: [11:06:06] Rep: 40 Mol:15 +141: [11:06:06] Rep: 40 Mol:19 +141: [11:06:06] Rep: 40 Mol:23 +141: [11:06:06] Rep: 40 Mol:27 +141: [11:06:06] Rep: 40 Mol:31 +143: [11:06:06] Rep: 0 Mol:17 +143: [11:06:06] Rep: 0 Mol:8 +143: [11:06:06] Rep: 0 Mol:6 +143: [11:06:06] Rep: 0 Mol:10 +143: [11:06:06] Rep: 0 Mol:12 +143: [11:06:06] Rep: 0 Mol:16 +145: .[11:06:06] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +145: [11:06:06] Molecule does not have explicit Hs. Consider calling AddHs() +143: [11:06:06] Rep: 0 Mol:7 +143: [11:06:06] Rep: 0 Mol:20 +143: [11:06:06] Rep: 0 Mol:11 +145: .[11:06:06] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +145: [11:06:06] Molecule does not have explicit Hs. Consider calling AddHs() +143: [11:06:06] Rep: 0 Mol:14 +147: [11:06:06] [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: [11:06:06] [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)] +143: [11:06:06] Rep: 0 Mol:24 +143: [11:06:06] Rep: 0 Mol:21 +141: [11:06:06] Rep: 20 Mol:2 +141: [11:06:06] Rep: 20 Mol:6 +143: [11:06:06] Rep: 0 Mol:28 +141: [11:06:06] Rep: 20 Mol:10 +143: [11:06:06] Rep: 0 Mol:18 +147: [11:06:06] [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: [11:06:06] [OX2:1][CX4:2]!@;-[CX4:3][N:4]: 48 46 45 49, [(1 0), (1 0), (1 4), (1 0), (1 0), (1 0)] +141: [11:06:06] Rep: 20 Mol:14 +147: [11:06:06] [!#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: [11:06:06] [!#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: [11:06:06] [!#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: [11:06:06] [!#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: [11:06:06] [!#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: [11:06:06] [!#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: [11:06:06] [!#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: [11:06:06] [!#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: [11:06:06] [!#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: [11:06:06] [!#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: [11:06:06] [!#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: [11:06:06] [!#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: [11:06:06] [!#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: [11:06:06] [C:1][CX4H2:2]!@;-[CX3:3]=[O:4]: 85 86 87 88, [(1 -1), (1 -0.5), (1 -0.2), (1 -0.3), (1 0), (1 -0.3)] +141: [11:06:06] Rep: 20 Mol:18 +147: [11:06:06] [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)] +141: [11:06:06] Rep: 20 Mol:22 +143: [11:06:06] Rep: 0 Mol:25 +143: [11:06:06] Rep: 0 Mol:22 +143: [11:06:06] Rep: 0 Mol:26 +141: [11:06:06] Rep: 20 Mol:26 +141: [11:06:06] Rep: 20 Mol:30 +141: [11:06:06] Rep: 40 Mol:0 +141: [11:06:06] Rep: 40 Mol:4 +141: [11:06:06] Rep: 40 Mol:8 +141: [11:06:06] Rep: 40 Mol:12 +141: [11:06:06] Rep: 40 Mol:16 +141: [11:06:06] Rep: 40 Mol:20 +141: [11:06:06] Rep: 40 Mol:24 +145: .[11:06:06] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +145: [11:06:06] Molecule does not have explicit Hs. Consider calling AddHs() +145: .[11:06:06] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +145: [11:06:06] Molecule does not have explicit Hs. Consider calling AddHs() +145: .[11:06:06] UFFTYPER: Unrecognized hybridization for atom: 0 +145: [11:06:06] UFFTYPER: Unrecognized atom type: Cu+1 (0) +145: .[11:06:06] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +145: [11:06:06] Molecule does not have explicit Hs. Consider calling AddHs() +145: [11:06:06] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +145: [11:06:06] Molecule does not have explicit Hs. Consider calling AddHs() +145: [11:06:06] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +145: [11:06:06] Molecule does not have explicit Hs. Consider calling AddHs() +145: [11:06:06] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +145: [11:06:06] Molecule does not have explicit Hs. Consider calling AddHs() +143: [11:06:06] Rep: 0 Mol:15 +143: [11:06:06] Rep: 0 Mol:19 +143: [11:06:06] Rep: 0 Mol:29 +147: [11:06:06] [*: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: [11:06:06] [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: [11:06:06] [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: [11:06:06] [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: [11:06:06] [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: [11:06:06] [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: [11:06:06] [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: [11:06:06] [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: [11:06:06] [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: [11:06:06] [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: [11:06:06] [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: [11:06:06] [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)] +143: [11:06:06] Rep: 0 Mol:23 +147: [11:06:06] [$([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)] +143: [11:06:06] Rep: 0 Mol:27 +147: [11:06:06] [$(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: [11:06:06] [$(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: [11:06:06] [$(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: [11:06:06] [$(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: [11:06:06] [$(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: [11:06:06] [$(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: [11:06:06] [$(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: [11:06:06] [$(C=O):1][NX3H1;r{9-}:2]@;-[CX4H1;r{9-}:3][H:4]: 105 107 52 171, [(-1 5), (1 0), (1 0), (1 0), (1 0), (1 0)] +141: [11:06:06] Rep: 40 Mol:28 +143: [11:06:06] Rep: 0 Mol:31 +145: [11:06:06] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +145: [11:06:06] Molecule does not have explicit Hs. Consider calling AddHs() +145: .[11:06:06] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +145: [11:06:06] Molecule does not have explicit Hs. Consider calling AddHs() +145: .[11:06:06] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +145: [11:06:06] Molecule does not have explicit Hs. Consider calling AddHs() +147: [11:06:06] [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)] +145: .[11:06:06] Molecule does not have explicit Hs. Consider calling AddHs() +145: [11:06:06] Molecule does not have explicit Hs. Consider calling AddHs() +147: [11:06:06] [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: [11:06:06] [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: [11:06:06] [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: [11:06:06] [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: [11:06:06] 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: [11:06:06] [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)] +145: ...[11:06:06] Molecule does not have explicit Hs. Consider calling AddHs() +145: [11:06:06] Molecule does not have explicit Hs. Consider calling AddHs() +143: [11:06:06] Rep: 0 Mol:30 +147: [11:06:06] [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: [11:06:06] [!#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: [11:06:06] [!#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: [11:06:06] [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: [11:06:06] [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: [11:06:06] [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: [11:06:06] [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: [11:06:06] [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: [11:06:06] [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: [11:06:06] [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: [11:06:06] [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: [11:06:06] [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)] +141: [11:06:06] Rep: 40 Mol:1 +141: [11:06:06] Rep: 40 Mol:5 +141: [11:06:06] Rep: 40 Mol:9 +141: [11:06:06] Rep: 40 Mol:13 +147: [11:06:06] [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: [11:06:06] [$([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: [11:06:06] [$([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: [11:06:06] [$(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: [11:06:06] [$(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: [11:06:06] [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: [11:06:06] [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: [11:06:06] 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: [11:06:06] 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: [11:06:06] [!#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: [11:06:06] [!#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: [11:06:06] [!#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: [11:06:06] [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: [11:06:06] [C:1][CX4;r{9-}:2]@;-[CX3;r{9-}:3]=[O:4]: 7 6 4 5, [(1 0), (1 0), (-1 1), (1 0), (1 0), (1 0)] +147: ----------- +147: [11:06:06] [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: [11:06:06] [$([CX3]=O):1][NX3H1;r{9-}:2]@;-[CX4H2;r{9-}:3][C:4]: 10 12 13 14, [(1 0), (1 0), (1 4), (1 0), (1 0), (1 0)] +141: [11:06:06] Rep: 40 Mol:17 +145: [11:06:06] Molecule does not have explicit Hs. Consider calling AddHs() +147: [11:06:06] [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: [11:06:06] 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: [11:06:06] Rep: 40 Mol:21 +141: [11:06:06] Rep: 40 Mol:25 +141: [11:06:06] Rep: 40 Mol:29 +147: ----------- +147: [11:06:06] [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: [11:06:06] [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: [11:06:06] [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: [11:06:06] [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: [11:06:06] [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: [11:06:06] [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: [11:06:06] [$(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: [11:06:06] [$(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: [11:06:06] [$(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: [11:06:06] [$(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: [11:06:06] [$(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: [11:06:06] [$(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: [11:06:06] [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: [11:06:06] [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: [11:06:06] [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: [11:06:06] [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: [11:06:06] [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: [11:06:06] [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: [11:06:06] Rep: 60 Mol:3 +141: [11:06:06] Rep: 60 Mol:7 +141: [11:06:06] Rep: 60 Mol:11 +141: [11:06:06] Rep: 60 Mol:15 +141: [11:06:06] Rep: 60 Mol:19 +141: [11:06:06] Rep: 60 Mol:23 +141: [11:06:06] Rep: 60 Mol:27 +141: [11:06:06] Rep: 60 Mol:31 145: ... 145: ---------------------------------------------------------------------- -145: Ran 19 tests in 0.102s +145: Ran 19 tests in 0.196s 145: 145: OK -141: [02:19:10] Rep: 0 Mol:28 -141: [02:19:10] Rep: 0 Mol:25 -141: [02:19:10] Rep: 0 Mol:7 -141: [02:19:10] Rep: 0 Mol:29 -141: [02:19:10] Rep: 0 Mol:11 -141: [02:19:10] Rep: 0 Mol:15 -141: [02:19:10] Rep: 0 Mol:14 -141: [02:19:10] Rep: 0 Mol:19 -141: [02:19:10] Rep: 0 Mol:18 -141: [02:19:10] Rep: 0 Mol:23 -141: [02:19:10] Rep: 0 Mol:27 -141: [02:19:10] Rep: 0 Mol:31 -136/238 Test #145: pyForceFieldHelpers .................... Passed 0.36 sec -141: [02:19:10] Rep: 0 Mol:22 +147: [11:06:06] UFFTYPER: Unrecognized atom type: Pt5+2 (1) +147: [11:06:06] UFFTYPER: Unrecognized charge state for atom: 1 +147: [11:06:06] UFFTYPER: Unrecognized charge state for atom: 1 +147: [11:06:06] UFFTYPER: Unrecognized charge state for atom: 1 +141: [11:06:06] Rep: 60 Mol:0 +141: [11:06:06] Rep: 60 Mol:4 +141: [11:06:06] Rep: 60 Mol:8 +141: [11:06:06] Rep: 60 Mol:12 +141: [11:06:06] Rep: 60 Mol:16 +141: [11:06:06] Rep: 60 Mol:20 +141: [11:06:06] Rep: 60 Mol:24 +141: [11:06:06] Rep: 40 Mol:2 +141: [11:06:06] Rep: 40 Mol:6 +141: [11:06:06] Rep: 40 Mol:10 +141: [11:06:06] Rep: 60 Mol:28 +141: [11:06:06] Rep: 40 Mol:14 +141: [11:06:06] Rep: 40 Mol:18 +141: [11:06:06] Rep: 40 Mol:22 +147: [11:06:06] UFFTYPER: Unrecognized charge state for atom: 5 +141: [11:06:06] Rep: 40 Mol:26 +141: [11:06:06] Rep: 40 Mol:30 +147: [11:06:06] UFFTYPER: Unrecognized charge state for atom: 5 +147: [11:06:06] UFFTYPER: Unrecognized charge state for atom: 5 +136/238 Test #145: pyForceFieldHelpers .................... Passed 0.62 sec +141: [11:06:06] Rep: 60 Mol:1 +141: [11:06:06] Rep: 60 Mol:5 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 -147: [02:19:10] UFFTYPER: Unrecognized charge state for atom: 6 -141: [02:19:10] Rep: 0 Mol:26 -147: [02:19:10] UFFTYPER: Unrecognized charge state for atom: 6 -141: [02:19:10] Rep: 0 Mol:30 -147: [02:19:10] UFFTYPER: Unrecognized charge state for atom: 6 -141: [02:19:10] Rep: 20 Mol:1 -141: [02:19:10] Rep: 20 Mol:5 -141: [02:19:10] Rep: 20 Mol:9 -141: [02:19:10] Rep: 20 Mol:13 -141: [02:19:10] Rep: 20 Mol:17 -141: [02:19:10] Rep: 20 Mol:21 -141: [02:19:10] Rep: 20 Mol:25 -141: [02:19:10] Rep: 20 Mol:29 -141: [02:19:10] Rep: 20 Mol:0 -141: [02:19:10] Rep: 20 Mol:4 -141: [02:19:10] Rep: 20 Mol:8 -141: [02:19:10] Rep: 20 Mol:12 -141: [02:19:10] Rep: 20 Mol:16 -141: [02:19:10] Rep: 20 Mol:20 -141: [02:19:10] Rep: 20 Mol:24 -141: [02:19:10] Rep: 20 Mol:28 -141: [02:19:10] Rep: 20 Mol:3 -141: [02:19:10] Rep: 20 Mol:7 -141: [02:19:10] Rep: 20 Mol:11 -141: [02:19:10] Rep: 20 Mol:15 -141: [02:19:10] Rep: 20 Mol:19 -141: [02:19:10] Rep: 20 Mol:23 -141: [02:19:10] Rep: 20 Mol:27 -141: [02:19:10] Rep: 20 Mol:31 -143: [02:19:10] Rep: 100 Mol:3 -143: [02:19:10] Rep: 100 Mol:7 -143: [02:19:10] Rep: 100 Mol:11 -143: [02:19:10] Rep: 100 Mol:15 -143: [02:19:10] Rep: 100 Mol:19 -143: [02:19:10] Rep: 100 Mol:23 -143: [02:19:10] Rep: 100 Mol:27 -143: [02:19:10] Rep: 100 Mol:31 -148: .[02:19:10] Molecule does not have explicit Hs. Consider calling AddHs() -148: [02:19:10] Molecule does not have explicit Hs. Consider calling AddHs() -148: [02:19:10] Molecule does not have explicit Hs. Consider calling AddHs() -148: [02:19:10] Molecule does not have explicit Hs. Consider calling AddHs() -148: ..[02:19:10] Molecule does not have explicit Hs. Consider calling AddHs() -141: [02:19:10] Rep: 20 Mol:2 -141: [02:19:10] Rep: 20 Mol:6 -141: [02:19:10] Rep: 20 Mol:10 -141: [02:19:10] Rep: 20 Mol:14 -141: [02:19:10] Rep: 20 Mol:18 -141: [02:19:10] Rep: 20 Mol:22 -141: [02:19:10] Rep: 20 Mol:26 -141: [02:19:10] Rep: 20 Mol:30 -148: [02:19:10] Molecule does not have explicit Hs. Consider calling AddHs() -148: [02:19:10] Molecule does not have explicit Hs. Consider calling AddHs() -148: [02:19:10] Molecule does not have explicit Hs. Consider calling AddHs() -148: [02:19:10] Molecule does not have explicit Hs. Consider calling AddHs() -148: [02:19:10] Molecule does not have explicit Hs. Consider calling AddHs() -148: [02:19:10] Molecule does not have explicit Hs. Consider calling AddHs() -148: [02:19:10] Molecule does not have explicit Hs. Consider calling AddHs() -148: [02:19:10] Molecule does not have explicit Hs. Consider calling AddHs() -148: [02:19:10] Molecule does not have explicit Hs. Consider calling AddHs() -148: [02:19:10] Molecule does not have explicit Hs. Consider calling AddHs() -148: ..[02:19:10] Molecule does not have explicit Hs. Consider calling AddHs() -141: [02:19:10] Rep: 40 Mol:1 -148: .[02:19:10] Molecule does not have explicit Hs. Consider calling AddHs() -148: [02:19:10] Molecule does not have explicit Hs. Consider calling AddHs() -141: [02:19:10] Rep: 40 Mol:3 -141: [02:19:10] Rep: 40 Mol:7 -148: [02:19:10] Molecule does not have explicit Hs. Consider calling AddHs() -148: [02:19:10] Molecule does not have explicit Hs. Consider calling AddHs() -148: [02:19:10] Molecule does not have explicit Hs. Consider calling AddHs() -148: [02:19:10] Molecule does not have explicit Hs. Consider calling AddHs() -141: [02:19:10] Rep: 40 Mol:11 -141: [02:19:10] Rep: 40 Mol:5 -148: [02:19:10] Molecule does not have explicit Hs. Consider calling AddHs() -141: [02:19:10] [02:19:10] Rep: 40 Mol:0 -141: [02:19:10] Rep: 40 Mol:4 -141: [02:19:10] Rep: 40 Mol:8 -141: [02:19:10] Rep: 40 Mol:12 -148: [02:19:10] Molecule does not have explicit Hs. Consider calling AddHs() -141: [02:19:10] Rep: 40 Mol:16 -141: Rep: 40 Mol:9 -141: [02:19:10] Rep: 40 Mol:20 -141: [02:19:10] Rep: 40 Mol:13 -141: [02:19:10] Rep: 40 Mol:24 -141: [02:19:10] Rep: 40 Mol:17 -141: [02:19:10] Rep: 40 Mol:28 -141: [02:19:10] Rep: 40 Mol:15 -148: [02:19:10] Molecule does not have explicit Hs. Consider calling AddHs() -141: [02:19:10] Rep: 40 Mol:19 -141: [02:19:10] Rep: 40 Mol:23 -141: [02:19:10] Rep: 40 Mol:21 -141: [02:19:10] Rep: 40 Mol:27 -141: [02:19:10] Rep: 40 Mol:31 -141: [02:19:10] Rep: 40 Mol:25 -141: [02:19:10] Rep: 40 Mol:29 -148: [02:19:10] Molecule does not have explicit Hs. Consider calling AddHs() -148: [02:19:10] Molecule does not have explicit Hs. Consider calling AddHs() -148: [02:19:10] Molecule does not have explicit Hs. Consider calling AddHs() -148: [02:19:10] Molecule does not have explicit Hs. Consider calling AddHs() -148: [02:19:10] Molecule does not have explicit Hs. Consider calling AddHs() -148: [02:19:10] Molecule does not have explicit Hs. Consider calling AddHs() -148: [02:19:10] Molecule does not have explicit Hs. Consider calling AddHs() -148: [02:19:10] Molecule does not have explicit Hs. Consider calling AddHs() -148: [02:19:10] Molecule does not have explicit Hs. Consider calling AddHs() -148: [02:19:10] Molecule does not have explicit Hs. Consider calling AddHs() -148: [02:19:10] Molecule does not have explicit Hs. Consider calling AddHs() -148: [02:19:10] Molecule does not have explicit Hs. Consider calling AddHs() -148: [02:19:10] Molecule does not have explicit Hs. Consider calling AddHs() -148: [02:19:10] Molecule does not have explicit Hs. Consider calling AddHs() -148: [02:19:10] Molecule does not have explicit Hs. Consider calling AddHs() -148: [02:19:10] Molecule does not have explicit Hs. Consider calling AddHs() -148: [02:19:10] Molecule does not have explicit Hs. Consider calling AddHs() -148: [02:19:10] Molecule does not have explicit Hs. Consider calling AddHs() -148: [02:19:10] Molecule does not have explicit Hs. Consider calling AddHs() -148: [02:19:10] Molecule does not have explicit Hs. Consider calling AddHs() -148: [02:19:10] Molecule does not have explicit Hs. Consider calling AddHs() -148: [02:19:10] Molecule does not have explicit Hs. Consider calling AddHs() -148: [02:19:10] Molecule does not have explicit Hs. Consider calling AddHs() -148: [02:19:10] Molecule does not have explicit Hs. Consider calling AddHs() -148: [02:19:10] Molecule does not have explicit Hs. Consider calling AddHs() -148: [02:19:10] Molecule does not have explicit Hs. Consider calling AddHs() -148: [02:19:10] Molecule does not have explicit Hs. Consider calling AddHs() -148: [02:19:10] Molecule does not have explicit Hs. Consider calling AddHs() -148: [02:19:10] Molecule does not have explicit Hs. Consider calling AddHs() -148: [02:19:10] Molecule does not have explicit Hs. Consider calling AddHs() -148: [02:19:10] Molecule does not have explicit Hs. Consider calling AddHs() -148: [02:19:10] Molecule does not have explicit Hs. Consider calling AddHs() -148: [02:19:10] Molecule does not have explicit Hs. Consider calling AddHs() -148: [02:19:10] Molecule does not have explicit Hs. Consider calling AddHs() -148: [02:19:10] Molecule does not have explicit Hs. Consider calling AddHs() -148: [02:19:10] Molecule does not have explicit Hs. Consider calling AddHs() -143: [02:19:10] Rep: 100 Mol:1 -143: [02:19:10] Rep: 100 Mol:5 -143: [02:19:10] Rep: 100 Mol:9 -143: [02:19:10] Rep: 100 Mol:13 -143: [02:19:10] Rep: 100 Mol:17 -143: [02:19:10] Rep: 100 Mol:21 -143: [02:19:10] Rep: 100 Mol:25 -143: [02:19:10] Rep: 100 Mol:29 -148: [02:19:10] Molecule does not have explicit Hs. Consider calling AddHs() -148: [02:19:10] Molecule does not have explicit Hs. Consider calling AddHs() -148: [02:19:10] Molecule does not have explicit Hs. Consider calling AddHs() -148: [02:19:10] Molecule does not have explicit Hs. Consider calling AddHs() -141: [02:19:10] Rep: 60 Mol:3 -141: [02:19:10] Rep: 60 Mol:7 -141: [02:19:10] Rep: 60 Mol:11 -141: [02:19:10] Rep: 60 Mol:15 -141: [02:19:10] Rep: 60 Mol:19 -141: [02:19:10] Rep: 60 Mol:23 -141: [02:19:10] Rep: 60 Mol:27 -141: [02:19:10] Rep: 60 Mol:31 -148: [02:19:10] Molecule does not have explicit Hs. Consider calling AddHs() -148: [02:19:10] Molecule does not have explicit Hs. Consider calling AddHs() -148: [02:19:10] Molecule does not have explicit Hs. Consider calling AddHs() -128: [02:19:10] done -128: [02:19:10] ------------------------------------- -128: [02:19:10] Test GitHub Issue 258: Bad pattern fingerprint for query molecule -128: [02:19:10] done -128: [02:19:10] ------------------------------------- -128: [02:19:10] Test GitHub Issue 334: explicit Hs in SMILES modifies atom pair (and topological torsion) FP. -128: [02:19:10] DEPRECATION WARNING: please use AtomPairGenerator -128: [02:19:10] DEPRECATION WARNING: please use AtomPairGenerator -128: [02:19:10] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [02:19:10] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [02:19:10] done -128: [02:19:10] ------------------------------------- -128: [02:19:10] Test GitHub Issue 695: Include cis/trans stereochemistry when useChirality=true with the morgan fingerprints -128: [02:19:10] done -128: [02:19:10] ------------------------------------- -128: [02:19:10] Test GitHub Issue 811: rooted atom fingerprint non identical for the same molecules #811 -148: [02:19:10] Molecule does not have explicit Hs. Consider calling AddHs() -128: [02:19:10] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [02:19:10] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [02:19:10] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [02:19:10] done -128: [02:19:10] ------------------------------------- -128: [02:19:10] Test unfolded version of RDKFP -128: [02:19:10] ------------------------------------- -128: [02:19:10] Test bitinfo of RDKFP +141: [11:06:06] Rep: 60 Mol:9 +141: [11:06:06] Rep: 60 Mol:13 +141: [11:06:06] Rep: 60 Mol:17 +141: [11:06:06] Rep: 60 Mol:21 +141: [11:06:06] Rep: 60 Mol:25 +141: [11:06:06] [11:06:06] Rep: 60 Mol:29 +141: Rep: 80 Mol:3 +141: [11:06:06] Rep: 80 Mol:7 +141: [11:06:06] Rep: 80 Mol:11 +141: [11:06:06] Rep: 80 Mol:15 +141: [11:06:06] Rep: 80 Mol:19 +141: [11:06:06] Rep: 80 Mol:23 +141: [11:06:06] Rep: 80 Mol:27 +141: [11:06:06] Rep: 80 Mol:31 +147: [11:06:06] UFFTYPER: Unrecognized charge state for atom: 6 +147: [11:06:06] UFFTYPER: Unrecognized charge state for atom: 6 +147: [11:06:06] UFFTYPER: Unrecognized charge state for atom: 6 +141: [11:06:07] Rep: 80 Mol:0 +141: [11:06:07] Rep: 80 Mol:4 +141: [11:06:07] Rep: 80 Mol:8 +141: [11:06:07] Rep: 80 Mol:12 +141: [11:06:07] Rep: 80 Mol:16 +141: [11:06:07] Rep: 80 Mol:20 +141: [11:06:07] Rep: 80 Mol:24 +141: [11:06:07] Rep: 80 Mol:28 +141: [11:06:07] Rep: 60 Mol:2 +141: [11:06:07] Rep: 60 Mol:6 +141: [11:06:07] Rep: 60 Mol:10 +141: [11:06:07] Rep: 60 Mol:14 +141: [11:06:07] Rep: 60 Mol:18 +141: [11:06:07] Rep: 60 Mol:22 +141: [11:06:07] Rep: 60 Mol:26 +141: [11:06:07] Rep: 60 Mol:30 +141: [11:06:07] Rep: 80 Mol:1 +141: [11:06:07] Rep: 80 Mol:5 +141: [11:06:07] Rep: 80 Mol:9 +141: [11:06:07] Rep: 80 Mol:13 +141: [11:06:07] Rep: 80 Mol:17 +141: [11:06:07] Rep: 80 Mol:21 +141: [11:06:07] Rep: 80 Mol:25 +141: [11:06:07] Rep: 80 Mol:29 +143: [11:06:07] Rep: 100 Mol:3 +143: [11:06:07] Rep: 100 Mol:7 +143: [11:06:07] Rep: 100 Mol:11 +143: [11:06:07] Rep: 100 Mol:15 +143: [11:06:07] Rep: 100 Mol:19 +143: [11:06:07] Rep: 100 Mol:23 +143: [11:06:07] Rep: 100 Mol:27 +143: [11:06:07] Rep: 100 Mol:31 +143: [11:06:07] Rep: 100 Mol:0 +143: [11:06:07] Rep: 100 Mol:4 +143: [11:06:07] Rep: 100 Mol:8 +143: [11:06:07] Rep: 100 Mol:12 +143: [11:06:07] Rep: 100 Mol:16 +143: [11:06:07] Rep: 100 Mol:20 +143: [11:06:07] Rep: 100 Mol:24 +143: [11:06:07] Rep: 100 Mol:28 +143: [11:06:07] Rep: 100 Mol:1 +143: [11:06:07] Rep: 100 Mol:5 +143: [11:06:07] Rep: 100 Mol:9 +143: [11:06:07] Rep: 100 Mol:13 +143: [11:06:07] Rep: 100 Mol:17 +143: [11:06:07] Rep: 100 Mol:21 +143: [11:06:07] Rep: 100 Mol:25 +143: [11:06:07] Rep: 100 Mol:29 +148: .[11:06:07] Molecule does not have explicit Hs. Consider calling AddHs() +141: [11:06:07] Rep: 80 Mol:2 +141: [11:06:07] Rep: 80 Mol:6 +141: [11:06:07] Rep: 80 Mol:10 +148: [11:06:07] Molecule does not have explicit Hs. Consider calling AddHs() +141: [11:06:07] Rep: 80 Mol:14 +141: [11:06:07] Rep: 80 Mol:18 +141: [11:06:07] Rep: 80 Mol:22 +148: [11:06:07] Molecule does not have explicit Hs. Consider calling AddHs() +141: [11:06:07] Rep: 80 Mol:26 +141: [11:06:07] Rep: 80 Mol:30 +148: [11:06:07] Molecule does not have explicit Hs. Consider calling AddHs() +148: ..[11:06:07] Molecule does not have explicit Hs. Consider calling AddHs() +148: [11:06:07] Molecule does not have explicit Hs. Consider calling AddHs() +148: [11:06:07] Molecule does not have explicit Hs. Consider calling AddHs() +148: [11:06:07] Molecule does not have explicit Hs. Consider calling AddHs() +148: [11:06:07] Molecule does not have explicit Hs. Consider calling AddHs() +148: [11:06:07] Molecule does not have explicit Hs. Consider calling AddHs() +148: [11:06:07] Molecule does not have explicit Hs. Consider calling AddHs() +148: [11:06:07] Molecule does not have explicit Hs. Consider calling AddHs() +148: [11:06:07] Molecule does not have explicit Hs. Consider calling AddHs() +148: [11:06:07] Molecule does not have explicit Hs. Consider calling AddHs() +148: [11:06:07] Molecule does not have explicit Hs. Consider calling AddHs() +148: ..[11:06:07] Molecule does not have explicit Hs. Consider calling AddHs() +148: .[11:06:07] Molecule does not have explicit Hs. Consider calling AddHs() +148: [11:06:07] Molecule does not have explicit Hs. Consider calling AddHs() +148: [11:06:07] Molecule does not have explicit Hs. Consider calling AddHs() +148: [11:06:07] Molecule does not have explicit Hs. Consider calling AddHs() +148: [11:06:07] Molecule does not have explicit Hs. Consider calling AddHs() +148: [11:06:07] Molecule does not have explicit Hs. Consider calling AddHs() +148: [11:06:07] Molecule does not have explicit Hs. Consider calling AddHs() +148: [11:06:07] Molecule does not have explicit Hs. Consider calling AddHs() +148: [11:06:07] Molecule does not have explicit Hs. Consider calling AddHs() +148: [11:06:07] Molecule does not have explicit Hs. Consider calling AddHs() +148: [11:06:07] Molecule does not have explicit Hs. Consider calling AddHs() +148: [11:06:07] Molecule does not have explicit Hs. Consider calling AddHs() +148: [11:06:07] Molecule does not have explicit Hs. Consider calling AddHs() +148: [11:06:07] Molecule does not have explicit Hs. Consider calling AddHs() +148: [11:06:07] Molecule does not have explicit Hs. Consider calling AddHs() +148: [11:06:07] Molecule does not have explicit Hs. Consider calling AddHs() +148: [11:06:07] Molecule does not have explicit Hs. Consider calling AddHs() +148: [11:06:07] Molecule does not have explicit Hs. Consider calling AddHs() +148: [11:06:07] Molecule does not have explicit Hs. Consider calling AddHs() +148: [11:06:07] Molecule does not have explicit Hs. Consider calling AddHs() +148: [11:06:07] Molecule does not have explicit Hs. Consider calling AddHs() +148: [11:06:07] Molecule does not have explicit Hs. Consider calling AddHs() +148: [11:06:07] Molecule does not have explicit Hs. Consider calling AddHs() +148: [11:06:07] Molecule does not have explicit Hs. Consider calling AddHs() +148: [11:06:07] Molecule does not have explicit Hs. Consider calling AddHs() +148: [11:06:07] Molecule does not have explicit Hs. Consider calling AddHs() +148: [11:06:07] Molecule does not have explicit Hs. Consider calling AddHs() +148: [11:06:07] Molecule does not have explicit Hs. Consider calling AddHs() +148: [11:06:07] Molecule does not have explicit Hs. Consider calling AddHs() +141: [11:06:07] done +141: [11:06:07] ------------------------------------- +141: [11:06:07] Test MMFF multithreading2 +148: [11:06:07] Molecule does not have explicit Hs. Consider calling AddHs() +148: [11:06:07] Molecule does not have explicit Hs. Consider calling AddHs() +148: [11:06:07] Molecule does not have explicit Hs. Consider calling AddHs() +148: [11:06:07] Molecule does not have explicit Hs. Consider calling AddHs() +148: [11:06:07] Molecule does not have explicit Hs. Consider calling AddHs() +148: [11:06:07] Molecule does not have explicit Hs. Consider calling AddHs() +148: [11:06:07] Molecule does not have explicit Hs. Consider calling AddHs() +148: [11:06:07] Molecule does not have explicit Hs. Consider calling AddHs() +148: [11:06:07] Molecule does not have explicit Hs. Consider calling AddHs() +148: [11:06:07] Molecule does not have explicit Hs. Consider calling AddHs() +148: [11:06:07] Molecule does not have explicit Hs. Consider calling AddHs() +148: [11:06:07] Molecule does not have explicit Hs. Consider calling AddHs() +148: [11:06:07] Molecule does not have explicit Hs. Consider calling AddHs() +143: [11:06:07] Rep: 100 Mol:2 +143: [11:06:07] Rep: 100 Mol:6 +143: [11:06:07] Rep: 100 Mol:10 +143: [11:06:07] Rep: 100 Mol:14 +143: [11:06:07] Rep: 100 Mol:18 +143: [11:06:07] Rep: 100 Mol:22 +143: [11:06:07] Rep: 100 Mol:26 +143: [11:06:07] Rep: 100 Mol:30 +148: [11:06:07] Molecule does not have explicit Hs. Consider calling AddHs() +148: [11:06:07] Molecule does not have explicit Hs. Consider calling AddHs() +148: [11:06:07] Molecule does not have explicit Hs. Consider calling AddHs() +148: [11:06:07] Molecule does not have explicit Hs. Consider calling AddHs() +148: [11:06:07] Molecule does not have explicit Hs. Consider calling AddHs() +148: [11:06:07] Molecule does not have explicit Hs. Consider calling AddHs() +148: [11:06:07] Molecule does not have explicit Hs. Consider calling AddHs() +148: [11:06:07] Molecule does not have explicit Hs. Consider calling AddHs() +148: [11:06:07] Molecule does not have explicit Hs. Consider calling AddHs() +148: [11:06:07] Molecule does not have explicit Hs. Consider calling AddHs() +148: [11:06:07] Molecule does not have explicit Hs. Consider calling AddHs() +148: [11:06:07] Molecule does not have explicit Hs. Consider calling AddHs() +148: [11:06:07] Molecule does not have explicit Hs. Consider calling AddHs() +148: [11:06:07] Molecule does not have explicit Hs. Consider calling AddHs() +148: [11:06:07] Molecule does not have explicit Hs. Consider calling AddHs() +148: [11:06:07] Molecule does not have explicit Hs. Consider calling AddHs() +148: [11:06:07] Molecule does not have explicit Hs. Consider calling AddHs() +148: [11:06:07] Molecule does not have explicit Hs. Consider calling AddHs() +148: [11:06:07] Molecule does not have explicit Hs. Consider calling AddHs() +148: [11:06:07] Molecule does not have explicit Hs. Consider calling AddHs() +148: .[11:06:07] Molecule does not have explicit Hs. Consider calling AddHs() +141: [11:06:07] done +141: [11:06:07] ------------------------------------- +141: [11:06:07] Test MMFF multithreading3 +147: [11:06:07] UFFTYPER: Warning: hybridization set to SP3 for atom 6 +147: [11:06:07] UFFTYPER: Warning: hybridization set to SP3 for atom 6 +128: [11:06:07] done +128: [11:06:07] ------------------------------------- +128: [11:06:07] Test GitHub Issue 258: Bad pattern fingerprint for query molecule +128: [11:06:07] done +128: [11:06:07] ------------------------------------- +128: [11:06:07] Test GitHub Issue 334: explicit Hs in SMILES modifies atom pair (and topological torsion) FP. +128: [11:06:07] DEPRECATION WARNING: please use AtomPairGenerator +128: [11:06:07] DEPRECATION WARNING: please use AtomPairGenerator +128: [11:06:07] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [11:06:07] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [11:06:07] done +128: [11:06:07] ------------------------------------- +128: [11:06:07] Test GitHub Issue 695: Include cis/trans stereochemistry when useChirality=true with the morgan fingerprints +128: [11:06:07] done +128: [11:06:07] ------------------------------------- +128: [11:06:07] Test GitHub Issue 811: rooted atom fingerprint non identical for the same molecules #811 +128: [11:06:07] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [11:06:07] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [11:06:07] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [11:06:07] done +128: [11:06:07] ------------------------------------- +128: [11:06:07] Test unfolded version of RDKFP +128: [11:06:07] ------------------------------------- +128: [11:06:07] Test bitinfo of RDKFP 128: 562: [ 2 ], 128: 709: [ 0 1 ], 128: 1118: [ 0 1 2 ], @@ -26986,118 +27115,130 @@ 128: 1772: [ 0 ], [ 1 ], 128: 1813: [ 0 1 ], 128: ------------ -128: [02:19:10] ------------------------------------- -128: [02:19:10] Single atoms setting radius 1 bits in Morgan fingerprints -128: [02:19:10] done -128: [02:19:10] ------------------------------------- -128: [02:19:10] Github #879: Pattern fingerprint should set bits for single-atom fragments. -128: [02:19:10] done -128: [02:19:10] ------------------------------------- -128: [02:19:10] Github #1496: Pattern fingerprint setting bad bits for degree zero atoms -128: [02:19:10] done -128: [02:19:10] ------------------------------------- -128: [02:19:10] Github #1793: Fingerprint segfaults with branchedPaths=False and useHs=False -128: [02:19:10] done -128: [02:19:10] ------------------------------------- -128: [02:19:10] Github #1993: fingerprinters that use R/S labels should force a call to assignStereochemistry() if it hasn't already been called -128: [02:19:10] DEPRECATION WARNING: please use AtomPairGenerator -128: [02:19:10] DEPRECATION WARNING: please use AtomPairGenerator -128: [02:19:10] DEPRECATION WARNING: please use AtomPairGenerator -128: [02:19:10] DEPRECATION WARNING: please use AtomPairGenerator -128: [02:19:10] DEPRECATION WARNING: please use AtomPairGenerator -143: [02:19:10] Rep: 100 Mol:2 -128: [02:19:10] DEPRECATION WARNING: please use AtomPairGenerator -128: [02:19:10] DEPRECATION WARNING: please use AtomPairGenerator -128: [02:19:10] DEPRECATION WARNING: please use AtomPairGenerator -128: [02:19:10] DEPRECATION WARNING: please use AtomPairGenerator -128: [02:19:10] DEPRECATION WARNING: please use AtomPairGenerator -128: [02:19:10] DEPRECATION WARNING: please use AtomPairGenerator -128: [02:19:10] DEPRECATION WARNING: please use AtomPairGenerator -128: [02:19:10] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [02:19:10] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [02:19:10] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [02:19:10] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [02:19:10] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [02:19:10] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [02:19:10] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [02:19:10] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [02:19:10] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [02:19:10] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [02:19:10] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [02:19:10] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [02:19:10] done -128: [02:19:10] ------------------------------------- -128: [02:19:10] Github #2115: BitInfo not complete for RDKFingerprint -128: [02:19:10] done -128: [02:19:10] ------------------------------------- -128: [02:19:10] Github #3723: Fingerprint crash for mols with Zero order bonds -128: [02:19:10] done -148: [02:19:10] Molecule does not have explicit Hs. Consider calling AddHs() -141: [02:19:10] Rep: 60 Mol:0 -141: [02:19:10] Rep: 60 Mol:4 -141: [02:19:10] Rep: 60 Mol:1 -141: [02:19:10] Rep: 60 Mol:5 -141: [02:19:10] Rep: 60 Mol:8 -141: [02:19:10] Rep: 60 Mol:9 -137/238 Test #128: testFingerprints ....................... Passed 2.60 sec -141: [02:19:10] Rep: 60 Mol:12 -141: [02:19:10] Rep: 60 Mol:13 -141: [02:19:10] Rep: 60 Mol:16 -143: [02:19:10] Rep: 100 Mol:0 -143: [02:19:10] Rep: 100 Mol:6 +128: [11:06:07] ------------------------------------- +128: [11:06:07] Single atoms setting radius 1 bits in Morgan fingerprints +128: [11:06:07] done +128: [11:06:07] ------------------------------------- +128: [11:06:07] Github #879: Pattern fingerprint should set bits for single-atom fragments. +128: [11:06:07] done +128: [11:06:07] ------------------------------------- +128: [11:06:07] Github #1496: Pattern fingerprint setting bad bits for degree zero atoms +128: [11:06:07] done +128: [11:06:07] ------------------------------------- +128: [11:06:07] Github #1793: Fingerprint segfaults with branchedPaths=False and useHs=False +128: [11:06:07] done +128: [11:06:07] ------------------------------------- +128: [11:06:07] Github #1993: fingerprinters that use R/S labels should force a call to assignStereochemistry() if it hasn't already been called +128: [11:06:07] DEPRECATION WARNING: please use AtomPairGenerator +128: [11:06:07] DEPRECATION WARNING: please use AtomPairGenerator +128: [11:06:07] DEPRECATION WARNING: please use AtomPairGenerator +128: [11:06:07] DEPRECATION WARNING: please use AtomPairGenerator +128: [11:06:07] DEPRECATION WARNING: please use AtomPairGenerator +128: [11:06:07] DEPRECATION WARNING: please use AtomPairGenerator +128: [11:06:07] DEPRECATION WARNING: please use AtomPairGenerator +128: [11:06:07] DEPRECATION WARNING: please use AtomPairGenerator +128: [11:06:07] DEPRECATION WARNING: please use AtomPairGenerator +128: [11:06:07] DEPRECATION WARNING: please use AtomPairGenerator +128: [11:06:07] DEPRECATION WARNING: please use AtomPairGenerator +128: [11:06:07] DEPRECATION WARNING: please use AtomPairGenerator +128: [11:06:07] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [11:06:07] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [11:06:07] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [11:06:07] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [11:06:07] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [11:06:07] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [11:06:07] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [11:06:07] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [11:06:07] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [11:06:07] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [11:06:07] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [11:06:07] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [11:06:07] done +128: [11:06:07] ------------------------------------- +128: [11:06:07] Github #2115: BitInfo not complete for RDKFingerprint +128: [11:06:07] done +128: [11:06:07] ------------------------------------- +128: [11:06:07] Github #3723: Fingerprint crash for mols with Zero order bonds +128: [11:06:07] done +137/238 Test #128: testFingerprints ....................... Passed 3.33 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 -141: [02:19:10] Rep: 60 Mol:17 -141: [02:19:10] Rep: 60 Mol:20 -141: [02:19:10] Rep: 60 Mol:24 -141: [02:19:10] Rep: 60 Mol:21 -141: [02:19:10] Rep: 60 Mol:25 -141: [02:19:10] Rep: 60 Mol:29 -143: [02:19:10] Rep: 100 Mol:10 -143: [02:19:10] Rep: 100 Mol:14 -143: [02:19:10] Rep: 100 Mol:18 -143: [02:19:10] Rep: 100 Mol:22 -143: [02:19:10] Rep: 100 Mol:26 -143: [02:19:10] Rep: 100 Mol:30 -143: [02:19:10] Rep: 100 Mol:4 -143: [02:19:10] Rep: 100 Mol:8 -143: [02:19:10] Rep: 100 Mol:12 -143: [02:19:10] Rep: 100 Mol:16 -141: [02:19:10] Rep: 60 Mol:28 -148: [02:19:10] Molecule does not have explicit Hs. Consider calling AddHs() -143: [02:19:10] Rep: 100 Mol:20 -143: [02:19:10] Rep: 100 Mol:24 -143: [02:19:10] Rep: 100 Mol:28 -148: [02:19:10] Molecule does not have explicit Hs. Consider calling AddHs() -148: [02:19:10] Molecule does not have explicit Hs. Consider calling AddHs() -141: [02:19:10] Rep: 40 Mol:2 -148: [02:19:10] Molecule does not have explicit Hs. Consider calling AddHs() -141: [02:19:10] Rep: 40 Mol:6 -141: [02:19:10] Rep: 40 Mol:10 -141: [02:19:10] Rep: 40 Mol:14 -141: [02:19:10] Rep: 40 Mol:18 -141: [02:19:10] Rep: 40 Mol:22 -141: [02:19:10] Rep: 40 Mol:26 -141: [02:19:10] Rep: 40 Mol:30 -148: [02:19:10] Molecule does not have explicit Hs. Consider calling AddHs() -148: [02:19:10] Molecule does not have explicit Hs. Consider calling AddHs() -148: [02:19:10] Molecule does not have explicit Hs. Consider calling AddHs() -147: [02:19:10] UFFTYPER: Warning: hybridization set to SP3 for atom 6 -148: [02:19:10] Molecule does not have explicit Hs. Consider calling AddHs() -148: .[02:19:10] Molecule does not have explicit Hs. Consider calling AddHs() -141: [02:19:10] Rep: 80 Mol:3 -141: [02:19:10] Rep: 80 Mol:7 -141: [02:19:10] Rep: 80 Mol:11 -141: [02:19:10] Rep: 80 Mol:15 -141: [02:19:10] Rep: 80 Mol:19 -141: [02:19:10] Rep: 80 Mol:23 -141: [02:19:10] Rep: 80 Mol:27 -141: [02:19:10] Rep: 80 Mol:31 -147: [02:19:10] UFFTYPER: Warning: hybridization set to SP3 for atom 6 +147: [11:06:07] UFFTYPER: Warning: hybridization set to SP3 for atom 6 +146: [11:06:06] --------------------------------- +146: [11:06:06] test3 +146: +146: [11:06:06] --------------------------------- +146: [11:06:06] test4 +146: +146: [11:06:06] --------------------------------- +146: [11:06:06] test5 +146: +146: [11:06:07] --------------------------------- +146: [11:06:07] test6 +146: +146: [11:06:07] --------------------------------- +146: [11:06:07] test15Dists +146: +146: [11:06:07] --------------------------------- +146: [11:06:07] test Issue 215 +146: +146: [11:06:07] --------------------------------- +146: [11:06:07] testMultipleConfs +146: +146: [11:06:07] --------------------------------- +146: [11:06:07] testMultipleConfsExpTors +146: +146: [11:06:07] --------------------------------- +146: [11:06:07] testIssue227 +146: +146: [11:06:07] --------------------------------- +146: [11:06:07] testIssue236 +146: +146: [11:06:07] --------------------------------- +146: [11:06:07] testOrdering +146: +146: [11:06:07] --------------------------------- +146: [11:06:07] testIssue244 +146: +146: [11:06:07] --------------------------------- +146: [11:06:07] testIssue251 +146: +146: [11:06:07] --------------------------------- +146: [11:06:07] testIssue276 +146: [11:06:07] --------------------------------- +146: [11:06:07] testIssue284 +146: +146: [11:06:07] --------------------------------- +146: [11:06:07] testIssue285 +146: +146: [11:06:07] --------------------------------- +146: [11:06:07] testIssue355 +146: +146: [11:06:07] --------------------------------- +146: [11:06:07] testRandomCoords +146: +146: [11:06:07] --------------------------------- +146: [11:06:07] test sf.net issue 1989539 +146: +146: [11:06:07] --------------------------------- +146: [11:06:07] test sf.net issue 2091864 +146: +146: [11:06:07] --------------------------------- +146: [11:06:07] test constrained embedding +146: +146: [11:06:07] ssd: 0.0752641 +146: [11:06:07] ssd: 0.0659363 +148: [11:06:07] Molecule does not have explicit Hs. Consider calling AddHs() +143: [11:06:07] done +143: [11:06:07] ------------------------------------- +143: [11:06:07] Test UFF multithreading2 +147: [11:06:07] UFFTYPER: Warning: hybridization set to SP3 for atom 11 +147: [11:06:07] UFFTYPER: Warning: hybridization set to SP3 for atom 11 +147: [11:06:07] UFFTYPER: Warning: hybridization set to SP3 for atom 11 149: *********************************************************** 149: Testing MolAlign 149: --------------------------------- @@ -27119,8 +27260,7 @@ 149: testIssue241 149: 149: *********************************************************** -138/238 Test #149: testMolAlign ........................... Passed 0.12 sec -147: [02:19:10] UFFTYPER: Warning: hybridization set to SP3 for atom 6 +138/238 Test #149: testMolAlign ........................... Passed 0.15 sec test 150 Start 150: testO3AAlign @@ -27133,155 +27273,65 @@ 95: 1,1 0 95: 2,0 0 95: 2,1 0 -139/238 Test #95: testEnumeration ........................ Passed 5.60 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 -141: [02:19:10] Rep: 80 Mol:0 -141: [02:19:10] Rep: 80 Mol:4 -141: [02:19:10] Rep: 80 Mol:1 -141: [02:19:10] Rep: 80 Mol:8 -141: [02:19:10] Rep: 80 Mol:5 -141: [02:19:10] Rep: 80 Mol:9 -141: [02:19:10] Rep: 80 Mol:13 -141: [02:19:10] Rep: 80 Mol:12 -141: [02:19:10] Rep: 80 Mol:16 -141: [02:19:10] Rep: 80 Mol:17 -141: [02:19:10] Rep: 80 Mol:20 -141: [02:19:10] Rep: 80 Mol:21[02:19:10] Rep: 80 Mol:24 -141: [02:19:10] Rep: 80 Mol:28 -141: -146: [02:19:10] --------------------------------- -146: [02:19:10] test3 -146: -146: [02:19:10] --------------------------------- -146: [02:19:10] test4 -146: -146: [02:19:10] --------------------------------- -146: [02:19:10] test5 -146: -146: [02:19:10] --------------------------------- -146: [02:19:10] test6 -146: -146: [02:19:10] --------------------------------- -146: [02:19:10] test15Dists -146: -146: [02:19:10] --------------------------------- -146: [02:19:10] test Issue 215 -146: -146: [02:19:10] --------------------------------- -146: [02:19:10] testMultipleConfs -146: -146: [02:19:10] --------------------------------- -146: [02:19:10] testMultipleConfsExpTors -146: -146: [02:19:10] --------------------------------- -146: [02:19:10] testIssue227 -146: -146: [02:19:10] --------------------------------- -146: [02:19:10] testIssue236 -146: -146: [02:19:10] --------------------------------- -146: [02:19:10] testOrdering -146: -146: [02:19:10] --------------------------------- -146: [02:19:10] testIssue244 -146: -146: [02:19:10] --------------------------------- -146: [02:19:10] testIssue251 -146: -146: [02:19:10] --------------------------------- -146: [02:19:10] testIssue276 -146: [02:19:10] --------------------------------- -146: [02:19:10] testIssue284 -146: -146: [02:19:10] --------------------------------- -146: [02:19:10] testIssue285 -146: -146: [02:19:10] --------------------------------- -146: [02:19:10] testIssue355 -146: -146: [02:19:10] --------------------------------- -146: [02:19:10] testRandomCoords -146: -146: [02:19:10] --------------------------------- -146: [02:19:10] test sf.net issue 1989539 -146: -146: [02:19:10] --------------------------------- -146: [02:19:10] test sf.net issue 2091864 +146: [11:06:07] --------------------------------- +146: [11:06:07] test sf.net issue 2091974 146: -146: [02:19:10] --------------------------------- -146: [02:19:10] test constrained embedding +146: [11:06:07] --------------------------------- +146: [11:06:07] test sf.net issue 2835784 146: -146: [02:19:10] ssd: 0.0752641 -146: [02:19:10] ssd: 0.0659363 -147: [02:19:10] UFFTYPER: Warning: hybridization set to SP3 for atom 11 -141: [02:19:10] Rep: 80 Mol:25 -141: [02:19:10] Rep: 80 Mol:29 -147: [02:19:10] UFFTYPER: Warning: hybridization set to SP3 for atom 11 -147: [02:19:10] UFFTYPER: Warning: hybridization set to SP3 for atom 11 -148: [02:19:10] Molecule does not have explicit Hs. Consider calling AddHs() -141: [02:19:10] Rep: 60 Mol:2 -141: [02:19:10] Rep: 60 Mol:6 -141: [02:19:10] Rep: 60 Mol:10 -141: [02:19:10] Rep: 60 Mol:14 -141: [02:19:10] Rep: 60 Mol:18 -141: [02:19:11] Rep: 60 Mol:22 -141: [02:19:11] Rep: 60 Mol:26 -141: [02:19:11] Rep: 60 Mol:30 -151: Randomness seeded to: 1113701546 -151: 45633860 -151: 28572748 -146: [02:19:10] --------------------------------- -146: [02:19:10] test sf.net issue 2091974 +146: [11:06:07] --------------------------------- +146: [11:06:07] test sf.net issue 3019283 146: -146: [02:19:10] --------------------------------- -146: [02:19:10] test sf.net issue 2835784 +146: [11:06:07] --------------------------------- +146: [11:06:07] test sf.net issue 3238580 146: -146: [02:19:10] --------------------------------- -146: [02:19:10] test sf.net issue 3019283 +146: [11:06:07] --------------------------------- +146: [11:06:07] test sf.net issue 3483968 146: -146: [02:19:10] --------------------------------- -146: [02:19:10] test sf.net issue 3238580 +146: [11:06:07] --------------------------------- +146: [11:06:07] test github issue 55 146: -146: [02:19:10] --------------------------------- -146: [02:19:10] test sf.net issue 3483968 +146: [11:06:07] --------------------------------- +146: [11:06:07] test1 146: -146: [02:19:11] --------------------------------- -146: [02:19:11] test github issue 55 -146: -146: [02:19:11] --------------------------------- -146: [02:19:11] test1 -146: -146: [02:19:11] --------------------------------- -146: [02:19:11] test multi-threading +146: [11:06:07] --------------------------------- +146: [11:06:07] test multi-threading 146: 146: building molecules -148: [02:19:11] Molecule does not have explicit Hs. Consider calling AddHs() +139/238 Test #95: testEnumeration ........................ Passed 6.56 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 146: generating reference data -141: [02:19:11] Rep: 80 Mol:2 -141: [02:19:11] Rep: 80 Mol:6 -141: [02:19:11] Rep: 80 Mol:10 -141: [02:19:11] Rep: 80 Mol:14 -141: [02:19:11] Rep: 80 Mol:18 -141: [02:19:11] Rep: 80 Mol:22 -141: [02:19:11] Rep: 80 Mol:26 -141: [02:19:11] Rep: 80 Mol:30 -148: [02:19:11] Molecule does not have explicit Hs. Consider calling AddHs() -141: [02:19:11] done -141: [02:19:11] ------------------------------------- -141: [02:19:11] Test MMFF multithreading2 -143: [02:19:11] done -143: [02:19:11] ------------------------------------- -143: [02:19:11] Test UFF multithreading2 -148: [02:19:11] Molecule does not have explicit Hs. Consider calling AddHs() -141: [02:19:11] done -141: [02:19:11] ------------------------------------- -141: [02:19:11] Test MMFF multithreading3 -148: [02:19:11] Molecule does not have explicit Hs. Consider calling AddHs() +141: [11:06:08] done +141: [11:06:08] ------------------------------------- +141: [11:06:08] Testing github 162: Incorrect SMILES after MMFF parameterization . +141: [11:06:08] done +141: [11:06:08] ------------------------------------- +141: [11:06:08] Testing github 224: crash during MMFF parameterization . +141: [11:06:08] done +141: [11:06:08] ------------------------------------- +141: [11:06:08] Testing github6728: crash due to missing stretch-bend params. +140/238 Test #141: testMMFFForceFieldHelpers .............. Passed 2.22 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: [11:06:08] Molecule does not have explicit Hs. Consider calling AddHs() +151: Randomness seeded to: 2786208239 +151: 40735880 +151: 34553040 +148: [11:06:08] Molecule does not have explicit Hs. Consider calling AddHs() +143: [11:06:08] done +143: [11:06:08] ------------------------------------- +143: [11:06:08] Test UFF multithreading3 +148: [11:06:08] Molecule does not have explicit Hs. Consider calling AddHs() +148: [11:06:08] 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 @@ -27289,61 +27339,65 @@ 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: .[02:19:11] DEPRECATION WARNING: please use MorganGenerator -126: .[02:19:11] DEPRECATION WARNING: please use MorganGenerator -126: ..[02:19:11] DEPRECATION WARNING: please use AtomPairGenerator -126: [02:19:11] DEPRECATION WARNING: please use AtomPairGenerator -126: [02:19:11] DEPRECATION WARNING: please use AtomPairGenerator -126: [02:19:11] DEPRECATION WARNING: please use AtomPairGenerator -126: [02:19:11] DEPRECATION WARNING: please use AtomPairGenerator -126: [02:19:11] DEPRECATION WARNING: please use AtomPairGenerator -126: .[02:19:11] DEPRECATION WARNING: please use TopologicalTorsionGenerator -126: [02:19:11] DEPRECATION WARNING: please use TopologicalTorsionGenerator -126: ...[02:19:11] DEPRECATION WARNING: please use MorganGenerator -126: [02:19:11] DEPRECATION WARNING: please use MorganGenerator -126: [02:19:11] DEPRECATION WARNING: please use MorganGenerator -126: [02:19:11] DEPRECATION WARNING: please use MorganGenerator -126: [02:19:11] DEPRECATION WARNING: please use MorganGenerator -126: [02:19:11] DEPRECATION WARNING: please use MorganGenerator -126: [02:19:11] DEPRECATION WARNING: please use MorganGenerator -126: [02:19:11] DEPRECATION WARNING: please use MorganGenerator -126: [02:19:11] DEPRECATION WARNING: please use MorganGenerator -126: [02:19:11] DEPRECATION WARNING: please use MorganGenerator -126: [02:19:11] DEPRECATION WARNING: please use MorganGenerator -126: [02:19:11] DEPRECATION WARNING: please use MorganGenerator -126: [02:19:11] DEPRECATION WARNING: please use MorganGenerator -126: [02:19:11] DEPRECATION WARNING: please use MorganGenerator -126: [02:19:11] DEPRECATION WARNING: please use MorganGenerator -126: [02:19:11] DEPRECATION WARNING: please use MorganGenerator -126: [02:19:11] DEPRECATION WARNING: please use MorganGenerator -126: [02:19:11] DEPRECATION WARNING: please use MorganGenerator -126: [02:19:11] DEPRECATION WARNING: please use MorganGenerator -126: [02:19:11] DEPRECATION WARNING: please use MorganGenerator -126: [02:19:11] DEPRECATION WARNING: please use MorganGenerator -126: [02:19:11] DEPRECATION WARNING: please use MorganGenerator -143: [02:19:11] done -143: [02:19:11] ------------------------------------- -143: [02:19:11] Test UFF multithreading3 -126: ....[02:19:11] DEPRECATION WARNING: please use AtomPairGenerator -126: [02:19:11] DEPRECATION WARNING: please use AtomPairGenerator -126: ....[02:19:11] DEPRECATION WARNING: please use AtomPairGenerator -126: [02:19:11] DEPRECATION WARNING: please use AtomPairGenerator -126: .[02:19:11] DEPRECATION WARNING: please use TopologicalTorsionGenerator -126: [02:19:11] DEPRECATION WARNING: please use TopologicalTorsionGenerator -126: [02:19:11] DEPRECATION WARNING: please use TopologicalTorsionGenerator -126: [02:19:11] DEPRECATION WARNING: please use TopologicalTorsionGenerator -126: [02:19:11] DEPRECATION WARNING: please use TopologicalTorsionGenerator -126: ..[02:19:11] DEPRECATION WARNING: please use TopologicalTorsionGenerator -126: [02:19:11] DEPRECATION WARNING: please use TopologicalTorsionGenerator -126: [02:19:11] DEPRECATION WARNING: please use TopologicalTorsionGenerator -126: [02:19:11] DEPRECATION WARNING: please use TopologicalTorsionGenerator -126: [02:19:11] DEPRECATION WARNING: please use TopologicalTorsionGenerator -126: [02:19:11] DEPRECATION WARNING: please use TopologicalTorsionGenerator -126: .[02:19:11] DEPRECATION WARNING: please use TopologicalTorsionGenerator -126: [02:19:11] DEPRECATION WARNING: please use TopologicalTorsionGenerator +126: .[11:06:08] DEPRECATION WARNING: please use MorganGenerator +126: .[11:06:08] DEPRECATION WARNING: please use MorganGenerator +126: ..[11:06:08] DEPRECATION WARNING: please use AtomPairGenerator +126: [11:06:08] DEPRECATION WARNING: please use AtomPairGenerator +126: [11:06:08] DEPRECATION WARNING: please use AtomPairGenerator +126: [11:06:08] DEPRECATION WARNING: please use AtomPairGenerator +126: [11:06:08] DEPRECATION WARNING: please use AtomPairGenerator +126: [11:06:08] DEPRECATION WARNING: please use AtomPairGenerator +126: .[11:06:08] DEPRECATION WARNING: please use TopologicalTorsionGenerator +126: [11:06:08] DEPRECATION WARNING: please use TopologicalTorsionGenerator +126: ...[11:06:08] DEPRECATION WARNING: please use MorganGenerator +126: [11:06:08] DEPRECATION WARNING: please use MorganGenerator +126: [11:06:08] DEPRECATION WARNING: please use MorganGenerator +126: [11:06:08] DEPRECATION WARNING: please use MorganGenerator +126: [11:06:08] DEPRECATION WARNING: please use MorganGenerator +126: [11:06:08] DEPRECATION WARNING: please use MorganGenerator +126: [11:06:08] DEPRECATION WARNING: please use MorganGenerator +126: [11:06:08] DEPRECATION WARNING: please use MorganGenerator +126: [11:06:08] DEPRECATION WARNING: please use MorganGenerator +126: [11:06:08] DEPRECATION WARNING: please use MorganGenerator +126: [11:06:08] DEPRECATION WARNING: please use MorganGenerator +126: [11:06:08] DEPRECATION WARNING: please use MorganGenerator +126: [11:06:08] DEPRECATION WARNING: please use MorganGenerator +126: [11:06:08] DEPRECATION WARNING: please use MorganGenerator +126: [11:06:08] DEPRECATION WARNING: please use MorganGenerator +126: [11:06:08] DEPRECATION WARNING: please use MorganGenerator +126: [11:06:08] DEPRECATION WARNING: please use MorganGenerator +126: [11:06:08] DEPRECATION WARNING: please use MorganGenerator +126: [11:06:08] DEPRECATION WARNING: please use MorganGenerator +126: [11:06:08] DEPRECATION WARNING: please use MorganGenerator +126: [11:06:08] DEPRECATION WARNING: please use MorganGenerator +126: [11:06:08] DEPRECATION WARNING: please use MorganGenerator +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 +126: ....[11:06:08] DEPRECATION WARNING: please use AtomPairGenerator +126: [11:06:08] DEPRECATION WARNING: please use AtomPairGenerator +125: Warning: Atom Count for residue GLU150A does not match expected count +125: Warning: Atom Count for residue ASN157A does not match expected count +126: ....[11:06:08] DEPRECATION WARNING: please use AtomPairGenerator +126: [11:06:08] DEPRECATION WARNING: please use AtomPairGenerator +126: .[11:06:08] DEPRECATION WARNING: please use TopologicalTorsionGenerator +126: [11:06:08] DEPRECATION WARNING: please use TopologicalTorsionGenerator +126: [11:06:08] DEPRECATION WARNING: please use TopologicalTorsionGenerator +126: [11:06:08] DEPRECATION WARNING: please use TopologicalTorsionGenerator +126: [11:06:08] DEPRECATION WARNING: please use TopologicalTorsionGenerator +126: ..[11:06:08] DEPRECATION WARNING: please use TopologicalTorsionGenerator +126: [11:06:08] DEPRECATION WARNING: please use TopologicalTorsionGenerator +126: [11:06:08] DEPRECATION WARNING: please use TopologicalTorsionGenerator +126: [11:06:08] DEPRECATION WARNING: please use TopologicalTorsionGenerator +126: [11:06:08] DEPRECATION WARNING: please use TopologicalTorsionGenerator +126: [11:06:08] DEPRECATION WARNING: please use TopologicalTorsionGenerator +126: .[11:06:08] DEPRECATION WARNING: please use TopologicalTorsionGenerator +126: [11:06:08] DEPRECATION WARNING: please use TopologicalTorsionGenerator 126: ... 126: ---------------------------------------------------------------------- -126: Ran 31 tests in 3.641s +126: Ran 31 tests in 4.315s 126: 126: OK 126: exactmw 78.046950192 @@ -27392,96 +27446,74 @@ 126: CustomNumAtoms 6.0 126: exactmw 78.046950192 126: lipinskiHBA 0.0 -29: Checking against /build/reproducible-path/rdkit-202503.1/Code/ForceField/MMFF/test_data/MMFF94_reference.log... -140/238 Test #126: pyMolDescriptors ....................... Passed 4.15 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 -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. -141: [02:19:12] done -141: [02:19:12] ------------------------------------- -141: [02:19:12] Testing github 162: Incorrect SMILES after MMFF parameterization . -141: [02:19:12] done -141: [02:19:12] ------------------------------------- -141: [02:19:12] Testing github 224: crash during MMFF parameterization . -141: [02:19:12] done -141: [02:19:12] ------------------------------------- -141: [02:19:12] Testing github6728: crash due to missing stretch-bend params. -141/238 Test #141: testMMFFForceFieldHelpers .............. Passed 2.44 sec +125: =============================================================================== +125: All tests passed (515 assertions in 10 test cases) +125: +141/238 Test #125: descriptorsTestCatch ................... Passed 4.91 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: [02:19:12] ------------------------------------- -153: [02:19:12] AtomType parser testing. -153: [02:19:12] SMARTS Parse Error: syntax error while parsing: [$([!$([NH0])_100;N,O,$([S])_101,$([N,O)_102])_103] -153: [02:19:12] SMARTS Parse Error: Failed parsing SMARTS '[$([!$([NH0])_100;N,O,$([S])_101,$([N,O)_102])_103]' for input: '[$([!$([NH0]);N,O,$([S]),$([N,O)])]' -153: [02:19:12] done -153: [02:19:12] ------------------------------------- -153: [02:19:12] FeatureDefinition parser testing. -153: [02:19:12] done -153: [02:19:12] ------------------------------------- -153: [02:19:12] Test pulling feat defs from a string. -153: [02:19:12] done -153: [02:19:12] ------------------------------------- -153: [02:19:12] FeatureDef functionality testing. -153: [02:19:12] done -153: [02:19:12] ------------------------------------- -153: [02:19:12] FeatureFactory testing. -153: [02:19:12] 1 -153: [02:19:12] 2 -153: [02:19:12] 3 -153: [02:19:12] 4 -153: [02:19:12] 5 -153: [02:19:12] 6 -153: [02:19:12] done -153: [02:19:12] ------------------------------------- -153: [02:19:12] Feature Location testing. -153: [02:19:12] done -153: [02:19:12] ------------------------------------- -153: [02:19:12] Test building a FeatureFactory from a file -153: [02:19:12] done -153: [02:19:12] ------------------------------------- -153: [02:19:12] Testing Issue 224. -153: [02:19:12] done -153: [02:19:12] ------------------------------------- -153: [02:19:12] Testing Issue 225. -153: [02:19:12] done -153: [02:19:12] ------------------------------------- -153: [02:19:12] Test Issue346 -153: [02:19:12] done -153: [02:19:12] ------------------------------------- -153: [02:19:12] Test Issue347 -153: [02:19:12] done -153: [02:19:12] ------------------------------------- -153: [02:19:12] Testing Issue 348. -153: [02:19:12] SMARTS Parse Error: syntax error while parsing: [C[C] -153: [02:19:12] SMARTS Parse Error: Failed parsing SMARTS '[C[C]' for input: '[C[C]' -153: [02:19:12] ------------------------------------- -153: [02:19:12] Testing Nested AtomType definitions. +153: [11:06:08] ------------------------------------- +153: [11:06:08] AtomType parser testing. +153: [11:06:08] SMARTS Parse Error: syntax error while parsing: [$([!$([NH0])_100;N,O,$([S])_101,$([N,O)_102])_103] +153: [11:06:08] 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: [11:06:08] done +153: [11:06:08] ------------------------------------- +153: [11:06:08] FeatureDefinition parser testing. +153: [11:06:08] done +153: [11:06:08] ------------------------------------- +153: [11:06:08] Test pulling feat defs from a string. +153: [11:06:08] done +153: [11:06:08] ------------------------------------- +153: [11:06:08] FeatureDef functionality testing. +153: [11:06:08] done +153: [11:06:08] ------------------------------------- +153: [11:06:08] FeatureFactory testing. +153: [11:06:08] 1 +153: [11:06:08] 2 +153: [11:06:08] 3 +153: [11:06:08] 4 +153: [11:06:08] 5 +153: [11:06:08] 6 +153: [11:06:08] done +153: [11:06:08] ------------------------------------- +153: [11:06:08] Feature Location testing. +153: [11:06:08] done +153: [11:06:08] ------------------------------------- +153: [11:06:08] Test building a FeatureFactory from a file +153: [11:06:08] done +153: [11:06:08] ------------------------------------- +153: [11:06:08] Testing Issue 224. +153: [11:06:08] done +153: [11:06:08] ------------------------------------- +153: [11:06:08] Testing Issue 225. +153: [11:06:08] done +153: [11:06:08] ------------------------------------- +143: [11:06:08] done +143: [11:06:08] ------------------------------------- +143: [11:06:08] Testing GitHubIssue62. +153: [11:06:08] Test Issue346 +153: [11:06:08] done +153: [11:06:08] ------------------------------------- +153: [11:06:08] Test Issue347 +143: [11:06:08] beta-lactam 39.6387 +153: [11:06:08] done +153: [11:06:08] ------------------------------------- +153: [11:06:08] Testing Issue 348. +153: [11:06:08] SMARTS Parse Error: syntax error while parsing: [C[C] +153: [11:06:08] SMARTS Parse Error: Failed parsing SMARTS '[C[C]' for input: '[C[C]' +153: [11:06:08] ------------------------------------- +153: [11:06:08] Testing Nested AtomType definitions. +143: [11:06:08] cyclopropanone 174.698 153: [$([$([$([C;!$(C=[O,N,P,S]);!$(C#N)]),c]);R])] -153: [02:19:12] ------------------------------------- -153: [02:19:12] Testing Github Issue #252: crash when calling getPos() with no conformer. -153: [02:19:12] expect a precondition failure message below -153: [02:19:12] +153: [11:06:08] ------------------------------------- +153: [11:06:08] Testing Github Issue #252: crash when calling getPos() with no conformer. +143: [11:06:08] aziridine 337.986 +153: [11:06:08] expect a precondition failure message below +153: [11:06:08] 153: 153: **** 153: Pre-condition Violation @@ -27494,18 +27526,18 @@ 153: 1# Invar::operator<<(std::ostream&, Invar::Invariant const&) in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu//lib/libRDKitRDGeneral.so.1 153: 2# RDKit::MolChemicalFeature::getPos(int) const in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu//lib/libRDKitMolChemicalFeatures.so.1 153: 3# RDKit::MolChemicalFeature::getPos() const in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu//lib/libRDKitMolChemicalFeatures.so.1 -153: 4# 0x0000AAAAD9531AB0 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/MolChemicalFeatures/testFeatures -153: 5# 0x0000AAAAD9524568 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/MolChemicalFeatures/testFeatures -153: 6# 0x0000FFFFBB38229C in /lib/aarch64-linux-gnu/libc.so.6 +153: 4# 0x0000AAAAAED01AB0 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/MolChemicalFeatures/testFeatures +153: 5# 0x0000AAAAAECF4568 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/MolChemicalFeatures/testFeatures +153: 6# 0x0000FFFFAD57229C in /lib/aarch64-linux-gnu/libc.so.6 153: 7# __libc_start_main in /lib/aarch64-linux-gnu/libc.so.6 -153: 8# 0x0000AAAAD9524730 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/MolChemicalFeatures/testFeatures +153: 8# 0x0000AAAAAECF4730 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/MolChemicalFeatures/testFeatures 153: ---------- 153: **** 153: -153: [02:19:12] Done -153: [02:19:12] ------------------------------------- -153: [02:19:12] Testing github 2077: add confId argument to MolChemicalFeatureFactor::getFeaturesForMol() -153: [02:19:12] done +153: [11:06:08] Done +153: [11:06:08] ------------------------------------- +153: [11:06:08] Testing github 2077: add confId argument to MolChemicalFeatureFactor::getFeaturesForMol() +153: [11:06:08] done 142/238 Test #153: testFeatures ........................... Passed 0.04 sec test 154 Start 154: pyChemicalFeatures @@ -27513,15 +27545,23 @@ 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 -29: done -143/238 Test #29: testMMFFForceField ..................... Passed 8.90 sec +143: [11:06:08] aziridinone 115.248 +143: [11:06:08] isobutene 2.48217 +143: [11:06:08] acetone 1.91788 +143: [11:06:08] cyclopentanone 10.1648 +143: [11:06:08] cyclopropene 99.4921 +143: [11:06:08] cyclobutene 41.0156 +143: [11:06:08] cyclopropane 267.236 +143: [11:06:08] gamma-lactam 15.7471 +143/238 Test #126: pyMolDescriptors ....................... Passed 4.91 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 -148: [02:19:12] Molecule does not have explicit Hs. Consider calling AddHs() +143: [11:06:08] trans-2,3-diphenylcyclopropan-1-one 203.398 +29: Checking against /build/reproducible-path/rdkit-202503.1/Code/ForceField/MMFF/test_data/MMFF94_reference.log... 155: *********************************************************** 155: Testing ShapeHelpers 155: --------------------------------- @@ -27534,142 +27574,91 @@ 155: testGithub4364 155: 155: *********************************************************** -144/238 Test #155: testShapeHelpers ....................... Passed 0.03 sec +144/238 Test #155: testShapeHelpers ....................... Passed 0.04 sec +143: [11:06:08] cis-2,3-diphenylcyclopropan-1-one 206.852 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 -51: Randomness seeded to: 2023979262 -51: =============================================================================== -51: All tests passed (14835 assertions in 14 test cases) -51: -145/238 Test #51: canonTestsCatch ........................ Passed 8.69 sec +143: [11:06:08] 2,3-diphenylcyclopropa-2-en-1-one 20.0443 +143: [11:06:08] cyclopropylidencyclobutane 218.879 +143: [11:06:08] diphenylmethylidencyclobutane 79.6139 +143: [11:06:08] done +143: [11:06:08] ------------------------------------- +143: [11:06:08] Test Github Issue 613: UFF Atom type not properly assigned to lanthanides. +143: [11:06:08] done +143: [11:06:08] ------------------------------------- +143: [11:06:08] Test square planar complexes +143: [11:06:08] done +143: [11:06:08] ------------------------------------- +143: [11:06:08] Test octahedral complexes +143: [11:06:08] done +145/238 Test #143: testUFFForceFieldHelpers ............... Passed 2.73 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 -146/238 Test #157: testMolCatalog ......................... Passed 0.01 sec +29: All 191 tests passed +29: done +29: ------------------------------------- +29: Unit tests for all MMFF constraint terms. +146/238 Test #157: testMolCatalog ......................... Passed 0.02 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: [02:19:12] done -143: [02:19:12] ------------------------------------- -143: [02:19:12] Testing GitHubIssue62. -143: [02:19:12] beta-lactam 39.6387 -143: [02:19:12] cyclopropanone 174.698 -143: [02:19:12] aziridine 337.986 -143: [02:19:12] aziridinone 115.248 -143: [02:19:12] isobutene 2.48217 -143: [02:19:12] acetone 1.91788 -148: [02:19:12] Molecule does not have explicit Hs. Consider calling AddHs() -143: [02:19:12] cyclopentanone 10.1648 -143: [02:19:12] cyclopropene 99.4921 -143: [02:19:12] cyclobutene 41.0156 -143: [02:19:12] cyclopropane 267.236 -143: [02:19:12] gamma-lactam 15.7471 -143: [02:19:12] trans-2,3-diphenylcyclopropan-1-one 203.398 -143: [02:19:12] cis-2,3-diphenylcyclopropan-1-one 206.852 -143: [02:19:12] 2,3-diphenylcyclopropa-2-en-1-one 20.0443 -143: [02:19:12] cyclopropylidencyclobutane 218.879 -151: 1316560453 -143: [02:19:12] diphenylmethylidencyclobutane 79.6139 -143: [02:19:12] done -143: [02:19:12] ------------------------------------- -143: [02:19:12] Test Github Issue 613: UFF Atom type not properly assigned to lanthanides. -143: [02:19:12] done -143: [02:19:12] ------------------------------------- -143: [02:19:12] Test square planar complexes -143: [02:19:12] done -143: [02:19:12] ------------------------------------- -143: [02:19:12] Test octahedral complexes -143: [02:19:12] done -147/238 Test #143: testUFFForceFieldHelpers ............... Passed 2.69 sec +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. +148: [11:06:08] Molecule does not have explicit Hs. Consider calling AddHs() +151: 854486240 +148: [11:06:09] Molecule does not have explicit Hs. Consider calling AddHs() +154: .[11:06:09] Molecule does not have explicit Hs. Consider calling AddHs() +154: .[11:06:09] Molecule does not have explicit Hs. Consider calling AddHs() +29: done +147/238 Test #29: testMMFFForceField ..................... Passed 9.62 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 -154: .[02:19:12] Molecule does not have explicit Hs. Consider calling AddHs() -154: .[02:19:12] Molecule does not have explicit Hs. Consider calling AddHs() -125: Warning: Atom Count for residue GLU5A does not match expected count -125: Warning: Atom Count for residue ASN39A does not match expected count -125: Warning: Atom Count for residue GLU53A does not match expected count -125: Warning: Atom Count for residue ARG64A does not match expected count -125: Warning: Atom Count for residue LYS80A does not match expected count -125: Warning: Atom Count for residue GLU150A does not match expected count -125: Warning: Atom Count for residue ASN157A does not match expected count -125: =============================================================================== -125: All tests passed (515 assertions in 10 test cases) -125: -154: ..[02:19:12] Molecule does not have explicit Hs. Consider calling AddHs() -148/238 Test #125: descriptorsTestCatch ................... Passed 4.85 sec -154: .[02:19:12] Molecule does not have explicit Hs. Consider calling AddHs() -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 -154: .[02:19:12] SMARTS Parse Error: syntax error while parsing: [N,O;!HQ] -154: [02:19:12] SMARTS Parse Error: Failed parsing SMARTS '[N,O;!HQ]' for input: '[N,O;!HQ]' +148: [11:06:09] Molecule does not have explicit Hs. Consider calling AddHs() +154: ..[11:06:09] Molecule does not have explicit Hs. Consider calling AddHs() +154: .[11:06:09] Molecule does not have explicit Hs. Consider calling AddHs() +154: .[11:06:09] SMARTS Parse Error: syntax error while parsing: [N,O;!HQ] +154: [11:06:09] SMARTS Parse Error: Failed parsing SMARTS '[N,O;!HQ]' for input: '[N,O;!HQ]' +154: ... +154: ---------------------------------------------------------------------- +154: Ran 9 tests in 0.068s +154: +154: OK 156: . 156: ---------------------------------------------------------------------- -156: Ran 1 test in 0.025s +156: Ran 1 test in 0.047s 156: 156: OK 156: Testing Shape Helpers wrapper -158: . -158: ---------------------------------------------------------------------- -158: Ran 1 test in 0.006s -158: -158: OK -154: ... -154: ---------------------------------------------------------------------- -154: Ran 9 tests in 0.060s -154: -154: OK 159: ----------------- Test 1 -148: [02:19:12] Molecule does not have explicit Hs. Consider calling AddHs() -149/238 Test #156: pyShapeHelpers ......................... Passed 0.29 sec -150/238 Test #158: pyMolCatalog ........................... Passed 0.19 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 -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 +148: [11:06:09] Molecule does not have explicit Hs. Consider calling AddHs() 159: file test1_6.svg gave hash 1109656969U not the expected 2635907956U 159: Done 159: ----------------- Test 2 -160: Randomness seeded to: 4209345306 -160: file contourMol_1.svg gave hash 4125787245U not the expected 3634867913U -160: file contourMol_2.svg gave hash 2761342533U not the expected 1815941817U -151/238 Test #154: pyChemicalFeatures ..................... Passed 0.38 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 +146: validating reference data 159: file test2_1.png gave hash 2467931916U not the expected 638584804U -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 -161: ----------------- Test 1 159: file test2_2.png gave hash 3737953282U not the expected 610424244U 159: file test2_3.png gave hash 2294574389U not the expected 2179746375U 159: Done @@ -27677,22 +27666,33 @@ 159: file test4_1.png gave hash 516573244U not the expected 3993974247U 159: Done 159: ----------------- Test 5 -161: file rxn_test1_1.png gave hash 2332294744U not the expected 801892091U -160: file testGithub3226_1.png gave hash 632134109U not the expected 3165135374U +148/238 Test #156: pyShapeHelpers ......................... Passed 0.38 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: file test5_1.png gave hash 2590128341U not the expected 571291290U -160: file testGithub3226_2.png gave hash 1790248804U not the expected 643975155U -160: file testGithub3226_3.png gave hash 1296655029U not the expected 3119571946U +158: . +158: ---------------------------------------------------------------------- +158: Ran 1 test in 0.014s +158: +158: OK 159: file test5_2.png gave hash 2869651309U not the expected 97265124U -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 +149/238 Test #154: pyChemicalFeatures ..................... Passed 0.47 sec +test 161 + Start 161: moldraw2DRxnTest1 + +161: Test command: /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/MolDraw2D/moldraw2DRxnTest1 +161: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/MolDraw2D +161: Test timeout computed to be: 1500 159: file test5_3.png gave hash 4285469383U not the expected 606188176U 159: Done 159: ----------------- Test 6 (atom labels) -148: [02:19:12] Molecule does not have explicit Hs. Consider calling AddHs() 159: Done 159: ----------------- Test 7 (backgrounds) -160: file testPNGMetadata_2.png gave hash 1147517534U not the expected 1797853056U -161: file rxn_test1_3.png gave hash 2120547110U not the expected 1590809137U +161: ----------------- Test 1 159: 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 @@ -27700,77 +27700,107 @@ 159: Done 159: ----------------- Test multi-threaded drawing 159: reading molecules +148: [11:06:09] Molecule does not have explicit Hs. Consider calling AddHs() +161: file rxn_test1_1.png gave hash 2332294744U not the expected 801892091U +159: generating reference drawings +150/238 Test #158: pyMolCatalog ........................... Passed 0.38 sec +161: file rxn_test1_2.png gave hash 3186000742U not the expected 507435337U +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 +160: Randomness seeded to: 502835860 +160: file contourMol_1.svg gave hash 4125787245U not the expected 3634867913U +160: file contourMol_2.svg gave hash 2761342533U not the expected 1815941817U +161: file rxn_test1_3.png gave hash 2120547110U not the expected 1590809137U +160: file contourMol_3.svg gave hash 1333854566U not the expected 2579392727U 161: file rxn_test1_4.png gave hash 59268109U not the expected 1766700542U +160: file contourMol_4.svg gave hash 4249475618U not the expected 2914799663U +151: 350085640 +151: =============================================================================== +151: All tests passed (73 assertions in 3 test cases) +151: +151/238 Test #151: molAlignCatchTest ...................... Passed 1.37 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 contourMol_5.svg gave hash 3376179346U not the expected 3792684719U +159: processing +159: launch :0 +159: launch :1 +159: launch :2 +159: launch :3 161: file rxn_test1_5.png gave hash 3733738372U not the expected 2552100594U -160: [02:19:12] Font file /build/reproducible-path/rdkit-202503.1/Data/Fonts/ComicNeue-Regular.ttf not found. -160: [02:19:12] Falling back to original font file /build/reproducible-path/rdkit-202503.1/Data/Fonts/Telex-Regular.ttf. -159: generating reference drawings -160: file testHandDrawn-1.svg gave hash 1143910631U not the expected 2253418236U -160: [02:19:12] Font file /build/reproducible-path/rdkit-202503.1/Data/Fonts/ComicNeue-Regular.ttf not found. -160: [02:19:12] Falling back to original font file /build/reproducible-path/rdkit-202503.1/Data/Fonts/Telex-Regular.ttf. +148: [11:06:09] Molecule does not have explicit Hs. Consider calling AddHs() 161: file rxn_test1_6.png gave hash 2102224395U not the expected 3791582903U -160: file testHandDrawn-1.png gave hash 1854123184U not the expected 3894611804U 161: file rxn_test1_7.png gave hash 3541821286U not the expected 1461397406U 161: Done 161: ----------------- Test 2: some examples that caused problems in testing +160: file testGithub3226_1.png gave hash 632134109U not the expected 3165135374U +160: file testGithub3226_2.png gave hash 1790248804U not the expected 643975155U 161: file rxn_test2_1.png gave hash 2631413446U not the expected 3551633840U -160: [02:19:12] Font file /build/reproducible-path/rdkit-202503.1/Data/Fonts/ComicNeue-Regular.ttf not found. +160: file testGithub3226_3.png gave hash 1296655029U not the expected 3119571946U +160: file testPNGMetadata_1.png gave hash 2053548476U not the expected 997629701U 161: 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: [02:19:12] 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: [02:19:12] Font file /build/reproducible-path/rdkit-202503.1/Data/Fonts/ComicNeue-Regular.ttf not found. -160: [02:19:12] 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 +160: file testPNGMetadata_2.png gave hash 1147517534U not the expected 1797853056U 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: file testHandDrawn-2.png gave hash 3861646972U not the expected 1443443188U -160: [02:19:12] Font file /build/reproducible-path/rdkit-202503.1/Data/Fonts/ComicNeue-Regular.ttf not found. -160: [02:19:12] Falling back to original font file /build/reproducible-path/rdkit-202503.1/Data/Fonts/Telex-Regular.ttf. -160: file testHandDrawn-3.svg gave hash 2359787964U not the expected 3982694296U -160: [02:19:12] Font file /build/reproducible-path/rdkit-202503.1/Data/Fonts/ComicNeue-Regular.ttf not found. -160: [02:19:12] Falling back to original font file /build/reproducible-path/rdkit-202503.1/Data/Fonts/Telex-Regular.ttf. 161: file rxn_test2_2_3.png gave hash 351157945U not the expected 3828365604U -160: file testHandDrawn-3.png gave hash 2744546773U not the expected 865629432U 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: [02:19:12] Font file /build/reproducible-path/rdkit-202503.1/Data/Fonts/ComicNeue-Regular.ttf not found. -160: [02:19:12] 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: [02:19:12] Font file /build/reproducible-path/rdkit-202503.1/Data/Fonts/ComicNeue-Regular.ttf not found. -160: [02:19:12] 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-4.png gave hash 2378590163U not the expected 3919767093U -159: processing -159: launch :0 +160: [11:06:09] Font file /build/reproducible-path/rdkit-202503.1/Data/Fonts/ComicNeue-Regular.ttf not found. +160: [11:06:09] 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: [11:06:09] Font file /build/reproducible-path/rdkit-202503.1/Data/Fonts/ComicNeue-Regular.ttf not found. +160: [11:06:09] Falling back to original font file /build/reproducible-path/rdkit-202503.1/Data/Fonts/Telex-Regular.ttf. 161: file rxn_test3_1.png gave hash 3254654119U not the expected 4189980366U -159: launch :1 -159: launch :2 -159: launch :3 161: Done 161: ----------------- Test 4: some examples from SMARTS in testing 161: draw! -162: ...[02:19:12] Font file /build/reproducible-path/rdkit-202503.1/Code/GraphMol/MolDraw2D/Amadeus.ttf not found. -162: [02:19:12] Falling back to original font file /build/reproducible-path/rdkit-202503.1/Data/Fonts/Telex-Regular.ttf. -151: 358895039 -151: =============================================================================== -151: All tests passed (73 assertions in 3 test cases) -151: -152/238 Test #151: molAlignCatchTest ...................... Passed 1.82 sec +160: file testHandDrawn-1.png gave hash 1854123184U not the expected 3894611804U +161: file rxn_test4_1.png gave hash 4262495936U not the expected 2745201873U +161: done +160: [11:06:09] Font file /build/reproducible-path/rdkit-202503.1/Data/Fonts/ComicNeue-Regular.ttf not found. +160: [11:06:09] 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: [11:06:09] Font file /build/reproducible-path/rdkit-202503.1/Data/Fonts/ComicNeue-Regular.ttf not found. +160: [11:06:09] Falling back to original font file /build/reproducible-path/rdkit-202503.1/Data/Fonts/Telex-Regular.ttf. +160: file testHandDrawn-2.png gave hash 3861646972U not the expected 1443443188U +160: [11:06:09] Font file /build/reproducible-path/rdkit-202503.1/Data/Fonts/ComicNeue-Regular.ttf not found. +160: [11:06:09] Falling back to original font file /build/reproducible-path/rdkit-202503.1/Data/Fonts/Telex-Regular.ttf. +160: file testHandDrawn-3.svg gave hash 2359787964U not the expected 3982694296U +160: [11:06:09] Font file /build/reproducible-path/rdkit-202503.1/Data/Fonts/ComicNeue-Regular.ttf not found. +160: [11:06:09] 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: file testHandDrawn-3.png gave hash 2744546773U not the expected 865629432U +161: Done +160: [11:06:09] Font file /build/reproducible-path/rdkit-202503.1/Data/Fonts/ComicNeue-Regular.ttf not found. +160: [11:06:09] Falling back to original font file /build/reproducible-path/rdkit-202503.1/Data/Fonts/Telex-Regular.ttf. +152/238 Test #161: moldraw2DRxnTest1 ...................... Passed 0.30 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 -146: validating reference data -161: file rxn_test4_1.png gave hash 4262495936U not the expected 2745201873U -161: done -148: [02:19:12] Molecule does not have explicit Hs. Consider calling AddHs() -162: ..........[02:19:12] +160: file testHandDrawn-4.svg gave hash 1880974760U not the expected 2146113517U +160: [11:06:09] Font file /build/reproducible-path/rdkit-202503.1/Data/Fonts/ComicNeue-Regular.ttf not found. +160: [11:06:09] 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: ...[11:06:09] Font file /build/reproducible-path/rdkit-202503.1/Code/GraphMol/MolDraw2D/Amadeus.ttf not found. +162: [11:06:09] Falling back to original font file /build/reproducible-path/rdkit-202503.1/Data/Fonts/Telex-Regular.ttf. +162: ..........[11:06:09] 162: 162: **** 162: Pre-condition Violation @@ -27784,7 +27814,7 @@ 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# 0x0000FFFFB3362680 in /lib/aarch64-linux-gnu/libboost_python313.so.1.83.0 +162: 5# 0x0000FFFFA5A52680 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 @@ -27795,17 +27825,17 @@ 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# 0x0000FFFFB296C320 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so -162: 17# 0x0000FFFFB296C2B8 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so -162: 18# 0x0000FFFFB296C248 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so -162: 19# 0x0000FFFFB296C1E0 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so -162: 20# 0x0000FFFFB296C178 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so +162: 16# 0x0000FFFFA505C320 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so +162: 17# 0x0000FFFFA505C2B8 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so +162: 18# 0x0000FFFFA505C248 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so +162: 19# 0x0000FFFFA505C1E0 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so +162: 20# 0x0000FFFFA505C178 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# 0x0000FFFFB335F25C in /lib/aarch64-linux-gnu/libboost_python313.so.1.83.0 +162: 26# 0x0000FFFFA5A4F25C in /lib/aarch64-linux-gnu/libboost_python313.so.1.83.0 162: 27# _PyObject_MakeTpCall in /usr/bin/python3 162: 28# _PyEval_EvalFrameDefault in /usr/bin/python3 162: 29# 0x000000000053D3B0 in /usr/bin/python3 @@ -27837,15 +27867,20 @@ 162: 55# 0x000000000065EE50 in /usr/bin/python3 162: 56# Py_RunMain in /usr/bin/python3 162: 57# Py_BytesMain in /usr/bin/python3 -162: 58# 0x0000FFFFB4CC229C in /lib/aarch64-linux-gnu/libc.so.6 +162: 58# 0x0000FFFFA73B229C 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: -161: file rxn_test4_2.png gave hash 2281531937U not the expected 3094925886U -161: Done -153/238 Test #161: moldraw2DRxnTest1 ...................... Passed 0.31 sec +148: .[11:06:09] Molecule does not have explicit Hs. Consider calling AddHs() +162: ...................... +162: ---------------------------------------------------------------------- +162: Ran 35 tests in 0.230s +162: +162: OK +162: json lasso +153/238 Test #162: pyMolDraw2D ............................ Passed 0.62 sec test 165 Start 165: FMCStest @@ -29817,32 +29852,71 @@ 165: 165: testFileSDF_RandomSet(): benchmark/chembl13_threshold_90.smi 165: ERROR: RDKit could not load input file -148: [02:19:12] Molecule does not have explicit Hs. Consider calling AddHs() -154/238 Test #165: FMCStest ............................... Passed 0.06 sec +154/238 Test #165: FMCStest ............................... Passed 0.04 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 -162: ...................... -162: ---------------------------------------------------------------------- -162: Ran 35 tests in 0.134s -162: -162: OK -162: json lasso -155/238 Test #162: pyMolDraw2D ............................ Passed 0.42 sec +166: Randomness seeded to: 1270443401 +166: =============================================================================== +166: All tests passed (363 assertions in 14 test cases) +166: +155/238 Test #166: molHashCatchTest ....................... Passed 0.08 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 -166: Randomness seeded to: 192888335 -166: =============================================================================== -166: All tests passed (363 assertions in 14 test cases) -166: -156/238 Test #166: molHashCatchTest ....................... Passed 0.07 sec +160: file testHandDrawn-5a.svg gave hash 2796249138U not the expected 1567781555U +160: [11:06:10] Font file /build/reproducible-path/rdkit-202503.1/Data/Fonts/ComicNeue-Regular.ttf not found. +160: [11:06:10] Falling back to original font file /build/reproducible-path/rdkit-202503.1/Data/Fonts/Telex-Regular.ttf. +150: *********************************************************** +150: Testing O3AAlign +150: --------------------------------- +150: testMMFFO3A +150: +150: --------------------------------- +150: testMMFFO3A with pre-computed dmat and MolHistogram +150: +150: --------------------------------- +150: testMMFFO3A with constraints +150: +150: --------------------------------- +150: testMMFFO3A with variable weight constraints followed by local-only optimization +150: +150: --------------------------------- +150: testCrippenO3A +150: +150: --------------------------------- +150: testCrippenO3A with pre-computed dmat and MolHistogram +150: +150: --------------------------------- +150: testCrippenO3A with constraints +150: +150: --------------------------------- +150: testCrippenO3A with variable weight constraints followed by local-only optimization +150: +150: --------------------------------- +150: testMMFFO3A multithreading +150: +150: generating reference data +160: file testHandDrawn-5b.svg gave hash 4043231252U not the expected 66354106U +160: [11:06:10] Font file /build/reproducible-path/rdkit-202503.1/Data/Fonts/ComicNeue-Regular.ttf not found. +160: [11:06:10] 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 +160: [11:06:10] 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 0.021s +167: +167: OK +156/238 Test #167: pyMolHash .............................. Passed 0.40 sec test 168 Start 168: testMMPA @@ -29851,7 +29925,7 @@ 168: Test timeout computed to be: 1500 168: 168: TEST mol: Case1 Cc1ccccc1NC(=O)[C:7](C)[NH+]1CCCC1 Case1 -168: Time elapsed 0.006510 seconds +168: Time elapsed 0.002263 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 @@ -29892,7 +29966,7 @@ 168: --- UNMATCHED Reference RESULTS: --- 168: 1: Cc1ccccc1NC(=O)[C:7](C)[NH+]1CCCC1,Case1,[*:1][C:7]([*:2])[*:3],C1CC[NH+]([*:3])C1.C[*:2].Cc1ccccc1NC(=O)[*:1] 168: ----------------------------------- -168: Time elapsed 0.006222 seconds +168: Time elapsed 0.001962 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 @@ -29934,11 +30008,12 @@ 168: ----------------------------------- 168: 168: TEST mol: ZINC21984717 Cc1c(C(=O)NCCO)[n+](=O)c2ccccc2n1[O-] ZINC21984717 -168: Time elapsed 0.006252 seconds +168: Time elapsed 0.001961 seconds 168: 1: res= NULL,C[*:1].O=C(NCCO)c1c([*:1])n([O-])c2ccccc2[n+]1=O 168: 1: PASSED. matchedRefRes = 4 168: 2: res= O=[n+]1c([*:2])c([*:1])n([O-])c2ccccc21,C[*:1].O=C(NCCO)[*:2] 168: 2: PASSED. matchedRefRes = 1 +160: file testGithub4323_3.png gave hash 2734641420U not the expected 381907253U 168: 3: res= O=C(N[*:2])c1c([*:1])n([O-])c2ccccc2[n+]1=O,C[*:1].OCC[*:2] 168: 3: PASSED. matchedRefRes = 6 168: 4: res= O=C(NC[*:2])c1c([*:1])n([O-])c2ccccc2[n+]1=O,C[*:1].OC[*:2] @@ -29953,6 +30028,7 @@ 168: 8: NOREF. Reference data NOT LISTED in test case. 168: 9: res= O=C(NCC[*:1])[*:2],Cc1c([*:2])[n+](=O)c2ccccc2n1[O-].O[*:1] 168: 9: NOREF. Reference data NOT LISTED in test case. +160: [11:06:10] FIELDDISP info not found for DAT SGroup which isn't associated with an atom. SGroup will not be rendered. 168: 10: res= NULL,Cc1c(C(=O)N[*:1])[n+](=O)c2ccccc2n1[O-].OCC[*:1] 168: 10: PASSED. matchedRefRes = 3 168: 11: res= C([*:1])[*:2],Cc1c(C(=O)N[*:2])[n+](=O)c2ccccc2n1[O-].OC[*:1] @@ -29974,7 +30050,7 @@ 168: ----------------------------------- 168: 168: TEST mol: Case1-SIMPLE CC(N1CC1)C(=O) Case1-SIMPLE -168: Time elapsed 0.004746 seconds +168: Time elapsed 0.000562 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] @@ -29996,7 +30072,7 @@ 168: ----------------------------------- 168: 168: TEST mol: Case1 Cc1ccccc1NC(=O)[C:7](C)[NH+]1CCCC1 Case1 -168: Time elapsed 0.006375 seconds +168: Time elapsed 0.002150 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 @@ -30039,7 +30115,7 @@ 168: ----------------------------------- 168: 168: TEST mol: Case2 O=C(OCc1ccccc1)C(O)c1ccccc1 Case2 -168: Time elapsed 0.006504 seconds +168: Time elapsed 0.002339 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 @@ -30087,71 +30163,40 @@ 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 -148: .[02:19:13] Molecule does not have explicit Hs. Consider calling AddHs() -160: file testHandDrawn-5a.svg gave hash 2796249138U not the expected 1567781555U -160: [02:19:13] Font file /build/reproducible-path/rdkit-202503.1/Data/Fonts/ComicNeue-Regular.ttf not found. -160: [02:19:13] Falling back to original font file /build/reproducible-path/rdkit-202503.1/Data/Fonts/Telex-Regular.ttf. -160: file testHandDrawn-5b.svg gave hash 4043231252U not the expected 66354106U -160: [02:19:13] Font file /build/reproducible-path/rdkit-202503.1/Data/Fonts/ComicNeue-Regular.ttf not found. -160: [02:19:13] Falling back to original font file /build/reproducible-path/rdkit-202503.1/Data/Fonts/Telex-Regular.ttf. -167: .... -167: ---------------------------------------------------------------------- -167: Ran 4 tests in 0.017s -167: -167: OK -160: file testHandDrawn-5.png gave hash 2095603616U not the expected 828378555U -160: file testBrackets-5a.svg gave hash 279553678U not the expected 1447240271U -160: file testPositionVariation-1b.svg gave hash 3055422087U not the expected 3269244452U -158/238 Test #167: pyMolHash .............................. Passed 0.38 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 -160: [02:19:13] 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 -160: file testGithub4323_3.png gave hash 2734641420U not the expected 381907253U -160: [02:19:13] FIELDDISP info not found for DAT SGroup which isn't associated with an atom. SGroup will not be rendered. -146: processing -146: launch :0 -146: launch :1 -146: launch :2 -146: launch :3 163: MCS: [#6]-[#6]1-[#6]-[#6]-[#6]-[#6]-[#6]-1 7 atoms, 7 bonds 163: Time elapsed 0.000 seconds 163: 163: test32() 163: MCS: [#6]1:[#6]:[#6]:[#6](:[#6]:[#6]:1)-[#6]=[#6]-[#6](-[#7]-[#6]1:[#6]:[#6](-[#16](-[#7]2-[#6]-[#6]-[#8]-[#6]-[#6]-2)(=[#8])=[#8]):[#6]:[#6]:[#6]:1-[#7](-[#6]-[#6])-[#6]-[#6])=[#8] 31 atoms, 33 bonds -163: Time elapsed 0.034 seconds +163: Time elapsed 0.066 seconds 163: 163: test190() 163: MCS: [#6]1:[#6]:[#6]2:[#8]:[#6](:[#7]:[#6]:2:[#6]:[#6]:1)-[#6]1:[#6]:[#6](-[#7]-[#6](=[#8])-[#6]):[#6]:[#6]:[#6]:1 19 atoms, 21 bonds -163: Time elapsed 0.005 seconds +163: Time elapsed 0.009 seconds 163: 163: test3() 163: MCS: [#6]1:[#6]:[#6]:[#6]:[#6]:[#6]:1-[#6]-[#6](=[#8])-[#7]-[#6]-[#6]-[#6]-[#6] 14 atoms, 14 bonds -163: Time elapsed 0.007 seconds +163: Time elapsed 0.011 seconds 163: 163: testSimpleFast() 163: MCS: [#6]-[#8]-[#6]-[#6]1:[#6]:[#7]:[#6]:[#6](:[#6]:1):[#7]:[#6]1:[#6]:[#6]:[#6]:[#6](:[#6]:1)-[#8]-[#6]1:[#6]:[#6]:[#6](:[#6]:[#6]:1)-[#17] 24 atoms, 26 bonds -163: Time elapsed 0.056 seconds +163: Time elapsed 0.090 seconds 163: 163: testSimple() 163: MCS: [#6]-&!@[#6]-&!@[#6](-&!@[#7]-&!@[#6](=&!@[#8])-&!@[#6]-&!@[#7]-&!@[#6](=&!@[#8])-&!@[#6])-&!@[#6](-&!@[#7]-&!@[#6])=&!@[#8] 15 atoms, 14 bonds -163: Time elapsed 0.051 seconds +163: Time elapsed 0.053 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 0.074 seconds +163: Time elapsed 0.061 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 0.127 seconds +163: Time elapsed 0.060 seconds 163: 163: testSegFault() 163: MCS: [#6]1:&@[#6]:&@[#6]:&@[#6]:&@[#6]:&@[#6]:&@1 6 atoms, 6 bonds -163: Time elapsed 0.009 seconds +163: Time elapsed 0.005 seconds 163: MCS MatchFusedRings: [#6]1:&@[#6]:&@[#6]:&@[#6]:&@[#6]:&@[#6]:&@1 6 atoms, 6 bonds -163: Time elapsed 0.015 seconds +163: Time elapsed 0.007 seconds 163: MCS MatchFusedRingsStrict: [#6;r6,!R1]1:&@[#6;r6,!R1]:&@[#6;r6,!R1]:&@[#6;r6,!R1]:&@[#6;r6,!R1]:&@[#6;r6,!R1]:&@1 6 atoms, 6 bonds -163: Time elapsed 0.015 seconds +163: Time elapsed 0.007 seconds 163: 163: testThreshold() 163: MCS: [#6]-[#6]-[#6] 3 atoms, 2 bonds @@ -30159,11 +30204,11 @@ 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 0.337 seconds +163: Time elapsed 0.189 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 0.190 seconds +163: Time elapsed 0.346 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 0.193 seconds +163: Time elapsed 0.270 seconds 163: 163: testAtomCompareIsotopes() 163: MCS: [0*]-[0*]-[13*] 3 atoms, 2 bonds @@ -30187,39 +30232,9 @@ 163: 163: testJnk1LigandsDistance() 163: MCS: [#6]-[#6]-[#8]-[#6]1:[#6](:[#6](:[#6]:[#6](:[#7]:1)-[#7]-[#6](=[#8])-[#6]-[#6]1:[#6]:[#6]:[#6]:[#6]:[#6]:1)-[#7])-[#6]#[#7] CCOc1nc(NC(=O)Cc2ccccc2)cc(N)c1C#N 22 atoms, 23 bonds -163: Time elapsed 0.009 seconds +163: Time elapsed 0.011 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 -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 -163: Time elapsed 0.007 seconds +163: Time elapsed 0.001 seconds 163: 163: test18() 163: Query +MAP [CH3:0][c:1]1[n:2][c:3]([CH2:4][N:5]([CH:6]([CH3:7])[c:8]2[n:9][cH:10][cH:11][cH:12][cH:13]2)[CH2:14][CH2:15][CH2:16][CH2:17][NH2:18])[cH:19][cH:20][cH:21]1 @@ -30229,15 +30244,15 @@ 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 0.095 seconds +163: Time elapsed 0.047 seconds 163: MCS: [#6]-[#6]1-[#6]-[#6]-[#6]-[#6]-[#6]-1 7 atoms, 7 bonds 163: Time elapsed 0.001 seconds 163: MCS: [#6]1-[#6]-[#7]-[#6](-[#6]-[#7]-1-[#6]1:[#6](:[#6]:[#6]2:[#6](:[#6](:[#6]:[#7](-[#6]3-[#6]-[#6]-3):[#6]:2:[#6]:1)-[#6](=[#8])-[#8])=[#8])-[#9])-[#6] 25 atoms, 28 bonds -163: Time elapsed 0.026 seconds +163: Time elapsed 0.019 seconds 163: Query Cc1c(F)c(N2CCNC(C)C2)cc2c1c(=O)c(C(=O)O)cn2C1CC1 26(26) atoms, 29(28) bonds -163: 1 Seeds:1 MCS 25 atoms, 28 bonds for 0.0007 seconds. bond[0]=6 +163: 1 Seeds:1 MCS 25 atoms, 28 bonds for 0.0008 seconds. bond[0]=6 163: STATISTICS: -163: Total Growing Steps = 1, MCS found on 1 step, for 0.0007 seconds +163: Total Growing Steps = 1, MCS found on 1 step, for 0.0008 seconds 163: Initial Seeds = 1, Mismatched 0 163: Inspected Seeds = 2 163: Rejected by BestSize = 0 @@ -30352,6 +30367,27 @@ 163: res sub = 1 size=3 163: MCS: [#6]-[#6]-[#6] 3 atoms, 2 bonds 163: done +51: Randomness seeded to: 2233565772 +51: =============================================================================== +51: All tests passed (14835 assertions in 14 test cases) +51: +158/238 Test #51: canonTestsCatch ........................ Passed 10.85 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 +150: processing +150: launch :0 +150: launch :1 +150: launch :2 +150: launch :3 +146: processing +146: launch :0 +146: launch :1 +146: launch :2 +146: launch :3 160: 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 @@ -30365,26 +30401,15 @@ 160: file github5383_1.png gave hash 482266761U not the expected 2893520928U 160: file acs1996_1.png gave hash 2331419344U not the expected 2329725800U 160: file acs1996_2.png gave hash 2927836808U not the expected 2996350718U -169: ......... -169: ---------------------------------------------------------------------- -169: Ran 9 tests in 0.839s -169: -169: OK 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: [02:19:14] 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. -159/238 Test #169: pyMMPA ................................. Passed 1.13 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: [11:06:11] 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 160: file github6336_1.png gave hash 1930712448U not the expected 2958833204U +163: [11:06:11] The provided InitialSeed is not an MCS and will be ignored 160: file AtropManyChiralsEnhanced.svg gave hash 643650995U not the expected 2256768013U 160: file testWedgingShouldBeOnSingleBond.svg gave hash 2637422009U not the expected 1002741488U 160: file testHighlightHeteroAtoms_1.svg gave hash 4006401146U not the expected 1769258632U @@ -30393,52 +30418,62 @@ 160: file testGithub_7739_3.svg gave hash 3850267352U not the expected 1037942338U 160: file testGithub_7739_4.svg gave hash 1411616678U not the expected 3549083171U 160: file testSmallReactionCanvas.svg gave hash 3859901121U not the expected 2238356155U +169: ......... +169: ---------------------------------------------------------------------- +169: Ran 9 tests in 1.625s +169: +169: OK 160: =============================================================================== 160: All tests passed (6857 assertions in 116 test cases) 160: -160/238 Test #160: moldraw2DTestCatch ..................... Passed 2.26 sec +159/238 Test #160: moldraw2DTestCatch ..................... Passed 3.30 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 +160/238 Test #169: pyMMPA ................................. Passed 1.98 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 -150: processing -150: launch :0 -150: launch :1 -150: launch :2 -150: launch :3 -163: [02:19:15] The provided InitialSeed is not an MCS and will be ignored -172: ..........[02:19:15] Too many matching bond pairs (1032) so can't continue. -164: ........................................[02:19:16] The provided InitialSeed is not an MCS and will be ignored -164: [02:19:16] The provided InitialSeed is not an MCS and will be ignored -164: [02:19:16] The provided InitialSeed is not an MCS and will be ignored -164: .[02:19:16] The provided InitialSeed is not an MCS and will be ignored -164: [02:19:16] The provided InitialSeed is not an MCS and will be ignored -164: [02:19:16] The provided InitialSeed is not an MCS and will be ignored -164: .[02:19:16] The provided InitialSeed is not an MCS and will be ignored -164: [02:19:16] The provided InitialSeed is not an MCS and will be ignored -164: [02:19:16] The provided InitialSeed is not an MCS and will be ignored -164: .[02:19:16] The provided InitialSeed is not an MCS and will be ignored -164: [02:19:16] The provided InitialSeed is not an MCS and will be ignored -164: [02:19:16] The provided InitialSeed is not an MCS and will be ignored +172: ..........[11:06:13] Too many matching bond pairs (1032) so can't continue. +164: ........................................[11:06:13] The provided InitialSeed is not an MCS and will be ignored +164: [11:06:13] The provided InitialSeed is not an MCS and will be ignored +164: [11:06:13] The provided InitialSeed is not an MCS and will be ignored +164: .[11:06:13] The provided InitialSeed is not an MCS and will be ignored +164: [11:06:13] The provided InitialSeed is not an MCS and will be ignored +164: [11:06:13] The provided InitialSeed is not an MCS and will be ignored +164: .[11:06:13] The provided InitialSeed is not an MCS and will be ignored +164: [11:06:13] The provided InitialSeed is not an MCS and will be ignored +164: [11:06:13] The provided InitialSeed is not an MCS and will be ignored +164: .[11:06:13] The provided InitialSeed is not an MCS and will be ignored +164: [11:06:13] The provided InitialSeed is not an MCS and will be ignored +164: [11:06:13] The provided InitialSeed is not an MCS and will be ignored 164: ................. 164: ---------------------------------------------------------------------- -164: Ran 60 tests in 3.715s +164: Ran 60 tests in 3.947s 164: 164: OK -172: .... -172: ---------------------------------------------------------------------- -172: Ran 14 tests in 1.563s -172: -172: OK -161/238 Test #164: pyFMCS ................................. Passed 4.01 sec +161/238 Test #164: pyFMCS ................................. Passed 4.43 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 +172: .... +172: ---------------------------------------------------------------------- +172: Ran 14 tests in 1.735s +172: +172: OK +159: Done +159: ----------------- Test Github #781: Rendering single-atom molecules +159: Done +159: ----------------- Test 3 162/238 Test #172: pyRascalMCES ........................... Passed 2.09 sec test 174 Start 174: testSynthonSpaceRascalSearch @@ -30446,10 +30481,6 @@ 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: Done -159: ----------------- Test Github #781: Rendering single-atom molecules -159: Done -159: ----------------- Test 3 159: file test3_1.png gave hash 3115155176U not the expected 675908852U 159: file test3_2.png gave hash 907411238U not the expected 2452584093U 159: file test3_3.png gave hash 2790716736U not the expected 1907006999U @@ -30458,8 +30489,6 @@ 159: file test3_4.svg gave hash 2680534430U not the expected 187720898U 159: file test3_5.png gave hash 268184992U not the expected 3842605920U 159: file test3_5.svg gave hash 3625812711U not the expected 300865579U -173: Randomness seeded to: 2928504206 -173: [02:19:18] Writing the enumerated file may take quite some time and result in a large file. 159: file test3_6.png gave hash 3400306190U not the expected 662622011U 159: file test3_7.png gave hash 2184493535U not the expected 469729412U 159: Done @@ -30490,6 +30519,8 @@ 159: ----------------- Test Github #953: default color should not be cyan 159: Done 159: ----------------- Test Github #983: wedged bonds between chiral centers drawn improperly +173: Randomness seeded to: 4155807365 +173: [11:06:15] Writing the enumerated file may take quite some time and result in a large file. 159: Done 159: ----------------- Test Deuterium, Tritium 159: Done @@ -30571,28 +30602,26 @@ 159: Done 159: ----------------- Test AND queries 159: Done -163/238 Test #159: moldraw2DTest1 ......................... Passed 6.12 sec +163/238 Test #159: moldraw2DTest1 ......................... Passed 6.42 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: 3368398384 -175: [02:19:18] non kekulizable aromatic bond being treated as bond order 1 -175: [02:19:18] non kekulizable aromatic bond being treated as bond order 1 -175: [02:19:18] non kekulizable aromatic bond being treated as bond order 1 -175: [02:19:18] non kekulizable aromatic bond being treated as bond order 1 -175: [02:19:18] non kekulizable aromatic bond being treated as bond order 1 -175: [02:19:18] non kekulizable aromatic bond being treated as bond order 1 -171: Randomness seeded to: 2426224808 -171: /build/reproducible-path/rdkit-202503.1/Code/GraphMol/RascalMCES/data/chembl_1907596.smi -175: [02:19:18] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored -175: [02:19:18] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored +175: Randomness seeded to: 2935914476 +175: [11:06:15] non kekulizable aromatic bond being treated as bond order 1 +175: [11:06:15] non kekulizable aromatic bond being treated as bond order 1 +175: [11:06:15] non kekulizable aromatic bond being treated as bond order 1 +175: [11:06:15] non kekulizable aromatic bond being treated as bond order 1 +175: [11:06:15] non kekulizable aromatic bond being treated as bond order 1 +175: [11:06:15] non kekulizable aromatic bond being treated as bond order 1 +175: [11:06:15] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored +175: [11:06:15] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored 175: =============================================================================== 175: All tests passed (6577 assertions in 19 test cases) 175: -164/238 Test #175: testCIPLabeler ......................... Passed 0.15 sec +164/238 Test #175: testCIPLabeler ......................... Passed 0.18 sec test 176 Start 176: pyCIPLabelsWrapTest @@ -30601,18 +30630,18 @@ 176: Test timeout computed to be: 1500 176: .... 176: ---------------------------------------------------------------------- -176: Ran 4 tests in 0.022s +176: Ran 4 tests in 0.019s 176: 176: OK -165/238 Test #176: pyCIPLabelsWrapTest .................... Passed 0.40 sec +165/238 Test #176: pyCIPLabelsWrapTest .................... Passed 0.41 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: [02:19:19] Building the fingerprints may take some time. -173: [02:19:20] +173: [11:06:16] Building the fingerprints may take some time. +173: [11:06:17] 173: 173: **** 173: Invariant Violation @@ -30628,65 +30657,69 @@ 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# 0x0000AAAAE922DB50 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/SynthonSpaceSearch/testSynthonSpaceSubstructureSearch -173: 8# 0x0000AAAAE92766EC in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/SynthonSpaceSearch/testSynthonSpaceSubstructureSearch -173: 9# 0x0000AAAAE92770A0 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/SynthonSpaceSearch/testSynthonSpaceSubstructureSearch -173: 10# 0x0000AAAAE92774D4 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/SynthonSpaceSearch/testSynthonSpaceSubstructureSearch -173: 11# 0x0000AAAAE924A958 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/SynthonSpaceSearch/testSynthonSpaceSubstructureSearch -173: 12# 0x0000AAAAE924AEA4 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/SynthonSpaceSearch/testSynthonSpaceSubstructureSearch -173: 13# 0x0000AAAAE922CC10 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/SynthonSpaceSearch/testSynthonSpaceSubstructureSearch -173: 14# 0x0000FFFFB7E0229C in /lib/aarch64-linux-gnu/libc.so.6 +173: 7# 0x0000AAAAB038DB50 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/SynthonSpaceSearch/testSynthonSpaceSubstructureSearch +173: 8# 0x0000AAAAB03D66EC in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/SynthonSpaceSearch/testSynthonSpaceSubstructureSearch +173: 9# 0x0000AAAAB03D70A0 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/SynthonSpaceSearch/testSynthonSpaceSubstructureSearch +173: 10# 0x0000AAAAB03D74D4 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/SynthonSpaceSearch/testSynthonSpaceSubstructureSearch +173: 11# 0x0000AAAAB03AA958 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/SynthonSpaceSearch/testSynthonSpaceSubstructureSearch +173: 12# 0x0000AAAAB03AAEA4 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/SynthonSpaceSearch/testSynthonSpaceSubstructureSearch +173: 13# 0x0000AAAAB038CC10 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/SynthonSpaceSearch/testSynthonSpaceSubstructureSearch +173: 14# 0x0000FFFFA1E2229C in /lib/aarch64-linux-gnu/libc.so.6 173: 15# __libc_start_main in /lib/aarch64-linux-gnu/libc.so.6 -173: 16# 0x0000AAAAE922CCF0 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/SynthonSpaceSearch/testSynthonSpaceSubstructureSearch +173: 16# 0x0000AAAAB038CCF0 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/SynthonSpaceSearch/testSynthonSpaceSubstructureSearch 173: ---------- 173: **** 173: -173: [02:19:20] Error:: in reaction amide-1 :: building molecule from synthons : 1-1 (c1cc[1*]ccc1C(=O)[1*]) and 2-1 ([1*]N1CCCC1) +173: [11:06:17] 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: [02:19:20] Explicit valence for atom # 4 C, 5, is greater than permitted -173: [02:19:20] Error:: in reaction error-1 :: building molecule from synthons : 1-1 (C(=[2*])=CC=[1*]) and 2-1 (ClC([2*])=CN=[1*]) +173: [11:06:17] Explicit valence for atom # 4 C, 5, is greater than permitted +173: [11:06:17] 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: [02:19:20] Complex queries can be slow. -173: [02:19:20] Complex queries can be slow. -173: [02:19:20] Complex queries can be slow. -173: [02:19:20] Complex queries can be slow. -152: .............[02:19:20] Molecule does not have explicit Hs. Consider calling AddHs() -173: [02:19:20] Complex queries can be slow. -152: [02:19:21] Molecule does not have explicit Hs. Consider calling AddHs() -152: [02:19:21] Molecule does not have explicit Hs. Consider calling AddHs() -152: [02:19:21] Molecule does not have explicit Hs. Consider calling AddHs() -152: [02:19:21] Molecule does not have explicit Hs. Consider calling AddHs() -152: [02:19:21] Molecule does not have explicit Hs. Consider calling AddHs() -152: [02:19:21] Molecule does not have explicit Hs. Consider calling AddHs() -173: [02:19:21] Complex queries can be slow. -152: [02:19:21] Molecule does not have explicit Hs. Consider calling AddHs() -152: [02:19:21] Molecule does not have explicit Hs. Consider calling AddHs() -152: [02:19:21] Molecule does not have explicit Hs. Consider calling AddHs() -152: [02:19:21] Molecule does not have explicit Hs. Consider calling AddHs() -173: [02:19:21] Complex queries can be slow. -173: [02:19:21] Complex queries can be slow. -173: [02:19:21] Complex queries can be slow. -173: [02:19:21] Complex queries can be slow. -173: [02:19:21] Complex queries can be slow. -152: ...[02:19:24] Molecule does not have explicit Hs. Consider calling AddHs() -152: [02:19:24] Molecule does not have explicit Hs. Consider calling AddHs() -152: [02:19:24] Molecule does not have explicit Hs. Consider calling AddHs() -152: [02:19:24] Molecule does not have explicit Hs. Consider calling AddHs() -152: [02:19:24] Molecule does not have explicit Hs. Consider calling AddHs() +173: [11:06:17] Complex queries can be slow. +173: [11:06:17] Complex queries can be slow. +171: Randomness seeded to: 839569508 +171: /build/reproducible-path/rdkit-202503.1/Code/GraphMol/RascalMCES/data/chembl_1907596.smi +173: [11:06:17] Complex queries can be slow. +173: [11:06:17] Complex queries can be slow. +173: [11:06:17] Complex queries can be slow. +173: [11:06:17] Complex queries can be slow. +173: [11:06:17] Complex queries can be slow. +173: [11:06:17] Complex queries can be slow. +173: [11:06:18] Complex queries can be slow. +152: .............[11:06:18] Molecule does not have explicit Hs. Consider calling AddHs() +152: [11:06:18] Molecule does not have explicit Hs. Consider calling AddHs() +173: [11:06:18] Complex queries can be slow. +152: [11:06:18] Molecule does not have explicit Hs. Consider calling AddHs() +152: [11:06:18] Molecule does not have explicit Hs. Consider calling AddHs() +152: [11:06:18] Molecule does not have explicit Hs. Consider calling AddHs() +152: [11:06:18] Molecule does not have explicit Hs. Consider calling AddHs() +152: [11:06:18] Molecule does not have explicit Hs. Consider calling AddHs() +152: [11:06:18] Molecule does not have explicit Hs. Consider calling AddHs() +152: [11:06:18] Molecule does not have explicit Hs. Consider calling AddHs() +152: [11:06:18] Molecule does not have explicit Hs. Consider calling AddHs() +152: [11:06:18] Molecule does not have explicit Hs. Consider calling AddHs() +173: [11:06:18] Complex queries can be slow. +170: Randomness seeded to: 436153241 +170: [11:06:21] Timed out after 11 seconds. +152: ...[11:06:21] Molecule does not have explicit Hs. Consider calling AddHs() +152: [11:06:21] Molecule does not have explicit Hs. Consider calling AddHs() +152: [11:06:21] Molecule does not have explicit Hs. Consider calling AddHs() +152: [11:06:21] Molecule does not have explicit Hs. Consider calling AddHs() +152: [11:06:21] Molecule does not have explicit Hs. Consider calling AddHs() 152: ... 152: ---------------------------------------------------------------------- -152: Ran 19 tests in 11.851s +152: Ran 19 tests in 13.523s 152: 152: OK 152: Testing MolAlign Wrappers -166/238 Test #152: pyMolAlign ............................. Passed 12.26 sec +166/238 Test #152: pyMolAlign ............................. Passed 14.05 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: 1268538722 +178: Randomness seeded to: 1918715346 178: =============================================================================== 178: All tests passed (111 assertions in 3 test cases) 178: @@ -30697,119 +30730,6 @@ 179: Test command: /usr/bin/python3 "/build/reproducible-path/rdkit-202503.1/Code/GraphMol/Deprotect/Wrap/rough_test.py" 179: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/Deprotect/Wrap 179: Test timeout computed to be: 1500 -170: Randomness seeded to: 1931028285 -170: [02:19:24] Timed out after 11 seconds. -179: ..... -179: ---------------------------------------------------------------------- -179: Ran 5 tests in 0.044s -179: -179: OK -179: Testing tert-butyldimethylsilyl -179: Testing methoxytrityl -179: Testing tetrahydropyranyl -179: Testing methoxymethyl_ether -179: Testing beta-Methoxyethoxymethyl_ether -179: Testing benzyl -179: Testing trimethylsilyl -179: Testing benzoyl -179: Testing pivaloyl -179: Testing triisopropylsilyl -179: Testing acetyl -179: Testing para-methoxybenzyl_ether -179: Testing triphenylmethyl -179: Testing phthaloyl -179: Testing trimethylsilylethoxymethyl -179: Testing para-methoxyphenyl -179: Testing tosyl -179: Testing tert-butyloxycarbonyl -179: Testing trifluoroacetyl -179: Testing benzoyl -179: Testing 9-fluorenylmethyloxycarbonyl -179: Testing benzylamine -179: Testing acetamide -179: Testing carbobenzyloxy -179: Testing Acetal/Ketal -179: Testing tert-butyldimethylsilyl -179: Testing methoxytrityl -179: Testing tetrahydropyranyl -179: Testing methoxymethyl_ether -179: Testing beta-Methoxyethoxymethyl_ether -179: Testing benzyl -179: Testing trimethylsilyl -179: Testing benzoyl -179: Testing pivaloyl -179: Testing triisopropylsilyl -179: Testing acetyl -179: Testing para-methoxybenzyl_ether -179: Testing triphenylmethyl -179: Testing phthaloyl -179: Testing trimethylsilylethoxymethyl -179: Testing para-methoxyphenyl -179: Testing tosyl -179: Testing tert-butyloxycarbonyl -179: Testing trifluoroacetyl -179: Testing benzoyl -179: Testing 9-fluorenylmethyloxycarbonyl -179: Testing benzylamine -179: Testing acetamide -179: Testing carbobenzyloxy -179: Testing Acetal/Ketal -168/238 Test #179: pyDeprotect ............................ Passed 0.43 sec -test 180 - Start 180: testReducedGraphs - -180: Test command: /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/ReducedGraphs/testReducedGraphs -180: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/ReducedGraphs -180: Test timeout computed to be: 1500 -180: Size: 315 [ 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0.3, 1, 0.3, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0.3, 1, 0.3, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 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0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0.3, 1, 0.3, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, ] -180: -169/238 Test #180: testReducedGraphs ...................... Passed 0.04 sec -test 181 - Start 181: pyReducedGraphs - -181: Test command: /usr/bin/python3 "/build/reproducible-path/rdkit-202503.1/Code/GraphMol/ReducedGraphs/Wrap/testReducedGraphs.py" -181: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/ReducedGraphs/Wrap -181: Test timeout computed to be: 1500 -181: ..... -181: ---------------------------------------------------------------------- -181: Ran 5 tests in 0.017s -181: -181: OK -170/238 Test #181: pyReducedGraphs ........................ Passed 0.39 sec -test 182 - Start 182: trajectoryTest - -182: Test command: /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/Trajectory/trajectoryTest -182: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/Trajectory -182: Test timeout computed to be: 1500 -171/238 Test #182: trajectoryTest ......................... Passed 0.29 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: [02:19:25] ------------------------------------- -183: [02:19:25] Test1 -183: [02:19:25] done -183: [02:19:25] ------------------------------------- -183: [02:19:25] Test2 177: VS001: PASSED 177: VS002: PASSED 177: VS003: PASSED @@ -31112,1260 +31032,1364 @@ 177: VS300: PASSED 177: Check finished: 0 molecules failed. 177: Failed: -183: [02:19:25] done -183: [02:19:25] ------------------------------------- -183: [02:19:25] Test3 (stereo options) -183: [02:19:25] Done (stereo options) -172/238 Test #177: pyCIPLabelsValidation .................. Passed 6.89 sec -183: [02:19:25] ------------------------------------- +168/238 Test #177: pyCIPLabelsValidation .................. Passed 6.30 sec +test 180 + Start 180: testReducedGraphs + +180: Test command: /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/ReducedGraphs/testReducedGraphs +180: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/ReducedGraphs +180: Test timeout computed to be: 1500 +180: Size: 315 [ 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0.3, 1, 0.3, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0.3, 1, 0.3, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 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0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0.3, 1, 0.3, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, ] +180: +169/238 Test #180: testReducedGraphs ...................... Passed 0.04 sec +test 181 + Start 181: pyReducedGraphs + +181: Test command: /usr/bin/python3 "/build/reproducible-path/rdkit-202503.1/Code/GraphMol/ReducedGraphs/Wrap/testReducedGraphs.py" +181: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/ReducedGraphs/Wrap +181: Test timeout computed to be: 1500 +179: ..... +179: ---------------------------------------------------------------------- +179: Ran 5 tests in 0.046s +179: +179: OK +179: Testing tert-butyldimethylsilyl +179: Testing methoxytrityl +179: Testing tetrahydropyranyl +179: Testing methoxymethyl_ether +179: Testing beta-Methoxyethoxymethyl_ether +179: Testing benzyl +179: Testing trimethylsilyl +179: Testing benzoyl +179: Testing pivaloyl +179: Testing triisopropylsilyl +179: Testing acetyl +179: Testing para-methoxybenzyl_ether +179: Testing triphenylmethyl +179: Testing phthaloyl +179: Testing trimethylsilylethoxymethyl +179: Testing para-methoxyphenyl +179: Testing tosyl +179: Testing tert-butyloxycarbonyl +179: Testing trifluoroacetyl +179: Testing benzoyl +179: Testing 9-fluorenylmethyloxycarbonyl +179: Testing benzylamine +179: Testing acetamide +179: Testing carbobenzyloxy +179: Testing Acetal/Ketal +179: Testing tert-butyldimethylsilyl +179: Testing methoxytrityl +179: Testing tetrahydropyranyl +179: Testing methoxymethyl_ether +179: Testing beta-Methoxyethoxymethyl_ether +179: Testing benzyl +179: Testing trimethylsilyl +179: Testing benzoyl +179: Testing pivaloyl +179: Testing triisopropylsilyl +179: Testing acetyl +179: Testing para-methoxybenzyl_ether +179: Testing triphenylmethyl +179: Testing phthaloyl +179: Testing trimethylsilylethoxymethyl +179: Testing para-methoxyphenyl +179: Testing tosyl +179: Testing tert-butyloxycarbonyl +179: Testing trifluoroacetyl +179: Testing benzoyl +179: Testing 9-fluorenylmethyloxycarbonyl +179: Testing benzylamine +179: Testing acetamide +179: Testing carbobenzyloxy +179: Testing Acetal/Ketal +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 13.26 seconds +170/238 Test #179: pyDeprotect ............................ Passed 0.45 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 +148: .........[11:06:22] Molecule does not have explicit Hs. Consider calling AddHs() +148: .[11:06:22] Molecule does not have explicit Hs. Consider calling AddHs() +171/238 Test #163: testFMCS ............................... Passed 13.31 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 +148: [11:06:22] Molecule does not have explicit Hs. Consider calling AddHs() +148: [11:06:22] Molecule does not have explicit Hs. Consider calling AddHs() +148: [11:06:22] Molecule does not have explicit Hs. Consider calling AddHs() +148: [11:06:22] Molecule does not have explicit Hs. Consider calling AddHs() +148: [11:06:22] Molecule does not have explicit Hs. Consider calling AddHs() +148: [11:06:22] Molecule does not have explicit Hs. Consider calling AddHs() +148: [11:06:22] Molecule does not have explicit Hs. Consider calling AddHs() +148: [11:06:22] Molecule does not have explicit Hs. Consider calling AddHs() +148: [11:06:22] Molecule does not have explicit Hs. Consider calling AddHs() +148: .[11:06:22] Molecule does not have explicit Hs. Consider calling AddHs() +148: [11:06:22] Molecule does not have explicit Hs. Consider calling AddHs() +148: [11:06:22] Molecule does not have explicit Hs. Consider calling AddHs() +148: [11:06:22] Molecule does not have explicit Hs. Consider calling AddHs() +148: [11:06:22] Molecule does not have explicit Hs. Consider calling AddHs() +148: [11:06:22] Molecule does not have explicit Hs. Consider calling AddHs() +148: [11:06:22] Molecule does not have explicit Hs. Consider calling AddHs() +148: [11:06:22] Molecule does not have explicit Hs. Consider calling AddHs() +148: [11:06:22] Molecule does not have explicit Hs. Consider calling AddHs() +148: [11:06:22] Molecule does not have explicit Hs. Consider calling AddHs() +183: [11:06:22] ------------------------------------- +183: [11:06:22] Test1 +181: ..... +181: ---------------------------------------------------------------------- +181: Ran 5 tests in 0.020s +181: +181: OK +172/238 Test #181: pyReducedGraphs ........................ Passed 0.42 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: [02:19:25] Test4 (trusted smiles) -183: [02:19:25] Done (trusted smiles) -183: [02:19:25] ------------------------------------- -183: [02:19:25] Testing C++ docs -183: [02:19:25] Done (C++ doc tests) -183: [02:19:25] ------------------------------------- -183: [02:19:25] Testing C++ ring query: PatternHolder -183: [02:19:25] Done (C++ ring query tests) -183: [02:19:25] ------------------------------------- -183: [02:19:25] Testing C++ ring query: TautomerPatternHolder -183: [02:19:25] Done (C++ ring query tests) -183: [02:19:25] ------------------------------------- -183: [02:19:25] Add Patterns -184: Randomness seeded to: 1770461295 -184: =============================================================================== -184: All tests passed (171 assertions in 5 test cases) -184: -173/238 Test #184: substructLibraryCatchTest .............. Passed 0.47 sec +183: [11:06:22] done +183: [11:06:22] ------------------------------------- +183: [11:06:22] Test2 +173/238 Test #182: trajectoryTest ......................... Passed 0.30 sec test 185 Start 185: pySubstructLibrary 185: Test command: /usr/bin/python3 "/build/reproducible-path/rdkit-202503.1/Code/GraphMol/SubstructLibrary/Wrap/rough_test.py" 185: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/SubstructLibrary/Wrap 185: Test timeout computed to be: 1500 -148: .........[02:19:26] Molecule does not have explicit Hs. Consider calling AddHs() -148: .[02:19:26] Molecule does not have explicit Hs. Consider calling AddHs() -148: [02:19:26] Molecule does not have explicit Hs. Consider calling AddHs() -148: [02:19:26] Molecule does not have explicit Hs. Consider calling AddHs() -148: [02:19:26] Molecule does not have explicit Hs. Consider calling AddHs() -148: [02:19:26] Molecule does not have explicit Hs. Consider calling AddHs() -148: [02:19:26] Molecule does not have explicit Hs. Consider calling AddHs() -148: [02:19:26] Molecule does not have explicit Hs. Consider calling AddHs() -148: [02:19:26] Molecule does not have explicit Hs. Consider calling AddHs() -148: [02:19:26] Molecule does not have explicit Hs. Consider calling AddHs() -148: [02:19:26] Molecule does not have explicit Hs. Consider calling AddHs() -148: .[02:19:26] Molecule does not have explicit Hs. Consider calling AddHs() -148: [02:19:26] Molecule does not have explicit Hs. Consider calling AddHs() -148: [02:19:26] Molecule does not have explicit Hs. Consider calling AddHs() -148: [02:19:26] Molecule does not have explicit Hs. Consider calling AddHs() -148: [02:19:26] Molecule does not have explicit Hs. Consider calling AddHs() -148: [02:19:26] Molecule does not have explicit Hs. Consider calling AddHs() -148: [02:19:26] Molecule does not have explicit Hs. Consider calling AddHs() -148: [02:19:26] Molecule does not have explicit Hs. Consider calling AddHs() -148: [02:19:26] Molecule does not have explicit Hs. Consider calling AddHs() -148: [02:19:26] Molecule does not have explicit Hs. Consider calling AddHs() -173: [02:19:27] Complex queries can be slow. -163: MCS MatchStereo false : [#6]-[#6]-[#6]=[#6]-[#6]-[#6] 6 atoms, 5 bonds -163: MCS MatchStereo true : [#6]-[#6]-[#6] 3 atoms, 2 bonds -163: MCS MatchStereo false : [#6]-[#6]-[#6]=[#6]-[#6]-[#6] 6 atoms, 5 bonds -163: MCS MatchStereo true : [#6]-[#6]-[#6] 3 atoms, 2 bonds -163: MCS MatchStereo false : [#6]-[#6]-[#6]=[#6]-[#6]-[#6] 6 atoms, 5 bonds -163: MCS MatchStereo true : [#6]-[#6]-[#6]=[#6]-[#6]-[#6] 6 atoms, 5 bonds -163: TOTAL Time elapsed 14.96 seconds -173: [02:19:27] Complex queries can be slow. -174/238 Test #163: testFMCS ............................... Passed 14.99 sec +183: [11:06:23] done +183: [11:06:23] ------------------------------------- +183: [11:06:23] Test3 (stereo options) +183: [11:06:23] Done (stereo options) +183: [11:06:23] ------------------------------------- +183: [11:06:23] Test4 (trusted smiles) +183: [11:06:23] Done (trusted smiles) +183: [11:06:23] ------------------------------------- +183: [11:06:23] Testing C++ docs +183: [11:06:23] Done (C++ doc tests) +183: [11:06:23] ------------------------------------- +183: [11:06:23] Testing C++ ring query: PatternHolder +183: [11:06:23] Done (C++ ring query tests) +183: [11:06:23] ------------------------------------- +183: [11:06:23] Testing C++ ring query: TautomerPatternHolder +183: [11:06:23] Done (C++ ring query tests) +183: [11:06:23] ------------------------------------- +183: [11:06:23] Add Patterns +184: Randomness seeded to: 3619570554 +184: =============================================================================== +184: All tests passed (171 assertions in 5 test cases) +184: +174/238 Test #184: substructLibraryCatchTest .............. Passed 0.43 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 -173: [02:19:27] Complex queries can be slow. -173: [02:19:27] Complex queries can be slow. -183: [02:19:27] ------------------------------------- -183: [02:19:27] testing PatternHolder -186: [02:19:27] Non terminal R group defined. To allow set allowNonTerminalRGroups in RGroupDecompositionParameters -186: [02:19:27] WARNING: not removing hydrogen atom with dummy atom neighbors -183: [02:19:27] ------------------------------------- -183: [02:19:27] testing TautomerPatternHolder -173: [02:19:27] Complex queries can be slow. -183: [02:19:27] ------------------------------------- -183: [02:19:27] testSegFaultInHolder -183: [02:19:27] SMILES Parse Error: syntax error while parsing: dsafsdf -183: [02:19:27] SMILES Parse Error: check for mistakes around position 1: -183: [02:19:27] dsafsdf[02:19:27] SMILES Parse Error: syntax error while parsing: dsafsdf -183: [02:19:27] SMILES Parse Error: check for mistakes around position 1: -183: [02:19:27] dsafsdf -183: [02:19:27] ^ -183: [02:19:27] SMILES Parse Error: syntax error while parsing: dsafsdf -183: [02:19:27] SMILES Parse Error: check for mistakes around position 1: -183: [02:19:27] dsafsdf -183: [02:19:27] ^ -183: [02:19:27] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -183: [02:19:27] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -183: [02:19:27] SMILES Parse Error: syntax error while parsing: dsafsdf -183: [02:19:27] SMILES Parse Error: check for mistakes around position 1: -183: [02:19:27] dsafsdf -183: [02:19:27] ^ -183: [02:19:27] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -183: [02:19:27] SMILES Parse Error: syntax error while parsing: dsafsdf -183: [02:19:27] SMILES Parse Error: check for mistakes around position 1: -183: [02:19:27] dsafsdf -183: [02:19:27] ^ -183: [02:19:27] SMILES Parse Error: syntax error while parsing: dsafsdf -183: [02:19:27] SMILES Parse Error: check for mistakes around position 1 -183: [02:19:27] ^ -183: [02:19:27] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +186: [11:06:23] Non terminal R group defined. To allow set allowNonTerminalRGroups in RGroupDecompositionParameters +186: [11:06:23] WARNING: not removing hydrogen atom with dummy atom neighbors +186: iterative +150: --------------------------------- +150: test O3A multithreading bug +150: +150: --------------------------------- +150: testCrippenO3A multithreading +150: +150: generating reference data +183: [11:06:25] ------------------------------------- +183: [11:06:25] testing PatternHolder +173: [11:06:25] Complex queries can be slow. +173: [11:06:25] Complex queries can be slow. +183: [11:06:25] ------------------------------------- +183: [11:06:25] testing TautomerPatternHolder +173: [11:06:25] Complex queries can be slow. +148: ... +148: ---------------------------------------------------------------------- +148: Ran 22 tests in 18.159s +148: +148: OK +173: [11:06:25] Complex queries can be slow. +175/238 Test #148: pyDistGeomHelpers ...................... Passed 18.48 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 +183: [11:06:25] ------------------------------------- +183: [11:06:25] testSegFaultInHolder +183: [11:06:25] SMILES Parse Error: syntax error while parsing: dsafsdf +183: [11:06:25] SMILES Parse Error: syntax error while parsing: dsafsdf +183: [11:06:25] SMILES Parse Error: check for mistakes around position 1: +183: [11:06:25] dsafsdf +183: [11:06:25] ^ +183: [11:06:25] SMILES Parse Error: syntax error while parsing: dsafsdf +183: [11:06:25] SMILES Parse Error: check for mistakes around position 1: +183: [11:06:25] [11:06:25] dsafsdf +183: [11:06:25] [11:06:25] SMILES Parse Error: syntax error while parsing: dsafsdf[11:06:25] [11:06:25] SMILES Parse Error: [11:06:25] [11:06:25] [11:06:25] ^SMILES Parse Error: SMILES Parse Error: [11:06:25] SMILES Parse Error: SMILESsyntax error +183: Parse Error: Failed parsing SMILES 'dsafsdf'[11:06:25] SMILES Parse Error: check for mistakes around position 1: +183: [11:06:25] dsafsdf +183: [11:06:25] +183: SMILES Parse Error: syntax error while parsing: dsafsdfsyntax error while parsing: dsafsdf +183: SMILES Parse Error: syntax error while parsing: dsafsdf while parsing: syntax errorSMILES Parse Error: dsafsdf +183: [11:06:25] [11:06:25] SMILES Parse Error: check for mistakes around position syntax error while parsing: dsafsdf[11:06:25] +183: 1 183: : -183: [02:19:27] dsafsdf -183: [02:19:27] ^ -183: [02:19:27] SMILES Parse Error: syntax error while parsing: dsafsdf[02:19:27] [02:19:27] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -183: SMILES Parse Error: syntax error while parsing: dsafsdf -183: [02:19:27] SMILES Parse Error: check for mistakes around position 1: -183: [02:19:27] dsafsdf -183: [02:19:27] ^ -183: [02:19:27] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -183: [02:19:27] SMILES Parse Error: syntax error while parsing: dsafsdf -183: [02:19:27] SMILES Parse Error: check for mistakes around position 1: -183: [02:19:27] dsafsdf -183: [02:19:27] ^ -183: [02:19:27] SMILES Parse Error: syntax error[02:19:27] [02:19:27] SMILES Parse Error: syntax error while parsing: while parsing: -183: [02:19:27] SMILES Parse Error: check for mistakes around position [02:19:27] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -183: 1: -183: [02:19:27] dsafsdf -183: [02:19:27] ^ -183: [02:19:27] SMILES Parse Error: syntax error while parsing: dsafsdf -183: [02:19:27] SMILES Parse Error: check for mistakes around position 1: -183: [02:19:27] dsafsdf -183: [02:19:27] ^ -183: [02:19:27] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -183: [02:19:27] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -183: [02:19:27] SMILES Parse Error: syntax error while parsing: dsafsdf -183: [02:19:27] SMILES Parse Error: check for mistakes around position 1: -183: [02:19:27] SMILES Parse Error: syntax error while parsing: dsafsdf -183: [02:19:27] SMILES Parse Error: check for mistakes around position 1: -183: [02:19:27] [02:19:27] SMILES Parse Error: syntax error while parsing: dsafsdf -183: [02:19:27] SMILES Parse Error: check for mistakes around position 1: -183: [02:19:27] dsafsdf -183: [02:19:27] SMILES Parse Error: check for mistakes around position 1: -183: [02:19:27] dsafsdf -183: [02:19:27] ^ -183: [02:19:27] dsafsdf -183: SMILES Parse Error: [02:19:27] SMILES Parse Error: Failed parsing SMILES 'dsafsdf'dsafsdf -183: for input: 'syntax errordsafsdf[02:19:27] ^' while parsing: dsafsdf +183: syntax error for input: ' while parsing: +183: ^[11:06:25] [11:06:25] dsafsdfSMILES Parse Error: check for mistakes around position dsafsdf +183: [11:06:25] 'SMILES Parse Error: check for mistakes around position [11:06:25] 1: +183: [11:06:25] SMILES Parse Error: check for mistakes around position 1: +183: dsafsdf[11:06:25] dsafsdf 183: +183: [11:06:25] SMILES Parse Error: check for mistakes around position 1 while parsing: dsafsdf: +183: [11:06:25] 1[11:06:25] [11:06:25] SMILESSMILESdsafsdf 183: -183: [02:19:27] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -183: [02:19:27] SMILES Parse Error: syntax error while parsing: dsafsdf -183: [02:19:27] SMILES Parse Error: check for mistakes around position 1: -183: [02:19:27] dsafsdf -183: [02:19:27] ^ -183: [02:19:27] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -183: [02:19:27] SMILES Parse Error: syntax error while parsing: dsafsdf -183: [02:19:27] SMILES Parse Error: check for mistakes around position 1: -183: [02:19:27] dsafsdf -183: [02:19:27] ^ -183: [02:19:27] SMILES Parse Error: syntax error while parsing: [02:19:27] [02:19:27] ^ -183: [02:19:27] SMILES Parse Error: check for mistakes around position dsafsdf -183: 1: -183: [02:19:27] dsafsdf -183: [02:19:27] ^ -183: [02:19:27] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -183: [02:19:27] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -183: [02:19:27] SMILES Parse Error: syntax error while parsing: dsafsdf -183: [02:19:27] SMILES Parse Error: check for mistakes around position 1: -183: [02:19:27] dsafsdf -183: [02:19:27] ^ -183: [02:19:27] SMILES Parse Error: syntax error while parsing: dsafsdf -183: [02:19:27] SMILES Parse Error: check for mistakes around position [02:19:27] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: '[02:19:27] SMILES Parse Error: check for mistakes around position 1:dsafsdfSMILES Parse Error: Failed parsing SMILES 'dsafsdf'' -183: [02:19:27] dsafsdf -183: for input: 'dsafsdf'1: 183: -183: [02:19:27] ^ -183: [02:19:27] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -183: [02:19:27] SMILES Parse Error: syntax error while parsing: dsafsdf -183: [02:19:27] SMILES Parse Error: check for mistakes around position 1: -183: [02:19:27] dsafsdf -183: [02:19:27] ^ -183: [02:19:27] SMILES Parse Error: syntax error while parsing: dsafsdf -183: [02:19:27] -183: SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -183: [02:19:27] SMILES Parse Error: syntax error while parsing: dsafsdf -183: [02:19:27] SMILES Parse Error: check for mistakes around position 1: -183: [02:19:27] dsafsdf[02:19:27] [02:19:27] SMILES Parse Error: -183: [02:19:27] ^ -183: [02:19:27] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -183: [02:19:27] dsafsdf -183: [02:19:27] ^ -183: SMILES Parse Error: check for mistakes around position 1syntax error while parsing: dsafsdf -183: : -183: [02:19:27] dsafsdf -183: [02:19:27] ^ -183: [02:19:27] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf[02:19:27] [02:19:27] SMILES' +183: [11:06:25] ^ +183: Parse Error: [11:06:25] SMILES Parse Error: check for mistakes around position 1[11:06:25] SMILESdsafsdf: +183: [11:06:25] 183: Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -183: [02:19:27] SMILES Parse Error: syntax error while parsing: dsafsdf -183: [02:19:27] SMILES Parse Error: check for mistakes around position 1: -183: [02:19:27] dsafsdf -183: [02:19:27] ^ -183: [02:19:27] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -183: [02:19:27] SMILES Parse Error: syntax error while parsing: dsafsdf -183: [02:19:27] SMILES Parse Error: check for mistakes around position 1: -183: [02:19:27] [02:19:27] SMILES Parse Error: check for mistakes around position 1: -183: [02:19:27] dsafsdf -183: [02:19:27] ^ +183: SMILES Parse Error: check for mistakes around position 1:Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +183: [11:06:25] ^: +183: Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf^ +183: ' +183: +183: [11:06:25] [11:06:25] [11:06:25] dsafsdf 183: SMILES Parse Error: syntax error while parsing: dsafsdf -183: [02:19:27] [02:19:27] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +183: [11:06:25] [11:06:25] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +183: ^[11:06:25] [11:06:25] +183: ^[11:06:25] SMILES Parse Error: [11:06:25] syntax error while parsing: SMILES Parse Error: syntax error while parsing: dsafsdf 183: SMILES Parse Error: check for mistakes around position dsafsdf -183: [02:19:27] 1: -183: [02:19:27] dsafsdf -183: [02:19:27] ^ -183: [02:19:27] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -183: ^ -183: [02:19:27] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -183: [02:19:27] SMILES Parse Error: syntax error while parsing: dsafsdf -183: [02:19:27] SMILES Parse Error: check for mistakes around position 1: -183: [02:19:27] dsafsdf -183: [02:19:27] ^ -183: [02:19:27] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -183: [02:19:27] dsafsdf -183: [02:19:27] ^ -183: [02:19:27] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -183: [02:19:27] SMILES Parse Error: syntax error while parsing: dsafsdf -183: [02:19:27] SMILES Parse Error: check for mistakes around position 1: -183: [02:19:27] dsafsdf -183: [02:19:27] ^ -183: [02:19:27] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -183: dsafsdf[02:19:27] SMILES Parse Error: syntax error while parsing: dsafsdf -183: [02:19:27] -183: [02:19:27] SMILES Parse Error: check for mistakes around position 1: -183: [02:19:27] dsafsdf -183: [02:19:27] ^ -183: [02:19:27] SMILES Parse Error: syntax error while parsing: dsafsdf -183: [02:19:27] [02:19:27] SMILES Parse Error: check for mistakes around position 1: -183: [02:19:27] dsafsdf -183: [02:19:27] ^ -183: SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -183: [02:19:27] SMILES Parse Error: [02:19:27] SMILES Parse Error: check for mistakes around position 1: -183: SMILESsyntax error Parse Error: [02:19:27] dsafsdf -183: Failed parsing SMILES 'dsafsdf'[02:19:27] [02:19:27] [02:19:27] while parsing: dsafsdf -183: [02:19:27] SMILES Parse Error: check for mistakes around position 1SMILES Parse Error: SMILES Parse Error: syntax error while parsing: dsafsdf for input: 'dsafsdf' -183: syntax error while parsing: : -183: dsafsdf[02:19:27] -183: [02:19:27] SMILES Parse Error: check for mistakes around position 1: -183: [02:19:27] ^ -183: dsafsdf -183: [02:19:27] ^ -183: [02:19:27] SMILES Parse Error: syntax error while parsing: dsafsdf -183: [02:19:27] [02:19:27] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -183: SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -183: [02:19:27] SMILES Parse Error: check for mistakes around position 1: -183: [02:19:27] dsafsdf -183: [02:19:27] ^ -183: [02:19:27] SMILES Parse Error: syntax error while parsing: dsafsdf -183: [02:19:27] SMILES Parse Error: check for mistakes around position 1: -183: [02:19:27] dsafsdf -183: [02:19:27] ^ -183: [02:19:27] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -183: [02:19:27] SMILES Parse Error: syntax error while parsing: dsafsdf -183: [02:19:27] dsafsdf -183: [02:19:27] [02:19:27] SMILESSMILES Parse Error: syntax error while parsing: ^ Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -183: -183: dsafsdf -183: [02:19:27] SMILES Parse Error: check for mistakes around position 1: -183: [02:19:27] dsafsdf -183: [02:19:27] ^ -183: [02:19:27] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -183: [02:19:27] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -183: [02:19:27] SMILES Parse Error: syntax error while parsing: dsafsdf -183: [02:19:27] SMILES Parse Error: check for mistakes around position 1: -183: [02:19:27] dsafsdf -183: [02:19:27] [02:19:27] SMILES Parse Error: check for mistakes around position 1:SMILES Parse Error: [02:19:27] ^syntax error -183: [02:19:27] dsafsdf -183: [02:19:27] ^ -183: while parsing: dsafsdf -183: [02:19:27] SMILES Parse Error: check for mistakes around position 1: -183: [02:19:27] [02:19:27] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -183: dsafsdf -183: [02:19:27] ^ -183: [02:19:27] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -183: [02:19:27] SMILES Parse Error: syntax error while parsing: dsafsdf -183: [02:19:27] SMILES Parse Error: check for mistakes around position 1: -183: [02:19:27] dsafsdf -183: [02:19:27] ^ -183: [02:19:27] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -183: [02:19:27] SMILES Parse Error: syntax error while parsing: dsafsdf -183: [02:19:27] SMILES Parse Error: check for mistakes around position 1: -183: [02:19:27] dsafsdf -183: [02:19:27] ^ -183: [02:19:27] SMILES Parse Error: syntax error while parsing: dsafsdf[02:19:27] -183: SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -183: [02:19:27] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -183: [02:19:27] SMILES Parse Error: syntax error while parsing: dsafsdf -183: [02:19:27] SMILES Parse Error: check for mistakes around position 1: -183: [02:19:27] dsafsdf -183: [02:19:27] ^ -183: [02:19:27] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -183: [02:19:27] SMILES Parse Error: syntax error while parsing: dsafsdf -183: [02:19:27] SMILES Parse Error: check for mistakes around position 1: -183: [02:19:27] dsafsdf -183: [02:19:27] ^ -183: [02:19:27] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' 183: -183: [02:19:27] SMILES Parse Error: check for mistakes around position 1: -183: [02:19:27] dsafsdf -183: [02:19:27] ^ -183: [02:19:27] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -183: [02:19:27] SMILES Parse Error: syntax error while parsing: dsafsdf -183: [02:19:27] SMILES Parse Error: check for mistakes around position 1: -183: [02:19:27] dsafsdf -183: [02:19:27] ^ -183: [02:19:27] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +183: [11:06:25] [11:06:25] SMILES Parse Error: check for mistakes around position 11:SMILES: +183: [11:06:25] dsafsdf +183: [11:06:25] ^[11:06:25] [11:06:25] SMILES Parse Error: +183: Failed parsing SMILES 'dsafsdf' Parse Error: Failed parsing SMILES 'dsafsdf'[11:06:25] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf for input: 'dsafsdf' 183: -183: [02:19:27] SMILES Parse Error: check for mistakes around position 1: -183: [02:19:27] dsafsdf -183: [02:19:27] ^ -183: [02:19:27] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -183: [02:19:27] SMILES Parse Error: syntax error while parsing: dsafsdf -183: [02:19:27] SMILES Parse Error: check for mistakes around position 1: -183: [02:19:27] dsafsdf -183: [02:19:27] ^ -183: [02:19:27] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -183: [02:19:27] SMILES Parse Error: syntax error while parsing: dsafsdf -183: [02:19:27] SMILES Parse Error: check for mistakes around position 1: -183: [02:19:27] dsafsdf -183: [02:19:27] ^ -183: [02:19:27] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -183: [02:19:27] SMILES Parse Error: syntax error while parsing: dsafsdf -183: [02:19:27] SMILES Parse Error: check for mistakes around position 1: -183: [02:19:27] dsafsdf -183: [02:19:27] ^ -183: [02:19:27] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -183: SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -183: [02:19:27] SMILES Parse Error: syntax error while parsing: dsafsdf -183: [02:19:27] SMILES Parse Error: check for mistakes around position 1: -183: [02:19:27] dsafsdf -183: [02:19:27] ^ -183: [02:19:27] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -183: [02:19:27] SMILES Parse Error: syntax error while parsing: dsafsdf -183: [02:19:27] SMILES Parse Error: check for mistakes around position 1: -183: [02:19:27] dsafsdf -183: [02:19:27] ^ -183: [02:19:27] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -183: [02:19:27] SMILES Parse Error: syntax error while parsing: dsafsdf -183: [02:19:27] SMILES Parse Error: check for mistakes around position 1: -183: [02:19:27] dsafsdf -183: [02:19:27] ^ -183: [02:19:27] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -183: [02:19:27] SMILES Parse Error: syntax error while parsing: dsafsdf -183: [02:19:27] SMILES Parse Error: check for mistakes around position 1: -183: [02:19:27] dsafsdf -183: [02:19:27] ^ -183: [02:19:27] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -183: [02:19:27] SMILES Parse Error: syntax error while parsing: dsafsdf -183: [02:19:27] SMILES Parse Error: check for mistakes around position 1: -183: [02:19:27] dsafsdf -183: [02:19:27] ^ -183: [02:19:27] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -183: [02:19:27] SMILES Parse Error: syntax error while parsing: dsafsdf -183: [02:19:27] SMILES Parse Error: check for mistakes around position 1: -183: [02:19:27] dsafsdf -183: [02:19:27] ^ -183: [02:19:27] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -183: [02:19:27] SMILES Parse Error: syntax error while parsing: dsafsdf -183: [02:19:27] SMILES Parse Error: check for mistakes around position 1: -183: [02:19:27] dsafsdf -183: [02:19:27] ^ -183: [02:19:27] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -183: [02:19:27] SMILES Parse Error: syntax error while parsing: dsafsdf -183: [02:19:27] SMILES Parse Error: check for mistakes around position 1: -183: [02:19:27] dsafsdf -183: [02:19:27] ^ -183: [02:19:27] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -183: [02:19:27] SMILES Parse Error: syntax error while parsing: dsafsdf -183: [02:19:27] SMILES Parse Error: check for mistakes around position 1: -183: [02:19:27] dsafsdf -183: [02:19:27] ^ -183: [02:19:27] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -183: [02:19:27] SMILES Parse Error: syntax error while parsing: dsafsdf -183: [02:19:27] SMILES Parse Error: check for mistakes around position 1: -183: [02:19:27] dsafsdf -183: [02:19:27] ^ -183: [02:19:27] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -183: [02:19:27] SMILES Parse Error: syntax error while parsing: dsafsdf -183: [02:19:27] SMILES Parse Error: check for mistakes around position 1: -183: [02:19:27] dsafsdf -183: [02:19:27] ^ -183: [02:19:27] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -183: [02:19:27] SMILES Parse Error: syntax error while parsing: dsafsdf -183: [02:19:27] SMILES Parse Error: check for mistakes around position 1: -183: [02:19:27] dsafsdf -183: [02:19:27] ^ -183: [02:19:27] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -183: [02:19:27] SMILES Parse Error: syntax error while parsing: dsafsdf -183: [02:19:27] SMILES Parse Error: check for mistakes around position 1:[02:19:27] [02:19:27] SMILES Parse Error: syntax error while parsing: dsafsdf -183: [02:19:27] SMILES Parse Error: check for mistakes around position 1: -183: [02:19:27] dsafsdf -183: [02:19:27] ^ -183: SMILES Parse Error: syntax error while parsing: dsafsdf -183: [02:19:27] SMILES Parse Error: check for mistakes around position 1[02:19:27] [02:19:27] SMILES Parse Error: syntax error while parsing: dsafsdf -183: [02:19:27] SMILES Parse Error: check for mistakes around position 1: -183: [02:19:27] -183: SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -183: :[02:19:27] SMILES Parse Error: syntax error while parsing: -183: [02:19:27] dsafsdf -183: [02:19:27] ^ -183: [02:19:27] dsafsdf -183: [02:19:27] ^ -183: [02:19:27] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -183: [02:19:27] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf'[02:19:27] [02:19:27] SMILES Parse Error: syntax error -183: while parsing: dsafsdfdsafsdfSMILES Parse Error: [02:19:27] syntax error while parsing: dsafsdf -183: SMILES Parse Error: syntax error while parsing: dsafsdf -183: [02:19:27] SMILES Parse Error: check for mistakes around position 1 +183: [11:06:25] SMILES Parse Error: check for mistakes around position 183: dsafsdf -183: [02:19:27] [02:19:27] : -183: [02:19:27] dsafsdf -183: [02:19:27] [02:19:27] ^ -183: ^ -183: [02:19:27] [02:19:27] SMILES Parse Error: SMILES Parse Error: check for mistakes around position 1:Failed parsing SMILES 'dsafsdf'SMILES Parse Error: check for mistakes around position 1: -183: for input: 'dsafsdf +183: [11:06:25] ^ +183: [11:06:25] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +183: [11:06:25] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +183: [11:06:25] SMILES Parse Error: syntax error while parsing: dsafsdf +183: [11:06:25] [11:06:25] SMILES Parse Error: check for mistakes around position 1: +183: [11:06:25] dsafsdf +183: [11:06:25] ^ +183: SMILES Parse Error: +183: syntax error while parsing: dsafsdf[11:06:25] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +183: 1[11:06:25] : +183: [11:06:25] dsafsdf +183: [11:06:25] ^ +183: SMILES Parse Error: syntax error while parsing: dsafsdf +183: [11:06:25] [11:06:25] SMILES Parse Error: check for mistakes around position '1 183: -183: [02:19:27] SMILES Parse Error: syntax error while parsing: dsafsdf -183: [02:19:27] [02:19:27] '[02:19:27] -183: SMILES Parse Error: syntax error while parsing: dsafsdf[02:19:27] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf +183: [11:06:25] : for input: 'dsafsdf'SMILES Parse Error: check for mistakes around position SMILES Parse Error: syntax error while parsing: dsafsdf[11:06:25] SMILES Parse Error: syntax errordsafsdf +183: [11:06:25] [11:06:25] dsafsdf +183: [11:06:25] ^ +183: SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: ' while parsing: 1 +183: : +183: [11:06:25] [11:06:25] SMILES Parse Error: check for mistakes around position [11:06:25] SMILES Parse Error: syntax error while parsing: dsafsdf +183: [11:06:25] SMILES Parse Error: check for mistakes around position 1: +183: [11:06:25] dsafsdf +183: [11:06:25] ^ +183: [11:06:25] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +187: [11:06:25] WARNING: not removing hydrogen atom with dummy atom neighbors +187: [11:06:25] WARNING: not removing hydrogen atom with dummy atom neighbors +187: [11:06:25] WARNING: not removing hydrogen atom with dummy atom neighbors +187: [11:06:25] WARNING: not removing hydrogen atom with dummy atom neighbors +187: [11:06:25] WARNING: not removing hydrogen atom with dummy atom neighbors +187: [11:06:25] WARNING: not removing hydrogen atom with dummy atom neighbors +187: [11:06:25] WARNING: not removing hydrogen atom with dummy atom neighbors +187: [11:06:25] WARNING: not removing hydrogen atom with dummy atom neighbors +187: [11:06:25] WARNING: not removing hydrogen atom with dummy atom neighbors +187: [11:06:25] WARNING: not removing hydrogen atom with dummy atom neighbors +187: [11:06:25] WARNING: not removing hydrogen atom with dummy atom neighbors +187: [11:06:25] WARNING: not removing hydrogen atom with dummy atom neighbors +187: [11:06:25] WARNING: not removing hydrogen atom with dummy atom neighbors +187: [11:06:25] WARNING: not removing hydrogen atom with dummy atom neighbors +187: [11:06:25] WARNING: not removing hydrogen atom with dummy atom neighbors +187: [11:06:25] WARNING: not removing hydrogen atom with dummy atom neighbors +187: [11:06:25] WARNING: not removing hydrogen atom with dummy atom neighbors +187: [11:06:25] WARNING: not removing hydrogen atom with dummy atom neighbors +187: [11:06:25] WARNING: not removing hydrogen atom with dummy atom neighbors +187: [11:06:25] WARNING: not removing hydrogen atom with dummy atom neighbors +187: [11:06:25] WARNING: not removing hydrogen atom with dummy atom neighbors +183: [11:06:25] SMILES Parse Error: syntax error while parsing: dsafsdf +183: [11:06:25] SMILES Parse Error: check for mistakes around position 1: +183: [11:06:25] dsafsdf +183: [11:06:25] ^ +183: [11:06:25] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' 183: dsafsdf' -183: [02:19:27] ^ +183: [11:06:25] SMILES Parse Error: syntax error while parsing: dsafsdf +183: [11:06:25] SMILES Parse Error: check for mistakes around position 1: +183: [11:06:25] dsafsdf +183: [11:06:25] ^ +183: [11:06:25] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +183: [11:06:25] SMILES Parse Error: syntax error while parsing: dsafsdf +183: [11:06:25] SMILES Parse Error: check for mistakes around position 1: +183: [11:06:25] dsafsdf +183: [11:06:25] ^ +183: [11:06:25] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +183: [11:06:25] dsafsdf +183: [11:06:25] ^ +183: [11:06:25] dsafsdf 183: -183: [02:19:27] SMILES Parse Error: check for mistakes around position 1: -183: [02:19:27] dsafsdf -183: [02:19:27] ^ -183: [02:19:27] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -183: [02:19:27] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -183: [02:19:27] [02:19:27] SMILES Parse Error: syntax error while parsing: dsafsdf -183: [02:19:27] SMILES Parse Error: [02:19:27] SMILES Parse Error: check for mistakes around position 1: -183: syntax error[02:19:27] [02:19:27] SMILES Parse Error: syntax error while parsing: SMILES Parse Error: SMILES Parse Error: check for mistakes around position 1 while parsing: syntax error: -183: [02:19:27] dsafsdf while parsing: dsafsdf +183: [11:06:25] SMILES Parse Error: check for mistakes around position 1: +183: [11:06:25] dsafsdf[11:06:25] SMILES Parse Error: +183: [11:06:25] [11:06:25] ^ +183: SMILES Parse Error: syntax errorSMILES[11:06:25] [11:06:25] SMILES Parse Error: Failed parsing SMILES 'dsafsdf'dsafsdf +183: [11:06:25] ^ +183: for input: '[11:06:25] SMILES1: +183: [11:06:25] dsafsdf +183: [11:06:25] ^[11:06:25] SMILES Parse Error: SMILES Parse Error: [11:06:25] +183: ^ +183: dsafsdf'[11:06:25] SMILES Parse Error: check for mistakes around position +183: Parse Error: syntax error while parsing: dsafsdf +183: Failed parsing SMILES 'dsafsdf'[11:06:25] SMILES Parse Error: check for mistakes around position 1: for input: 'dsafsdf' +183: while parsing: dsafsdf 183: -183: [02:19:27] ^ -183: [02:19:27] SMILES Parse Error: check for mistakes around position 1: +183: [11:06:25] SMILES Parse Error: syntax error while parsing: dsafsdfFailed parsing SMILES 'dsafsdf'1[11:06:25] SMILES Parse Error: check for mistakes around position for input: ' +183: [11:06:25] [11:06:25] dsafsdf +183: [11:06:25] dsafsdf:[11:06:25] 1[11:06:25] SMILES Parse Error: SMILES Parse Error: check for mistakes around position ^syntax error'1 +183: while parsing: : +183: dsafsdf: +183: SMILES +183: Parse Error: [11:06:25] +183: [11:06:25] dsafsdf 183: dsafsdf -183: [02:19:27] dsafsdf -183: [02:19:27] ^ -183: [02:19:27] SMILES Parse Error: check for mistakes around position 1: -183: SMILES Parse Error: check for mistakes around position [02:19:27] [02:19:27] [02:19:27] dsafsdfdsafsdfSMILES -183: 1dsafsdf[02:19:27] [02:19:27] -183: SMILES: -183: SMILES Parse Error: check for mistakes around position Parse Error: [02:19:27] -183: ^[02:19:27] -183: [02:19:27] ^ -183: Failed parsing SMILES 'dsafsdf'dsafsdf -183: 1 for input: 'dsafsdf' -183: :[02:19:27] [02:19:27] ^ -183: SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf -183: [02:19:27] dsafsdf -183: [02:19:27] SMILES Parse Error: Failed parsing SMILES 'dsafsdf'[02:19:27] ^[02:19:27] for input: 'dsafsdf' +183: syntax error[11:06:25] ^ +183: while parsing: dsafsdf +183: [11:06:25] [11:06:25] +183: Failed parsing SMILES 'dsafsdf'SMILES Parse Error: check for mistakes around position [11:06:25] for input: 'SMILES[11:06:25] dsafsdf' +183: Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +183: dsafsdfSMILES Parse Error: +183: syntax error1 while parsing: dsafsdf +183: [11:06:25] SMILES Parse Error: check for mistakes around position :[11:06:25] +183: 1: +183: [11:06:25] [11:06:25] ^[11:06:25] dsafsdf +183: [11:06:25] ^ +183: dsafsdf[11:06:25] +183: [11:06:25] SMILES Parse Error: ^ +183: syntax error[11:06:25] while parsing: dsafsdf +183: [11:06:25] SMILES Parse Error: [11:06:25] +183: SMILES Parse Error: [11:06:25] SMILES Parse Error: check for mistakes around position ^Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf 183: ' +183: syntax error while parsing: dsafsdfSMILES Parse Error: check for mistakes around position [11:06:25] 1SMILES Parse Error: Failed parsing SMILES 'dsafsdf'[11:06:25] +183: SMILES[11:06:25] : +183: [11:06:25] dsafsdf for input: 'SMILES Parse Error: check for mistakes around position [11:06:25] dsafsdf Parse Error: SMILES1Failed parsing SMILES 'dsafsdf'1[11:06:25] :SMILES Parse Error: syntax error while parsing: +183: ' +183: :dsafsdf[11:06:25] +183: [11:06:25] Parse Error: [11:06:25] dsafsdfSMILESFailed parsing SMILES 'dsafsdf' for input: 'dsafsdf' for input: ' +183: dsafsdf[11:06:25] ^ 183: -183: SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -183: [02:19:27] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -183: [02:19:27] SMILES Parse Error: syntax error while parsing: dsafsdf -183: [02:19:27] SMILES Parse Error: check for mistakes around position 1: -183: [02:19:27] dsafsdf -183: [02:19:27] ^ -183: [02:19:27] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -183: [02:19:27] [02:19:27] SMILES Parse Error: syntax error while parsing: [02:19:27] [02:19:27] SMILES Parse Error: syntax error while parsing: [02:19:27] SMILES Parse Error: dsafsdf Parse Error: syntax error while parsing: SMILES Parse Error: syntax error while parsing: dsafsdfdsafsdf -183: SMILES Parse Error: syntax error[02:19:27] -183: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf[02:19:27] SMILES Parse Error: check for mistakes around position 1dsafsdfSMILES Parse Error: check for mistakes around position -183: [02:19:27] SMILES Parse Error: check for mistakes around position 1 -183: '[02:19:27] SMILES Parse Error: check for mistakes around position :11: -183: : -183: [02:19:27] : -183: dsafsdf -183: [02:19:27] dsafsdf -183: [02:19:27] [02:19:27] dsafsdf -183: ^ -183: [02:19:27] ^ +183: dsafsdf[11:06:25] SMILES Parse Error: check for mistakes around position Parse Error: ' 183: -183: [02:19:27] ^ -183: [02:19:27] SMILES Parse Error: Failed parsing SMILES 'dsafsdf'[02:19:27] SMILES Parse Error: [02:19:27] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -183: for input: 'dsafsdf' -183: [02:19:27] SMILES Parse Error: syntax error while parsing: dsafsdf -183: [02:19:27] Failed parsing SMILES 'dsafsdf' while parsing: dsafsdf -183: [02:19:27] for input: ' -183: dsafsdfSMILES Parse Error: check for mistakes around position 1SMILES Parse Error: check for mistakes around position 1[02:19:27] dsafsdf -183: ' -183: [02:19:27] ^ -183: [02:19:27] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -183: [02:19:27] [02:19:27] : -183: [02:19:27] dsafsdf -183: [02:19:27] ^ -183: [02:19:27] SMILES Parse Error: syntax error while parsing: dsafsdf -183: [02:19:27] SMILES Parse Error: check for mistakes around position 1: -183: [02:19:27] dsafsdf -183: [02:19:27] ^ -183: [02:19:27] SMILES Parse Error: Failed parsing SMILES 'dsafsdf'[02:19:27] : -183: SMILES for input: 'dsafsdf'SMILES Parse Error: syntax error while parsing: dsafsdf -183: [02:19:27] dsafsdf -183: Parse Error: -183: Failed parsing SMILES 'dsafsdf'[02:19:27] [02:19:27] SMILES Parse Error: check for mistakes around position 1: -183: [02:19:27] dsafsdf -183: [02:19:27] ^ -183: [02:19:27] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -183: [02:19:27] SMILES Parse Error: syntax error while parsing: dsafsdf -183: [02:19:27] SMILES Parse Error: check for mistakes around position 1: -183: [02:19:27] dsafsdf -183: [02:19:27] ^ -183: [02:19:27] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -183: for input: 'dsafsdf' +183: [11:06:25] 1: 183: ^ -183: [02:19:27] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -183: [02:19:27] SMILES Parse Error: syntax error while parsing: dsafsdf -183: [02:19:27] SMILES Parse Error: check for mistakes around position 1: -183: [02:19:27] dsafsdf -183: [02:19:27] ^ -183: [02:19:27] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +183: +183: Failed parsing SMILES 'dsafsdf'[11:06:25] +183: SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +183: [11:06:25] [11:06:25] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +183: SMILES Parse Error: [11:06:25] SMILES Parse Error: syntax error while parsing: dsafsdf +183: [11:06:25] SMILES Parse Error: check for mistakes around position 1: +183: [11:06:25] [11:06:25] [11:06:25] [11:06:25] dsafsdf +183: SMILES Parse Error: dsafsdf +183: [11:06:25] ^syntax error[11:06:25] while parsing: +183: SMILES Parse Error: syntax errorsyntax error while parsing: dsafsdf +183: [11:06:25] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +183: while parsing: ^ +183: dsafsdfdsafsdf[11:06:25] [11:06:25] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdfSMILES Parse Error: check for mistakes around position 1 +183: : for input: ''dsafsdf' +183: +183: [11:06:25] +183: [11:06:25] SMILES Parse Error: check for mistakes around position 1SMILES Parse Error: check for mistakes around position +183: 1: +183: :[11:06:25] dsafsdf +183: [11:06:25] ^ +183: +183: [11:06:25] dsafsdf +183: [11:06:25] [11:06:25] [11:06:25] [11:06:25] ^ 183: SMILES Parse Error: syntax error while parsing: dsafsdf -183: [02:19:27] SMILES Parse Error: check for mistakes around position 1: -183: [02:19:27] dsafsdf -183: [02:19:27] ^ -183: [02:19:27] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -183: [02:19:27] SMILES Parse Error: syntax error while parsing: dsafsdf -183: [02:19:27] SMILES Parse Error: check for mistakes around position 1: -183: [02:19:27] dsafsdf -183: [02:19:27] ^ -183: [02:19:27] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -183: [02:19:27] SMILES Parse Error: syntax error while parsing: dsafsdf -183: [02:19:27] SMILES Parse Error: check for mistakes around position 1: -183: [02:19:27] dsafsdf -183: [02:19:27] ^ -183: [02:19:27] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -183: [02:19:27] SMILES Parse Error: syntax error while parsing: dsafsdf -183: [02:19:27] SMILES Parse Error: check for mistakes around position 1: -183: [02:19:27] dsafsdf -183: [02:19:27] ^ -183: [02:19:27] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -183: [02:19:27] SMILES Parse Error: syntax error while parsing: dsafsdf -183: [02:19:27] SMILES Parse Error: check for mistakes around position 1: -183: [02:19:27] dsafsdf -183: [02:19:27] ^ -183: [02:19:27] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -183: dsafsdf -183: [02:19:27] ^ -183: [02:19:27] SMILES Parse Error: syntax error while parsing: dsafsdf -183: [02:19:27] SMILES Parse Error: check for mistakes around position 1: -183: [02:19:27] dsafsdf -183: [02:19:27] ^ -183: [02:19:27] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -183: [02:19:27] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -183: [02:19:27] [02:19:27] SMILES Parse Error: syntax error while parsing: dsafsdf -183: [02:19:27] SMILES Parse Error: check for mistakes around position 1: -183: [02:19:27] SMILES Parse Error: syntax error while parsing: dsafsdf -183: [02:19:27] SMILES Parse Error: check for mistakes around position 1: -183: [02:19:27] dsafsdf -183: [02:19:27] ^ -183: [02:19:27] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -183: [02:19:27] SMILES Parse Error: syntax error while parsing: dsafsdf -183: [02:19:27] SMILES Parse Error: check for mistakes around position 1: -183: [02:19:27] dsafsdf -183: [02:19:27] ^ -183: [02:19:27] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -183: [02:19:27] SMILES Parse Error: syntax error while parsing: dsafsdf -183: [02:19:27] SMILES Parse Error: check for mistakes around position 1: -183: [02:19:27] dsafsdf -183: [02:19:27] ^ -183: [02:19:27] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -183: [02:19:27] SMILES Parse Error: syntax error while parsing: dsafsdf -183: [02:19:27] SMILES Parse Error: check for mistakes around position 1: -183: [02:19:27] dsafsdf -183: [02:19:27] ^ -183: [02:19:27] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -183: dsafsdf -183: [02:19:27] ^ -183: [02:19:27] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -183: [02:19:27] SMILES Parse Error: syntax error while parsing: dsafsdf -183: [02:19:27] SMILES Parse Error: check for mistakes around position 1: -183: [02:19:27] dsafsdf -183: [02:19:27] ^ -183: [02:19:27] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -183: [02:19:27] SMILES Parse Error: syntax error while parsing: dsafsdf -183: [02:19:27] SMILES Parse Error: check for mistakes around position 1: -183: [02:19:27] dsafsdf -183: [02:19:27] ^ -183: [02:19:27] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -183: [02:19:27] SMILES Parse Error: syntax error while parsing: dsafsdf -183: [02:19:27] SMILES Parse Error: check for mistakes around position 1: -183: [02:19:27] dsafsdf -183: [02:19:27] ^ -183: [02:19:27] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -183: [02:19:27] SMILES Parse Error: syntax error while parsing: dsafsdf -183: [02:19:27] SMILES Parse Error: check for mistakes around position 1: -183: [02:19:27] dsafsdf -183: [02:19:27] ^ -183: [02:19:27] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -183: [02:19:27] SMILES Parse Error: syntax error while parsing: dsafsdf -183: [02:19:27] SMILES Parse Error: check for mistakes around position 1: -183: [02:19:27] dsafsdf -183: [02:19:27] ^ -183: [02:19:27] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -183: [02:19:27] SMILES Parse Error: syntax error while parsing: dsafsdf -183: [02:19:27] SMILES Parse Error: check for mistakes around position 1: -183: [02:19:27] dsafsdf -183: [02:19:27] ^ -183: [02:19:27] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -183: [02:19:27] SMILES Parse Error: syntax error while parsing: dsafsdf -183: [02:19:27] SMILES Parse Error: check for mistakes around position 1: -183: [02:19:27] dsafsdf -183: [02:19:27] ^ -183: [02:19:27] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -183: [02:19:27] SMILES Parse Error: syntax error while parsing: dsafsdf -183: [02:19:27] SMILES Parse Error: check for mistakes around position 1: -183: [02:19:27] dsafsdf -183: [02:19:27] ^ -183: [02:19:27] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -183: [02:19:27] SMILES Parse Error: syntax error while parsing: dsafsdf -183: [02:19:27] SMILES Parse Error: check for mistakes around position 1: -183: [02:19:27] dsafsdf -183: [02:19:27] ^ -183: [02:19:27] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -183: [02:19:27] SMILES Parse Error: syntax error while parsing: dsafsdf -183: [02:19:27] SMILES Parse Error: check for mistakes around position 1: -183: [02:19:27] dsafsdf -183: [02:19:27] ^ -183: [02:19:27] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -183: [02:19:27] SMILES Parse Error: syntax error while parsing: dsafsdf -183: [02:19:27] SMILES Parse Error: check for mistakes around position 1: -183: [02:19:27] dsafsdf -183: [02:19:27] ^ -183: [02:19:27] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -183: [02:19:27] SMILES Parse Error: syntax error while parsing: dsafsdf -183: [02:19:27] SMILES Parse Error: check for mistakes around position 1: -183: [02:19:27] dsafsdf -183: [02:19:27] ^ -183: [02:19:27] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -183: [02:19:27] SMILES Parse Error: syntax error while parsing: dsafsdf -183: [02:19:27] SMILES Parse Error: check for mistakes around position 1: -183: [02:19:27] dsafsdf -183: [02:19:27] ^ -183: [02:19:27] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -183: [02:19:27] SMILES Parse Error: syntax error while parsing: dsafsdf -183: [02:19:27] SMILES Parse Error: check for mistakes around position 1: -183: [02:19:27] dsafsdf -183: [02:19:27] ^ -183: [02:19:27] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -183: [02:19:27] SMILES Parse Error: syntax error while parsing: dsafsdf -183: [02:19:27] SMILES Parse Error: check for mistakes around position 1: -183: [02:19:27] dsafsdf -183: [02:19:27] ^ -183: [02:19:27] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -183: [02:19:27] SMILES Parse Error: syntax error while parsing: dsafsdf -183: [02:19:27] SMILES Parse Error: check for mistakes around position 1: -183: [02:19:27] dsafsdf -183: [02:19:27] ^ -183: [02:19:27] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -183: [02:19:27] SMILES Parse Error: syntax error while parsing: dsafsdf -183: [02:19:27] SMILES Parse Error: check for mistakes around position 1: -183: [02:19:27] dsafsdf -183: [02:19:27] ^ -183: [02:19:27] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -183: [02:19:27] SMILES Parse Error: syntax error while parsing: dsafsdf -183: [02:19:27] SMILES Parse Error: check for mistakes around position 1: -183: [02:19:27] dsafsdf -183: [02:19:27] ^ -183: [02:19:27] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -183: [02:19:27] SMILES Parse Error: syntax error while parsing: dsafsdf -183: [02:19:27] SMILES Parse Error: check for mistakes around position 1: -183: [02:19:27] dsafsdf -183: [02:19:27] ^ -183: [02:19:27] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -183: [02:19:27] SMILES Parse Error: syntax error while parsing: dsafsdf -183: [02:19:27] SMILES Parse Error: check for mistakes around position 1: -183: [02:19:27] dsafsdf -183: [02:19:27] ^ -183: [02:19:27] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -183: [02:19:27] SMILES Parse Error: syntax error while parsing: dsafsdf -183: [02:19:27] SMILES Parse Error: check for mistakes around position 1: -183: [02:19:27] dsafsdf -183: [02:19:27] ^ -183: [02:19:27] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -183: [02:19:27] SMILES Parse Error: syntax error while parsing: dsafsdf -183: [02:19:27] SMILES Parse Error: check for mistakes around position 1: -183: [02:19:27] dsafsdf -183: [02:19:27] ^ -183: [02:19:27] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -183: [02:19:27] SMILES Parse Error: syntax error while parsing: dsafsdf -183: [02:19:27] SMILES Parse Error: check for mistakes around position 1: -183: [02:19:27] dsafsdf -183: [02:19:27] ^ -183: [02:19:27] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -183: [02:19:27] SMILES Parse Error: syntax error while parsing: dsafsdf -183: [02:19:27] SMILES Parse Error: check for mistakes around position 1: -183: [02:19:27] dsafsdf -183: [02:19:27] ^ -183: [02:19:27] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -183: [02:19:27] SMILES Parse Error: syntax error while parsing: dsafsdf -183: [02:19:27] SMILES Parse Error: check for mistakes around position 1: -183: [02:19:27] dsafsdf -183: [02:19:27] ^ -183: [02:19:27] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -183: [02:19:27] SMILES Parse Error: syntax error while parsing: dsafsdf -183: [02:19:27] SMILES Parse Error: check for mistakes around position 1: -183: [02:19:27] dsafsdf -183: [02:19:27] ^ -183: [02:19:27] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -183: [02:19:27] SMILES Parse Error: syntax error while parsing: dsafsdf -183: [02:19:27] SMILES Parse Error: check for mistakes around position 1: -183: [02:19:27] dsafsdf -183: [02:19:27] ^ -183: [02:19:27] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -183: [02:19:27] SMILES Parse Error: syntax error while parsing: dsafsdf -183: [02:19:27] SMILES Parse Error: check for mistakes around position 1: -183: [02:19:27] dsafsdf -183: [02:19:27] ^ -183: [02:19:27] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -183: [02:19:27] SMILES Parse Error: syntax error while parsing: dsafsdf -183: [02:19:27] SMILES Parse Error: check for mistakes around position 1: -183: [02:19:27] dsafsdf -183: [02:19:27] ^ -183: [02:19:27] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -183: [02:19:27] SMILES Parse Error: syntax error while parsing: dsafsdf -183: [02:19:27] SMILES Parse Error: check for mistakes around position 1: -183: [02:19:27] dsafsdf -183: [02:19:27] ^ -183: [02:19:27] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -183: [02:19:27] SMILES Parse Error: syntax error while parsing: dsafsdf -183: [02:19:27] SMILES Parse Error: check for mistakes around position 1: -183: [02:19:27] dsafsdf -183: [02:19:27] ^ -183: [02:19:27] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -183: [02:19:27] SMILES Parse Error: syntax error while parsing: dsafsdf -183: [02:19:27] SMILES Parse Error: check for mistakes around position 1: -183: [02:19:27] dsafsdf -183: [02:19:27] ^ -183: [02:19:27] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -183: [02:19:27] SMILES Parse Error: syntax error while parsing: dsafsdf -183: [02:19:27] SMILES Parse Error: check for mistakes around position 1: -183: [02:19:27] dsafsdf -183: [02:19:27] ^ -183: [02:19:27] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -183: [02:19:27] SMILES Parse Error: syntax error while parsing: dsafsdf -183: [02:19:27] SMILES Parse Error: check for mistakes around position 1: -183: [02:19:27] dsafsdf -183: [02:19:27] ^ -183: [02:19:27] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -183: [02:19:27] SMILES Parse Error: syntax error while parsing: dsafsdf -183: [02:19:27] SMILES Parse Error: check for mistakes around position 1: -183: [02:19:27] dsafsdf -183: [02:19:27] ^ -183: [02:19:27] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -183: [02:19:27] SMILES Parse Error: syntax error while parsing: dsafsdf -183: [02:19:27] SMILES Parse Error: check for mistakes around position 1: -183: [02:19:27] dsafsdf -183: [02:19:27] ^ -183: [02:19:27] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -183: [02:19:27] SMILES Parse Error: syntax error while parsing: dsafsdf -183: [02:19:27] SMILES Parse Error: check for mistakes around position 1: -183: [02:19:27] dsafsdf -183: [02:19:27] ^ -183: [02:19:27] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -183: [02:19:27] SMILES Parse Error: syntax error while parsing: dsafsdf -183: [02:19:27] SMILES Parse Error: check for mistakes around position 1: -183: [02:19:27] dsafsdf -183: [02:19:27] ^ -183: [02:19:27] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -183: [02:19:27] SMILES Parse Error: syntax error while parsing: dsafsdf -183: [02:19:27] SMILES Parse Error: check for mistakes around position 1: -183: [02:19:27] dsafsdf -183: [02:19:27] ^ -183: [02:19:27] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -183: [02:19:27] SMILES Parse Error: syntax error while parsing: dsafsdf -183: [02:19:27] SMILES Parse Error: check for mistakes around position 1: -183: [02:19:27] dsafsdf -183: [02:19:27] ^ -183: [02:19:27] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -183: [02:19:27] SMILES Parse Error: syntax error while parsing: dsafsdf -183: [02:19:27] SMILES Parse Error: check for mistakes around position 1: -183: [02:19:27] dsafsdf -183: [02:19:27] ^ -183: [02:19:27] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -183: [02:19:27] SMILES Parse Error: syntax error while parsing: dsafsdf -183: [02:19:27] SMILES Parse Error: check for mistakes around position 1: -183: [02:19:27] dsafsdf -183: [02:19:27] ^ -183: [02:19:27] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -183: [02:19:27] SMILES Parse Error: syntax error while parsing: dsafsdf -183: [02:19:27] SMILES Parse Error: check for mistakes around position 1: -183: [02:19:27] dsafsdf -183: [02:19:27] ^ -183: [02:19:27] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -183: [02:19:27] SMILES Parse Error: syntax error while parsing: dsafsdf -183: [02:19:27] SMILES Parse Error: check for mistakes around position 1: -183: [02:19:27] dsafsdf -183: [02:19:27] ^ -183: [02:19:27] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -183: [02:19:27] SMILES Parse Error: syntax error while parsing: dsafsdf -183: [02:19:27] SMILES Parse Error: check for mistakes around position 1: -183: [02:19:27] dsafsdf -183: [02:19:27] ^ -183: [02:19:27] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -183: [02:19:27] SMILES Parse Error: syntax error while parsing: dsafsdf -183: [02:19:27] SMILES Parse Error: check for mistakes around position 1: -183: [02:19:27] dsafsdf -183: [02:19:27] ^ -183: [02:19:27] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -183: [02:19:27] SMILES Parse Error: syntax error while parsing: dsafsdf -183: [02:19:27] SMILES Parse Error: check for mistakes around position 1: -183: [02:19:27] dsafsdf -183: [02:19:27] ^ -183: [02:19:27] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -183: [02:19:27] SMILES Parse Error: syntax error while parsing: dsafsdf -183: [02:19:27] SMILES Parse Error: check for mistakes around position 1: -183: [02:19:27] dsafsdf -183: [02:19:27] ^ -183: [02:19:27] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -183: [02:19:27] SMILES Parse Error: syntax error while parsing: dsafsdf -183: [02:19:27] SMILES Parse Error: check for mistakes around position 1: -183: [02:19:27] dsafsdf -183: [02:19:27] ^ -183: [02:19:27] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -183: [02:19:27] SMILES Parse Error: syntax error while parsing: dsafsdf -183: [02:19:27] SMILES Parse Error: check for mistakes around position 1: -183: [02:19:27] dsafsdf -183: [02:19:27] ^ -183: [02:19:27] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -183: [02:19:27] SMILES Parse Error: syntax error while parsing: dsafsdf -183: [02:19:27] SMILES Parse Error: check for mistakes around position 1: -183: [02:19:27] dsafsdf -183: [02:19:27] ^ -183: [02:19:27] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -183: [02:19:27] SMILES Parse Error: syntax error while parsing: dsafsdf -183: [02:19:27] SMILES Parse Error: check for mistakes around position 1: -183: [02:19:27] dsafsdf -183: [02:19:27] ^ -183: [02:19:27] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -173: [02:19:27] Complex queries can be slow. -183: [02:19:27] SMILES Parse Error: syntax error while parsing: dsafsdf -183: [02:19:27] SMILES Parse Error: check for mistakes around position 1: -183: [02:19:27] dsafsdf -183: [02:19:27] ^ -183: [02:19:27] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -183: [02:19:27] SMILES Parse Error: syntax error while parsing: dsafsdf -183: [02:19:27] SMILES Parse Error: check for mistakes around position 1: -183: [02:19:27] dsafsdf -183: [02:19:27] ^ -183: [02:19:27] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -183: [02:19:27] SMILES Parse Error: syntax error while parsing: dsafsdf -183: [02:19:27] SMILES Parse Error: check for mistakes around position 1: -183: [02:19:27] dsafsdf -183: [02:19:27] ^ -183: [02:19:27] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -183: [02:19:27] SMILES Parse Error: syntax error while parsing: dsafsdf -183: [02:19:27] SMILES Parse Error: check for mistakes around position 1: -183: [02:19:27] dsafsdf -183: [02:19:27] ^ -183: [02:19:27] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -183: [02:19:27] SMILES Parse Error: syntax error while parsing: dsafsdf -183: [02:19:27] SMILES Parse Error: check for mistakes around position 1: -183: [02:19:27] dsafsdf -183: [02:19:27] ^ -183: [02:19:27] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -183: [02:19:27] SMILES Parse Error: syntax error while parsing: dsafsdf -183: [02:19:27] SMILES Parse Error: check for mistakes around position 1: -183: [02:19:27] dsafsdf -183: [02:19:27] ^ -183: [02:19:27] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -183: [02:19:27] SMILES Parse Error: syntax error while parsing: dsafsdf -183: [02:19:27] SMILES Parse Error: check for mistakes around position 1: -183: [02:19:27] dsafsdf -183: [02:19:27] ^ -183: [02:19:27] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -183: [02:19:27] SMILES Parse Error: syntax error while parsing: dsafsdf -183: [02:19:27] SMILES Parse Error: check for mistakes around position 1: -183: [02:19:27] dsafsdf -183: [02:19:27] ^ -183: [02:19:27] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -183: [02:19:27] SMILES Parse Error: syntax error while parsing: dsafsdf -183: [02:19:27] SMILES Parse Error: check for mistakes around position 1: -183: [02:19:27] dsafsdf -183: [02:19:27] ^ -183: [02:19:27] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -183: [02:19:27] SMILES Parse Error: syntax error while parsing: dsafsdf -183: [02:19:27] SMILES Parse Error: check for mistakes around position 1: -183: [02:19:27] dsafsdf -183: [02:19:27] ^ -183: [02:19:27] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -183: [02:19:27] SMILES Parse Error: syntax error while parsing: dsafsdf -183: [02:19:27] SMILES Parse Error: check for mistakes around position 1: -183: [02:19:27] dsafsdf -183: [02:19:27] ^ -183: [02:19:27] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -183: [02:19:27] SMILES Parse Error: syntax error while parsing: dsafsdf -183: [02:19:27] SMILES Parse Error: check for mistakes around position 1: -183: [02:19:27] dsafsdf -183: [02:19:27] ^ -183: [02:19:27] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -183: [02:19:27] SMILES Parse Error: syntax error while parsing: dsafsdf -183: [02:19:27] SMILES Parse Error: check for mistakes around position 1: -183: [02:19:27] dsafsdf -183: [02:19:27] ^ -183: [02:19:27] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -183: [02:19:27] SMILES Parse Error: syntax error while parsing: dsafsdf -183: [02:19:27] SMILES Parse Error: check for mistakes around position 1: -183: [02:19:27] dsafsdf -183: [02:19:27] ^ -183: [02:19:27] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -183: [02:19:27] SMILES Parse Error: syntax error while parsing: dsafsdf -183: [02:19:27] SMILES Parse Error: check for mistakes around position 1: -183: [02:19:27] dsafsdf -183: [02:19:27] ^ -183: [02:19:27] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -183: [02:19:27] SMILES Parse Error: syntax error while parsing: dsafsdf -183: [02:19:27] SMILES Parse Error: check for mistakes around position 1: -183: [02:19:27] dsafsdf -183: [02:19:27] ^ -183: [02:19:27] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -183: [02:19:27] SMILES Parse Error: syntax error while parsing: dsafsdf -183: [02:19:27] SMILES Parse Error: check for mistakes around position 1: -183: [02:19:27] dsafsdf -183: [02:19:27] ^ -183: [02:19:27] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -183: [02:19:27] SMILES Parse Error: syntax error while parsing: dsafsdf -183: [02:19:27] SMILES Parse Error: check for mistakes around position 1: -183: [02:19:27] dsafsdf -183: [02:19:27] ^ -183: [02:19:27] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -183: [02:19:27] SMILES Parse Error: syntax error while parsing: dsafsdf -183: [02:19:27] SMILES Parse Error: check for mistakes around position 1: -183: [02:19:27] dsafsdf -183: [02:19:27] ^ -183: [02:19:27] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -183: [02:19:27] SMILES Parse Error: syntax error while parsing: dsafsdf -183: [02:19:27] SMILES Parse Error: check for mistakes around position 1: -183: [02:19:27] dsafsdf -183: [02:19:27] ^ -183: [02:19:27] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -183: [02:19:27] SMILES Parse Error: syntax error while parsing: dsafsdf -183: [02:19:27] SMILES Parse Error: check for mistakes around position 1: -183: [02:19:27] dsafsdf -183: [02:19:27] ^ -183: [02:19:27] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -183: [02:19:27] SMILES Parse Error: syntax error while parsing: dsafsdf -183: [02:19:27] SMILES Parse Error: check for mistakes around position 1: -183: [02:19:27] dsafsdf -183: [02:19:27] ^ -183: [02:19:27] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -183: [02:19:27] SMILES Parse Error: syntax error while parsing: dsafsdf -183: [02:19:27] SMILES Parse Error: check for mistakes around position 1: -183: [02:19:27] dsafsdf -183: [02:19:27] ^ -183: [02:19:27] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -183: [02:19:27] SMILES Parse Error: syntax error while parsing: dsafsdf -183: [02:19:27] SMILES Parse Error: check for mistakes around position 1: -183: [02:19:27] dsafsdf -183: [02:19:27] ^ -183: [02:19:27] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -183: [02:19:27] SMILES Parse Error: syntax error while parsing: dsafsdf -183: [02:19:27] SMILES Parse Error: check for mistakes around position 1: -183: [02:19:27] dsafsdf -183: [02:19:27] ^ -183: [02:19:27] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -183: [02:19:27] SMILES Parse Error: syntax error while parsing: dsafsdf -183: [02:19:27] SMILES Parse Error: check for mistakes around position 1: -183: [02:19:27] dsafsdf -183: [02:19:27] ^ -183: [02:19:27] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -183: [02:19:27] SMILES Parse Error: syntax error while parsing: dsafsdf -183: [02:19:27] SMILES Parse Error: check for mistakes around position 1: -183: [02:19:27] dsafsdf -183: [02:19:27] ^ -183: [02:19:27] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -183: [02:19:27] SMILES Parse Error: syntax error while parsing: dsafsdf -183: [02:19:27] SMILES Parse Error: check for mistakes around position 1: -183: [02:19:27] dsafsdf -183: [02:19:27] ^ -183: [02:19:27] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -183: [02:19:27] SMILES Parse Error: syntax error while parsing: dsafsdf -183: [02:19:27] SMILES Parse Error: check for mistakes around position 1: -183: [02:19:27] dsafsdf -183: [02:19:27] ^ -183: [02:19:27] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -183: [02:19:27] SMILES Parse Error: syntax error while parsing: dsafsdf -183: [02:19:27] SMILES Parse Error: check for mistakes around position 1: -183: [02:19:27] dsafsdf -183: [02:19:27] ^ -183: [02:19:27] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -183: [02:19:27] SMILES Parse Error: syntax error while parsing: dsafsdf -183: [02:19:27] SMILES Parse Error: check for mistakes around position 1: -183: [02:19:27] dsafsdf -183: [02:19:27] ^ -183: [02:19:27] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -183: [02:19:27] SMILES Parse Error: syntax error while parsing: dsafsdf -183: [02:19:27] SMILES Parse Error: check for mistakes around position 1: -183: [02:19:27] dsafsdf -183: [02:19:27] ^ -183: [02:19:27] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -183: [02:19:27] SMILES Parse Error: syntax error while parsing: dsafsdf -183: [02:19:27] SMILES Parse Error: check for mistakes around position 1: -183: [02:19:27] dsafsdf -183: [02:19:27] ^ -183: [02:19:27] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -183: [02:19:27] SMILES Parse Error: syntax error while parsing: dsafsdf -183: [02:19:27] SMILES Parse Error: check for mistakes around position 1: -183: [02:19:27] dsafsdf -183: [02:19:27] ^ -183: [02:19:27] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -183: [02:19:27] SMILES Parse Error: syntax error while parsing: dsafsdf -183: [02:19:27] SMILES Parse Error: check for mistakes around position 1: -183: [02:19:27] dsafsdf -183: [02:19:27] ^ -183: [02:19:27] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -183: [02:19:27] SMILES Parse Error: syntax error while parsing: dsafsdf -183: [02:19:27] SMILES Parse Error: check for mistakes around position 1: -183: [02:19:27] dsafsdf -183: [02:19:27] ^ -183: [02:19:27] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -183: [02:19:27] SMILES Parse Error: syntax error while parsing: dsafsdf -183: [02:19:27] SMILES Parse Error: check for mistakes around position 1: -183: [02:19:27] dsafsdf -183: [02:19:27] ^ -183: [02:19:27] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -183: [02:19:27] SMILES Parse Error: syntax error while parsing: dsafsdf -183: [02:19:27] SMILES Parse Error: check for mistakes around position 1: -183: [02:19:27] dsafsdf -183: [02:19:27] ^ -183: [02:19:27] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -183: [02:19:27] SMILES Parse Error: syntax error while parsing: dsafsdf -183: [02:19:27] SMILES Parse Error: check for mistakes around position 1: -183: [02:19:27] dsafsdf -183: [02:19:27] ^ -183: [02:19:27] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -183: [02:19:27] SMILES Parse Error: syntax error while parsing: dsafsdf -183: [02:19:27] SMILES Parse Error: check for mistakes around position 1: -183: [02:19:27] dsafsdf -183: [02:19:27] ^ -183: [02:19:27] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -183: [02:19:27] SMILES Parse Error: syntax error while parsing: dsafsdf -183: [02:19:27] SMILES Parse Error: check for mistakes around position 1: -183: [02:19:27] dsafsdf -183: [02:19:27] ^ -183: [02:19:27] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -183: [02:19:27] SMILES Parse Error: syntax error while parsing: dsafsdf -183: [02:19:27] SMILES Parse Error: check for mistakes around position 1: -183: [02:19:27] dsafsdf -183: [02:19:27] ^ -183: [02:19:27] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -183: [02:19:27] SMILES Parse Error: syntax error while parsing: dsafsdf -183: [02:19:27] SMILES Parse Error: check for mistakes around position 1: -183: [02:19:27] dsafsdf -183: [02:19:27] ^ -183: [02:19:27] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -183: [02:19:27] SMILES Parse Error: syntax error while parsing: dsafsdf -183: [02:19:27] SMILES Parse Error: check for mistakes around position 1: -183: [02:19:27] dsafsdf -183: [02:19:27] ^ -183: [02:19:27] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -183: [02:19:27] SMILES Parse Error: syntax error while parsing: dsafsdf -183: [02:19:27] SMILES Parse Error: check for mistakes around position 1: -183: [02:19:27] dsafsdf -183: [02:19:27] ^ -183: [02:19:27] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -183: [02:19:27] SMILES Parse Error: syntax error while parsing: dsafsdf -183: [02:19:27] SMILES Parse Error: check for mistakes around position 1: -183: [02:19:27] dsafsdf -183: [02:19:27] ^ -183: [02:19:27] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -183: [02:19:27] SMILES Parse Error: syntax error while parsing: dsafsdf -183: [02:19:27] SMILES Parse Error: check for mistakes around position 1: -183: [02:19:27] dsafsdf -183: [02:19:27] ^ -183: [02:19:27] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -183: [02:19:27] SMILES Parse Error: syntax error while parsing: dsafsdf -183: [02:19:27] SMILES Parse Error: check for mistakes around position 1: -183: [02:19:27] dsafsdf -183: [02:19:27] ^ -183: [02:19:27] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -183: [02:19:27] SMILES Parse Error: syntax error while parsing: dsafsdf -183: [02:19:27] SMILES Parse Error: check for mistakes around position 1: -183: [02:19:27] dsafsdf -183: [02:19:27] ^ -183: [02:19:27] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -183: [02:19:27] SMILES Parse Error: syntax error while parsing: dsafsdf -183: [02:19:27] SMILES Parse Error: check for mistakes around position 1: -183: [02:19:27] dsafsdf -183: [02:19:27] ^ -183: [02:19:27] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -183: [02:19:27] ------------------------------------- -183: [02:19:27] Results do not depend on numThreads -173: [02:19:28] Complex queries can be slow. -173: [02:19:28] Complex queries can be slow. -173: [02:19:28] Complex queries can be slow. -173: [02:19:28] Complex queries can be slow. -173: [02:19:28] Complex queries can be slow. -173: [02:19:28] Complex queries can be slow. -173: [02:19:28] Complex queries can be slow. -173: [02:19:28] Complex queries can be slow. -173: [02:19:28] Complex queries can be slow. -173: [02:19:28] Complex queries can be slow. -173: [02:19:29] Complex queries can be slow. -186: iterative -173: [02:19:29] Complex queries can be slow. -150: --------------------------------- -150: test O3A multithreading bug -150: -150: --------------------------------- -150: testCrippenO3A multithreading -150: -150: generating reference data -173: [02:19:29] Complex queries can be slow. -173: =============================================================================== -173: All tests passed (121 assertions in 17 test cases) -173: -175/238 Test #173: testSynthonSpaceSubstructureSearch ..... Passed 12.71 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 -148: ... -148: ---------------------------------------------------------------------- -148: Ran 22 tests in 18.982s -148: -148: OK -187: [02:19:29] WARNING: not removing hydrogen atom with dummy atom neighbors -187: [02:19:29] WARNING: not removing hydrogen atom with dummy atom neighbors -187: [02:19:29] WARNING: not removing hydrogen atom with dummy atom neighbors -187: [02:19:29] WARNING: not removing hydrogen atom with dummy atom neighbors -187: [02:19:29] WARNING: not removing hydrogen atom with dummy atom neighbors -187: [02:19:29] WARNING: not removing hydrogen atom with dummy atom neighbors -187: [02:19:29] WARNING: not removing hydrogen atom with dummy atom neighbors -187: [02:19:29] WARNING: not removing hydrogen atom with dummy atom neighbors -187: [02:19:29] WARNING: not removing hydrogen atom with dummy atom neighbors -187: [02:19:29] WARNING: not removing hydrogen atom with dummy atom neighbors -187: [02:19:29] WARNING: not removing hydrogen atom with dummy atom neighbors -187: [02:19:29] WARNING: not removing hydrogen atom with dummy atom neighbors -187: [02:19:29] WARNING: not removing hydrogen atom with dummy atom neighbors -187: [02:19:29] WARNING: not removing hydrogen atom with dummy atom neighbors -187: [02:19:29] WARNING: not removing hydrogen atom with dummy atom neighbors -187: [02:19:29] WARNING: not removing hydrogen atom with dummy atom neighbors -187: [02:19:29] WARNING: not removing hydrogen atom with dummy atom neighbors -187: [02:19:29] WARNING: not removing hydrogen atom with dummy atom neighbors -187: [02:19:29] WARNING: not removing hydrogen atom with dummy atom neighbors -187: [02:19:29] WARNING: not removing hydrogen atom with dummy atom neighbors -187: [02:19:29] WARNING: not removing hydrogen atom with dummy atom neighbors -176/238 Test #187: testRGroupDecompInternals .............. Passed 0.03 sec +183: SMILESdsafsdf +183: Parse Error: [11:06:25] ^[11:06:25] [11:06:25] +183: SMILES Parse Error: [11:06:25] [11:06:25] SMILES Parse Error: check for mistakes around position 1: +183: [11:06:25] dsafsdf[11:06:25] SMILESSMILESFailed parsing SMILES 'dsafsdf'^ for input: ' +183: dsafsdf'syntax error +183: while parsing: Parse Error: dsafsdf +183: [11:06:25] [11:06:25] Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +183: SMILES Parse Error: check for mistakes around position SMILES Parse Error: +183: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +183: 1 Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +183: : +183: [11:06:25] dsafsdf +183: [11:06:25] ^ +183: [11:06:25] SMILES Parse Error: syntax error while parsing: dsafsdf +183: [11:06:25] SMILES Parse Error: check for mistakes around position 1: +183: [11:06:25] dsafsdf +183: [11:06:25] ^ +183: [11:06:25] SMILES Parse Error: Failed parsing SMILES 'dsafsdf'[11:06:25] SMILES Parse Error: syntax error while parsing: dsafsdf +183: [11:06:25] SMILES Parse Error: check for mistakes around position 1: +183: [11:06:25] dsafsdf +183: [11:06:25] ^ +183: [11:06:25] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +183: [11:06:25] SMILES Parse Error: syntax error while parsing: dsafsdf +183: [11:06:25] SMILES Parse Error: check for mistakes around position 1: +183: [11:06:25] dsafsdf +183: [11:06:25] ^ +183: [11:06:25] SMILES Parse Error: syntax error while parsing: dsafsdf +183: [11:06:25] SMILES Parse Error: check for mistakes around position 1[11:06:25] for input: 'dsafsdf'SMILES: +183: Parse Error: +183: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +183: [11:06:25] SMILES Parse Error: syntax error while parsing: dsafsdf +183: [11:06:25] SMILES Parse Error: check for mistakes around position 1: +183: [11:06:25] dsafsdf +183: [11:06:25] ^ +183: [11:06:25] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +183: [11:06:25] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +183: [11:06:25] dsafsdf +183: [11:06:25] ^ +183: [11:06:25] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +183: [11:06:25] SMILES Parse Error: syntax error while parsing: dsafsdf +183: [11:06:25] SMILES Parse Error: check for mistakes around position 1: +183: [11:06:25] dsafsdf +183: [11:06:25] ^ +183: [11:06:25] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +183: +183: [11:06:25] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +183: [11:06:25] SMILES Parse Error: syntax error while parsing: dsafsdf +183: [11:06:25] SMILES Parse Error: check for mistakes around position 1: +183: [11:06:25] dsafsdf +183: [11:06:25] ^ +183: [11:06:25] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +183: [11:06:25] SMILES Parse Error: syntax error while parsing: dsafsdf +183: [11:06:25] SMILES Parse Error: check for mistakes around position 1: +183: [11:06:25] dsafsdf +183: [11:06:25] ^ +183: [11:06:25] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +183: Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +183: [11:06:25] SMILES Parse Error: syntax error while parsing: dsafsdf +183: [11:06:25] SMILES Parse Error: check for mistakes around position 1: +183: [11:06:25] dsafsdf +183: [11:06:25] ^ +183: [11:06:25] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +183: [11:06:25] SMILES Parse Error: syntax error while parsing: dsafsdf +183: [11:06:25] SMILES Parse Error: check for mistakes around position 1: +183: [11:06:25] dsafsdf +183: [11:06:25] ^ +183: [11:06:25] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +183: [11:06:25] SMILES Parse Error: syntax error while parsing: dsafsdf +183: [11:06:25] SMILES Parse Error: check for mistakes around position 1: +183: [11:06:25] dsafsdf +183: [11:06:25] ^ +183: [11:06:25] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +183: [11:06:25] ^ +183: [11:06:25] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +183: [11:06:25] SMILES Parse Error: syntax error while parsing: dsafsdf +183: [11:06:25] SMILES Parse Error: check for mistakes around position 1: +183: [11:06:25] dsafsdf +183: [11:06:25] ^ +183: [11:06:25] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +183: [11:06:25] SMILES Parse Error: syntax error while parsing: dsafsdf +183: [11:06:25] SMILES Parse Error: check for mistakes around position 1: +183: [11:06:25] dsafsdf +183: [11:06:25] ^ +183: [11:06:25] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +183: [11:06:25] SMILES Parse Error: syntax error while parsing: dsafsdf +183: [11:06:25] SMILES Parse Error: check for mistakes around position 1: +183: [11:06:25] dsafsdf +183: [11:06:25] ^ +183: [11:06:25] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +183: [11:06:25] SMILES Parse Error: syntax error while parsing: dsafsdf +183: [11:06:25] SMILES Parse Error: check for mistakes around position 1: +183: [11:06:25] dsafsdf +183: [11:06:25] ^ +183: [11:06:25] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +183: [11:06:25] SMILES Parse Error: syntax error while parsing: dsafsdf +183: [11:06:25] SMILES Parse Error: check for mistakes around position 1: +183: [11:06:25] dsafsdf +183: [11:06:25] ^ +183: [11:06:25] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +183: [11:06:25] SMILES Parse Error: syntax error while parsing: dsafsdf +183: [11:06:25] SMILES Parse Error: check for mistakes around position 1: +183: [11:06:25] dsafsdf +183: [11:06:25] ^ +183: [11:06:25] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +183: [11:06:25] SMILES Parse Error: syntax error while parsing: dsafsdf +183: [11:06:25] SMILES Parse Error: check for mistakes around position 1: +183: [11:06:25] dsafsdf +183: [11:06:25] ^ +183: [11:06:25] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +183: [11:06:25] SMILES Parse Error: syntax error while parsing: dsafsdf +183: [11:06:25] SMILES Parse Error: check for mistakes around position 1: +183: [11:06:25] dsafsdf +183: [11:06:25] ^ +183: [11:06:25] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +183: [11:06:25] SMILES Parse Error: syntax error while parsing: dsafsdf +183: [11:06:25] SMILES Parse Error: check for mistakes around position 1: +183: [11:06:25] dsafsdf +183: [11:06:25] ^ +183: [11:06:25] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +183: [11:06:25] SMILES Parse Error: syntax error while parsing: dsafsdf +183: [11:06:25] SMILES Parse Error: check for mistakes around position 1: +183: [11:06:25] dsafsdf +183: [11:06:25] ^ +183: [11:06:25] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +183: [11:06:25] SMILES Parse Error: syntax error while parsing: dsafsdf +183: [11:06:25] SMILES Parse Error: check for mistakes around position 1: +183: [11:06:25] dsafsdf +183: [11:06:25] ^ +183: [11:06:25] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +183: [11:06:25] SMILES Parse Error: syntax error while parsing: dsafsdf +183: [11:06:25] SMILES Parse Error: check for mistakes around position 1: +183: [11:06:25] dsafsdf +183: [11:06:25] ^ +183: [11:06:25] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +183: [11:06:25] SMILES Parse Error: syntax error while parsing: dsafsdf +183: [11:06:25] SMILES Parse Error: check for mistakes around position 1: +183: [11:06:25] dsafsdf +183: [11:06:25] ^ +183: [11:06:25] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +176/238 Test #187: testRGroupDecompInternals .............. Passed 0.04 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 -177/238 Test #148: pyDistGeomHelpers ...................... Passed 19.24 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 +183: [11:06:25] SMILES Parse Error: syntax error while parsing: dsafsdf +183: [11:06:25] SMILES Parse Error: check for mistakes around position 1: +183: [11:06:25] dsafsdf +183: [11:06:25] ^ +183: [11:06:25] SMILES Parse Error: syntax error while parsing: dsafsdf +183: [11:06:25] SMILES Parse Error: check for mistakes around position 1: +183: [11:06:25] [11:06:25] [11:06:25] SMILES Parse Error: syntax error while parsing: dsafsdf +183: SMILESdsafsdf Parse Error: [11:06:25] +183: [11:06:25] ^ +183: SMILES Parse Error: syntax error while parsing: dsafsdf +183: [11:06:25] SMILES Parse Error: check for mistakes around position 1: +183: [11:06:25] dsafsdf +183: [11:06:25] ^ +183: [11:06:25] SMILES Parse Error: syntax error while parsing: dsafsdf +183: [11:06:25] SMILES Parse Error: check for mistakes around position 1: +183: [11:06:25] Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +183: SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf'[11:06:25] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +183: +183: [11:06:25] SMILES Parse Error: syntax error while parsing: dsafsdf +183: [11:06:25] SMILES Parse Error: check for mistakes around position 1: +183: [11:06:25] dsafsdf +183: [11:06:25] ^ +183: [11:06:25] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +183: [11:06:25] SMILES Parse Error: syntax error while parsing: dsafsdf +183: [11:06:25] SMILES Parse Error: check for mistakes around position 1: +183: [11:06:25] SMILES Parse Error: syntax error while parsing: dsafsdf +183: [11:06:25] SMILES Parse Error: check for mistakes around position 1: +183: [11:06:25] dsafsdf +183: [11:06:25] ^ +183: [11:06:25] SMILES Parse Error: [11:06:25] [11:06:25] SMILES Parse Error: SMILES Parse Error: syntax error while parsing: Failed parsing SMILES 'dsafsdf'[11:06:25] [11:06:25] dsafsdf +183: [11:06:25] ^[11:06:25] SMILES Parse Error: SMILES Parse Error: check for mistakes around position +183: 1 for input: 'dsafsdf' +183: : +183: syntax errorsyntax error while parsing: dsafsdfdsafsdf +183: [11:06:25] SMILES Parse Error: check for mistakes around position 1: while parsing: +183: [11:06:25] SMILES Parse Error: check for mistakes around position 1: +183: [11:06:25] dsafsdf +183: [11:06:25] ^ +183: dsafsdf +183: [11:06:25] SMILES Parse Error: check for mistakes around position [11:06:25] SMILES Parse Error: Failed parsing SMILES 'dsafsdf'1 +183: [11:06:25] : +183: [11:06:25] dsafsdf +183: [11:06:25] ^ +183: SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: '[11:06:25] [11:06:25] for input: '[11:06:25] [11:06:25] dsafsdfdsafsdfSMILESSMILES Parse Error: 'dsafsdfdsafsdf' +183: Parse Error: [11:06:25] syntax error^ +183: Failed parsing SMILES 'dsafsdf' +183: [11:06:25] +183: [11:06:25] while parsing: SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +183: dsafsdf +183: [11:06:25] SMILES Parse Error: check for mistakes around position 1: +183: [11:06:25] dsafsdf +183: [11:06:25] ^ +183: for input: 'dsafsdf' +183: [11:06:25] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +183: [11:06:25] SMILES Parse Error: syntax error while parsing: dsafsdf +183: [11:06:25] SMILES Parse Error: check for mistakes around position 1: +183: [11:06:25] dsafsdf +183: [11:06:25] [11:06:25] SMILES Parse Error: syntax error while parsing: dsafsdf +183: [11:06:25] SMILES Parse Error: check for mistakes around position [11:06:25] +183: SMILES Parse Error: syntax error while parsing: dsafsdf +183: ^[11:06:25] +183: [11:06:25] SMILES Parse Error: check for mistakes around position 1: +183: SMILES Parse Error: ^ +183: syntax error while parsing: [11:06:25] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf[11:06:25] dsafsdf +183: [11:06:25] SMILES Parse Error: check for mistakes around position 1:' +183: [11:06:25] dsafsdf +183: [11:06:25] dsafsdf +183: [11:06:25] +183: [11:06:25] SMILES[11:06:25] ^ +183: Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +183: 1: +183: [11:06:25] dsafsdf +183: [11:06:25] ^ +183: [11:06:25] SMILES Parse Error: syntax error while parsing: SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +183: [11:06:25] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +183: [11:06:25] SMILES Parse Error: syntax error while parsing: dsafsdf +183: [11:06:25] SMILES Parse Error: check for mistakes around position 1: +183: [11:06:25] dsafsdf +183: [11:06:25] ^ +183: [11:06:25] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +183: [11:06:25] SMILES Parse Error: syntax error while parsing: dsafsdf +183: [11:06:25] SMILES Parse Error: check for mistakes around position 1: +183: [11:06:25] dsafsdf +183: [11:06:25] ^ +183: [11:06:25] SMILES Parse Error: [11:06:25] ^ +183: [11:06:25] [11:06:25] Failed parsing SMILES 'dsafsdf'[11:06:25] for input: 'dsafsdf'SMILES Parse Error: syntax error while parsing: dsafsdf +183: +183: [11:06:25] SMILES Parse Error: check for mistakes around position SMILES Parse Error: dsafsdfsyntax error while parsing: dsafsdf +183: [11:06:25] SMILES Parse Error: SMILES Parse Error: check for mistakes around position 1: +183: +183: dsafsdf +183: [11:06:25] syntax error while parsing: dsafsdf +183: 1[11:06:25] [11:06:25] [11:06:25] ^ +183: dsafsdf +183: [11:06:25] [11:06:25] SMILES Parse Error: check for mistakes around position 1: +183: [11:06:25] SMILES Parse Error: ^syntax error while parsing: dsafsdf +183: [11:06:25] SMILES Parse Error: check for mistakes around position 1: +183: [11:06:25] [11:06:25] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf[11:06:25] :SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: ' +183: +183: [11:06:25] dsafsdf +183: dsafsdfdsafsdf +183: [11:06:25] ^ +183: '[11:06:25] SMILES Parse Error: check for mistakes around position SMILES +183: dsafsdf Parse Error: 1': +183: +183: [11:06:25] dsafsdfFailed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +183: +183: [11:06:25] ^ +183: [11:06:25] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +183: [11:06:25] SMILES Parse Error: syntax error while parsing: dsafsdf +183: [11:06:25] SMILES Parse Error: check for mistakes around position 1: +183: [11:06:25] dsafsdf +183: [11:06:25] ^ +183: [11:06:25] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +183: [11:06:25] SMILES Parse Error: syntax error while parsing: dsafsdf +183: [11:06:25] SMILES Parse Error: check for mistakes around position 1: +183: [11:06:25] dsafsdf +183: [11:06:25] ^ +183: [11:06:25] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +183: [11:06:25] [11:06:25] SMILES Parse Error: syntax error while parsing: dsafsdf +183: [11:06:25] SMILES Parse Error: check for mistakes around position 1: +183: [11:06:25] dsafsdf +183: [11:06:25] ^ +183: [11:06:25] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +183: [11:06:25] SMILES Parse Error: syntax error while parsing: dsafsdf +183: [11:06:25] SMILES Parse Error: check for mistakes around position 1: +183: [11:06:25] dsafsdf +183: [11:06:25] ^ +183: [11:06:25] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +183: [11:06:25] SMILES Parse Error: syntax error while parsing: dsafsdf +183: [11:06:25] SMILES Parse Error: check for mistakes around position 1: +183: [11:06:25] dsafsdf +183: [11:06:25] ^ +183: [11:06:25] SMILES +183: [11:06:25] ^ +183: Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +183: [11:06:25] SMILES[11:06:25] SMILES Parse Error: syntax error while parsing: dsafsdf +183: [11:06:25] SMILES Parse Error: check for mistakes around position 1: +183: [11:06:25] Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +183: dsafsdf +183: [11:06:25] ^ +183: SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf'[11:06:25] [11:06:25] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf'[11:06:25] ^ +183: +183: SMILES Parse Error: syntax error while parsing: dsafsdf +183: [11:06:25] SMILES Parse Error: check for mistakes around position 1: +183: [11:06:25] dsafsdf +183: [11:06:25] ^ +183: +183: [11:06:25] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +183: [11:06:25] SMILES Parse Error: syntax error while parsing: dsafsdf +183: [11:06:25] SMILES Parse Error: check for mistakes around position 1: +183: [11:06:25] dsafsdf +183: [11:06:25] ^ +183: [11:06:25] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +183: [11:06:25] SMILES Parse Error: syntax error while parsing: dsafsdf +183: [11:06:25] SMILES Parse Error: check for mistakes around position 1[11:06:25] SMILES Parse Error: syntax error while parsing: dsafsdf +183: [11:06:25] SMILES Parse Error: check for mistakes around position 1: +183: [11:06:25] dsafsdf +183: [11:06:25] ^ +183: : +183: [11:06:25] [11:06:25] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +183: SMILES Parse Error: syntax error while parsing: dsafsdf +183: [11:06:25] SMILES Parse Error: check for mistakes around position 1: +183: [11:06:25] [11:06:25] dsafsdf +183: [11:06:25] ^ +183: dsafsdf +183: [11:06:25] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +183: [11:06:25] ^ +183: [11:06:25] SMILES Parse Error: syntax error while parsing: dsafsdf +183: [11:06:25] SMILES Parse Error: check for mistakes around position 1: +183: [11:06:25] dsafsdf +183: [11:06:25] [11:06:25] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +183: [11:06:25] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +183: [11:06:25] SMILES Parse Error: syntax error while parsing: dsafsdf +183: [11:06:25] SMILES Parse Error: check for mistakes around position 1: +183: [11:06:25] dsafsdf +183: [11:06:25] ^ +183: [11:06:25] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +183: [11:06:25] SMILES Parse Error: syntax error while parsing: dsafsdf +183: [11:06:25] SMILES Parse Error: check for mistakes around position 1: +183: [11:06:25] dsafsdf +183: [11:06:25] ^ +183: [11:06:25] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +183: ^ +183: [11:06:25] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +183: [11:06:25] SMILES Parse Error: syntax error while parsing: dsafsdf +183: [11:06:25] SMILES Parse Error: check for mistakes around position 1: +183: [11:06:25] dsafsdf +183: [11:06:25] ^ +183: [11:06:25] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +183: [11:06:25] SMILES Parse Error: syntax error while parsing: dsafsdf +183: [11:06:25] SMILES Parse Error: check for mistakes around position 1: +183: [11:06:25] dsafsdf +183: [11:06:25] ^ +183: [11:06:25] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +183: [11:06:25] SMILES Parse Error: syntax error while parsing: dsafsdf +183: [11:06:25] SMILES Parse Error: check for mistakes around position 1: +183: [11:06:25] dsafsdf +183: [11:06:25] ^ +183: [11:06:25] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +183: [11:06:25] SMILES Parse Error: syntax error while parsing: dsafsdf +183: [11:06:25] SMILES Parse Error: check for mistakes around position 1: +183: [11:06:25] dsafsdf +183: [11:06:25] ^ +183: [11:06:25] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +183: [11:06:25] SMILES Parse Error: syntax error while parsing: dsafsdf +183: [11:06:25] SMILES Parse Error: check for mistakes around position 1: +183: [11:06:25] dsafsdf +183: [11:06:25] ^ +183: [11:06:25] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +183: [11:06:25] SMILES Parse Error: syntax error while parsing: dsafsdf +183: [11:06:25] SMILES Parse Error: check for mistakes around position 1: +183: [11:06:25] dsafsdf +183: [11:06:25] ^ +183: [11:06:25] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +183: [11:06:25] SMILES Parse Error: syntax error while parsing: dsafsdf +183: [11:06:25] SMILES Parse Error: check for mistakes around position 1: +183: [11:06:25] dsafsdf +183: [11:06:25] ^ +183: [11:06:25] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +183: [11:06:25] SMILES Parse Error: syntax error while parsing: dsafsdf +183: [11:06:25] SMILES Parse Error: check for mistakes around position 1: +183: [11:06:25] dsafsdf +183: [11:06:25] ^ +183: [11:06:25] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +183: [11:06:25] SMILES Parse Error: syntax error while parsing: dsafsdf +183: [11:06:25] SMILES Parse Error: check for mistakes around position 1: +183: [11:06:25] dsafsdf +183: [11:06:25] ^ +183: [11:06:25] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +183: [11:06:25] SMILES Parse Error: syntax error while parsing: dsafsdf +183: [11:06:25] SMILES Parse Error: check for mistakes around position 1: +183: [11:06:25] dsafsdf +183: [11:06:25] ^ +183: [11:06:25] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +183: [11:06:25] SMILES Parse Error: syntax error while parsing: dsafsdf +183: [11:06:25] SMILES Parse Error: check for mistakes around position 1: +183: [11:06:25] dsafsdf +183: [11:06:25] ^ +183: [11:06:25] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +183: [11:06:25] SMILES Parse Error: syntax error while parsing: dsafsdf +183: [11:06:25] SMILES Parse Error: check for mistakes around position 1: +183: [11:06:25] dsafsdf +183: [11:06:25] ^ +183: [11:06:25] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +183: [11:06:25] SMILES Parse Error: syntax error while parsing: dsafsdf +183: [11:06:25] SMILES Parse Error: check for mistakes around position 1: +183: [11:06:25] dsafsdf +183: [11:06:25] ^ +183: [11:06:25] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +183: [11:06:25] SMILES Parse Error: syntax error while parsing: dsafsdf +183: [11:06:25] SMILES Parse Error: check for mistakes around position 1: +183: [11:06:25] dsafsdf +183: [11:06:25] ^ +183: [11:06:25] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +183: [11:06:25] SMILES Parse Error: syntax error while parsing: dsafsdf +183: [11:06:25] SMILES Parse Error: check for mistakes around position 1: +183: [11:06:25] dsafsdf +183: [11:06:25] ^ +183: [11:06:25] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +183: [11:06:25] SMILES Parse Error: syntax error while parsing: dsafsdf +183: [11:06:25] SMILES Parse Error: check for mistakes around position 1: +183: [11:06:25] dsafsdf +183: [11:06:25] ^ +183: [11:06:25] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +183: [11:06:25] SMILES Parse Error: syntax error while parsing: dsafsdf +183: [11:06:25] SMILES Parse Error: check for mistakes around position 1: +183: [11:06:25] dsafsdf +183: [11:06:25] ^ +183: [11:06:25] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +183: [11:06:25] SMILES Parse Error: syntax error while parsing: dsafsdf +183: [11:06:25] SMILES Parse Error: check for mistakes around position 1: +183: [11:06:25] dsafsdf +183: [11:06:25] ^ +183: [11:06:25] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +183: [11:06:25] SMILES Parse Error: syntax error while parsing: dsafsdf +183: [11:06:25] SMILES Parse Error: check for mistakes around position 1: +183: [11:06:25] dsafsdf +183: [11:06:25] ^ +183: [11:06:25] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +183: [11:06:25] SMILES Parse Error: syntax error while parsing: dsafsdf +183: [11:06:25] SMILES Parse Error: check for mistakes around position 1: +183: [11:06:25] dsafsdf +183: [11:06:25] ^ +183: [11:06:25] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +183: [11:06:25] SMILES Parse Error: syntax error while parsing: dsafsdf +183: [11:06:25] SMILES Parse Error: check for mistakes around position 1: +183: [11:06:25] dsafsdf +183: [11:06:25] ^ +183: [11:06:25] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +183: [11:06:25] SMILES Parse Error: syntax error while parsing: dsafsdf +183: [11:06:25] SMILES Parse Error: check for mistakes around position 1: +183: [11:06:25] dsafsdf +183: [11:06:25] ^ +183: [11:06:25] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +183: [11:06:25] SMILES Parse Error: syntax error while parsing: dsafsdf +183: [11:06:25] SMILES Parse Error: check for mistakes around position 1: +183: [11:06:25] dsafsdf +183: [11:06:25] ^ +183: [11:06:25] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +183: [11:06:25] SMILES Parse Error: syntax error while parsing: dsafsdf +183: [11:06:25] SMILES Parse Error: check for mistakes around position 1: +183: [11:06:25] dsafsdf +183: [11:06:25] ^ +183: [11:06:25] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +183: [11:06:25] SMILES Parse Error: syntax error while parsing: dsafsdf +183: [11:06:25] SMILES Parse Error: check for mistakes around position 1: +183: [11:06:25] dsafsdf +183: [11:06:25] ^ +183: [11:06:25] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +183: [11:06:25] SMILES Parse Error: syntax error while parsing: dsafsdf +183: [11:06:25] SMILES Parse Error: check for mistakes around position 1: +183: [11:06:25] dsafsdf +183: [11:06:25] ^ +183: [11:06:25] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +183: [11:06:25] SMILES Parse Error: syntax error while parsing: dsafsdf +183: [11:06:25] SMILES Parse Error: check for mistakes around position 1: +183: [11:06:25] dsafsdf +183: [11:06:25] ^ +183: [11:06:25] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +183: [11:06:25] SMILES Parse Error: syntax error while parsing: dsafsdf +183: [11:06:25] SMILES Parse Error: check for mistakes around position 1: +183: [11:06:25] dsafsdf +183: [11:06:25] ^ +183: [11:06:25] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +183: [11:06:25] SMILES Parse Error: syntax error while parsing: dsafsdf +183: [11:06:25] SMILES Parse Error: check for mistakes around position 1: +183: [11:06:25] dsafsdf +183: [11:06:25] ^ +183: [11:06:25] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +183: [11:06:25] SMILES Parse Error: syntax error while parsing: dsafsdf +183: [11:06:25] SMILES Parse Error: check for mistakes around position 1: +183: [11:06:25] dsafsdf +183: [11:06:25] ^ +183: [11:06:25] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +183: [11:06:25] SMILES Parse Error: syntax error while parsing: dsafsdf +183: [11:06:25] SMILES Parse Error: check for mistakes around position 1: +183: [11:06:25] dsafsdf +183: [11:06:25] ^ +183: [11:06:25] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +183: [11:06:25] SMILES Parse Error: syntax error while parsing: dsafsdf +183: [11:06:25] SMILES Parse Error: check for mistakes around position 1: +183: [11:06:25] dsafsdf +183: [11:06:25] ^ +183: [11:06:25] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +183: [11:06:25] SMILES Parse Error: syntax error while parsing: dsafsdf +183: [11:06:25] SMILES Parse Error: check for mistakes around position 1: +183: [11:06:25] dsafsdf +183: [11:06:25] ^ +183: [11:06:25] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +183: [11:06:25] SMILES Parse Error: syntax error while parsing: dsafsdf +183: [11:06:25] SMILES Parse Error: check for mistakes around position 1: +183: [11:06:25] dsafsdf +183: [11:06:25] ^ +183: [11:06:25] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +183: [11:06:25] SMILES Parse Error: syntax error while parsing: dsafsdf +183: [11:06:25] SMILES Parse Error: check for mistakes around position 1: +183: [11:06:25] dsafsdf +183: [11:06:25] ^ +183: [11:06:25] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +183: [11:06:25] SMILES Parse Error: syntax error while parsing: dsafsdf +183: [11:06:25] SMILES Parse Error: check for mistakes around position 1: +183: [11:06:25] dsafsdf +183: [11:06:25] ^ +183: [11:06:25] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +183: [11:06:25] SMILES Parse Error: syntax error while parsing: dsafsdf +183: [11:06:25] SMILES Parse Error: check for mistakes around position 1: +183: [11:06:25] dsafsdf +183: [11:06:25] ^ +183: [11:06:25] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +183: [11:06:25] SMILES Parse Error: syntax error while parsing: dsafsdf +183: [11:06:25] SMILES Parse Error: check for mistakes around position 1: +183: [11:06:25] dsafsdf +183: [11:06:25] ^ +183: [11:06:25] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +183: [11:06:25] SMILES Parse Error: syntax error while parsing: dsafsdf +183: [11:06:25] SMILES Parse Error: check for mistakes around position 1: +183: [11:06:25] dsafsdf +183: [11:06:25] ^ +183: [11:06:25] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +183: [11:06:25] SMILES Parse Error: syntax error while parsing: dsafsdf +183: [11:06:25] SMILES Parse Error: check for mistakes around position 1: +183: [11:06:25] dsafsdf +183: [11:06:25] ^ +183: [11:06:25] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +183: [11:06:25] SMILES Parse Error: syntax error while parsing: dsafsdf +183: [11:06:25] SMILES Parse Error: check for mistakes around position 1: +183: [11:06:25] dsafsdf +183: [11:06:25] ^ +183: [11:06:25] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +183: [11:06:25] SMILES Parse Error: syntax error while parsing: dsafsdf +183: [11:06:25] SMILES Parse Error: check for mistakes around position 1: +183: [11:06:25] dsafsdf +183: [11:06:25] ^ +183: [11:06:25] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +183: [11:06:25] SMILES Parse Error: syntax error while parsing: dsafsdf +183: [11:06:25] SMILES Parse Error: check for mistakes around position 1: +183: [11:06:25] dsafsdf +183: [11:06:25] ^ +183: [11:06:25] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +183: [11:06:25] SMILES Parse Error: syntax error while parsing: dsafsdf +183: [11:06:25] SMILES Parse Error: check for mistakes around position 1: +183: [11:06:25] dsafsdf +183: [11:06:25] ^ +183: [11:06:25] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +183: [11:06:25] SMILES Parse Error: syntax error while parsing: dsafsdf +183: [11:06:25] SMILES Parse Error: check for mistakes around position 1: +183: [11:06:25] dsafsdf +183: [11:06:25] ^ +183: [11:06:25] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +183: [11:06:25] SMILES Parse Error: syntax error while parsing: dsafsdf +183: [11:06:25] SMILES Parse Error: check for mistakes around position 1: +183: [11:06:25] dsafsdf +183: [11:06:25] ^ +183: [11:06:25] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +183: [11:06:25] SMILES Parse Error: syntax error while parsing: dsafsdf +183: [11:06:25] SMILES Parse Error: check for mistakes around position 1: +183: [11:06:25] dsafsdf +183: [11:06:25] ^ +183: [11:06:25] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +183: [11:06:25] SMILES Parse Error: syntax error while parsing: dsafsdf +183: [11:06:25] SMILES Parse Error: check for mistakes around position 1: +183: [11:06:25] dsafsdf +183: [11:06:25] ^ +183: [11:06:25] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +183: [11:06:25] SMILES Parse Error: syntax error while parsing: dsafsdf +183: [11:06:25] SMILES Parse Error: check for mistakes around position 1: +183: [11:06:25] dsafsdf +183: [11:06:25] ^ +183: [11:06:25] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +183: [11:06:25] SMILES Parse Error: syntax error while parsing: dsafsdf +183: [11:06:25] SMILES Parse Error: check for mistakes around position 1: +183: [11:06:25] dsafsdf +183: [11:06:25] ^ +183: [11:06:25] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +183: [11:06:25] SMILES Parse Error: syntax error while parsing: dsafsdf +183: [11:06:25] SMILES Parse Error: check for mistakes around position 1: +183: [11:06:25] dsafsdf +183: [11:06:25] ^ +183: [11:06:25] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +183: [11:06:25] SMILES Parse Error: syntax error while parsing: dsafsdf +183: [11:06:25] SMILES Parse Error: check for mistakes around position 1: +183: [11:06:25] dsafsdf +183: [11:06:25] ^ +183: [11:06:25] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +183: [11:06:25] SMILES Parse Error: syntax error while parsing: dsafsdf +183: [11:06:25] SMILES Parse Error: check for mistakes around position 1: +183: [11:06:25] dsafsdf +183: [11:06:25] ^ +183: [11:06:25] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +183: [11:06:25] SMILES Parse Error: syntax error while parsing: dsafsdf +183: [11:06:25] SMILES Parse Error: check for mistakes around position 1: +183: [11:06:25] dsafsdf +183: [11:06:25] ^ +183: [11:06:25] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +183: [11:06:25] SMILES Parse Error: syntax error while parsing: dsafsdf +183: [11:06:25] SMILES Parse Error: check for mistakes around position 1: +183: [11:06:25] dsafsdf +183: [11:06:25] ^ +183: [11:06:25] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +183: [11:06:25] SMILES Parse Error: syntax error while parsing: dsafsdf +183: [11:06:25] SMILES Parse Error: check for mistakes around position 1: +183: [11:06:25] dsafsdf +183: [11:06:25] ^ +183: [11:06:25] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +183: [11:06:25] SMILES Parse Error: syntax error while parsing: dsafsdf +183: [11:06:25] SMILES Parse Error: check for mistakes around position 1: +183: [11:06:25] dsafsdf +183: [11:06:25] ^ +183: [11:06:25] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +183: [11:06:25] SMILES Parse Error: syntax error while parsing: dsafsdf +183: [11:06:25] SMILES Parse Error: check for mistakes around position 1: +183: [11:06:25] dsafsdf +183: [11:06:25] ^ +183: [11:06:25] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +183: [11:06:25] SMILES Parse Error: syntax error while parsing: dsafsdf +183: [11:06:25] SMILES Parse Error: check for mistakes around position 1: +183: [11:06:25] dsafsdf +183: [11:06:25] ^ +183: [11:06:25] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +183: [11:06:25] SMILES Parse Error: syntax error while parsing: dsafsdf +183: [11:06:25] SMILES Parse Error: check for mistakes around position 1: +183: [11:06:25] dsafsdf +183: [11:06:25] ^ +183: [11:06:25] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +183: [11:06:25] SMILES Parse Error: syntax error while parsing: dsafsdf +183: [11:06:25] SMILES Parse Error: check for mistakes around position 1: +183: [11:06:25] dsafsdf +183: [11:06:25] ^ +183: [11:06:25] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +183: [11:06:25] SMILES Parse Error: syntax error while parsing: dsafsdf +183: [11:06:25] SMILES Parse Error: check for mistakes around position 1: +183: [11:06:25] dsafsdf +183: [11:06:25] ^ +183: [11:06:25] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +183: [11:06:25] SMILES Parse Error: syntax error while parsing: dsafsdf +183: [11:06:25] SMILES Parse Error: check for mistakes around position 1: +183: [11:06:25] dsafsdf +183: [11:06:25] ^ +183: [11:06:25] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +183: [11:06:25] SMILES Parse Error: syntax error while parsing: dsafsdf +183: [11:06:25] SMILES Parse Error: check for mistakes around position 1: +183: [11:06:25] dsafsdf +183: [11:06:25] ^ +183: [11:06:25] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +183: [11:06:25] SMILES Parse Error: syntax error while parsing: dsafsdf +183: [11:06:25] SMILES Parse Error: check for mistakes around position 1: +183: [11:06:25] dsafsdf +183: [11:06:25] ^ +183: [11:06:25] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +183: [11:06:25] SMILES Parse Error: syntax error while parsing: dsafsdf +183: [11:06:25] SMILES Parse Error: check for mistakes around position 1: +183: [11:06:25] dsafsdf +183: [11:06:25] ^ +183: [11:06:25] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +183: [11:06:25] SMILES Parse Error: syntax error while parsing: dsafsdf +183: [11:06:25] SMILES Parse Error: check for mistakes around position 1: +183: [11:06:25] dsafsdf +183: [11:06:25] ^ +183: [11:06:25] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +183: [11:06:25] SMILES Parse Error: syntax error while parsing: dsafsdf +183: [11:06:25] SMILES Parse Error: check for mistakes around position 1: +183: [11:06:25] dsafsdf +183: [11:06:25] ^ +183: [11:06:25] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +183: [11:06:25] SMILES Parse Error: syntax error while parsing: dsafsdf +183: [11:06:25] SMILES Parse Error: check for mistakes around position 1: +183: [11:06:25] dsafsdf +183: [11:06:25] ^ +183: [11:06:25] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +183: [11:06:25] SMILES Parse Error: syntax error while parsing: dsafsdf +183: [11:06:25] SMILES Parse Error: check for mistakes around position 1: +183: [11:06:25] dsafsdf +183: [11:06:25] ^ +183: [11:06:25] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +183: [11:06:25] SMILES Parse Error: syntax error while parsing: dsafsdf +183: [11:06:25] SMILES Parse Error: check for mistakes around position 1: +183: [11:06:25] dsafsdf +183: [11:06:25] ^ +183: [11:06:25] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +183: [11:06:25] SMILES Parse Error: syntax error while parsing: dsafsdf +183: [11:06:25] SMILES Parse Error: check for mistakes around position 1: +183: [11:06:25] dsafsdf +183: [11:06:25] ^ +183: [11:06:25] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +183: [11:06:25] SMILES Parse Error: syntax error while parsing: dsafsdf +183: [11:06:25] SMILES Parse Error: check for mistakes around position 1: +183: [11:06:25] dsafsdf +183: [11:06:25] ^ +183: [11:06:25] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +183: [11:06:25] SMILES Parse Error: syntax error while parsing: dsafsdf +183: [11:06:25] SMILES Parse Error: check for mistakes around position 1: +183: [11:06:25] dsafsdf +183: [11:06:25] ^ +183: [11:06:25] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +183: [11:06:25] SMILES Parse Error: syntax error while parsing: dsafsdf +183: [11:06:25] SMILES Parse Error: check for mistakes around position 1: +183: [11:06:25] dsafsdf +183: [11:06:25] ^ +183: [11:06:25] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +183: [11:06:25] SMILES Parse Error: syntax error while parsing: dsafsdf +183: [11:06:25] SMILES Parse Error: check for mistakes around position 1: +183: [11:06:25] dsafsdf +183: [11:06:25] ^ +183: [11:06:25] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +183: [11:06:25] SMILES Parse Error: syntax error while parsing: dsafsdf +183: [11:06:25] SMILES Parse Error: check for mistakes around position 1: +183: [11:06:25] dsafsdf +183: [11:06:25] ^ +183: [11:06:25] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +183: [11:06:25] SMILES Parse Error: syntax error while parsing: dsafsdf +183: [11:06:25] SMILES Parse Error: check for mistakes around position 1: +183: [11:06:25] dsafsdf +183: [11:06:25] ^ +183: [11:06:25] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +183: [11:06:25] SMILES Parse Error: syntax error while parsing: dsafsdf +183: [11:06:25] SMILES Parse Error: check for mistakes around position 1: +183: [11:06:25] dsafsdf +183: [11:06:25] ^ +183: [11:06:25] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +183: [11:06:25] SMILES Parse Error: syntax error while parsing: dsafsdf +183: [11:06:25] SMILES Parse Error: check for mistakes around position 1: +183: [11:06:25] dsafsdf +183: [11:06:25] ^ +183: [11:06:25] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +183: [11:06:25] SMILES Parse Error: syntax error while parsing: dsafsdf +183: [11:06:25] SMILES Parse Error: check for mistakes around position 1: +183: [11:06:25] dsafsdf +183: [11:06:25] ^ +183: [11:06:25] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +183: [11:06:25] SMILES Parse Error: syntax error while parsing: dsafsdf +183: [11:06:25] SMILES Parse Error: check for mistakes around position 1: +183: [11:06:25] dsafsdf +183: [11:06:25] ^ +183: [11:06:25] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +183: [11:06:25] SMILES Parse Error: syntax error while parsing: dsafsdf +183: [11:06:25] SMILES Parse Error: check for mistakes around position 1: +183: [11:06:25] dsafsdf +183: [11:06:25] ^ +183: [11:06:25] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +183: [11:06:25] SMILES Parse Error: syntax error while parsing: dsafsdf +183: [11:06:25] SMILES Parse Error: check for mistakes around position 1: +183: [11:06:25] dsafsdf +183: [11:06:25] ^ +183: [11:06:25] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +183: [11:06:25] SMILES Parse Error: syntax error while parsing: dsafsdf +183: [11:06:25] SMILES Parse Error: check for mistakes around position 1: +183: [11:06:25] dsafsdf +183: [11:06:25] ^ +183: [11:06:25] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +183: [11:06:25] SMILES Parse Error: syntax error while parsing: dsafsdf +183: [11:06:25] SMILES Parse Error: check for mistakes around position 1: +183: [11:06:25] dsafsdf +183: [11:06:25] ^ +183: [11:06:25] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +183: [11:06:25] SMILES Parse Error: syntax error while parsing: dsafsdf +183: [11:06:25] SMILES Parse Error: check for mistakes around position 1: +183: [11:06:25] dsafsdf +183: [11:06:25] ^ +183: [11:06:25] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +183: [11:06:25] SMILES Parse Error: syntax error while parsing: dsafsdf +183: [11:06:25] SMILES Parse Error: check for mistakes around position 1: +183: [11:06:25] dsafsdf +183: [11:06:25] ^ +183: [11:06:25] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +183: [11:06:25] SMILES Parse Error: syntax error while parsing: dsafsdf +183: [11:06:25] SMILES Parse Error: check for mistakes around position 1: +183: [11:06:25] dsafsdf +183: [11:06:25] ^ +183: [11:06:25] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +183: [11:06:25] SMILES Parse Error: syntax error while parsing: dsafsdf +183: [11:06:25] SMILES Parse Error: check for mistakes around position 1: +183: [11:06:25] dsafsdf +183: [11:06:25] ^ +183: [11:06:25] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +183: [11:06:25] SMILES Parse Error: syntax error while parsing: dsafsdf +183: [11:06:25] SMILES Parse Error: check for mistakes around position 1: +183: [11:06:25] dsafsdf +183: [11:06:25] ^ +183: [11:06:25] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +183: [11:06:25] SMILES Parse Error: syntax error while parsing: dsafsdf +183: [11:06:25] SMILES Parse Error: check for mistakes around position 1: +183: [11:06:25] dsafsdf +183: [11:06:25] ^ +183: [11:06:25] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +183: [11:06:25] SMILES Parse Error: syntax error while parsing: dsafsdf +183: [11:06:25] SMILES Parse Error: check for mistakes around position 1: +183: [11:06:25] dsafsdf +183: [11:06:25] ^ +183: [11:06:25] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +183: [11:06:25] SMILES Parse Error: syntax error while parsing: dsafsdf +183: [11:06:25] SMILES Parse Error: check for mistakes around position 1: +183: [11:06:25] dsafsdf +183: [11:06:25] ^ +183: [11:06:25] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +183: [11:06:25] SMILES Parse Error: syntax error while parsing: dsafsdf +183: [11:06:25] SMILES Parse Error: check for mistakes around position 1: +183: [11:06:25] dsafsdf +183: [11:06:25] ^ +183: [11:06:25] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +183: [11:06:25] SMILES Parse Error: syntax error while parsing: dsafsdf +183: [11:06:25] SMILES Parse Error: check for mistakes around position 1: +183: [11:06:25] dsafsdf +183: [11:06:25] ^ +183: [11:06:25] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +183: [11:06:25] SMILES Parse Error: syntax error while parsing: dsafsdf +183: [11:06:25] SMILES Parse Error: check for mistakes around position 1: +183: [11:06:25] dsafsdf +183: [11:06:25] ^ +183: [11:06:25] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +183: [11:06:25] SMILES Parse Error: syntax error while parsing: dsafsdf +183: [11:06:25] SMILES Parse Error: check for mistakes around position 1: +183: [11:06:25] dsafsdf +183: [11:06:25] ^ +183: [11:06:25] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +183: [11:06:25] SMILES Parse Error: syntax error while parsing: dsafsdf +183: [11:06:25] SMILES Parse Error: check for mistakes around position 1: +183: [11:06:25] dsafsdf +183: [11:06:25] ^ +183: [11:06:25] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +183: [11:06:25] SMILES Parse Error: syntax error while parsing: dsafsdf +183: [11:06:25] SMILES Parse Error: check for mistakes around position 1: +183: [11:06:25] dsafsdf +183: [11:06:25] ^ +183: [11:06:25] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +183: [11:06:25] SMILES Parse Error: syntax error while parsing: dsafsdf +183: [11:06:25] SMILES Parse Error: check for mistakes around position 1: +183: [11:06:25] dsafsdf +183: [11:06:25] ^ +183: [11:06:25] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +183: [11:06:25] ------------------------------------- +183: [11:06:25] Results do not depend on numThreads +173: [11:06:25] Complex queries can be slow. 150: processing 150: launch :0 150: launch :1 150: launch :2 150: launch :3 -188: Randomness seeded to: 3946715193 +173: [11:06:25] Complex queries can be slow. +173: [11:06:25] Complex queries can be slow. +188: Randomness seeded to: 3813058219 188: =============================================================================== 188: All tests passed (1475 assertions in 14 test cases) 188: -178/238 Test #188: rgroupCatchTests ....................... Passed 0.23 sec +177/238 Test #188: rgroupCatchTests ....................... Passed 0.23 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 +173: [11:06:25] Complex queries can be slow. +173: [11:06:25] Complex queries can be slow. +173: [11:06:25] Complex queries can be slow. +173: [11:06:26] Complex queries can be slow. +173: [11:06:26] Complex queries can be slow. +173: [11:06:26] Complex queries can be slow. +173: [11:06:26] Complex queries can be slow. +173: [11:06:26] Complex queries can be slow. +173: [11:06:26] Complex queries can be slow. +173: [11:06:26] Complex queries can be slow. +173: [11:06:26] Complex queries can be slow. +173: [11:06:26] Complex queries can be slow. +173: =============================================================================== +173: All tests passed (121 assertions in 17 test cases) +173: +178/238 Test #173: testSynthonSpaceSubstructureSearch ..... Passed 12.93 sec test 190 Start 190: determineBondsCatchTest 190: Test command: /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/DetermineBonds/determineBondsCatchTest 190: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/DetermineBonds 190: Test timeout computed to be: 1500 -186: bulk -183: [02:19:30] ------------------------------------- -183: [02:19:30] Results do not depend on numThreads (all same) -183: [02:19:30] ------------------------------------- -183: [02:19:30] testTautomerQueries -183: [02:19:30] Pattern fingerprints for tautomersearch aren't tautomer fingerprints, ignoring... -183: [02:19:30] ------------------------------------- -183: [02:19:30] github3881 recursive smarts with rings -179/238 Test #183: substructLibraryTest ................... Passed 4.76 sec +189: .................... +189: ---------------------------------------------------------------------- +189: Ran 20 tests in 1.220s +189: +189: OK +179/238 Test #189: pyRGroupDecomposition .................. Passed 1.43 sec test 191 Start 191: pyDetermineBonds 191: Test command: /usr/bin/python3 "/build/reproducible-path/rdkit-202503.1/Code/GraphMol/DetermineBonds/Wrap/testDetermineBonds.py" 191: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/DetermineBonds/Wrap 191: Test timeout computed to be: 1500 -190: Randomness seeded to: 347332760 +190: Randomness seeded to: 2925208004 190: =============================================================================== 190: All tests passed (5174 assertions in 7 test cases) 190: -180/238 Test #190: determineBondsCatchTest ................ Passed 0.68 sec +180/238 Test #190: determineBondsCatchTest ................ Passed 0.38 sec test 192 Start 192: molInterchangeTest1 192: Test command: /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/MolInterchange/molInterchangeTest1 192: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/MolInterchange 192: Test timeout computed to be: 1500 -192: [02:19:30] test1: basics -192: [02:19:30] done -192: [02:19:30] test2: basic writing +192: [11:06:27] test1: basics +192: [11:06:27] done +192: [11:06:27] test2: basic writing 192: {"rdkitjson":{"version":11},"defaults":{"atom":{"z":6,"impHs":0,"chg":0,"nRad":0,"isotope":0,"stereo":"unspecified"},"bond":{"bo":1,"stereo":"unspecified"}},"molecules":[{"name":"mol1 name","atoms":[{"impHs":3},{"impHs":3}],"bonds":[{"atoms":[0,1]}],"extensions":[{"name":"rdkitRepresentation","formatVersion":2,"toolkitVersion":"2025.03.1","cipRanks":[0,0]}]}]} 192: {"rdkitjson":{"version":11},"defaults":{"atom":{"z":6,"impHs":0,"chg":0,"nRad":0,"isotope":0,"stereo":"unspecified"},"bond":{"bo":1,"stereo":"unspecified"}},"molecules":[{"name":"test mol","atoms":[{"z":9},{"stereo":"cw"},{"z":17},{"z":8,"impHs":1},{"impHs":3}],"bonds":[{"atoms":[0,1]},{"atoms":[1,2]},{"atoms":[1,3]},{"atoms":[1,4]}],"extensions":[{"name":"rdkitRepresentation","formatVersion":2,"toolkitVersion":"2025.03.1","cipRanks":[3,1,4,2,0],"cipCodes":[[1,"S"]]}]}]} 192: {"rdkitjson":{"version":11},"defaults":{"atom":{"z":6,"impHs":0,"chg":0,"nRad":0,"isotope":0,"stereo":"unspecified"},"bond":{"bo":1,"stereo":"unspecified"}},"molecules":[{"name":"test mol","atoms":[{"impHs":1},{"impHs":1},{"impHs":1},{"impHs":1},{"impHs":1},{"impHs":1}],"bonds":[{"bo":2,"atoms":[0,1]},{"atoms":[1,2]},{"bo":2,"atoms":[2,3]},{"atoms":[3,4]},{"bo":2,"atoms":[4,5]},{"atoms":[5,0]}],"extensions":[{"name":"rdkitRepresentation","formatVersion":2,"toolkitVersion":"2025.03.1","aromaticAtoms":[0,1,2,3,4,5],"aromaticBonds":[0,1,2,3,4,5],"cipRanks":[0,0,0,0,0,0],"atomRings":[[0,5,4,3,2,1]]}]}]} 192: {"rdkitjson":{"version":11},"defaults":{"atom":{"z":6,"impHs":0,"chg":0,"nRad":0,"isotope":0,"stereo":"unspecified"},"bond":{"bo":1,"stereo":"unspecified"}},"molecules":[{"name":"test mol","atoms":[{"impHs":3},{"impHs":2},{},{},{"z":7,"impHs":2},{"impHs":1},{},{"impHs":3},{"z":7},{"impHs":1}],"bonds":[{"atoms":[0,1]},{"atoms":[1,2]},{"bo":2,"atoms":[2,3]},{"atoms":[3,4]},{"atoms":[3,5]},{"bo":2,"atoms":[5,6]},{"atoms":[6,7]},{"atoms":[6,8]},{"bo":2,"atoms":[8,9]},{"atoms":[9,2]}],"extensions":[{"name":"rdkitRepresentation","formatVersion":2,"toolkitVersion":"2025.03.1","aromaticAtoms":[2,3,5,6,8,9],"aromaticBonds":[2,4,5,7,8,9],"cipRanks":[0,2,4,5,8,3,7,1,9,6],"atomRings":[[2,9,8,6,5,3]]}]}]} -192: [02:19:30] done -192: [02:19:30] test3: writing conformers +192: [11:06:27] done +192: [11:06:27] test3: writing conformers 192: {"rdkitjson":{"version":11},"defaults":{"atom":{"z":6,"impHs":0,"chg":0,"nRad":0,"isotope":0,"stereo":"unspecified"},"bond":{"bo":1,"stereo":"unspecified"}},"molecules":[{"name":"example 2","atoms":[{"z":8},{"stereo":"cw"},{"z":17,"isotope":35},{"z":9},{"z":1},{"z":1}],"bonds":[{"atoms":[0,1]},{"atoms":[1,2]},{"atoms":[1,3]},{"atoms":[0,4]},{"atoms":[1,5]}],"conformers":[{"dim":2,"coords":[[-1.1988,-0.0452],[-0.3332,0.4556],[0.166,1.322],[0.5332,-0.0438],[-2.0652,0.4542],[-0.834,1.3212]]},{"dim":3,"coords":[[0.9554,-0.3743,-0.4679],[-0.3616,-0.1311,-0.0795],[-0.5097,1.6256,0.1706],[-0.5779,-0.792,1.1042],[1.5277,0.1064,0.1628],[-1.0339,-0.4346,-0.8902]]}],"extensions":[{"name":"rdkitRepresentation","formatVersion":2,"toolkitVersion":"2025.03.1","cipCodes":[[1,"S"]]},{"name":"partialCharges","generator":"RDKit","formatVersion":10,"generatorVersion":"2025.03.1","values":[-0.352,0.273,-0.055,-0.198,0.215,0.117]}]}]} -192: [02:19:30] done -192: [02:19:30] test4: writing properties +192: [11:06:27] done +192: [11:06:27] test4: writing properties 192: {"rdkitjson":{"version":11},"defaults":{"atom":{"z":6,"impHs":0,"chg":0,"nRad":0,"isotope":0,"stereo":"unspecified"},"bond":{"bo":1,"stereo":"unspecified"}},"molecules":[{"atoms":[{"impHs":3},{"impHs":3}],"bonds":[{"atoms":[0,1]}],"properties":{"foo_string":"bar","foo_int":1,"foo_double":1.2},"extensions":[{"name":"rdkitRepresentation","formatVersion":2,"toolkitVersion":"2025.03.1","cipRanks":[0,0]}]}]} -192: [02:19:30] done -192: [02:19:30] test5: writing partial charges +192: [11:06:27] done +192: [11:06:27] test5: writing partial charges 192: {"rdkitjson":{"version":11},"defaults":{"atom":{"z":6,"impHs":0,"chg":0,"nRad":0,"isotope":0,"stereo":"unspecified"},"bond":{"bo":1,"stereo":"unspecified"}},"molecules":[{"atoms":[{"impHs":3},{"z":8,"impHs":1}],"bonds":[{"atoms":[0,1]}],"extensions":[{"name":"rdkitRepresentation","formatVersion":2,"toolkitVersion":"2025.03.1","cipRanks":[0,1]},{"name":"partialCharges","generator":"RDKit","formatVersion":10,"generatorVersion":"2025.03.1","values":[0.5,-0.5]}]}]} -192: [02:19:30] testing parse options -192: [02:19:30] done -192: [02:19:30] testing github #2046: CIPRank values from JSONDataToMols are not unsigned +192: [11:06:27] testing parse options +192: [11:06:27] done +192: [11:06:27] testing github #2046: CIPRank values from JSONDataToMols are not unsigned 192: {"rdkitjson":{"version":11},"defaults":{"atom":{"z":6,"impHs":0,"chg":0,"nRad":0,"isotope":0,"stereo":"unspecified"},"bond":{"bo":1,"stereo":"unspecified"}},"molecules":[{"name":"test mol","atoms":[{"impHs":2},{"impHs":2},{"impHs":2},{"z":8},{"impHs":1,"stereo":"cw"},{"z":9}],"bonds":[{"atoms":[0,1]},{"atoms":[1,2]},{"atoms":[2,3]},{"atoms":[3,4]},{"atoms":[4,5]},{"atoms":[4,0]}],"extensions":[{"name":"rdkitRepresentation","formatVersion":2,"toolkitVersion":"2025.03.1","cipRanks":[1,0,2,4,3,5],"cipCodes":[[4,"S"]],"atomRings":[[0,1,2,3,4]]}]}]} -192: [02:19:30] done -192: [02:19:30] testing 'either' stereochemistry -192: [02:19:30] done -181/238 Test #192: molInterchangeTest1 .................... Passed 0.04 sec +192: [11:06:27] done +192: [11:06:27] testing 'either' stereochemistry +192: [11:06:27] done +181/238 Test #192: molInterchangeTest1 .................... Passed 0.02 sec test 193 Start 193: molInterchangeCatchTest 193: Test command: /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/MolInterchange/molInterchangeCatchTest 193: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/MolInterchange 193: Test timeout computed to be: 1500 -193: Randomness seeded to: 777127133 -193: [02:19:30] unrecognized bond type 12 set to zero while writing -193: [02:19:30] unrecognized bond type 0 set to zero while writing +193: Randomness seeded to: 2889416567 +193: [11:06:27] unrecognized bond type 12 set to zero while writing +193: [11:06:27] unrecognized bond type 0 set to zero while writing 193: =============================================================================== 193: All tests passed (125 assertions in 7 test cases) 193: -182/238 Test #193: molInterchangeCatchTest ................ Passed 0.05 sec +182/238 Test #193: molInterchangeCatchTest ................ Passed 0.03 sec test 194 Start 194: pyMolInterchange 194: Test command: /usr/bin/python3 "/build/reproducible-path/rdkit-202503.1/Code/GraphMol/MolInterchange/Wrap/testMolInterchange.py" 194: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/MolInterchange/Wrap 194: Test timeout computed to be: 1500 -194: .. -194: ---------------------------------------------------------------------- -194: Ran 2 tests in 0.022s -194: -194: OK 191: .s.. 191: ---------------------------------------------------------------------- -191: Ran 4 tests in 0.312s +191: Ran 4 tests in 0.172s 191: 191: OK (skipped=1) -183/238 Test #191: pyDetermineBonds ....................... Passed 0.66 sec +183/238 Test #191: pyDetermineBonds ....................... Passed 0.36 sec test 195 Start 195: testSLNParse @@ -32379,46 +32403,51 @@ 195: 3 1 H chg: 0 deg: 1 exp: N/A imp: N/A hyb: 195: 4 1 H chg: 0 deg: 1 exp: N/A imp: N/A hyb: 195: 5 1 H chg: 0 deg: 1 exp: N/A imp: N/A hyb: -184/238 Test #194: pyMolInterchange ....................... Passed 0.41 sec -test 196 - Start 196: pySLNParse - -196: Test command: /usr/bin/python3 "/build/reproducible-path/rdkit-202503.1/Code/GraphMol/SLNParse/Wrap/testSLN.py" -196: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/SLNParse/Wrap -196: Test timeout computed to be: 1500 195: Bonds: 195: 0 0->1 order: 1 195: 1 0->2 order: 1 195: 2 0->3 order: 1 195: 3 0->4 order: 1 195: 4 0->5 order: 1 -195: [02:19:30] SLN Parse Error: syntax error while parsing: CH4[I=13] -195: [02:19:30] Failed parsing SLN 'CH4[I=13]' -195: [02:19:30] SLN Parser error: Atom ID 1 appears *after* its ring closure. -195: [02:19:30] SLN Parser error: Ring closure 1 does not have a corresponding opener. -195: [02:19:30] SLN Parse Error: syntax error while parsing: CH2(C@1H2)CH2(CH2CH2C[1]H2) -195: [02:19:30] Failed parsing SLN 'CH2(C@1H2)CH2(CH2CH2C[1]H2)' -195: [02:19:30] SLN Parse Error: syntax error while parsing: CH2(CH2[1])CH2(CH2CH2CH2@1) -195: [02:19:30] Failed parsing SLN 'CH2(CH2[1])CH2(CH2CH2CH2@1)' -195: [02:19:30] SLN Parse Error: syntax error while parsing: CH4 fff -195: [02:19:30] Failed parsing SLN 'CH4 fff' -195: [02:19:30] SLN Parse Error: syntax error while parsing: C[charge=+1] foo -195: [02:19:30] Failed parsing SLN 'C[charge=+1] foo' -195: [02:19:30] Query property 'is' ignored on non-query atom -195: [02:19:30] Query property 'is' ignored on non-query atom -185/238 Test #195: testSLNParse ........................... Passed 0.03 sec +195: [11:06:27] SLN Parse Error: syntax error while parsing: CH4[I=13] +195: [11:06:27] Failed parsing SLN 'CH4[I=13]' +195: [11:06:27] SLN Parser error: Atom ID 1 appears *after* its ring closure. +195: [11:06:27] SLN Parser error: Ring closure 1 does not have a corresponding opener. +195: [11:06:27] SLN Parse Error: syntax error while parsing: CH2(C@1H2)CH2(CH2CH2C[1]H2) +195: [11:06:27] Failed parsing SLN 'CH2(C@1H2)CH2(CH2CH2C[1]H2)' +195: [11:06:27] SLN Parse Error: syntax error while parsing: CH2(CH2[1])CH2(CH2CH2CH2@1) +195: [11:06:27] Failed parsing SLN 'CH2(CH2[1])CH2(CH2CH2CH2@1)' +195: [11:06:27] SLN Parse Error: syntax error while parsing: CH4 fff +195: [11:06:27] Failed parsing SLN 'CH4 fff' +195: [11:06:27] SLN Parse Error: syntax error while parsing: C[charge=+1] foo +195: [11:06:27] Failed parsing SLN 'C[charge=+1] foo' +195: [11:06:27] Query property 'is' ignored on non-query atom +195: [11:06:27] Query property 'is' ignored on non-query atom +184/238 Test #195: testSLNParse ........................... Passed 0.03 sec +test 196 + Start 196: pySLNParse + +196: Test command: /usr/bin/python3 "/build/reproducible-path/rdkit-202503.1/Code/GraphMol/SLNParse/Wrap/testSLN.py" +196: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/SLNParse/Wrap +196: Test timeout computed to be: 1500 +194: .. +194: ---------------------------------------------------------------------- +194: Ran 2 tests in 0.008s +194: +194: OK +185/238 Test #194: pyMolInterchange ....................... Passed 0.20 sec test 197 Start 197: pyGraphMolWrap 197: Test command: /usr/bin/python3 "/build/reproducible-path/rdkit-202503.1/Code/GraphMol/Wrap/rough_test.py" 197: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/Wrap 197: Test timeout computed to be: 1500 -189: .................... -189: ---------------------------------------------------------------------- -189: Ran 20 tests in 1.150s -189: -189: OK -186/238 Test #189: pyRGroupDecomposition .................. Passed 1.49 sec +196: .. +196: ---------------------------------------------------------------------- +196: Ran 2 tests in 0.006s +196: +196: OK +186/238 Test #196: pySLNParse ............................. Passed 0.20 sec test 198 Start 198: pyTestConformerWrap @@ -32430,67 +32459,192 @@ 198: Ran 6 tests in 0.009s 198: 198: OK -196: .. -196: ---------------------------------------------------------------------- -196: Ran 2 tests in 0.018s -196: -196: OK -187/238 Test #198: pyTestConformerWrap .................... Passed 0.22 sec +187/238 Test #198: pyTestConformerWrap .................... Passed 0.24 sec test 199 Start 199: pyTestTrajectory 199: Test command: /usr/bin/python3 "/build/reproducible-path/rdkit-202503.1/Code/GraphMol/Wrap/testTrajectory.py" 199: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/Wrap 199: Test timeout computed to be: 1500 -188/238 Test #196: pySLNParse ............................. Passed 0.41 sec -test 200 - Start 200: pyTestSGroups - -200: Test command: /usr/bin/python3 "/build/reproducible-path/rdkit-202503.1/Code/GraphMol/Wrap/testSGroups.py" -200: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/Wrap -200: Test timeout computed to be: 1500 -197: ..............[02:19:31] SMARTS Parse Error: syntax error while parsing: fiib -197: [02:19:31] SMARTS Parse Error: Failed parsing SMARTS 'fiib' for input: 'fiib' -197: ....[02:19:31] ERROR: Problems encountered parsing data fields -197: [02:19:31] ERROR: moving to the beginning of the next molecule -197: [02:19:31] ERROR: Problems encountered parsing data fields -197: [02:19:31] ERROR: moving to the beginning of the next molecule -197: [02:19:31] Spurious data before the first property will be ignored -197: [02:19:31] Property will be truncated after the first blank line -197: [02:19:31] Property will be truncated after the first blank line -197: [02:19:31] Property will be truncated after the first blank line -197: [02:19:31] ERROR: Problems encountered parsing data fields -197: [02:19:31] ERROR: moving to the beginning of the next molecule -197: [02:19:31] ERROR: Problems encountered parsing data fields -197: [02:19:31] ERROR: moving to the beginning of the next molecule -197: [02:19:31] Spurious data before the first property will be ignored -197: [02:19:31] Property will be truncated after the first blank line -197: [02:19:31] Property will be truncated after the first blank line -197: [02:19:31] Property will be truncated after the first blank line -197: [02:19:31] ERROR: Problems encountered parsing data fields -197: [02:19:31] ERROR: moving to the beginning of the next molecule -197: [02:19:31] Property will be truncated after the first blank line -197: [02:19:31] ERROR: Problems encountered parsing data fields -197: [02:19:31] ERROR: moving to the beginning of the next molecule -197: [02:19:31] Property will be truncated after the first blank line -197: .[02:19:31] SMILES Parse Error: syntax error while parsing: fail -197: [02:19:31] SMILES Parse Error: check for mistakes around position 1: -197: [02:19:31] fail -197: [02:19:31] ^ -197: [02:19:31] SMILES Parse Error: Failed parsing SMILES 'fail' for input: 'fail' -197: [02:19:31] ERROR: Smiles parse error on line 2 -197: [02:19:31] ERROR: Cannot create molecule from : 'fail' +197: ..............[11:06:28] SMARTS Parse Error: syntax error while parsing: fiib +197: [11:06:28] SMARTS Parse Error: Failed parsing SMARTS 'fiib' for input: 'fiib' +197: ....[11:06:28] ERROR: Problems encountered parsing data fields +197: [11:06:28] ERROR: moving to the beginning of the next molecule +197: [11:06:28] ERROR: Problems encountered parsing data fields +197: [11:06:28] ERROR: moving to the beginning of the next molecule +197: [11:06:28] Spurious data before the first property will be ignored +197: [11:06:28] Property will be truncated after the first blank line +197: [11:06:28] Property will be truncated after the first blank line +197: [11:06:28] Property will be truncated after the first blank line +197: [11:06:28] ERROR: Problems encountered parsing data fields +197: [11:06:28] ERROR: moving to the beginning of the next molecule +197: [11:06:28] ERROR: Problems encountered parsing data fields +197: [11:06:28] ERROR: moving to the beginning of the next molecule +197: [11:06:28] Spurious data before the first property will be ignored +197: [11:06:28] Property will be truncated after the first blank line +197: [11:06:28] Property will be truncated after the first blank line +197: [11:06:28] Property will be truncated after the first blank line +197: [11:06:28] ERROR: Problems encountered parsing data fields +197: [11:06:28] ERROR: moving to the beginning of the next molecule +197: [11:06:28] Property will be truncated after the first blank line +197: [11:06:28] ERROR: Problems encountered parsing data fields +197: [11:06:28] ERROR: moving to the beginning of the next molecule +197: [11:06:28] Property will be truncated after the first blank line +197: .[11:06:28] SMILES Parse Error: syntax error while parsing: fail +197: [11:06:28] SMILES Parse Error: check for mistakes around position 1: +197: [11:06:28] fail +197: [11:06:28] ^ +197: [11:06:28] SMILES Parse Error: Failed parsing SMILES 'fail' for input: 'fail' +197: [11:06:28] ERROR: Smiles parse error on line 2 +197: [11:06:28] ERROR: Cannot create molecule from : 'fail' 197: >>> This may result in an infinite loop. It should finish almost instantly 197: <<< OK, it finished. -197: ............[02:19:31] Explicit valence for atom # 1 C, 5, is greater than permitted -197: ......[02:19:31] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -197: [02:19:31] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -197: [02:19:31] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -197: [02:19:31] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +199: [11:06:28] +199: +199: **** +199: Pre-condition Violation +199: from must be < size() +199: Violation occurred on line 91 in file ./Code/GraphMol/Trajectory/Trajectory.cpp +199: Failed Expression: from < static_cast(size()) +199: ---------- +199: Stacktrace: +199: 0# Invar::Invariant::toString[abi:cxx11]() const in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu//lib/libRDKitRDGeneral.so.1 +199: 1# Invar::operator<<(std::ostream&, Invar::Invariant const&) in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu//lib/libRDKitRDGeneral.so.1 +199: 2# RDKit::Trajectory::addConformersToMol(RDKit::ROMol&, int, int) in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu//lib/libRDKitTrajectory.so.1 +199: 3# boost::python::objects::caller_py_function_impl > >::operator()(_object*, _object*) in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdtrajectory.so +199: 4# boost::python::objects::function::call(_object*, _object*) const in /lib/aarch64-linux-gnu/libboost_python313.so.1.83.0 +199: 5# 0x0000FFFF8AF52680 in /lib/aarch64-linux-gnu/libboost_python313.so.1.83.0 +199: 6# boost::python::detail::exception_handler::operator()(boost::function0 const&) const in /lib/aarch64-linux-gnu/libboost_python313.so.1.83.0 +199: 7# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdmolfiles.so +199: 8# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdmolfiles.so +199: 9# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdCIPLabeler.so +199: 10# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so +199: 11# 0x0000FFFF894DC320 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so +199: 12# 0x0000FFFF894DC2B8 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so +199: 13# 0x0000FFFF894DC248 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so +199: 14# 0x0000FFFF894DC1E0 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so +199: 15# 0x0000FFFF894DC178 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so +199: 16# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/rdBase.so +199: 17# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/rdBase.so +199: 18# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/rdBase.so +199: 19# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/rdBase.so +199: 20# boost::python::handle_exception_impl(boost::function0) in /lib/aarch64-linux-gnu/libboost_python313.so.1.83.0 +199: 21# 0x0000FFFF8AF4F25C in /lib/aarch64-linux-gnu/libboost_python313.so.1.83.0 +199: 22# _PyObject_MakeTpCall in /usr/bin/python3 +199: 23# _PyEval_EvalFrameDefault in /usr/bin/python3 +199: 24# 0x000000000053D3B0 in /usr/bin/python3 +199: 25# _PyEval_EvalFrameDefault in /usr/bin/python3 +199: 26# 0x000000000061C8E0 in /usr/bin/python3 +199: 27# 0x00000000005A787C in /usr/bin/python3 +199: 28# _PyObject_MakeTpCall in /usr/bin/python3 +199: 29# _PyEval_EvalFrameDefault in /usr/bin/python3 +199: 30# 0x000000000053D3B0 in /usr/bin/python3 +199: 31# _PyEval_EvalFrameDefault in /usr/bin/python3 +199: 32# 0x000000000061C8E0 in /usr/bin/python3 +199: 33# 0x00000000005A787C in /usr/bin/python3 +199: 34# _PyObject_MakeTpCall in /usr/bin/python3 +199: 35# _PyEval_EvalFrameDefault in /usr/bin/python3 +199: 36# 0x000000000053D3B0 in /usr/bin/python3 +199: 37# _PyEval_EvalFrameDefault in /usr/bin/python3 +199: 38# 0x000000000061C8E0 in /usr/bin/python3 +199: 39# 0x00000000005A787C in /usr/bin/python3 +199: 40# _PyObject_MakeTpCall in /usr/bin/python3 +199: 41# _PyEval_EvalFrameDefault in /usr/bin/python3 +199: 42# 0x000000000050B030 in /usr/bin/python3 +199: 43# _PyObject_MakeTpCall in /usr/bin/python3 +199: 44# _PyEval_EvalFrameDefault in /usr/bin/python3 +199: 45# PyEval_EvalCode in /usr/bin/python3 +199: 46# 0x000000000064023C in /usr/bin/python3 +199: 47# 0x000000000063BC30 in /usr/bin/python3 +199: 48# 0x000000000065F810 in /usr/bin/python3 +199: 49# 0x000000000065F0B4 in /usr/bin/python3 +199: 50# 0x000000000065EE50 in /usr/bin/python3 +199: 51# Py_RunMain in /usr/bin/python3 +199: 52# Py_BytesMain in /usr/bin/python3 +199: 53# 0x0000FFFF8B73229C in /lib/aarch64-linux-gnu/libc.so.6 +199: 54# __libc_start_main in /lib/aarch64-linux-gnu/libc.so.6 +199: 55# _start in /usr/bin/python3 +199: ---------- +199: **** +199: +199: .[11:06:28] +199: +199: **** +199: Pre-condition Violation +199: from must be < size() +199: Violation occurred on line 91 in file ./Code/GraphMol/Trajectory/Trajectory.cpp +199: Failed Expression: from < static_cast(size()) +199: ---------- +199: Stacktrace: +199: 0# Invar::Invariant::toString[abi:cxx11]() const in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu//lib/libRDKitRDGeneral.so.1 +199: 1# Invar::operator<<(std::ostream&, Invar::Invariant const&) in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu//lib/libRDKitRDGeneral.so.1 +199: 2# RDKit::Trajectory::addConformersToMol(RDKit::ROMol&, int, int) in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu//lib/libRDKitTrajectory.so.1 +199: 3# boost::python::objects::caller_py_function_impl > >::operator()(_object*, _object*) in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdtrajectory.so +199: 4# boost::python::objects::function::call(_object*, _object*) const in /lib/aarch64-linux-gnu/libboost_python313.so.1.83.0 +199: 5# 0x0000FFFF8AF52680 in /lib/aarch64-linux-gnu/libboost_python313.so.1.83.0 +199: 6# boost::python::detail::exception_handler::operator()(boost::function0 const&) const in /lib/aarch64-linux-gnu/libboost_python313.so.1.83.0 +199: 7# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdmolfiles.so +199: 8# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdmolfiles.so +199: 9# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdCIPLabeler.so +199: 10# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so +199: 11# 0x0000FFFF894DC320 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so +199: 12# 0x0000FFFF894DC2B8 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so +199: 13# 0x0000FFFF894DC248 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so +199: 14# 0x0000FFFF894DC1E0 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so +199: 15# 0x0000FFFF894DC178 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so +199: 16# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/rdBase.so +199: 17# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/rdBase.so +199: 18# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/rdBase.so +199: 19# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/rdBase.so +199: 20# boost::python::handle_exception_impl(boost::function0) in /lib/aarch64-linux-gnu/libboost_python313.so.1.83.0 +199: 21# 0x0000FFFF8AF4F25C in /lib/aarch64-linux-gnu/libboost_python313.so.1.83.0 +199: 22# _PyObject_MakeTpCall in /usr/bin/python3 +199: 23# _PyEval_EvalFrameDefault in /usr/bin/python3 +199: 24# 0x000000000053D3B0 in /usr/bin/python3 +199: 25# _PyEval_EvalFrameDefault in /usr/bin/python3 +199: 26# 0x000000000061C8E0 in /usr/bin/python3 +199: 27# 0x00000000005A787C in /usr/bin/python3 +199: 28# _PyObject_MakeTpCall in /usr/bin/python3 +199: 29# _PyEval_EvalFrameDefault in /usr/bin/python3 +199: 30# 0x000000000053D3B0 in /usr/bin/python3 +199: 31# _PyEval_EvalFrameDefault in /usr/bin/python3 +199: 32# 0x000000000061C8E0 in /usr/bin/python3 +199: 33# 0x00000000005A787C in /usr/bin/python3 +199: 34# _PyObject_MakeTpCall in /usr/bin/python3 +199: 35# _PyEval_EvalFrameDefault in /usr/bin/python3 +199: 36# 0x000000000053D3B0 in /usr/bin/python3 +199: 37# _PyEval_EvalFrameDefault in /usr/bin/python3 +199: 38# 0x000000000061C8E0 in /usr/bin/python3 +199: 39# 0x00000000005A787C in /usr/bin/python3 +199: 40# _PyObject_MakeTpCall in /usr/bin/python3 +199: 41# _PyEval_EvalFrameDefault in /usr/bin/python3 +199: 42# 0x000000000050B030 in /usr/bin/python3 +199: 43# _PyObject_MakeTpCall in /usr/bin/python3 +199: 44# _PyEval_EvalFrameDefault in /usr/bin/python3 +199: 45# PyEval_EvalCode in /usr/bin/python3 +199: 46# 0x000000000064023C in /usr/bin/python3 +199: 47# 0x000000000063BC30 in /usr/bin/python3 +199: 48# 0x000000000065F810 in /usr/bin/python3 +199: 49# 0x000000000065F0B4 in /usr/bin/python3 +199: 50# 0x000000000065EE50 in /usr/bin/python3 +199: 51# Py_RunMain in /usr/bin/python3 +199: 52# Py_BytesMain in /usr/bin/python3 +199: 53# 0x0000FFFF8B73229C in /lib/aarch64-linux-gnu/libc.so.6 +199: 54# __libc_start_main in /lib/aarch64-linux-gnu/libc.so.6 +199: 55# _start in /usr/bin/python3 +199: ---------- +199: **** +199: +186: bulk, no symmetry +197: ............[11:06:28] Explicit valence for atom # 1 C, 5, is greater than permitted +197: ......[11:06:28] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +197: [11:06:28] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +197: [11:06:28] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +197: [11:06:28] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 197: .inWedges: [H]C12C3([H])C4([H])C1([H])C1([H])C2([H])C3([H])C41[H] |(-0.612,-0.6446,0.635;0.0021,-0.0041,0.002;-0.0187,1.5258,0.0104;-0.6498,2.1424,0.6504;1.5111,1.5466,-0.0041;2.1372,2.1804,0.624;1.5319,0.0168,-0.0125;2.175,-0.6067,0.6086;1.5173,0.025,-1.5424;2.1484,-0.5936,-2.1805;-0.0125,0.0041,-1.5279;-0.6405,-0.6297,-2.154;-0.0333,1.534,-1.5195;-0.6783,2.1574,-2.1387;1.4965,1.5548,-1.534;2.1106,2.1972,-2.1651)| -197: ........[02:19:31] non-ring atom 0 marked aromatic -197: [02:19:31] non-ring atom 0 marked aromatic -197: [02:19:31] +197: ........[11:06:28] non-ring atom 0 marked aromatic +197: [11:06:28] non-ring atom 0 marked aromatic +197: [11:06:28] 197: 197: **** 197: Range Error @@ -32503,9 +32657,9 @@ 197: 1# Invar::operator<<(std::ostream&, Invar::Invariant const&) in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu//lib/libRDKitRDGeneral.so.1 197: 2# RDKit::ROMol::getAtomWithIdx(unsigned int) in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu//lib/libRDKitGraphMol.so.1 197: 3# RDKit::RWMol::removeAtom(unsigned int) in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu//lib/libRDKitGraphMol.so.1 -197: 4# 0x0000FFFF884655F0 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so +197: 4# 0x0000FFFFAB2055F0 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so 197: 5# boost::python::objects::function::call(_object*, _object*) const in /lib/aarch64-linux-gnu/libboost_python313.so.1.83.0 -197: 6# 0x0000FFFF89EB2680 in /lib/aarch64-linux-gnu/libboost_python313.so.1.83.0 +197: 6# 0x0000FFFFACC52680 in /lib/aarch64-linux-gnu/libboost_python313.so.1.83.0 197: 7# boost::python::detail::exception_handler::operator()(boost::function0 const&) const in /lib/aarch64-linux-gnu/libboost_python313.so.1.83.0 197: 8# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdSLNParse.so 197: 9# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdChemReactions.so @@ -32516,17 +32670,17 @@ 197: 14# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdmolfiles.so 197: 15# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdCIPLabeler.so 197: 16# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so -197: 17# 0x0000FFFF8839C320 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so -197: 18# 0x0000FFFF8839C2B8 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so -197: 19# 0x0000FFFF8839C248 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so -197: 20# 0x0000FFFF8839C1E0 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so -197: 21# 0x0000FFFF8839C178 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so +197: 17# 0x0000FFFFAB13C320 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so +197: 18# 0x0000FFFFAB13C2B8 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so +197: 19# 0x0000FFFFAB13C248 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so +197: 20# 0x0000FFFFAB13C1E0 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so +197: 21# 0x0000FFFFAB13C178 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so 197: 22# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/rdBase.so 197: 23# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/rdBase.so 197: 24# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/rdBase.so 197: 25# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/rdBase.so 197: 26# boost::python::handle_exception_impl(boost::function0) in /lib/aarch64-linux-gnu/libboost_python313.so.1.83.0 -197: 27# 0x0000FFFF89EAF25C in /lib/aarch64-linux-gnu/libboost_python313.so.1.83.0 +197: 27# 0x0000FFFFACC4F25C in /lib/aarch64-linux-gnu/libboost_python313.so.1.83.0 197: 28# _PyObject_MakeTpCall in /usr/bin/python3 197: 29# _PyEval_EvalFrameDefault in /usr/bin/python3 197: 30# 0x000000000053D3B0 in /usr/bin/python3 @@ -32558,15 +32712,15 @@ 197: 56# 0x000000000065EE50 in /usr/bin/python3 197: 57# Py_RunMain in /usr/bin/python3 197: 58# Py_BytesMain in /usr/bin/python3 -197: 59# 0x0000FFFF8ABF229C in /lib/aarch64-linux-gnu/libc.so.6 +197: 59# 0x0000FFFFAD99229C in /lib/aarch64-linux-gnu/libc.so.6 197: 60# __libc_start_main in /lib/aarch64-linux-gnu/libc.so.6 197: 61# _start in /usr/bin/python3 197: ---------- 197: **** 197: -197: [02:19:31] non-ring atom 0 marked aromatic -197: [02:19:31] non-ring atom 0 marked aromatic -197: [02:19:31] +197: [11:06:28] non-ring atom 0 marked aromatic +197: [11:06:28] non-ring atom 0 marked aromatic +197: [11:06:28] 197: 197: **** 197: Range Error @@ -32579,9 +32733,9 @@ 197: 1# Invar::operator<<(std::ostream&, Invar::Invariant const&) in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu//lib/libRDKitRDGeneral.so.1 197: 2# RDKit::ROMol::getAtomWithIdx(unsigned int) in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu//lib/libRDKitGraphMol.so.1 197: 3# RDKit::RWMol::removeAtom(unsigned int) in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu//lib/libRDKitGraphMol.so.1 -197: 4# 0x0000FFFF884655F0 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so +197: 4# 0x0000FFFFAB2055F0 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so 197: 5# boost::python::objects::function::call(_object*, _object*) const in /lib/aarch64-linux-gnu/libboost_python313.so.1.83.0 -197: 6# 0x0000FFFF89EB2680 in /lib/aarch64-linux-gnu/libboost_python313.so.1.83.0 +197: 6# 0x0000FFFFACC52680 in /lib/aarch64-linux-gnu/libboost_python313.so.1.83.0 197: 7# boost::python::detail::exception_handler::operator()(boost::function0 const&) const in /lib/aarch64-linux-gnu/libboost_python313.so.1.83.0 197: 8# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdSLNParse.so 197: 9# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdChemReactions.so @@ -32592,17 +32746,17 @@ 197: 14# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdmolfiles.so 197: 15# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdCIPLabeler.so 197: 16# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so -197: 17# 0x0000FFFF8839C320 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so -197: 18# 0x0000FFFF8839C2B8 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so -197: 19# 0x0000FFFF8839C248 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so -197: 20# 0x0000FFFF8839C1E0 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so -197: 21# 0x0000FFFF8839C178 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so +197: 17# 0x0000FFFFAB13C320 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so +197: 18# 0x0000FFFFAB13C2B8 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so +197: 19# 0x0000FFFFAB13C248 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so +197: 20# 0x0000FFFFAB13C1E0 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so +197: 21# 0x0000FFFFAB13C178 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so 197: 22# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/rdBase.so 197: 23# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/rdBase.so 197: 24# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/rdBase.so 197: 25# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/rdBase.so 197: 26# boost::python::handle_exception_impl(boost::function0) in /lib/aarch64-linux-gnu/libboost_python313.so.1.83.0 -197: 27# 0x0000FFFF89EAF25C in /lib/aarch64-linux-gnu/libboost_python313.so.1.83.0 +197: 27# 0x0000FFFFACC4F25C in /lib/aarch64-linux-gnu/libboost_python313.so.1.83.0 197: 28# _PyObject_MakeTpCall in /usr/bin/python3 197: 29# _PyEval_EvalFrameDefault in /usr/bin/python3 197: 30# 0x000000000053D3B0 in /usr/bin/python3 @@ -32634,321 +32788,15 @@ 197: 56# 0x000000000065EE50 in /usr/bin/python3 197: 57# Py_RunMain in /usr/bin/python3 197: 58# Py_BytesMain in /usr/bin/python3 -197: 59# 0x0000FFFF8ABF229C in /lib/aarch64-linux-gnu/libc.so.6 +197: 59# 0x0000FFFFAD99229C in /lib/aarch64-linux-gnu/libc.so.6 197: 60# __libc_start_main in /lib/aarch64-linux-gnu/libc.so.6 197: 61# _start in /usr/bin/python3 197: ---------- 197: **** 197: -197: ...............[02:19:31] WARNING: the onlyHeavy argument to mol.GetNumAtoms() has been deprecated. Please use the onlyExplicit argument instead or mol.GetNumHeavyAtoms() if you want the heavy atom count. -197: [02:19:31] WARNING: the onlyHeavy argument to mol.GetNumAtoms() has been deprecated. Please use the onlyExplicit argument instead or mol.GetNumHeavyAtoms() if you want the heavy atom count. -197: ..............[02:19:31] Can't kekulize mol. Unkekulized atoms: 0 1 2 3 4 -197: [02:19:31] Explicit valence for atom # 1 C, 5, is greater than permitted -199: [02:19:31] -199: -199: **** -199: Pre-condition Violation -199: from must be < size() -199: Violation occurred on line 91 in file ./Code/GraphMol/Trajectory/Trajectory.cpp -199: Failed Expression: from < static_cast(size()) -199: ---------- -199: Stacktrace: -199: 0# Invar::Invariant::toString[abi:cxx11]() const in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu//lib/libRDKitRDGeneral.so.1 -199: 1# Invar::operator<<(std::ostream&, Invar::Invariant const&) in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu//lib/libRDKitRDGeneral.so.1 -199: 2# RDKit::Trajectory::addConformersToMol(RDKit::ROMol&, int, int) in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu//lib/libRDKitTrajectory.so.1 -199: 3# boost::python::objects::caller_py_function_impl > >::operator()(_object*, _object*) in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdtrajectory.so -199: 4# boost::python::objects::function::call(_object*, _object*) const in /lib/aarch64-linux-gnu/libboost_python313.so.1.83.0 -199: 5# 0x0000FFFF85442680 in /lib/aarch64-linux-gnu/libboost_python313.so.1.83.0 -199: 6# boost::python::detail::exception_handler::operator()(boost::function0 const&) const in /lib/aarch64-linux-gnu/libboost_python313.so.1.83.0 -199: 7# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdmolfiles.so -199: 8# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdmolfiles.so -199: 9# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdCIPLabeler.so -199: 10# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so -199: 11# 0x0000FFFF839CC320 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so -199: 12# 0x0000FFFF839CC2B8 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so -199: 13# 0x0000FFFF839CC248 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so -199: 14# 0x0000FFFF839CC1E0 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so -199: 15# 0x0000FFFF839CC178 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so -199: 16# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/rdBase.so -199: 17# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/rdBase.so -199: 18# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/rdBase.so -199: 19# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/rdBase.so -199: 20# boost::python::handle_exception_impl(boost::function0) in /lib/aarch64-linux-gnu/libboost_python313.so.1.83.0 -199: 21# 0x0000FFFF8543F25C in /lib/aarch64-linux-gnu/libboost_python313.so.1.83.0 -199: 22# _PyObject_MakeTpCall in /usr/bin/python3 -199: 23# _PyEval_EvalFrameDefault in /usr/bin/python3 -199: 24# 0x000000000053D3B0 in /usr/bin/python3 -199: 25# _PyEval_EvalFrameDefault in /usr/bin/python3 -199: 26# 0x000000000061C8E0 in /usr/bin/python3 -199: 27# 0x00000000005A787C in /usr/bin/python3 -199: 28# _PyObject_MakeTpCall in /usr/bin/python3 -199: 29# _PyEval_EvalFrameDefault in /usr/bin/python3 -199: 30# 0x000000000053D3B0 in /usr/bin/python3 -199: 31# _PyEval_EvalFrameDefault in /usr/bin/python3 -199: 32# 0x000000000061C8E0 in /usr/bin/python3 -199: 33# 0x00000000005A787C in /usr/bin/python3 -199: 34# _PyObject_MakeTpCall in /usr/bin/python3 -199: 35# _PyEval_EvalFrameDefault in /usr/bin/python3 -199: 36# 0x000000000053D3B0 in /usr/bin/python3 -199: 37# _PyEval_EvalFrameDefault in /usr/bin/python3 -199: 38# 0x000000000061C8E0 in /usr/bin/python3 -199: 39# 0x00000000005A787C in /usr/bin/python3 -199: 40# _PyObject_MakeTpCall in /usr/bin/python3 -199: 41# _PyEval_EvalFrameDefault in /usr/bin/python3 -199: 42# 0x000000000050B030 in /usr/bin/python3 -199: 43# _PyObject_MakeTpCall in /usr/bin/python3 -199: 44# _PyEval_EvalFrameDefault in /usr/bin/python3 -199: 45# PyEval_EvalCode in /usr/bin/python3 -199: 46# 0x000000000064023C in /usr/bin/python3 -199: 47# 0x000000000063BC30 in /usr/bin/python3 -199: 48# 0x000000000065F810 in /usr/bin/python3 -199: 49# 0x000000000065F0B4 in /usr/bin/python3 -199: 50# 0x000000000065EE50 in /usr/bin/python3 -199: 51# Py_RunMain in /usr/bin/python3 -199: 52# Py_BytesMain in /usr/bin/python3 -199: 53# 0x0000FFFF85C2229C in /lib/aarch64-linux-gnu/libc.so.6 -199: 54# __libc_start_main in /lib/aarch64-linux-gnu/libc.so.6 -199: 55# _start in /usr/bin/python3 -199: ---------- -199: **** -199: -199: .[02:19:31] -199: -199: **** -199: Pre-condition Violation -199: from must be < size() -199: Violation occurred on line 91 in file ./Code/GraphMol/Trajectory/Trajectory.cpp -199: Failed Expression: from < static_cast(size()) -199: ---------- -199: Stacktrace: -199: 0# Invar::Invariant::toString[abi:cxx11]() const in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu//lib/libRDKitRDGeneral.so.1 -199: 1# Invar::operator<<(std::ostream&, Invar::Invariant const&) in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu//lib/libRDKitRDGeneral.so.1 -199: 2# RDKit::Trajectory::addConformersToMol(RDKit::ROMol&, int, int) in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu//lib/libRDKitTrajectory.so.1 -199: 3# boost::python::objects::caller_py_function_impl > >::operator()(_object*, _object*) in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdtrajectory.so -199: 4# boost::python::objects::function::call(_object*, _object*) const in /lib/aarch64-linux-gnu/libboost_python313.so.1.83.0 -199: 5# 0x0000FFFF85442680 in /lib/aarch64-linux-gnu/libboost_python313.so.1.83.0 -199: 6# boost::python::detail::exception_handler::operator()(boost::function0 const&) const in /lib/aarch64-linux-gnu/libboost_python313.so.1.83.0 -199: 7# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdmolfiles.so -199: 8# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdmolfiles.so -199: 9# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdCIPLabeler.so -199: 10# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so -199: 11# 0x0000FFFF839CC320 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so -199: 12# 0x0000FFFF839CC2B8 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so -199: 13# 0x0000FFFF839CC248 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so -199: 14# 0x0000FFFF839CC1E0 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so -199: 15# 0x0000FFFF839CC178 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so -199: 16# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/rdBase.so -199: 17# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/rdBase.so -199: 18# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/rdBase.so -199: 19# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/rdBase.so -199: 20# boost::python::handle_exception_impl(boost::function0) in /lib/aarch64-linux-gnu/libboost_python313.so.1.83.0 -199: 21# 0x0000FFFF8543F25C in /lib/aarch64-linux-gnu/libboost_python313.so.1.83.0 -199: 22# _PyObject_MakeTpCall in /usr/bin/python3 -199: 23# _PyEval_EvalFrameDefault in /usr/bin/python3 -199: 24# 0x000000000053D3B0 in /usr/bin/python3 -199: 25# _PyEval_EvalFrameDefault in /usr/bin/python3 -199: 26# 0x000000000061C8E0 in /usr/bin/python3 -199: 27# 0x00000000005A787C in /usr/bin/python3 -199: 28# _PyObject_MakeTpCall in /usr/bin/python3 -199: 29# _PyEval_EvalFrameDefault in /usr/bin/python3 -199: 30# 0x000000000053D3B0 in /usr/bin/python3 -199: 31# _PyEval_EvalFrameDefault in /usr/bin/python3 -199: 32# 0x000000000061C8E0 in /usr/bin/python3 -199: 33# 0x00000000005A787C in /usr/bin/python3 -199: 34# _PyObject_MakeTpCall in /usr/bin/python3 -199: 35# _PyEval_EvalFrameDefault in /usr/bin/python3 -199: 36# 0x000000000053D3B0 in /usr/bin/python3 -199: 37# _PyEval_EvalFrameDefault in /usr/bin/python3 -199: 38# 0x000000000061C8E0 in /usr/bin/python3 -199: 39# 0x00000000005A787C in /usr/bin/python3 -199: 40# _PyObject_MakeTpCall in /usr/bin/python3 -199: 41# _PyEval_EvalFrameDefault in /usr/bin/python3 -199: 42# 0x000000000050B030 in /usr/bin/python3 -199: 43# _PyObject_MakeTpCall in /usr/bin/python3 -199: 44# _PyEval_EvalFrameDefault in /usr/bin/python3 -199: 45# PyEval_EvalCode in /usr/bin/python3 -199: 46# 0x000000000064023C in /usr/bin/python3 -199: 47# 0x000000000063BC30 in /usr/bin/python3 -199: 48# 0x000000000065F810 in /usr/bin/python3 -199: 49# 0x000000000065F0B4 in /usr/bin/python3 -199: 50# 0x000000000065EE50 in /usr/bin/python3 -199: 51# Py_RunMain in /usr/bin/python3 -199: 52# Py_BytesMain in /usr/bin/python3 -199: 53# 0x0000FFFF85C2229C in /lib/aarch64-linux-gnu/libc.so.6 -199: 54# __libc_start_main in /lib/aarch64-linux-gnu/libc.so.6 -199: 55# _start in /usr/bin/python3 -199: ---------- -199: **** -199: -200: ............. -200: ---------------------------------------------------------------------- -200: Ran 13 tests in 0.033s -200: -200: OK -200: Testing SubstanceGroups wrapper -189/238 Test #200: pyTestSGroups .......................... Passed 0.44 sec -test 201 - Start 201: pyTestThreads - -201: Test command: /usr/bin/python3 "/build/reproducible-path/rdkit-202503.1/Code/GraphMol/Wrap/testThreads.py" -201: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/Wrap -201: Test timeout computed to be: 1500 -185: ......[02:19:31] -185: -185: **** -185: Pre-condition Violation -185: RingInfo not initialized -185: Violation occurred on line 52 in file ./Code/GraphMol/RingInfo.cpp -185: Failed Expression: df_init -185: ---------- -185: Stacktrace: -185: 0# Invar::Invariant::toString[abi:cxx11]() const in /build/reproducible-path/rdkit-202503.1/obj-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::numAtomRings(unsigned int) const in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu//lib/libRDKitGraphMol.so.1 -185: 3# RDKit::AtomRingQuery::Match(RDKit::Atom const*) const in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu//lib/libRDKitSmilesParse.so.1 -185: 4# Queries::AndQuery::Match(RDKit::Atom const*) const in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu//lib/libRDKitGraphMol.so.1 -185: 5# RDKit::atomCompat(RDKit::Atom const*, RDKit::Atom const*, RDKit::SubstructMatchParameters const&) in /build/reproducible-path/rdkit-202503.1/obj-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 -185: 7# bool boost::detail::VF2SubState const, RDKit::detail::AtomLabelFunctor, RDKit::detail::BondLabelFunctor, RDKit::MolMatchFinalCheckFunctor>::MatchAll, std::allocator > >, std::allocator, std::allocator > > > > >(unsigned int*, unsigned int*, std::vector, std::allocator > >, std::allocator, std::allocator > > > >&, unsigned int) in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu//lib/libRDKitSubstructMatch.so.1 -185: 8# bool boost::vf2_all, RDKit::detail::AtomLabelFunctor, RDKit::detail::BondLabelFunctor, RDKit::MolMatchFinalCheckFunctor, std::vector, std::allocator > >, std::allocator, std::allocator > > > > >(boost::adjacency_list const&, boost::adjacency_list const&, RDKit::detail::AtomLabelFunctor&, RDKit::detail::BondLabelFunctor&, RDKit::MolMatchFinalCheckFunctor&, std::vector, std::allocator > >, std::allocator, std::allocator > > > >&, unsigned int) in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu//lib/libRDKitSubstructMatch.so.1 -185: 9# RDKit::SubstructMatch(RDKit::ROMol const&, RDKit::ROMol const&, RDKit::SubstructMatchParameters const&) in /build/reproducible-path/rdkit-202503.1/obj-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# 0x0000FFFF9F0CF530 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# 0x0000FFFFA0B82680 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# 0x0000FFFF9F02C320 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so -185: 21# 0x0000FFFF9F02C2B8 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so -185: 22# 0x0000FFFF9F02C248 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so -185: 23# 0x0000FFFF9F02C1E0 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so -185: 24# 0x0000FFFF9F02C178 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# 0x0000FFFFA0B7F25C in /lib/aarch64-linux-gnu/libboost_python313.so.1.83.0 -185: 31# _PyObject_MakeTpCall in /usr/bin/python3 -185: 32# _PyEval_EvalFrameDefault in /usr/bin/python3 -185: 33# 0x000000000053D3B0 in /usr/bin/python3 -185: 34# _PyEval_EvalFrameDefault in /usr/bin/python3 -185: 35# 0x000000000061C8E0 in /usr/bin/python3 -185: 36# 0x00000000005A787C in /usr/bin/python3 -185: 37# _PyObject_MakeTpCall in /usr/bin/python3 -185: 38# _PyEval_EvalFrameDefault in /usr/bin/python3 -185: 39# 0x000000000053D3B0 in /usr/bin/python3 -185: 40# _PyEval_EvalFrameDefault in /usr/bin/python3 -185: 41# 0x000000000061C8E0 in /usr/bin/python3 -185: 42# 0x00000000005A787C in /usr/bin/python3 -185: 43# _PyObject_MakeTpCall in /usr/bin/python3 -185: 44# _PyEval_EvalFrameDefault in /usr/bin/python3 -185: 45# 0x000000000053D3B0 in /usr/bin/python3 -185: 46# _PyEval_EvalFrameDefault in /usr/bin/python3 -185: 47# 0x000000000061C8E0 in /usr/bin/python3 -185: 48# 0x00000000005A787C in /usr/bin/python3 -185: 49# _PyObject_MakeTpCall in /usr/bin/python3 -185: 50# _PyEval_EvalFrameDefault in /usr/bin/python3 -185: 51# 0x000000000050B030 in /usr/bin/python3 -185: 52# _PyObject_MakeTpCall in /usr/bin/python3 -185: 53# _PyEval_EvalFrameDefault in /usr/bin/python3 -185: 54# PyEval_EvalCode in /usr/bin/python3 -185: 55# 0x000000000064023C in /usr/bin/python3 -185: 56# 0x000000000063BC30 in /usr/bin/python3 -185: 57# 0x000000000065F810 in /usr/bin/python3 -185: 58# 0x000000000065F0B4 in /usr/bin/python3 -185: 59# 0x000000000065EE50 in /usr/bin/python3 -185: 60# Py_RunMain in /usr/bin/python3 -185: 61# Py_BytesMain in /usr/bin/python3 -185: 62# 0x0000FFFFA156229C 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: [02:19:31] -185: -185: **** -185: Pre-condition Violation -185: RingInfo not initialized -185: Violation occurred on line 129 in file ./Code/GraphMol/RingInfo.cpp -185: Failed Expression: df_init -185: ---------- -185: Stacktrace: -185: 0# Invar::Invariant::toString[abi:cxx11]() const in /build/reproducible-path/rdkit-202503.1/obj-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# 0x0000FFFF9EB7FCE8 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 -185: 7# bool boost::detail::VF2SubState const, RDKit::detail::AtomLabelFunctor, RDKit::detail::BondLabelFunctor, RDKit::MolMatchFinalCheckFunctor>::MatchAll, std::allocator > >, std::allocator, std::allocator > > > > >(unsigned int*, unsigned int*, std::vector, std::allocator > >, std::allocator, std::allocator > > > >&, unsigned int) in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu//lib/libRDKitSubstructMatch.so.1 -185: 8# bool boost::detail::VF2SubState const, RDKit::detail::AtomLabelFunctor, RDKit::detail::BondLabelFunctor, RDKit::MolMatchFinalCheckFunctor>::MatchAll, std::allocator > >, std::allocator, std::allocator > > > > >(unsigned int*, unsigned int*, std::vector, std::allocator > >, std::allocator, std::allocator > > > >&, unsigned int) in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu//lib/libRDKitSubstructMatch.so.1 -185: 9# bool boost::vf2_all, RDKit::detail::AtomLabelFunctor, RDKit::detail::BondLabelFunctor, RDKit::MolMatchFinalCheckFunctor, std::vector, std::allocator > >, std::allocator, std::allocator > > > > >(boost::adjacency_list const&, boost::adjacency_list const&, RDKit::detail::AtomLabelFunctor&, RDKit::detail::BondLabelFunctor&, RDKit::MolMatchFinalCheckFunctor&, std::vector, std::allocator > >, std::allocator, std::allocator > > > >&, unsigned int) in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu//lib/libRDKitSubstructMatch.so.1 -185: 10# RDKit::SubstructMatch(RDKit::ROMol const&, RDKit::ROMol const&, RDKit::SubstructMatchParameters const&) in /build/reproducible-path/rdkit-202503.1/obj-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# 0x0000FFFF9F0CF530 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# 0x0000FFFFA0B82680 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# 0x0000FFFF9F02C320 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so -185: 22# 0x0000FFFF9F02C2B8 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so -185: 23# 0x0000FFFF9F02C248 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so -185: 24# 0x0000FFFF9F02C1E0 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so -185: 25# 0x0000FFFF9F02C178 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# 0x0000FFFFA0B7F25C in /lib/aarch64-linux-gnu/libboost_python313.so.1.83.0 -185: 32# _PyObject_MakeTpCall in /usr/bin/python3 -185: 33# _PyEval_EvalFrameDefault in /usr/bin/python3 -185: 34# 0x000000000053D3B0 in /usr/bin/python3 -185: 35# _PyEval_EvalFrameDefault in /usr/bin/python3 -185: 36# 0x000000000061C8E0 in /usr/bin/python3 -185: 37# 0x00000000005A787C in /usr/bin/python3 -185: 38# _PyObject_MakeTpCall in /usr/bin/python3 -185: 39# _PyEval_EvalFrameDefault in /usr/bin/python3 -185: 40# 0x000000000053D3B0 in /usr/bin/python3 -185: 41# _PyEval_EvalFrameDefault in /usr/bin/python3 -185: 42# 0x000000000061C8E0 in /usr/bin/python3 -185: 43# 0x00000000005A787C in /usr/bin/python3 -185: 44# _PyObject_MakeTpCall in /usr/bin/python3 -185: 45# _PyEval_EvalFrameDefault in /usr/bin/python3 -185: 46# 0x000000000053D3B0 in /usr/bin/python3 -185: 47# _PyEval_EvalFrameDefault in /usr/bin/python3 -185: 48# 0x000000000061C8E0 in /usr/bin/python3 -185: 49# 0x00000000005A787C in /usr/bin/python3 -185: 50# _PyObject_MakeTpCall in /usr/bin/python3 -185: 51# _PyEval_EvalFrameDefault in /usr/bin/python3 -185: 52# 0x000000000050B030 in /usr/bin/python3 -185: 53# _PyObject_MakeTpCall in /usr/bin/python3 -185: 54# _PyEval_EvalFrameDefault in /usr/bin/python3 -185: 55# PyEval_EvalCode in /usr/bin/python3 -185: 56# 0x000000000064023C in /usr/bin/python3 -185: 57# 0x000000000063BC30 in /usr/bin/python3 -185: 58# 0x000000000065F810 in /usr/bin/python3 -185: 59# 0x000000000065F0B4 in /usr/bin/python3 -185: 60# 0x000000000065EE50 in /usr/bin/python3 -185: 61# Py_RunMain in /usr/bin/python3 -185: 62# Py_BytesMain in /usr/bin/python3 -185: 63# 0x0000FFFFA156229C 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: -199: .[02:19:31] +197: ...............[11:06:28] WARNING: the onlyHeavy argument to mol.GetNumAtoms() has been deprecated. Please use the onlyExplicit argument instead or mol.GetNumHeavyAtoms() if you want the heavy atom count. +197: [11:06:28] 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. +199: .[11:06:28] 199: 199: **** 199: Range Error @@ -32963,23 +32811,23 @@ 199: 3# RDKit::getSnapshot_wrap(RDKit::Trajectory*, unsigned int) in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdtrajectory.so 199: 4# boost::python::objects::caller_py_function_impl, boost::mpl::vector3 > >::operator()(_object*, _object*) in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdtrajectory.so 199: 5# boost::python::objects::function::call(_object*, _object*) const in /lib/aarch64-linux-gnu/libboost_python313.so.1.83.0 -199: 6# 0x0000FFFF85442680 in /lib/aarch64-linux-gnu/libboost_python313.so.1.83.0 +199: 6# 0x0000FFFF8AF52680 in /lib/aarch64-linux-gnu/libboost_python313.so.1.83.0 199: 7# boost::python::detail::exception_handler::operator()(boost::function0 const&) const in /lib/aarch64-linux-gnu/libboost_python313.so.1.83.0 199: 8# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdmolfiles.so 199: 9# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdmolfiles.so 199: 10# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdCIPLabeler.so 199: 11# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so -199: 12# 0x0000FFFF839CC320 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so -199: 13# 0x0000FFFF839CC2B8 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so -199: 14# 0x0000FFFF839CC248 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so -199: 15# 0x0000FFFF839CC1E0 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so -199: 16# 0x0000FFFF839CC178 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so +199: 12# 0x0000FFFF894DC320 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so +199: 13# 0x0000FFFF894DC2B8 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so +199: 14# 0x0000FFFF894DC248 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so +199: 15# 0x0000FFFF894DC1E0 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so +199: 16# 0x0000FFFF894DC178 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so 199: 17# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/rdBase.so 199: 18# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/rdBase.so 199: 19# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/rdBase.so 199: 20# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/rdBase.so 199: 21# boost::python::handle_exception_impl(boost::function0) in /lib/aarch64-linux-gnu/libboost_python313.so.1.83.0 -199: 22# 0x0000FFFF8543F25C in /lib/aarch64-linux-gnu/libboost_python313.so.1.83.0 +199: 22# 0x0000FFFF8AF4F25C in /lib/aarch64-linux-gnu/libboost_python313.so.1.83.0 199: 23# _PyObject_MakeTpCall in /usr/bin/python3 199: 24# _PyEval_EvalFrameDefault in /usr/bin/python3 199: 25# 0x000000000053D3B0 in /usr/bin/python3 @@ -33011,13 +32859,13 @@ 199: 51# 0x000000000065EE50 in /usr/bin/python3 199: 52# Py_RunMain in /usr/bin/python3 199: 53# Py_BytesMain in /usr/bin/python3 -199: 54# 0x0000FFFF85C2229C in /lib/aarch64-linux-gnu/libc.so.6 +199: 54# 0x0000FFFF8B73229C in /lib/aarch64-linux-gnu/libc.so.6 199: 55# __libc_start_main in /lib/aarch64-linux-gnu/libc.so.6 199: 56# _start in /usr/bin/python3 199: ---------- 199: **** 199: -199: .[02:19:31] +199: .[11:06:28] 199: 199: **** 199: Pre-condition Violation @@ -33031,23 +32879,23 @@ 199: 2# RDKit::readAmberTrajectory(std::__cxx11::basic_string, std::allocator > const&, RDKit::Trajectory&) in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu//lib/libRDKitTrajectory.so.1 199: 3# boost::python::objects::caller_py_function_impl, std::allocator > const&, RDKit::Trajectory&), boost::python::default_call_policies, boost::mpl::vector3, std::allocator > const&, RDKit::Trajectory&> > >::operator()(_object*, _object*) in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdtrajectory.so 199: 4# boost::python::objects::function::call(_object*, _object*) const in /lib/aarch64-linux-gnu/libboost_python313.so.1.83.0 -199: 5# 0x0000FFFF85442680 in /lib/aarch64-linux-gnu/libboost_python313.so.1.83.0 +199: 5# 0x0000FFFF8AF52680 in /lib/aarch64-linux-gnu/libboost_python313.so.1.83.0 199: 6# boost::python::detail::exception_handler::operator()(boost::function0 const&) const in /lib/aarch64-linux-gnu/libboost_python313.so.1.83.0 199: 7# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdmolfiles.so 199: 8# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdmolfiles.so 199: 9# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdCIPLabeler.so 199: 10# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so -199: 11# 0x0000FFFF839CC320 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so -199: 12# 0x0000FFFF839CC2B8 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so -199: 13# 0x0000FFFF839CC248 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so -199: 14# 0x0000FFFF839CC1E0 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so -199: 15# 0x0000FFFF839CC178 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so +199: 11# 0x0000FFFF894DC320 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so +199: 12# 0x0000FFFF894DC2B8 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so +199: 13# 0x0000FFFF894DC248 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so +199: 14# 0x0000FFFF894DC1E0 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so +199: 15# 0x0000FFFF894DC178 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so 199: 16# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/rdBase.so 199: 17# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/rdBase.so 199: 18# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/rdBase.so 199: 19# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/rdBase.so 199: 20# boost::python::handle_exception_impl(boost::function0) in /lib/aarch64-linux-gnu/libboost_python313.so.1.83.0 -199: 21# 0x0000FFFF8543F25C in /lib/aarch64-linux-gnu/libboost_python313.so.1.83.0 +199: 21# 0x0000FFFF8AF4F25C in /lib/aarch64-linux-gnu/libboost_python313.so.1.83.0 199: 22# _PyObject_MakeTpCall in /usr/bin/python3 199: 23# _PyEval_EvalFrameDefault in /usr/bin/python3 199: 24# 0x000000000053D3B0 in /usr/bin/python3 @@ -33079,13 +32927,13 @@ 199: 50# 0x000000000065EE50 in /usr/bin/python3 199: 51# Py_RunMain in /usr/bin/python3 199: 52# Py_BytesMain in /usr/bin/python3 -199: 53# 0x0000FFFF85C2229C in /lib/aarch64-linux-gnu/libc.so.6 +199: 53# 0x0000FFFF8B73229C in /lib/aarch64-linux-gnu/libc.so.6 199: 54# __libc_start_main in /lib/aarch64-linux-gnu/libc.so.6 199: 55# _start in /usr/bin/python3 199: ---------- 199: **** 199: -199: ..[02:19:31] +199: ..[11:06:28] 199: 199: **** 199: Pre-condition Violation @@ -33099,23 +32947,23 @@ 199: 2# RDKit::readGromosTrajectory(std::__cxx11::basic_string, std::allocator > const&, RDKit::Trajectory&) in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu//lib/libRDKitTrajectory.so.1 199: 3# boost::python::objects::caller_py_function_impl, std::allocator > const&, RDKit::Trajectory&), boost::python::default_call_policies, boost::mpl::vector3, std::allocator > const&, RDKit::Trajectory&> > >::operator()(_object*, _object*) in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdtrajectory.so 199: 4# boost::python::objects::function::call(_object*, _object*) const in /lib/aarch64-linux-gnu/libboost_python313.so.1.83.0 -199: 5# 0x0000FFFF85442680 in /lib/aarch64-linux-gnu/libboost_python313.so.1.83.0 +199: 5# 0x0000FFFF8AF52680 in /lib/aarch64-linux-gnu/libboost_python313.so.1.83.0 199: 6# boost::python::detail::exception_handler::operator()(boost::function0 const&) const in /lib/aarch64-linux-gnu/libboost_python313.so.1.83.0 199: 7# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdmolfiles.so 199: 8# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdmolfiles.so 199: 9# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdCIPLabeler.so 199: 10# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so -199: 11# 0x0000FFFF839CC320 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so -199: 12# 0x0000FFFF839CC2B8 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so -199: 13# 0x0000FFFF839CC248 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so -199: 14# 0x0000FFFF839CC1E0 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so -199: 15# 0x0000FFFF839CC178 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so +199: 11# 0x0000FFFF894DC320 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so +199: 12# 0x0000FFFF894DC2B8 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so +199: 13# 0x0000FFFF894DC248 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so +199: 14# 0x0000FFFF894DC1E0 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so +199: 15# 0x0000FFFF894DC178 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so 199: 16# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/rdBase.so 199: 17# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/rdBase.so 199: 18# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/rdBase.so 199: 19# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/rdBase.so 199: 20# boost::python::handle_exception_impl(boost::function0) in /lib/aarch64-linux-gnu/libboost_python313.so.1.83.0 -199: 21# 0x0000FFFF8543F25C in /lib/aarch64-linux-gnu/libboost_python313.so.1.83.0 +199: 21# 0x0000FFFF8AF4F25C in /lib/aarch64-linux-gnu/libboost_python313.so.1.83.0 199: 22# _PyObject_MakeTpCall in /usr/bin/python3 199: 23# _PyEval_EvalFrameDefault in /usr/bin/python3 199: 24# 0x000000000053D3B0 in /usr/bin/python3 @@ -33147,13 +32995,13 @@ 199: 50# 0x000000000065EE50 in /usr/bin/python3 199: 51# Py_RunMain in /usr/bin/python3 199: 52# Py_BytesMain in /usr/bin/python3 -199: 53# 0x0000FFFF85C2229C in /lib/aarch64-linux-gnu/libc.so.6 +199: 53# 0x0000FFFF8B73229C in /lib/aarch64-linux-gnu/libc.so.6 199: 54# __libc_start_main in /lib/aarch64-linux-gnu/libc.so.6 199: 55# _start in /usr/bin/python3 199: ---------- 199: **** 199: -199: .[02:19:31] +199: .[11:06:28] 199: 199: **** 199: Pre-condition Violation @@ -33167,23 +33015,23 @@ 199: 2# RDKit::Snapshot::getPoint2D(unsigned int) const in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu//lib/libRDKitTrajectory.so.1 199: 3# boost::python::objects::caller_py_function_impl > >::operator()(_object*, _object*) in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdtrajectory.so 199: 4# boost::python::objects::function::call(_object*, _object*) const in /lib/aarch64-linux-gnu/libboost_python313.so.1.83.0 -199: 5# 0x0000FFFF85442680 in /lib/aarch64-linux-gnu/libboost_python313.so.1.83.0 +199: 5# 0x0000FFFF8AF52680 in /lib/aarch64-linux-gnu/libboost_python313.so.1.83.0 199: 6# boost::python::detail::exception_handler::operator()(boost::function0 const&) const in /lib/aarch64-linux-gnu/libboost_python313.so.1.83.0 199: 7# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdmolfiles.so 199: 8# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdmolfiles.so 199: 9# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdCIPLabeler.so 199: 10# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so -199: 11# 0x0000FFFF839CC320 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so -199: 12# 0x0000FFFF839CC2B8 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so -199: 13# 0x0000FFFF839CC248 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so -199: 14# 0x0000FFFF839CC1E0 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so -199: 15# 0x0000FFFF839CC178 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so +199: 11# 0x0000FFFF894DC320 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so +199: 12# 0x0000FFFF894DC2B8 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so +199: 13# 0x0000FFFF894DC248 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so +199: 14# 0x0000FFFF894DC1E0 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so +199: 15# 0x0000FFFF894DC178 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so 199: 16# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/rdBase.so 199: 17# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/rdBase.so 199: 18# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/rdBase.so 199: 19# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/rdBase.so 199: 20# boost::python::handle_exception_impl(boost::function0) in /lib/aarch64-linux-gnu/libboost_python313.so.1.83.0 -199: 21# 0x0000FFFF8543F25C in /lib/aarch64-linux-gnu/libboost_python313.so.1.83.0 +199: 21# 0x0000FFFF8AF4F25C in /lib/aarch64-linux-gnu/libboost_python313.so.1.83.0 199: 22# _PyObject_MakeTpCall in /usr/bin/python3 199: 23# _PyEval_EvalFrameDefault in /usr/bin/python3 199: 24# 0x000000000053D3B0 in /usr/bin/python3 @@ -33215,13 +33063,13 @@ 199: 50# 0x000000000065EE50 in /usr/bin/python3 199: 51# Py_RunMain in /usr/bin/python3 199: 52# Py_BytesMain in /usr/bin/python3 -199: 53# 0x0000FFFF85C2229C in /lib/aarch64-linux-gnu/libc.so.6 +199: 53# 0x0000FFFF8B73229C in /lib/aarch64-linux-gnu/libc.so.6 199: 54# __libc_start_main in /lib/aarch64-linux-gnu/libc.so.6 199: 55# _start in /usr/bin/python3 199: ---------- 199: **** 199: -199: [02:19:31] +199: [11:06:28] 199: 199: **** 199: Pre-condition Violation @@ -33235,23 +33083,23 @@ 199: 2# RDKit::Snapshot::getPoint2D(unsigned int) const in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu//lib/libRDKitTrajectory.so.1 199: 3# boost::python::objects::caller_py_function_impl > >::operator()(_object*, _object*) in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdtrajectory.so 199: 4# boost::python::objects::function::call(_object*, _object*) const in /lib/aarch64-linux-gnu/libboost_python313.so.1.83.0 -199: 5# 0x0000FFFF85442680 in /lib/aarch64-linux-gnu/libboost_python313.so.1.83.0 +199: 5# 0x0000FFFF8AF52680 in /lib/aarch64-linux-gnu/libboost_python313.so.1.83.0 199: 6# boost::python::detail::exception_handler::operator()(boost::function0 const&) const in /lib/aarch64-linux-gnu/libboost_python313.so.1.83.0 199: 7# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdmolfiles.so 199: 8# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdmolfiles.so 199: 9# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdCIPLabeler.so 199: 10# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so -199: 11# 0x0000FFFF839CC320 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so -199: 12# 0x0000FFFF839CC2B8 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so -199: 13# 0x0000FFFF839CC248 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so -199: 14# 0x0000FFFF839CC1E0 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so -199: 15# 0x0000FFFF839CC178 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so +199: 11# 0x0000FFFF894DC320 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so +199: 12# 0x0000FFFF894DC2B8 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so +199: 13# 0x0000FFFF894DC248 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so +199: 14# 0x0000FFFF894DC1E0 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so +199: 15# 0x0000FFFF894DC178 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so 199: 16# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/rdBase.so 199: 17# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/rdBase.so 199: 18# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/rdBase.so 199: 19# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/rdBase.so 199: 20# boost::python::handle_exception_impl(boost::function0) in /lib/aarch64-linux-gnu/libboost_python313.so.1.83.0 -199: 21# 0x0000FFFF8543F25C in /lib/aarch64-linux-gnu/libboost_python313.so.1.83.0 +199: 21# 0x0000FFFF8AF4F25C in /lib/aarch64-linux-gnu/libboost_python313.so.1.83.0 199: 22# _PyObject_MakeTpCall in /usr/bin/python3 199: 23# _PyEval_EvalFrameDefault in /usr/bin/python3 199: 24# 0x000000000053D3B0 in /usr/bin/python3 @@ -33283,13 +33131,13 @@ 199: 50# 0x000000000065EE50 in /usr/bin/python3 199: 51# Py_RunMain in /usr/bin/python3 199: 52# Py_BytesMain in /usr/bin/python3 -199: 53# 0x0000FFFF85C2229C in /lib/aarch64-linux-gnu/libc.so.6 +199: 53# 0x0000FFFF8B73229C in /lib/aarch64-linux-gnu/libc.so.6 199: 54# __libc_start_main in /lib/aarch64-linux-gnu/libc.so.6 199: 55# _start in /usr/bin/python3 199: ---------- 199: **** 199: -199: .[02:19:31] +199: .[11:06:28] 199: 199: **** 199: Range Error @@ -33304,23 +33152,23 @@ 199: 3# RDKit::getSnapshot_wrap(RDKit::Trajectory*, unsigned int) in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdtrajectory.so 199: 4# boost::python::objects::caller_py_function_impl, boost::mpl::vector3 > >::operator()(_object*, _object*) in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdtrajectory.so 199: 5# boost::python::objects::function::call(_object*, _object*) const in /lib/aarch64-linux-gnu/libboost_python313.so.1.83.0 -199: 6# 0x0000FFFF85442680 in /lib/aarch64-linux-gnu/libboost_python313.so.1.83.0 +199: 6# 0x0000FFFF8AF52680 in /lib/aarch64-linux-gnu/libboost_python313.so.1.83.0 199: 7# boost::python::detail::exception_handler::operator()(boost::function0 const&) const in /lib/aarch64-linux-gnu/libboost_python313.so.1.83.0 199: 8# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdmolfiles.so 199: 9# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdmolfiles.so 199: 10# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdCIPLabeler.so 199: 11# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so -199: 12# 0x0000FFFF839CC320 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so -199: 13# 0x0000FFFF839CC2B8 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so -199: 14# 0x0000FFFF839CC248 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so -199: 15# 0x0000FFFF839CC1E0 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so -199: 16# 0x0000FFFF839CC178 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so +199: 12# 0x0000FFFF894DC320 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so +199: 13# 0x0000FFFF894DC2B8 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so +199: 14# 0x0000FFFF894DC248 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so +199: 15# 0x0000FFFF894DC1E0 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so +199: 16# 0x0000FFFF894DC178 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so 199: 17# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/rdBase.so 199: 18# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/rdBase.so 199: 19# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/rdBase.so 199: 20# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/rdBase.so 199: 21# boost::python::handle_exception_impl(boost::function0) in /lib/aarch64-linux-gnu/libboost_python313.so.1.83.0 -199: 22# 0x0000FFFF8543F25C in /lib/aarch64-linux-gnu/libboost_python313.so.1.83.0 +199: 22# 0x0000FFFF8AF4F25C in /lib/aarch64-linux-gnu/libboost_python313.so.1.83.0 199: 23# _PyObject_MakeTpCall in /usr/bin/python3 199: 24# _PyEval_EvalFrameDefault in /usr/bin/python3 199: 25# 0x000000000053D3B0 in /usr/bin/python3 @@ -33352,13 +33200,13 @@ 199: 51# 0x000000000065EE50 in /usr/bin/python3 199: 52# Py_RunMain in /usr/bin/python3 199: 53# Py_BytesMain in /usr/bin/python3 -199: 54# 0x0000FFFF85C2229C in /lib/aarch64-linux-gnu/libc.so.6 +199: 54# 0x0000FFFF8B73229C in /lib/aarch64-linux-gnu/libc.so.6 199: 55# __libc_start_main in /lib/aarch64-linux-gnu/libc.so.6 199: 56# _start in /usr/bin/python3 199: ---------- 199: **** 199: -199: [02:19:31] +199: [11:06:28] 199: 199: **** 199: Range Error @@ -33372,23 +33220,23 @@ 199: 2# RDKit::Snapshot::getPoint2D(unsigned int) const in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu//lib/libRDKitTrajectory.so.1 199: 3# boost::python::objects::caller_py_function_impl > >::operator()(_object*, _object*) in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdtrajectory.so 199: 4# boost::python::objects::function::call(_object*, _object*) const in /lib/aarch64-linux-gnu/libboost_python313.so.1.83.0 -199: 5# 0x0000FFFF85442680 in /lib/aarch64-linux-gnu/libboost_python313.so.1.83.0 +199: 5# 0x0000FFFF8AF52680 in /lib/aarch64-linux-gnu/libboost_python313.so.1.83.0 199: 6# boost::python::detail::exception_handler::operator()(boost::function0 const&) const in /lib/aarch64-linux-gnu/libboost_python313.so.1.83.0 199: 7# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdmolfiles.so 199: 8# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdmolfiles.so 199: 9# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdCIPLabeler.so 199: 10# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so -199: 11# 0x0000FFFF839CC320 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so -199: 12# 0x0000FFFF839CC2B8 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so -199: 13# 0x0000FFFF839CC248 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so -199: 14# 0x0000FFFF839CC1E0 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so -199: 15# 0x0000FFFF839CC178 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so +199: 11# 0x0000FFFF894DC320 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so +199: 12# 0x0000FFFF894DC2B8 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so +199: 13# 0x0000FFFF894DC248 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so +199: 14# 0x0000FFFF894DC1E0 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so +199: 15# 0x0000FFFF894DC178 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so 199: 16# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/rdBase.so 199: 17# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/rdBase.so 199: 18# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/rdBase.so 199: 19# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/rdBase.so 199: 20# boost::python::handle_exception_impl(boost::function0) in /lib/aarch64-linux-gnu/libboost_python313.so.1.83.0 -199: 21# 0x0000FFFF8543F25C in /lib/aarch64-linux-gnu/libboost_python313.so.1.83.0 +199: 21# 0x0000FFFF8AF4F25C in /lib/aarch64-linux-gnu/libboost_python313.so.1.83.0 199: 22# _PyObject_MakeTpCall in /usr/bin/python3 199: 23# _PyEval_EvalFrameDefault in /usr/bin/python3 199: 24# 0x000000000053D3B0 in /usr/bin/python3 @@ -33420,13 +33268,13 @@ 199: 50# 0x000000000065EE50 in /usr/bin/python3 199: 51# Py_RunMain in /usr/bin/python3 199: 52# Py_BytesMain in /usr/bin/python3 -199: 53# 0x0000FFFF85C2229C in /lib/aarch64-linux-gnu/libc.so.6 +199: 53# 0x0000FFFF8B73229C in /lib/aarch64-linux-gnu/libc.so.6 199: 54# __libc_start_main in /lib/aarch64-linux-gnu/libc.so.6 199: 55# _start in /usr/bin/python3 199: ---------- 199: **** 199: -199: .[02:19:31] +199: .[11:06:28] 199: 199: **** 199: Range Error @@ -33441,23 +33289,23 @@ 199: 3# RDKit::getSnapshot_wrap(RDKit::Trajectory*, unsigned int) in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdtrajectory.so 199: 4# boost::python::objects::caller_py_function_impl, boost::mpl::vector3 > >::operator()(_object*, _object*) in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdtrajectory.so 199: 5# boost::python::objects::function::call(_object*, _object*) const in /lib/aarch64-linux-gnu/libboost_python313.so.1.83.0 -199: 6# 0x0000FFFF85442680 in /lib/aarch64-linux-gnu/libboost_python313.so.1.83.0 +199: 6# 0x0000FFFF8AF52680 in /lib/aarch64-linux-gnu/libboost_python313.so.1.83.0 199: 7# boost::python::detail::exception_handler::operator()(boost::function0 const&) const in /lib/aarch64-linux-gnu/libboost_python313.so.1.83.0 199: 8# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdmolfiles.so 199: 9# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdmolfiles.so 199: 10# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdCIPLabeler.so 199: 11# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so -199: 12# 0x0000FFFF839CC320 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so -199: 13# 0x0000FFFF839CC2B8 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so -199: 14# 0x0000FFFF839CC248 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so -199: 15# 0x0000FFFF839CC1E0 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so -199: 16# 0x0000FFFF839CC178 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so +199: 12# 0x0000FFFF894DC320 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so +199: 13# 0x0000FFFF894DC2B8 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so +199: 14# 0x0000FFFF894DC248 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so +199: 15# 0x0000FFFF894DC1E0 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so +199: 16# 0x0000FFFF894DC178 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so 199: 17# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/rdBase.so 199: 18# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/rdBase.so 199: 19# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/rdBase.so 199: 20# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/rdBase.so 199: 21# boost::python::handle_exception_impl(boost::function0) in /lib/aarch64-linux-gnu/libboost_python313.so.1.83.0 -199: 22# 0x0000FFFF8543F25C in /lib/aarch64-linux-gnu/libboost_python313.so.1.83.0 +199: 22# 0x0000FFFF8AF4F25C in /lib/aarch64-linux-gnu/libboost_python313.so.1.83.0 199: 23# _PyObject_MakeTpCall in /usr/bin/python3 199: 24# _PyEval_EvalFrameDefault in /usr/bin/python3 199: 25# 0x000000000053D3B0 in /usr/bin/python3 @@ -33489,13 +33337,13 @@ 199: 51# 0x000000000065EE50 in /usr/bin/python3 199: 52# Py_RunMain in /usr/bin/python3 199: 53# Py_BytesMain in /usr/bin/python3 -199: 54# 0x0000FFFF85C2229C in /lib/aarch64-linux-gnu/libc.so.6 +199: 54# 0x0000FFFF8B73229C in /lib/aarch64-linux-gnu/libc.so.6 199: 55# __libc_start_main in /lib/aarch64-linux-gnu/libc.so.6 199: 56# _start in /usr/bin/python3 199: ---------- 199: **** 199: -199: [02:19:31] +199: [11:06:28] 199: 199: **** 199: Pre-condition Violation @@ -33509,23 +33357,23 @@ 199: 2# RDKit::Snapshot::getPoint2D(unsigned int) const in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu//lib/libRDKitTrajectory.so.1 199: 3# boost::python::objects::caller_py_function_impl > >::operator()(_object*, _object*) in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdtrajectory.so 199: 4# boost::python::objects::function::call(_object*, _object*) const in /lib/aarch64-linux-gnu/libboost_python313.so.1.83.0 -199: 5# 0x0000FFFF85442680 in /lib/aarch64-linux-gnu/libboost_python313.so.1.83.0 +199: 5# 0x0000FFFF8AF52680 in /lib/aarch64-linux-gnu/libboost_python313.so.1.83.0 199: 6# boost::python::detail::exception_handler::operator()(boost::function0 const&) const in /lib/aarch64-linux-gnu/libboost_python313.so.1.83.0 199: 7# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdmolfiles.so 199: 8# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdmolfiles.so 199: 9# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdCIPLabeler.so 199: 10# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so -199: 11# 0x0000FFFF839CC320 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so -199: 12# 0x0000FFFF839CC2B8 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so -199: 13# 0x0000FFFF839CC248 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so -199: 14# 0x0000FFFF839CC1E0 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so -199: 15# 0x0000FFFF839CC178 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so +199: 11# 0x0000FFFF894DC320 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so +199: 12# 0x0000FFFF894DC2B8 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so +199: 13# 0x0000FFFF894DC248 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so +199: 14# 0x0000FFFF894DC1E0 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so +199: 15# 0x0000FFFF894DC178 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so 199: 16# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/rdBase.so 199: 17# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/rdBase.so 199: 18# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/rdBase.so 199: 19# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/rdBase.so 199: 20# boost::python::handle_exception_impl(boost::function0) in /lib/aarch64-linux-gnu/libboost_python313.so.1.83.0 -199: 21# 0x0000FFFF8543F25C in /lib/aarch64-linux-gnu/libboost_python313.so.1.83.0 +199: 21# 0x0000FFFF8AF4F25C in /lib/aarch64-linux-gnu/libboost_python313.so.1.83.0 199: 22# _PyObject_MakeTpCall in /usr/bin/python3 199: 23# _PyEval_EvalFrameDefault in /usr/bin/python3 199: 24# 0x000000000053D3B0 in /usr/bin/python3 @@ -33557,13 +33405,13 @@ 199: 50# 0x000000000065EE50 in /usr/bin/python3 199: 51# Py_RunMain in /usr/bin/python3 199: 52# Py_BytesMain in /usr/bin/python3 -199: 53# 0x0000FFFF85C2229C in /lib/aarch64-linux-gnu/libc.so.6 +199: 53# 0x0000FFFF8B73229C in /lib/aarch64-linux-gnu/libc.so.6 199: 54# __libc_start_main in /lib/aarch64-linux-gnu/libc.so.6 199: 55# _start in /usr/bin/python3 199: ---------- 199: **** 199: -199: [02:19:31] +199: [11:06:28] 199: 199: **** 199: Pre-condition Violation @@ -33577,23 +33425,23 @@ 199: 2# RDKit::Snapshot::getPoint2D(unsigned int) const in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu//lib/libRDKitTrajectory.so.1 199: 3# boost::python::objects::caller_py_function_impl > >::operator()(_object*, _object*) in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdtrajectory.so 199: 4# boost::python::objects::function::call(_object*, _object*) const in /lib/aarch64-linux-gnu/libboost_python313.so.1.83.0 -199: 5# 0x0000FFFF85442680 in /lib/aarch64-linux-gnu/libboost_python313.so.1.83.0 +199: 5# 0x0000FFFF8AF52680 in /lib/aarch64-linux-gnu/libboost_python313.so.1.83.0 199: 6# boost::python::detail::exception_handler::operator()(boost::function0 const&) const in /lib/aarch64-linux-gnu/libboost_python313.so.1.83.0 199: 7# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdmolfiles.so 199: 8# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdmolfiles.so 199: 9# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdCIPLabeler.so 199: 10# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so -199: 11# 0x0000FFFF839CC320 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so -199: 12# 0x0000FFFF839CC2B8 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so -199: 13# 0x0000FFFF839CC248 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so -199: 14# 0x0000FFFF839CC1E0 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so -199: 15# 0x0000FFFF839CC178 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so +199: 11# 0x0000FFFF894DC320 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so +199: 12# 0x0000FFFF894DC2B8 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so +199: 13# 0x0000FFFF894DC248 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so +199: 14# 0x0000FFFF894DC1E0 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so +199: 15# 0x0000FFFF894DC178 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so 199: 16# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/rdBase.so 199: 17# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/rdBase.so 199: 18# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/rdBase.so 199: 19# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/rdBase.so 199: 20# boost::python::handle_exception_impl(boost::function0) in /lib/aarch64-linux-gnu/libboost_python313.so.1.83.0 -199: 21# 0x0000FFFF8543F25C in /lib/aarch64-linux-gnu/libboost_python313.so.1.83.0 +199: 21# 0x0000FFFF8AF4F25C in /lib/aarch64-linux-gnu/libboost_python313.so.1.83.0 199: 22# _PyObject_MakeTpCall in /usr/bin/python3 199: 23# _PyEval_EvalFrameDefault in /usr/bin/python3 199: 24# 0x000000000053D3B0 in /usr/bin/python3 @@ -33625,7 +33473,7 @@ 199: 50# 0x000000000065EE50 in /usr/bin/python3 199: 51# Py_RunMain in /usr/bin/python3 199: 52# Py_BytesMain in /usr/bin/python3 -199: 53# 0x0000FFFF85C2229C in /lib/aarch64-linux-gnu/libc.so.6 +199: 53# 0x0000FFFF8B73229C in /lib/aarch64-linux-gnu/libc.so.6 199: 54# __libc_start_main in /lib/aarch64-linux-gnu/libc.so.6 199: 55# _start in /usr/bin/python3 199: ---------- @@ -33633,20 +33481,198 @@ 199: 199: . 199: ---------------------------------------------------------------------- -199: Ran 9 tests in 0.347s +199: Ran 9 tests in 0.187s 199: 199: OK 199: Testing Trajectory wrapper -186: bulk, no symmetry -190/238 Test #199: pyTestTrajectory ....................... Passed 0.75 sec +197: ..............[11:06:28] Can't kekulize mol. Unkekulized atoms: 0 1 2 3 4 +197: [11:06:28] Explicit valence for atom # 1 C, 5, is greater than permitted +188/238 Test #199: pyTestTrajectory ....................... Passed 0.39 sec +test 200 + Start 200: pyTestSGroups + +200: Test command: /usr/bin/python3 "/build/reproducible-path/rdkit-202503.1/Code/GraphMol/Wrap/testSGroups.py" +200: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/Wrap +200: Test timeout computed to be: 1500 +186: [11:06:28] Relabelling existing label +200: ............. +200: ---------------------------------------------------------------------- +200: Ran 13 tests in 0.013s +200: +200: OK +200: Testing SubstanceGroups wrapper +189/238 Test #200: pyTestSGroups .......................... Passed 0.21 sec +test 201 + Start 201: pyTestThreads + +201: Test command: /usr/bin/python3 "/build/reproducible-path/rdkit-202503.1/Code/GraphMol/Wrap/testThreads.py" +201: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/Wrap +201: Test timeout computed to be: 1500 +186: Best mapping +185: ......[11:06:28] +185: +185: **** +185: Pre-condition Violation +185: RingInfo not initialized +185: Violation occurred on line 52 in file ./Code/GraphMol/RingInfo.cpp +185: Failed Expression: df_init +185: ---------- +185: Stacktrace: +185: 0# Invar::Invariant::toString[abi:cxx11]() const in /build/reproducible-path/rdkit-202503.1/obj-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::numAtomRings(unsigned int) const in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu//lib/libRDKitGraphMol.so.1 +185: 3# RDKit::AtomRingQuery::Match(RDKit::Atom const*) const in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu//lib/libRDKitSmilesParse.so.1 +185: 4# Queries::AndQuery::Match(RDKit::Atom const*) const in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu//lib/libRDKitGraphMol.so.1 +185: 5# RDKit::atomCompat(RDKit::Atom const*, RDKit::Atom const*, RDKit::SubstructMatchParameters const&) in /build/reproducible-path/rdkit-202503.1/obj-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 +185: 7# bool boost::detail::VF2SubState const, RDKit::detail::AtomLabelFunctor, RDKit::detail::BondLabelFunctor, RDKit::MolMatchFinalCheckFunctor>::MatchAll, std::allocator > >, std::allocator, std::allocator > > > > >(unsigned int*, unsigned int*, std::vector, std::allocator > >, std::allocator, std::allocator > > > >&, unsigned int) in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu//lib/libRDKitSubstructMatch.so.1 +185: 8# bool boost::vf2_all, RDKit::detail::AtomLabelFunctor, RDKit::detail::BondLabelFunctor, RDKit::MolMatchFinalCheckFunctor, std::vector, std::allocator > >, std::allocator, std::allocator > > > > >(boost::adjacency_list const&, boost::adjacency_list const&, RDKit::detail::AtomLabelFunctor&, RDKit::detail::BondLabelFunctor&, RDKit::MolMatchFinalCheckFunctor&, std::vector, std::allocator > >, std::allocator, std::allocator > > > >&, unsigned int) in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu//lib/libRDKitSubstructMatch.so.1 +185: 9# RDKit::SubstructMatch(RDKit::ROMol const&, RDKit::ROMol const&, RDKit::SubstructMatchParameters const&) in /build/reproducible-path/rdkit-202503.1/obj-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# 0x0000FFFF9504F530 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# 0x0000FFFF96B02680 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# 0x0000FFFF94FAC320 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so +185: 21# 0x0000FFFF94FAC2B8 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so +185: 22# 0x0000FFFF94FAC248 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so +185: 23# 0x0000FFFF94FAC1E0 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so +185: 24# 0x0000FFFF94FAC178 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# 0x0000FFFF96AFF25C in /lib/aarch64-linux-gnu/libboost_python313.so.1.83.0 +185: 31# _PyObject_MakeTpCall in /usr/bin/python3 +185: 32# _PyEval_EvalFrameDefault in /usr/bin/python3 +185: 33# 0x000000000053D3B0 in /usr/bin/python3 +185: 34# _PyEval_EvalFrameDefault in /usr/bin/python3 +185: 35# 0x000000000061C8E0 in /usr/bin/python3 +185: 36# 0x00000000005A787C in /usr/bin/python3 +185: 37# _PyObject_MakeTpCall in /usr/bin/python3 +185: 38# _PyEval_EvalFrameDefault in /usr/bin/python3 +185: 39# 0x000000000053D3B0 in /usr/bin/python3 +185: 40# _PyEval_EvalFrameDefault in /usr/bin/python3 +185: 41# 0x000000000061C8E0 in /usr/bin/python3 +185: 42# 0x00000000005A787C in /usr/bin/python3 +185: 43# _PyObject_MakeTpCall in /usr/bin/python3 +185: 44# _PyEval_EvalFrameDefault in /usr/bin/python3 +185: 45# 0x000000000053D3B0 in /usr/bin/python3 +185: 46# _PyEval_EvalFrameDefault in /usr/bin/python3 +185: 47# 0x000000000061C8E0 in /usr/bin/python3 +185: 48# 0x00000000005A787C in /usr/bin/python3 +185: 49# _PyObject_MakeTpCall in /usr/bin/python3 +185: 50# _PyEval_EvalFrameDefault in /usr/bin/python3 +185: 51# 0x000000000050B030 in /usr/bin/python3 +185: 52# _PyObject_MakeTpCall in /usr/bin/python3 +185: 53# _PyEval_EvalFrameDefault in /usr/bin/python3 +185: 54# PyEval_EvalCode in /usr/bin/python3 +185: 55# 0x000000000064023C in /usr/bin/python3 +185: 56# 0x000000000063BC30 in /usr/bin/python3 +185: 57# 0x000000000065F810 in /usr/bin/python3 +185: 58# 0x000000000065F0B4 in /usr/bin/python3 +185: 59# 0x000000000065EE50 in /usr/bin/python3 +185: 60# Py_RunMain in /usr/bin/python3 +185: 61# Py_BytesMain in /usr/bin/python3 +185: 62# 0x0000FFFF974E229C 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: [11:06:28] +185: +185: **** +185: Pre-condition Violation +185: RingInfo not initialized +185: Violation occurred on line 129 in file ./Code/GraphMol/RingInfo.cpp +185: Failed Expression: df_init +185: ---------- +185: Stacktrace: +185: 0# Invar::Invariant::toString[abi:cxx11]() const in /build/reproducible-path/rdkit-202503.1/obj-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# 0x0000FFFF94AFFCE8 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 +185: 7# bool boost::detail::VF2SubState const, RDKit::detail::AtomLabelFunctor, RDKit::detail::BondLabelFunctor, RDKit::MolMatchFinalCheckFunctor>::MatchAll, std::allocator > >, std::allocator, std::allocator > > > > >(unsigned int*, unsigned int*, std::vector, std::allocator > >, std::allocator, std::allocator > > > >&, unsigned int) in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu//lib/libRDKitSubstructMatch.so.1 +185: 8# bool boost::detail::VF2SubState const, RDKit::detail::AtomLabelFunctor, RDKit::detail::BondLabelFunctor, RDKit::MolMatchFinalCheckFunctor>::MatchAll, std::allocator > >, std::allocator, std::allocator > > > > >(unsigned int*, unsigned int*, std::vector, std::allocator > >, std::allocator, std::allocator > > > >&, unsigned int) in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu//lib/libRDKitSubstructMatch.so.1 +185: 9# bool boost::vf2_all, RDKit::detail::AtomLabelFunctor, RDKit::detail::BondLabelFunctor, RDKit::MolMatchFinalCheckFunctor, std::vector, std::allocator > >, std::allocator, std::allocator > > > > >(boost::adjacency_list const&, boost::adjacency_list const&, RDKit::detail::AtomLabelFunctor&, RDKit::detail::BondLabelFunctor&, RDKit::MolMatchFinalCheckFunctor&, std::vector, std::allocator > >, std::allocator, std::allocator > > > >&, unsigned int) in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu//lib/libRDKitSubstructMatch.so.1 +185: 10# RDKit::SubstructMatch(RDKit::ROMol const&, RDKit::ROMol const&, RDKit::SubstructMatchParameters const&) in /build/reproducible-path/rdkit-202503.1/obj-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# 0x0000FFFF9504F530 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# 0x0000FFFF96B02680 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# 0x0000FFFF94FAC320 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so +185: 22# 0x0000FFFF94FAC2B8 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so +185: 23# 0x0000FFFF94FAC248 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so +185: 24# 0x0000FFFF94FAC1E0 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so +185: 25# 0x0000FFFF94FAC178 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# 0x0000FFFF96AFF25C in /lib/aarch64-linux-gnu/libboost_python313.so.1.83.0 +185: 32# _PyObject_MakeTpCall in /usr/bin/python3 +185: 33# _PyEval_EvalFrameDefault in /usr/bin/python3 +185: 34# 0x000000000053D3B0 in /usr/bin/python3 +185: 35# _PyEval_EvalFrameDefault in /usr/bin/python3 +185: 36# 0x000000000061C8E0 in /usr/bin/python3 +185: 37# 0x00000000005A787C in /usr/bin/python3 +185: 38# _PyObject_MakeTpCall in /usr/bin/python3 +185: 39# _PyEval_EvalFrameDefault in /usr/bin/python3 +185: 40# 0x000000000053D3B0 in /usr/bin/python3 +185: 41# _PyEval_EvalFrameDefault in /usr/bin/python3 +185: 42# 0x000000000061C8E0 in /usr/bin/python3 +185: 43# 0x00000000005A787C in /usr/bin/python3 +185: 44# _PyObject_MakeTpCall in /usr/bin/python3 +185: 45# _PyEval_EvalFrameDefault in /usr/bin/python3 +185: 46# 0x000000000053D3B0 in /usr/bin/python3 +185: 47# _PyEval_EvalFrameDefault in /usr/bin/python3 +185: 48# 0x000000000061C8E0 in /usr/bin/python3 +185: 49# 0x00000000005A787C in /usr/bin/python3 +185: 50# _PyObject_MakeTpCall in /usr/bin/python3 +185: 51# _PyEval_EvalFrameDefault in /usr/bin/python3 +185: 52# 0x000000000050B030 in /usr/bin/python3 +185: 53# _PyObject_MakeTpCall in /usr/bin/python3 +185: 54# _PyEval_EvalFrameDefault in /usr/bin/python3 +185: 55# PyEval_EvalCode in /usr/bin/python3 +185: 56# 0x000000000064023C in /usr/bin/python3 +185: 57# 0x000000000063BC30 in /usr/bin/python3 +185: 58# 0x000000000065F810 in /usr/bin/python3 +185: 59# 0x000000000065F0B4 in /usr/bin/python3 +185: 60# 0x000000000065EE50 in /usr/bin/python3 +185: 61# Py_RunMain in /usr/bin/python3 +185: 62# Py_BytesMain in /usr/bin/python3 +185: 63# 0x0000FFFF974E229C 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: +190/238 Test #186: testRGroupDecomp ....................... Passed 5.32 sec test 202 Start 202: pyTestMultithreadedMolSupplier 202: Test command: /usr/bin/python3 "/build/reproducible-path/rdkit-202503.1/Code/GraphMol/Wrap/testMultithreadedMolSupplier.py" 202: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/Wrap 202: Test timeout computed to be: 1500 -197: ............................[02:19:32] unable to set wavy bonds for double bonds: 3 -197: .............[02:19:32] +197: ............................[11:06:28] unable to set wavy bonds for double bonds: 3 +197: .............[11:06:28] 197: 197: **** 197: Range Error @@ -33661,7 +33687,7 @@ 197: 3# RDKit::RWMol::removeAtom(unsigned int) in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu//lib/libRDKitGraphMol.so.1 197: 4# boost::python::objects::caller_py_function_impl > >::operator()(_object*, _object*) in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so 197: 5# boost::python::objects::function::call(_object*, _object*) const in /lib/aarch64-linux-gnu/libboost_python313.so.1.83.0 -197: 6# 0x0000FFFF89EB2680 in /lib/aarch64-linux-gnu/libboost_python313.so.1.83.0 +197: 6# 0x0000FFFFACC52680 in /lib/aarch64-linux-gnu/libboost_python313.so.1.83.0 197: 7# boost::python::detail::exception_handler::operator()(boost::function0 const&) const in /lib/aarch64-linux-gnu/libboost_python313.so.1.83.0 197: 8# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdSLNParse.so 197: 9# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdChemReactions.so @@ -33672,17 +33698,17 @@ 197: 14# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdmolfiles.so 197: 15# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdCIPLabeler.so 197: 16# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so -197: 17# 0x0000FFFF8839C320 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so -197: 18# 0x0000FFFF8839C2B8 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so -197: 19# 0x0000FFFF8839C248 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so -197: 20# 0x0000FFFF8839C1E0 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so -197: 21# 0x0000FFFF8839C178 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so +197: 17# 0x0000FFFFAB13C320 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so +197: 18# 0x0000FFFFAB13C2B8 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so +197: 19# 0x0000FFFFAB13C248 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so +197: 20# 0x0000FFFFAB13C1E0 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so +197: 21# 0x0000FFFFAB13C178 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so 197: 22# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/rdBase.so 197: 23# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/rdBase.so 197: 24# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/rdBase.so 197: 25# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/rdBase.so 197: 26# boost::python::handle_exception_impl(boost::function0) in /lib/aarch64-linux-gnu/libboost_python313.so.1.83.0 -197: 27# 0x0000FFFF89EAF25C in /lib/aarch64-linux-gnu/libboost_python313.so.1.83.0 +197: 27# 0x0000FFFFACC4F25C in /lib/aarch64-linux-gnu/libboost_python313.so.1.83.0 197: 28# _PyObject_MakeTpCall in /usr/bin/python3 197: 29# _PyEval_EvalFrameDefault in /usr/bin/python3 197: 30# 0x000000000053D3B0 in /usr/bin/python3 @@ -33714,46 +33740,51 @@ 197: 56# 0x000000000065EE50 in /usr/bin/python3 197: 57# Py_RunMain in /usr/bin/python3 197: 58# Py_BytesMain in /usr/bin/python3 -197: 59# 0x0000FFFF8ABF229C in /lib/aarch64-linux-gnu/libc.so.6 +197: 59# 0x0000FFFFAD99229C in /lib/aarch64-linux-gnu/libc.so.6 197: 60# __libc_start_main in /lib/aarch64-linux-gnu/libc.so.6 197: 61# _start in /usr/bin/python3 197: ---------- 197: **** 197: -202: .s. -202: ---------------------------------------------------------------------- -202: Ran 3 tests in 0.099s -202: -202: OK (skipped=1) -202: Testing Smiles and SD MultithreadedMolSupplier -191/238 Test #202: pyTestMultithreadedMolSupplier ......... Passed 0.51 sec +183: [11:06:28] ------------------------------------- +183: [11:06:28] Results do not depend on numThreads (all same) +183: [11:06:28] ------------------------------------- +183: [11:06:28] testTautomerQueries +183: [11:06:28] Pattern fingerprints for tautomersearch aren't tautomer fingerprints, ignoring... +183: [11:06:28] ------------------------------------- +183: [11:06:28] github3881 recursive smarts with rings +191/238 Test #183: substructLibraryTest ................... Passed 6.21 sec test 203 Start 203: pyTestPropertyLists 203: Test command: /usr/bin/python3 "/build/reproducible-path/rdkit-202503.1/Code/GraphMol/Wrap/testPropertyLists.py" 203: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/Wrap 203: Test timeout computed to be: 1500 -186: [02:19:32] Relabelling existing label -186: Best mapping -192/238 Test #186: testRGroupDecomp ....................... Passed 5.32 sec +202: .s. +202: ---------------------------------------------------------------------- +202: Ran 3 tests in 0.091s +202: +202: OK (skipped=1) +202: Testing Smiles and SD MultithreadedMolSupplier +192/238 Test #202: pyTestMultithreadedMolSupplier ......... Passed 0.37 sec test 204 Start 204: pyCDXMLTest 204: Test command: /usr/bin/python3 "/build/reproducible-path/rdkit-202503.1/Code/GraphMol/Wrap/test_cdxml.py" 204: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/Wrap 204: Test timeout computed to be: 1500 -203: [02:19:32] Value [?] for property atom.iprop.PartiallyMissingInt of atom 0 can not be parsed. Ignoring it. -203: [02:19:32] Value ? for property atom.iprop.PartiallyMissingInt of atom 3 can not be parsed. Ignoring it. -203: [02:19:32] Value $$$$ for property atom.iprop.PartiallyMissingInt of atom 4 can not be parsed. Ignoring it. -203: .[02:19:32] Value [?] for property atom.iprop.PartiallyMissingInt of atom 0 can not be parsed. Ignoring it. -203: [02:19:32] Value ? for property atom.iprop.PartiallyMissingInt of atom 3 can not be parsed. Ignoring it. -203: [02:19:32] Value $$$$ for property atom.iprop.PartiallyMissingInt of atom 4 can not be parsed. Ignoring it. -203: ...[02:19:32] Value [?] for property atom.iprop.PartiallyMissingInt of atom 0 can not be parsed. Ignoring it. -203: [02:19:32] Value ? for property atom.iprop.PartiallyMissingInt of atom 3 can not be parsed. Ignoring it. -203: [02:19:32] Value $$$$ for property atom.iprop.PartiallyMissingInt of atom 4 can not be parsed. Ignoring it. +203: [11:06:29] Value [?] for property atom.iprop.PartiallyMissingInt of atom 0 can not be parsed. Ignoring it. +203: [11:06:29] Value ? for property atom.iprop.PartiallyMissingInt of atom 3 can not be parsed. Ignoring it. +203: [11:06:29] Value $$$$ for property atom.iprop.PartiallyMissingInt of atom 4 can not be parsed. Ignoring it. +203: .[11:06:29] Value [?] for property atom.iprop.PartiallyMissingInt of atom 0 can not be parsed. Ignoring it. +203: [11:06:29] Value ? for property atom.iprop.PartiallyMissingInt of atom 3 can not be parsed. Ignoring it. +203: [11:06:29] Value $$$$ for property atom.iprop.PartiallyMissingInt of atom 4 can not be parsed. Ignoring it. +203: ...[11:06:29] Value [?] for property atom.iprop.PartiallyMissingInt of atom 0 can not be parsed. Ignoring it. +203: [11:06:29] Value ? for property atom.iprop.PartiallyMissingInt of atom 3 can not be parsed. Ignoring it. +203: [11:06:29] Value $$$$ for property atom.iprop.PartiallyMissingInt of atom 4 can not be parsed. Ignoring it. 203: . 203: ---------------------------------------------------------------------- -203: Ran 5 tests in 0.013s +203: Ran 5 tests in 0.017s 203: 203: OK 193/238 Test #203: pyTestPropertyLists .................... Passed 0.40 sec @@ -33765,35 +33796,35 @@ 205: Test timeout computed to be: 1500 204: . 204: ---------------------------------------------------------------------- -204: Ran 1 test in 0.018s +204: Ran 1 test in 0.016s 204: 204: OK -197: ....................[02:19:33] Explicit valence for atom # 1 F, 2, is greater than permitted -197: [02:19:33] Explicit valence for atom # 6 F, 2, is greater than permitted -197: [02:19:33] Can't kekulize mol. Unkekulized atoms: 3 4 5 -194/238 Test #204: pyCDXMLTest ............................ Passed 0.27 sec +194/238 Test #204: pyCDXMLTest ............................ Passed 0.44 sec test 206 Start 206: molNormalizeTest 206: Test command: /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/MolStandardize/molNormalizeTest 206: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/MolStandardize 206: Test timeout computed to be: 1500 -206: [02:19:33] Can't kekulize mol. Unkekulized atoms: 3 7 8 9 -206: [02:19:33] Initializing Normalizer -206: [02:19:33] Running Normalizer -206: [02:19:33] Rule applied: BrokenazidetoN=N+=N- -206: [02:19:33] Initializing Normalizer -206: [02:19:33] Running Normalizer -206: [02:19:33] Initializing Normalizer -206: [02:19:33] Running Normalizer -195/238 Test #206: molNormalizeTest ....................... Passed 0.10 sec +206: [11:06:29] Can't kekulize mol. Unkekulized atoms: 3 7 8 9 +197: ....................[11:06:29] Explicit valence for atom # 1 F, 2, is greater than permitted +197: [11:06:29] Explicit valence for atom # 6 F, 2, is greater than permitted +197: [11:06:29] Can't kekulize mol. Unkekulized atoms: 3 4 5 +206: [11:06:29] Initializing Normalizer +206: [11:06:29] Running Normalizer +206: [11:06:29] Rule applied: BrokenazidetoN=N+=N- +206: [11:06:29] Initializing Normalizer +206: [11:06:29] Running Normalizer +206: [11:06:29] Initializing Normalizer +206: [11:06:29] Running Normalizer +195/238 Test #206: molNormalizeTest ....................... Passed 0.19 sec test 207 Start 207: molValidateTest 207: Test command: /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/MolStandardize/molValidateTest 207: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/MolStandardize 207: Test timeout computed to be: 1500 -197: .................[02:19:33] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +197: .................[11:06:29] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 207: ERROR: [FeaturesValidation] Query atom 0 is not allowed 207: ERROR: [FeaturesValidation] Dummy atom 0 is not allowed 207: ERROR: [FeaturesValidation] Query bond 0 is not allowed @@ -33812,7 +33843,7 @@ 207: ERROR: [StereoValidation] Bond 3 has assigned stereo type, but unexpected bond order. 207: there 207: ERROR: [StereoValidation] Atom 0 has stereo bonds, but less than 3 explicit substituents. -196/238 Test #207: molValidateTest ........................ Passed 0.04 sec +196/238 Test #207: molValidateTest ........................ Passed 0.07 sec test 208 Start 208: molChargeTest @@ -33826,8 +33857,7 @@ 209: Test command: /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/MolStandardize/molTautomerTest 209: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/MolStandardize 209: Test timeout computed to be: 1500 -209: [02:19:33] Tautomer enumeration stopped at 292 tautomers: max transforms reached -198/238 Test #205: molStandardizeTest ..................... Passed 1.09 sec +198/238 Test #205: molStandardizeTest ..................... Passed 0.79 sec test 210 Start 210: molStandardizeSmallTest @@ -33841,43 +33871,44 @@ 211: Test command: /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/MolStandardize/molFragmentTest 211: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/MolStandardize 211: Test timeout computed to be: 1500 -211: [02:19:34] SMARTS Parse Error: syntax error while parsing: [Cl -211: [02:19:34] SMARTS Parse Error: Failed parsing SMARTS '[Cl' for input: '[Cl' -200/238 Test #211: molFragmentTest ........................ Passed 0.07 sec +211: [11:06:30] SMARTS Parse Error: syntax error while parsing: [Cl +211: [11:06:30] SMARTS Parse Error: Failed parsing SMARTS '[Cl' for input: '[Cl' +200/238 Test #211: molFragmentTest ........................ Passed 0.08 sec test 212 Start 212: molStandardizeCatchTest 212: Test command: /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/MolStandardize/molStandardizeCatchTest 212: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/MolStandardize 212: Test timeout computed to be: 1500 -209: [02:19:34] Tautomer enumeration stopped at 292 tautomers: max transforms reached -209: [02:19:34] Tautomer enumeration stopped at 50 tautomers: max tautomers reached -209: [02:19:34] Tautomer enumeration stopped at 113 tautomers: canceled -209: Enumeration was canceled due to timeout (50 ms) -212: Randomness seeded to: 3873942915 +209: [11:06:30] Tautomer enumeration stopped at 292 tautomers: max transforms reached +209: [11:06:30] Tautomer enumeration stopped at 292 tautomers: max transforms reached +212: Randomness seeded to: 3746870425 212: * - * - * - * m1 212: * - * - * - * m2 212: * - * - * - * m1 212: * - * - * - * m2 -212: [02:19:34] Can't kekulize mol. Unkekulized atoms: 3 7 -212: [02:19:34] Can't kekulize mol. Unkekulized atoms: 3 8 -212: [02:19:34] Can't kekulize mol. Unkekulized atoms: 2 3 4 +212: [11:06:30] Can't kekulize mol. Unkekulized atoms: 3 7 +212: [11:06:30] Can't kekulize mol. Unkekulized atoms: 3 8 +212: [11:06:30] Can't kekulize mol. Unkekulized atoms: 2 3 4 +209: [11:06:30] Tautomer enumeration stopped at 50 tautomers: max tautomers reached +209: [11:06:30] Tautomer enumeration stopped at 114 tautomers: canceled +209: Enumeration was canceled due to timeout (50 ms) 209: 375 209: Enumeration has completed -209: [02:19:34] Tautomer enumeration stopped at 103 tautomers: canceled -201/238 Test #201: pyTestThreads .......................... Passed 3.31 sec +209: [11:06:31] Tautomer enumeration stopped at 85 tautomers: canceled +201/238 Test #201: pyTestThreads .......................... Passed 3.05 sec test 213 Start 213: molStandardizePipelineTest 213: Test command: /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/MolStandardize/molStandardizePipelineTest 213: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/MolStandardize 213: Test timeout computed to be: 1500 -213: Randomness seeded to: 893002082 +213: Randomness seeded to: 1068241562 213: 1 Counts line too short: '' on line4 213: 1 Could not instantiate a valid molecule from input 213: 8 Molecule has no atoms -213: [02:19:35] Explicit valence for atom # 1 N, 4, is greater than permitted -213: [02:19:35] Explicit valence for atom # 1 N, 4, is greater than permitted +213: [11:06:31] Explicit valence for atom # 1 N, 4, is greater than permitted +213: [11:06:31] Explicit valence for atom # 1 N, 4, is greater than permitted 213: 8 Explicit valence for atom # 1 N, 4, is greater than permitted 213: 128 An error occurred while preparing the molecule for standardization. 213: 8 The molecule contains an unknown isotope: 3C @@ -33892,26 +33923,19 @@ 213: 4 Bond 3 of dative type is not allowed 213: 4 Enhanced stereochemistry features are not allowed 213: 8 The radical at atom 0 is not allowed -213: [02:19:35] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +213: [11:06:31] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 213: 16 The molecule includes non-null Z coordinates 213: 32 Atom 0 too close to bond 2 213: 32 The length of bond 3 between atoms 0 and 3 exceeds a configured limit 213: 64 Atom 0 has 3 explicit substituents and multiple stereo bonds 213: 64 Atom 0 has adjacent stereo bonds with like orientation -213: [02:19:35] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +213: [11:06:31] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 213: 16 The molecule includes non-null Z coordinates 213: 64 Atom 0 has adjacent stereo bonds with like orientation 213: 32 The length of bond 16 between atoms 16 and 1 exceeds a configured limit 213: 8388608 One or more metal atoms were disconnected. 213: 33554432 One or more disconnected fragments (e.g., counterions) were removed. 213: 67108864 The protonation state was adjusted. -209: CN=c1cc[nH]cn1 -209: CN=c1ccnc[nH]1 -209: CNc1ccncn1 -209: res: CNc1ccncn1 -209: CN=c1cccc[nH]1 -209: CNc1ccccn1 -209: res: CNc1ccccn1 213: 16777216 The representation of some functional groups was adjusted. 213: 67108864 The protonation state was adjusted. 213: 16777216 The representation of some functional groups was adjusted. @@ -33951,34 +33975,38 @@ 213: 16777216 Double bond 2 was assigned an undefined/unknown stereochemical configuration 213: 16777216 The "wavy" style of bond 3 was removed 213: 16777216 The representation of some functional groups was adjusted. -202/238 Test #209: molTautomerTest ........................ Passed 1.96 sec +213: [11:06:31] Can't kekulize mol. Unkekulized atoms: 2 3 5 +213: =============================================================================== +213: All tests passed (268 assertions in 5 test cases) +213: +202/238 Test #213: molStandardizePipelineTest ............. Passed 0.26 sec test 214 Start 214: pyMolStandardize 214: Test command: /usr/bin/python3 "/build/reproducible-path/rdkit-202503.1/Code/GraphMol/MolStandardize/Wrap/testMolStandardize.py" 214: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/MolStandardize/Wrap 214: Test timeout computed to be: 1500 -213: [02:19:35] Can't kekulize mol. Unkekulized atoms: 2 3 5 -213: =============================================================================== -213: All tests passed (268 assertions in 5 test cases) -213: -203/238 Test #213: molStandardizePipelineTest ............. Passed 0.26 sec +209: CN=c1cc[nH]cn1 +209: CN=c1ccnc[nH]1 +209: CNc1ccncn1 +209: res: CNc1ccncn1 +209: CN=c1cccc[nH]1 +209: CNc1ccccn1 +209: res: CNc1ccccn1 +203/238 Test #209: molTautomerTest ........................ Passed 2.35 sec test 215 Start 215: testScaffoldNetwork 215: Test command: /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/ScaffoldNetwork/testScaffoldNetwork 215: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/ScaffoldNetwork 215: Test timeout computed to be: 1500 -147: [02:19:35] UFFTYPER: Unrecognized atom type: S_6+6 (0) -147: [02:19:35] UFFTYPER: Warning: hybridization set to SP3 for atom 0 -147: [02:19:35] UFFTYPER: Unrecognized charge state for atom: 0 -214: .....[02:19:36] Tautomer enumeration stopped at 292 tautomers: max transforms reached -214: [02:19:36] Tautomer enumeration stopped at 50 tautomers: max tautomers reached -214: .[02:19:36] Tautomer enumeration stopped at 79 tautomers: canceled +214: .....[11:06:32] Tautomer enumeration stopped at 292 tautomers: max transforms reached +214: [11:06:32] Tautomer enumeration stopped at 50 tautomers: max tautomers reached +214: .[11:06:32] Tautomer enumeration stopped at 89 tautomers: canceled 214: Enumeration was canceled due to timeout (50 ms) 185: ............. 185: ---------------------------------------------------------------------- -185: Ran 19 tests in 9.711s +185: Ran 19 tests in 10.220s 185: 185: OK 185: Testing atom rings @@ -33986,64 +34014,70 @@ 185: searching atom rings 185: searching bond rings 185: done -204/238 Test #185: pySubstructLibrary ..................... Passed 10.20 sec +215: Randomness seeded to: 1808682578 +215: =============================================================================== +215: All tests passed (273 assertions in 19 test cases) +215: +204/238 Test #185: pySubstructLibrary ..................... Passed 10.74 sec test 216 Start 216: pyScaffoldNetwork 216: Test command: /usr/bin/python3 "/build/reproducible-path/rdkit-202503.1/Code/GraphMol/ScaffoldNetwork/Wrap/testScaffoldNetwork.py" 216: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/ScaffoldNetwork/Wrap 216: Test timeout computed to be: 1500 -215: Randomness seeded to: 701376190 -215: =============================================================================== -215: All tests passed (273 assertions in 19 test cases) -215: -205/238 Test #215: testScaffoldNetwork .................... Passed 1.35 sec +205/238 Test #215: testScaffoldNetwork .................... Passed 1.50 sec test 217 Start 217: pyScaffoldNetworkPickling 217: Test command: /usr/bin/python3 "/build/reproducible-path/rdkit-202503.1/Code/GraphMol/ScaffoldNetwork/Wrap/testPickleScaffoldNetwork.py" 217: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/ScaffoldNetwork/Wrap 217: Test timeout computed to be: 1500 -216: ....... -216: ---------------------------------------------------------------------- -216: Ran 7 tests in 0.049s -216: -216: OK +214: Enumeration has completed +214: [11:06:34] Tautomer enumeration stopped at 63 tautomers: canceled 217: . 217: ---------------------------------------------------------------------- 217: Ran 1 test in 0.016s 217: 217: OK -206/238 Test #216: pyScaffoldNetwork ...................... Passed 0.46 sec +206/238 Test #217: pyScaffoldNetworkPickling .............. Passed 0.44 sec test 218 Start 218: testMolEnumerator 218: Test command: /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/MolEnumerator/testMolEnumerator 218: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/MolEnumerator 218: Test timeout computed to be: 1500 -207/238 Test #217: pyScaffoldNetworkPickling .............. Passed 0.46 sec +218: Randomness seeded to: 1179346020 +218: [11:06:34] can only enumerate SRUs with CONNECT=HT or CONNECT=HH +216: ....... +216: ---------------------------------------------------------------------- +216: Ran 7 tests in 0.075s +216: +216: OK +218: =============================================================================== +218: All tests passed (321 assertions in 16 test cases) +218: +207/238 Test #218: testMolEnumerator ...................... Passed 0.11 sec test 219 Start 219: pyMolEnumerator 219: Test command: /usr/bin/python3 "/build/reproducible-path/rdkit-202503.1/Code/GraphMol/MolEnumerator/Wrap/rough_test.py" 219: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/MolEnumerator/Wrap 219: Test timeout computed to be: 1500 -218: Randomness seeded to: 3004879795 -218: [02:19:37] can only enumerate SRUs with CONNECT=HT or CONNECT=HH -218: =============================================================================== -218: All tests passed (321 assertions in 16 test cases) -218: -208/238 Test #218: testMolEnumerator ...................... Passed 0.10 sec +214: ..........[11:06:34] Explicit valence for atom # 1 N, 4, is greater than permitted +214: [11:06:34] Explicit valence for atom # 1 N, 4, is greater than permitted +214: [11:06:34] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +214: [11:06:34] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +208/238 Test #216: pyScaffoldNetwork ...................... Passed 0.68 sec test 220 Start 220: testAbbreviations 220: Test command: /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/Abbreviations/testAbbreviations 220: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/Abbreviations 220: Test timeout computed to be: 1500 -220: Randomness seeded to: 360743837 -220: [02:19:37] SMARTS Parse Error: syntax error while parsing: *fail -220: [02:19:37] SMARTS Parse Error: Failed parsing SMARTS '*fail' for input: '*fail' -220: [02:19:37] no suitable SubstanceGroups found +220: Randomness seeded to: 4275485897 +220: [11:06:34] SMARTS Parse Error: syntax error while parsing: *fail +220: [11:06:34] SMARTS Parse Error: Failed parsing SMARTS '*fail' for input: '*fail' +220: [11:06:34] no suitable SubstanceGroups found 220: =============================================================================== 220: All tests passed (195 assertions in 12 test cases) 220: @@ -34054,86 +34088,7 @@ 221: Test command: /usr/bin/python3 "/build/reproducible-path/rdkit-202503.1/Code/GraphMol/Abbreviations/Wrap/testAbbreviations.py" 221: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/Abbreviations/Wrap 221: Test timeout computed to be: 1500 -219: ... -219: ---------------------------------------------------------------------- -219: Ran 3 tests in 0.016s -219: -219: OK -210/238 Test #219: pyMolEnumerator ........................ Passed 0.42 sec -test 222 - Start 222: generalizedSubstructCatch - -222: Test command: /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/GeneralizedSubstruct/generalizedSubstructCatch -222: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/GeneralizedSubstruct -222: Test timeout computed to be: 1500 -221: ....... -221: ---------------------------------------------------------------------- -221: Ran 7 tests in 0.024s -221: -221: OK -211/238 Test #221: pyAbbreviations ........................ Passed 0.41 sec -test 223 - Start 223: pyGeneralizedSubstruct - -223: Test command: /usr/bin/python3 "/build/reproducible-path/rdkit-202503.1/Code/GraphMol/GeneralizedSubstruct/Wrap/testGeneralizedSubstruct.py" -223: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/GeneralizedSubstruct/Wrap -223: Test timeout computed to be: 1500 -214: Enumeration has completed -214: [02:19:37] Tautomer enumeration stopped at 91 tautomers: canceled -222: Randomness seeded to: 2780732582 -222: =============================================================================== -222: All tests passed (486 assertions in 10 test cases) -222: -212/238 Test #222: generalizedSubstructCatch .............. Passed 0.28 sec -test 224 - Start 224: testMolProcessing - -224: Test command: /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/MolProcessing/testMolProcessing -224: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/MolProcessing -224: Test timeout computed to be: 1500 -214: ..........[02:19:37] Explicit valence for atom # 1 N, 4, is greater than permitted -214: [02:19:37] Explicit valence for atom # 1 N, 4, is greater than permitted -214: [02:19:37] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -214: [02:19:37] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -223: ....... -223: ---------------------------------------------------------------------- -223: Ran 7 tests in 0.157s -223: -223: OK -213/238 Test #223: pyGeneralizedSubstruct ................. Passed 0.56 sec -test 225 - Start 225: pyMolProcessing - -225: Test command: /usr/bin/python3 "/build/reproducible-path/rdkit-202503.1/Code/GraphMol/MolProcessing/Wrap/testMolProcessing.py" -225: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/MolProcessing/Wrap -225: Test timeout computed to be: 1500 -225: .. -225: ---------------------------------------------------------------------- -225: Ran 2 tests in 0.278s -225: -225: OK -214/238 Test #225: pyMolProcessing ........................ Passed 0.66 sec -test 226 - Start 226: testMIF - -226: Test command: /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/MolInteractionFields/testMIF -226: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/MolInteractionFields -226: Test timeout computed to be: 1500 -214: ............[02:19:38] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -214: [02:19:38] Warning: ambiguous stereochemistry - opposing bonds have opposite wedging - at atom 1 ignored. -214: [02:19:38] Warning: ambiguous stereochemistry - opposing bonds have opposite wedging - at atom 1 ignored. -226: Randomness seeded to: 4135192716 -226: =============================================================================== -226: All tests passed (27926 assertions in 8 test cases) -226: -215/238 Test #226: testMIF ................................ Passed 0.09 sec -test 227 - Start 227: pyMIF - -227: Test command: /usr/bin/python3 "/build/reproducible-path/rdkit-202503.1/Code/GraphMol/MolInteractionFields/Wrap/testMIF.py" -227: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/MolInteractionFields/Wrap -227: Test timeout computed to be: 1500 -197: ..[02:19:39] +197: ..[11:06:34] 197: 197: **** 197: Pre-condition Violation @@ -34147,7 +34102,7 @@ 197: 2# RDKit::Atom::getOwningMol() const in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so 197: 3# boost::python::objects::caller_py_function_impl, boost::mpl::vector2 > >::operator()(_object*, _object*) in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so 197: 4# boost::python::objects::function::call(_object*, _object*) const in /lib/aarch64-linux-gnu/libboost_python313.so.1.83.0 -197: 5# 0x0000FFFF89EB2680 in /lib/aarch64-linux-gnu/libboost_python313.so.1.83.0 +197: 5# 0x0000FFFFACC52680 in /lib/aarch64-linux-gnu/libboost_python313.so.1.83.0 197: 6# boost::python::detail::exception_handler::operator()(boost::function0 const&) const in /lib/aarch64-linux-gnu/libboost_python313.so.1.83.0 197: 7# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdSLNParse.so 197: 8# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdChemReactions.so @@ -34158,17 +34113,17 @@ 197: 13# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdmolfiles.so 197: 14# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdCIPLabeler.so 197: 15# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so -197: 16# 0x0000FFFF8839C320 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so -197: 17# 0x0000FFFF8839C2B8 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so -197: 18# 0x0000FFFF8839C248 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so -197: 19# 0x0000FFFF8839C1E0 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so -197: 20# 0x0000FFFF8839C178 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so +197: 16# 0x0000FFFFAB13C320 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so +197: 17# 0x0000FFFFAB13C2B8 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so +197: 18# 0x0000FFFFAB13C248 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so +197: 19# 0x0000FFFFAB13C1E0 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so +197: 20# 0x0000FFFFAB13C178 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so 197: 21# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/rdBase.so 197: 22# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/rdBase.so 197: 23# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/rdBase.so 197: 24# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/rdBase.so 197: 25# boost::python::handle_exception_impl(boost::function0) in /lib/aarch64-linux-gnu/libboost_python313.so.1.83.0 -197: 26# 0x0000FFFF89EAF25C in /lib/aarch64-linux-gnu/libboost_python313.so.1.83.0 +197: 26# 0x0000FFFFACC4F25C in /lib/aarch64-linux-gnu/libboost_python313.so.1.83.0 197: 27# _PyObject_MakeTpCall in /usr/bin/python3 197: 28# _PyEval_EvalFrameDefault in /usr/bin/python3 197: 29# 0x000000000053D3B0 in /usr/bin/python3 @@ -34200,13 +34155,13 @@ 197: 55# 0x000000000065EE50 in /usr/bin/python3 197: 56# Py_RunMain in /usr/bin/python3 197: 57# Py_BytesMain in /usr/bin/python3 -197: 58# 0x0000FFFF8ABF229C in /lib/aarch64-linux-gnu/libc.so.6 +197: 58# 0x0000FFFFAD99229C in /lib/aarch64-linux-gnu/libc.so.6 197: 59# __libc_start_main in /lib/aarch64-linux-gnu/libc.so.6 197: 60# _start in /usr/bin/python3 197: ---------- 197: **** 197: -197: [02:19:39] +197: [11:06:34] 197: 197: **** 197: Pre-condition Violation @@ -34220,7 +34175,7 @@ 197: 2# RDKit::AtomGetNeighbors(RDKit::Atom*) in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so 197: 3# boost::python::objects::caller_py_function_impl > >::operator()(_object*, _object*) in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so 197: 4# boost::python::objects::function::call(_object*, _object*) const in /lib/aarch64-linux-gnu/libboost_python313.so.1.83.0 -197: 5# 0x0000FFFF89EB2680 in /lib/aarch64-linux-gnu/libboost_python313.so.1.83.0 +197: 5# 0x0000FFFFACC52680 in /lib/aarch64-linux-gnu/libboost_python313.so.1.83.0 197: 6# boost::python::detail::exception_handler::operator()(boost::function0 const&) const in /lib/aarch64-linux-gnu/libboost_python313.so.1.83.0 197: 7# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdSLNParse.so 197: 8# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdChemReactions.so @@ -34231,17 +34186,17 @@ 197: 13# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdmolfiles.so 197: 14# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdCIPLabeler.so 197: 15# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so -197: 16# 0x0000FFFF8839C320 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so -197: 17# 0x0000FFFF8839C2B8 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so -197: 18# 0x0000FFFF8839C248 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so -197: 19# 0x0000FFFF8839C1E0 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so -197: 20# 0x0000FFFF8839C178 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so +197: 16# 0x0000FFFFAB13C320 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so +197: 17# 0x0000FFFFAB13C2B8 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so +197: 18# 0x0000FFFFAB13C248 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so +197: 19# 0x0000FFFFAB13C1E0 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so +197: 20# 0x0000FFFFAB13C178 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so 197: 21# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/rdBase.so 197: 22# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/rdBase.so 197: 23# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/rdBase.so 197: 24# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/rdBase.so 197: 25# boost::python::handle_exception_impl(boost::function0) in /lib/aarch64-linux-gnu/libboost_python313.so.1.83.0 -197: 26# 0x0000FFFF89EAF25C in /lib/aarch64-linux-gnu/libboost_python313.so.1.83.0 +197: 26# 0x0000FFFFACC4F25C in /lib/aarch64-linux-gnu/libboost_python313.so.1.83.0 197: 27# _PyObject_MakeTpCall in /usr/bin/python3 197: 28# _PyEval_EvalFrameDefault in /usr/bin/python3 197: 29# 0x000000000053D3B0 in /usr/bin/python3 @@ -34273,13 +34228,13 @@ 197: 55# 0x000000000065EE50 in /usr/bin/python3 197: 56# Py_RunMain in /usr/bin/python3 197: 57# Py_BytesMain in /usr/bin/python3 -197: 58# 0x0000FFFF8ABF229C in /lib/aarch64-linux-gnu/libc.so.6 +197: 58# 0x0000FFFFAD99229C in /lib/aarch64-linux-gnu/libc.so.6 197: 59# __libc_start_main in /lib/aarch64-linux-gnu/libc.so.6 197: 60# _start in /usr/bin/python3 197: ---------- 197: **** 197: -197: [02:19:39] +197: [11:06:34] 197: 197: **** 197: Pre-condition Violation @@ -34293,7 +34248,7 @@ 197: 2# RDKit::AtomGetBonds(RDKit::Atom*) in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so 197: 3# boost::python::objects::caller_py_function_impl > >::operator()(_object*, _object*) in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so 197: 4# boost::python::objects::function::call(_object*, _object*) const in /lib/aarch64-linux-gnu/libboost_python313.so.1.83.0 -197: 5# 0x0000FFFF89EB2680 in /lib/aarch64-linux-gnu/libboost_python313.so.1.83.0 +197: 5# 0x0000FFFFACC52680 in /lib/aarch64-linux-gnu/libboost_python313.so.1.83.0 197: 6# boost::python::detail::exception_handler::operator()(boost::function0 const&) const in /lib/aarch64-linux-gnu/libboost_python313.so.1.83.0 197: 7# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdSLNParse.so 197: 8# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdChemReactions.so @@ -34304,17 +34259,17 @@ 197: 13# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdmolfiles.so 197: 14# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdCIPLabeler.so 197: 15# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so -197: 16# 0x0000FFFF8839C320 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so -197: 17# 0x0000FFFF8839C2B8 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so -197: 18# 0x0000FFFF8839C248 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so -197: 19# 0x0000FFFF8839C1E0 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so -197: 20# 0x0000FFFF8839C178 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so +197: 16# 0x0000FFFFAB13C320 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so +197: 17# 0x0000FFFFAB13C2B8 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so +197: 18# 0x0000FFFFAB13C248 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so +197: 19# 0x0000FFFFAB13C1E0 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so +197: 20# 0x0000FFFFAB13C178 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so 197: 21# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/rdBase.so 197: 22# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/rdBase.so 197: 23# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/rdBase.so 197: 24# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/rdBase.so 197: 25# boost::python::handle_exception_impl(boost::function0) in /lib/aarch64-linux-gnu/libboost_python313.so.1.83.0 -197: 26# 0x0000FFFF89EAF25C in /lib/aarch64-linux-gnu/libboost_python313.so.1.83.0 +197: 26# 0x0000FFFFACC4F25C in /lib/aarch64-linux-gnu/libboost_python313.so.1.83.0 197: 27# _PyObject_MakeTpCall in /usr/bin/python3 197: 28# _PyEval_EvalFrameDefault in /usr/bin/python3 197: 29# 0x000000000053D3B0 in /usr/bin/python3 @@ -34346,13 +34301,13 @@ 197: 55# 0x000000000065EE50 in /usr/bin/python3 197: 56# Py_RunMain in /usr/bin/python3 197: 57# Py_BytesMain in /usr/bin/python3 -197: 58# 0x0000FFFF8ABF229C in /lib/aarch64-linux-gnu/libc.so.6 +197: 58# 0x0000FFFFAD99229C in /lib/aarch64-linux-gnu/libc.so.6 197: 59# __libc_start_main in /lib/aarch64-linux-gnu/libc.so.6 197: 60# _start in /usr/bin/python3 197: ---------- 197: **** 197: -197: [02:19:39] +197: [11:06:34] 197: 197: **** 197: Pre-condition Violation @@ -34366,7 +34321,7 @@ 197: 2# RDKit::AtomIsInRing(RDKit::Atom const*) in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so 197: 3# boost::python::objects::caller_py_function_impl > >::operator()(_object*, _object*) in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so 197: 4# boost::python::objects::function::call(_object*, _object*) const in /lib/aarch64-linux-gnu/libboost_python313.so.1.83.0 -197: 5# 0x0000FFFF89EB2680 in /lib/aarch64-linux-gnu/libboost_python313.so.1.83.0 +197: 5# 0x0000FFFFACC52680 in /lib/aarch64-linux-gnu/libboost_python313.so.1.83.0 197: 6# boost::python::detail::exception_handler::operator()(boost::function0 const&) const in /lib/aarch64-linux-gnu/libboost_python313.so.1.83.0 197: 7# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdSLNParse.so 197: 8# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdChemReactions.so @@ -34377,17 +34332,17 @@ 197: 13# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdmolfiles.so 197: 14# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdCIPLabeler.so 197: 15# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so -197: 16# 0x0000FFFF8839C320 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so -197: 17# 0x0000FFFF8839C2B8 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so -197: 18# 0x0000FFFF8839C248 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so -197: 19# 0x0000FFFF8839C1E0 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so -197: 20# 0x0000FFFF8839C178 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so +197: 16# 0x0000FFFFAB13C320 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so +197: 17# 0x0000FFFFAB13C2B8 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so +197: 18# 0x0000FFFFAB13C248 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so +197: 19# 0x0000FFFFAB13C1E0 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so +197: 20# 0x0000FFFFAB13C178 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so 197: 21# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/rdBase.so 197: 22# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/rdBase.so 197: 23# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/rdBase.so 197: 24# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/rdBase.so 197: 25# boost::python::handle_exception_impl(boost::function0) in /lib/aarch64-linux-gnu/libboost_python313.so.1.83.0 -197: 26# 0x0000FFFF89EAF25C in /lib/aarch64-linux-gnu/libboost_python313.so.1.83.0 +197: 26# 0x0000FFFFACC4F25C in /lib/aarch64-linux-gnu/libboost_python313.so.1.83.0 197: 27# _PyObject_MakeTpCall in /usr/bin/python3 197: 28# _PyEval_EvalFrameDefault in /usr/bin/python3 197: 29# 0x000000000053D3B0 in /usr/bin/python3 @@ -34419,13 +34374,13 @@ 197: 55# 0x000000000065EE50 in /usr/bin/python3 197: 56# Py_RunMain in /usr/bin/python3 197: 57# Py_BytesMain in /usr/bin/python3 -197: 58# 0x0000FFFF8ABF229C in /lib/aarch64-linux-gnu/libc.so.6 +197: 58# 0x0000FFFFAD99229C in /lib/aarch64-linux-gnu/libc.so.6 197: 59# __libc_start_main in /lib/aarch64-linux-gnu/libc.so.6 197: 60# _start in /usr/bin/python3 197: ---------- 197: **** 197: -197: [02:19:39] +197: [11:06:34] 197: 197: **** 197: Pre-condition Violation @@ -34439,7 +34394,7 @@ 197: 2# RDKit::AtomIsInRingSize(RDKit::Atom const*, int) in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so 197: 3# boost::python::objects::caller_py_function_impl > >::operator()(_object*, _object*) in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so 197: 4# boost::python::objects::function::call(_object*, _object*) const in /lib/aarch64-linux-gnu/libboost_python313.so.1.83.0 -197: 5# 0x0000FFFF89EB2680 in /lib/aarch64-linux-gnu/libboost_python313.so.1.83.0 +197: 5# 0x0000FFFFACC52680 in /lib/aarch64-linux-gnu/libboost_python313.so.1.83.0 197: 6# boost::python::detail::exception_handler::operator()(boost::function0 const&) const in /lib/aarch64-linux-gnu/libboost_python313.so.1.83.0 197: 7# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdSLNParse.so 197: 8# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdChemReactions.so @@ -34450,17 +34405,17 @@ 197: 13# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdmolfiles.so 197: 14# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdCIPLabeler.so 197: 15# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so -197: 16# 0x0000FFFF8839C320 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so -197: 17# 0x0000FFFF8839C2B8 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so -197: 18# 0x0000FFFF8839C248 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so -197: 19# 0x0000FFFF8839C1E0 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so -197: 20# 0x0000FFFF8839C178 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so +197: 16# 0x0000FFFFAB13C320 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so +197: 17# 0x0000FFFFAB13C2B8 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so +197: 18# 0x0000FFFFAB13C248 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so +197: 19# 0x0000FFFFAB13C1E0 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so +197: 20# 0x0000FFFFAB13C178 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so 197: 21# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/rdBase.so 197: 22# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/rdBase.so 197: 23# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/rdBase.so 197: 24# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/rdBase.so 197: 25# boost::python::handle_exception_impl(boost::function0) in /lib/aarch64-linux-gnu/libboost_python313.so.1.83.0 -197: 26# 0x0000FFFF89EAF25C in /lib/aarch64-linux-gnu/libboost_python313.so.1.83.0 +197: 26# 0x0000FFFFACC4F25C in /lib/aarch64-linux-gnu/libboost_python313.so.1.83.0 197: 27# _PyObject_MakeTpCall in /usr/bin/python3 197: 28# _PyEval_EvalFrameDefault in /usr/bin/python3 197: 29# 0x000000000053D3B0 in /usr/bin/python3 @@ -34492,13 +34447,13 @@ 197: 55# 0x000000000065EE50 in /usr/bin/python3 197: 56# Py_RunMain in /usr/bin/python3 197: 57# Py_BytesMain in /usr/bin/python3 -197: 58# 0x0000FFFF8ABF229C in /lib/aarch64-linux-gnu/libc.so.6 +197: 58# 0x0000FFFFAD99229C in /lib/aarch64-linux-gnu/libc.so.6 197: 59# __libc_start_main in /lib/aarch64-linux-gnu/libc.so.6 197: 60# _start in /usr/bin/python3 197: ---------- 197: **** 197: -197: .....[02:19:39] +197: .....[11:06:34] 197: 197: **** 197: Range Error @@ -34512,7 +34467,7 @@ 197: 2# RDKit::RWMol::addBond(unsigned int, unsigned int, RDKit::Bond::BondType) in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu//lib/libRDKitGraphMol.so.1 197: 3# boost::python::objects::caller_py_function_impl > >::operator()(_object*, _object*) in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so 197: 4# boost::python::objects::function::call(_object*, _object*) const in /lib/aarch64-linux-gnu/libboost_python313.so.1.83.0 -197: 5# 0x0000FFFF89EB2680 in /lib/aarch64-linux-gnu/libboost_python313.so.1.83.0 +197: 5# 0x0000FFFFACC52680 in /lib/aarch64-linux-gnu/libboost_python313.so.1.83.0 197: 6# boost::python::detail::exception_handler::operator()(boost::function0 const&) const in /lib/aarch64-linux-gnu/libboost_python313.so.1.83.0 197: 7# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdSLNParse.so 197: 8# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdChemReactions.so @@ -34523,17 +34478,17 @@ 197: 13# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdmolfiles.so 197: 14# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdCIPLabeler.so 197: 15# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so -197: 16# 0x0000FFFF8839C320 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so -197: 17# 0x0000FFFF8839C2B8 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so -197: 18# 0x0000FFFF8839C248 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so -197: 19# 0x0000FFFF8839C1E0 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so -197: 20# 0x0000FFFF8839C178 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so +197: 16# 0x0000FFFFAB13C320 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so +197: 17# 0x0000FFFFAB13C2B8 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so +197: 18# 0x0000FFFFAB13C248 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so +197: 19# 0x0000FFFFAB13C1E0 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so +197: 20# 0x0000FFFFAB13C178 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so 197: 21# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/rdBase.so 197: 22# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/rdBase.so 197: 23# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/rdBase.so 197: 24# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/rdBase.so 197: 25# boost::python::handle_exception_impl(boost::function0) in /lib/aarch64-linux-gnu/libboost_python313.so.1.83.0 -197: 26# 0x0000FFFF89EAF25C in /lib/aarch64-linux-gnu/libboost_python313.so.1.83.0 +197: 26# 0x0000FFFFACC4F25C in /lib/aarch64-linux-gnu/libboost_python313.so.1.83.0 197: 27# _PyObject_MakeTpCall in /usr/bin/python3 197: 28# _PyEval_EvalFrameDefault in /usr/bin/python3 197: 29# 0x000000000053D3B0 in /usr/bin/python3 @@ -34565,49 +34520,54 @@ 197: 55# 0x000000000065EE50 in /usr/bin/python3 197: 56# Py_RunMain in /usr/bin/python3 197: 57# Py_BytesMain in /usr/bin/python3 -197: 58# 0x0000FFFF8ABF229C in /lib/aarch64-linux-gnu/libc.so.6 +197: 58# 0x0000FFFFAD99229C in /lib/aarch64-linux-gnu/libc.so.6 197: 59# __libc_start_main in /lib/aarch64-linux-gnu/libc.so.6 197: 60# _start in /usr/bin/python3 197: ---------- 197: **** 197: -197: ......[02:19:39] SMILES Parse Error: unclosed ring for input: 'c1ccccc' -197: [02:19:39] ERROR: Smiles parse error on line 0 -197: [02:19:39] ERROR: Cannot create molecule from : 'c1ccccc' -197: [02:19:39] SMILES Parse Error: extra open parentheses while parsing: C(C -197: [02:19:39] SMILES Parse Error: check for mistakes around position 2: -197: [02:19:39] C(C -197: [02:19:39] ~^ -197: [02:19:39] SMILES Parse Error: Failed parsing SMILES 'C(C' for input: 'C(C' -197: [02:19:39] ERROR: Smiles parse error on line 3 -197: [02:19:39] ERROR: Cannot create molecule from : 'C(C' -197: [02:19:39] Explicit valence for atom # 1 C, 5, is greater than permitted -197: [02:19:39] ERROR: Could not sanitize molecule on line 6 -197: [02:19:39] ERROR: Explicit valence for atom # 1 C, 5, is greater than permitted -197: [02:19:39] SMILES Parse Error: unclosed ring for input: 'c1ccccc' -197: [02:19:39] ERROR: Smiles parse error on line 0 -197: [02:19:39] ERROR: Cannot create molecule from : 'c1ccccc' -197: [02:19:39] SMILES Parse Error: extra open parentheses while parsing: C(C -197: [02:19:39] SMILES Parse Error: check for mistakes around position 2: -197: [02:19:39] C(C -197: [02:19:39] ~^ -197: [02:19:39] SMILES Parse Error: Failed parsing SMILES 'C(C' for input: 'C(C' -197: [02:19:39] ERROR: Smiles parse error on line 3 -197: [02:19:39] ERROR: Cannot create molecule from : 'C(C' -197: [02:19:39] SMILES Parse Error: unclosed ring for input: 'C1C(Cl)CCCC' -197: [02:19:39] ERROR: Smiles parse error on line 6 -197: [02:19:39] ERROR: Cannot create molecule from : 'C1C(Cl)CCCC' -197: [02:19:39] Explicit valence for atom # 1 F, 2, is greater than permitted -197: [02:19:39] ERROR: Could not sanitize molecule ending on line 21 -197: [02:19:39] ERROR: Explicit valence for atom # 1 F, 2, is greater than permitted -197: [02:19:39] ERROR: EOF hit while reading atoms -197: [02:19:39] ERROR: moving to the beginning of the next molecule -197: [02:19:39] Explicit valence for atom # 1 F, 2, is greater than permitted -197: [02:19:39] ERROR: Could not sanitize molecule ending on line 21 -197: [02:19:39] ERROR: Explicit valence for atom # 1 F, 2, is greater than permitted -197: [02:19:39] ERROR: EOF hit while reading atoms -197: [02:19:39] ERROR: moving to the beginning of the next molecule -197: ....[02:19:39] +219: ... +219: ---------------------------------------------------------------------- +219: Ran 3 tests in 0.016s +219: +219: OK +197: ......[11:06:34] SMILES Parse Error: unclosed ring for input: 'c1ccccc' +197: [11:06:34] ERROR: Smiles parse error on line 0 +197: [11:06:34] ERROR: Cannot create molecule from : 'c1ccccc' +197: [11:06:34] SMILES Parse Error: extra open parentheses while parsing: C(C +197: [11:06:34] SMILES Parse Error: check for mistakes around position 2: +197: [11:06:34] C(C +197: [11:06:34] ~^ +197: [11:06:34] SMILES Parse Error: Failed parsing SMILES 'C(C' for input: 'C(C' +197: [11:06:34] ERROR: Smiles parse error on line 3 +197: [11:06:34] ERROR: Cannot create molecule from : 'C(C' +197: [11:06:34] Explicit valence for atom # 1 C, 5, is greater than permitted +197: [11:06:34] ERROR: Could not sanitize molecule on line 6 +197: [11:06:34] ERROR: Explicit valence for atom # 1 C, 5, is greater than permitted +197: [11:06:34] SMILES Parse Error: unclosed ring for input: 'c1ccccc' +197: [11:06:34] ERROR: Smiles parse error on line 0 +197: [11:06:34] ERROR: Cannot create molecule from : 'c1ccccc' +197: [11:06:34] SMILES Parse Error: extra open parentheses while parsing: C(C +197: [11:06:34] SMILES Parse Error: check for mistakes around position 2: +197: [11:06:34] C(C +197: [11:06:34] ~^ +197: [11:06:34] SMILES Parse Error: Failed parsing SMILES 'C(C' for input: 'C(C' +197: [11:06:34] ERROR: Smiles parse error on line 3 +197: [11:06:34] ERROR: Cannot create molecule from : 'C(C' +197: [11:06:34] SMILES Parse Error: unclosed ring for input: 'C1C(Cl)CCCC' +197: [11:06:34] ERROR: Smiles parse error on line 6 +197: [11:06:34] ERROR: Cannot create molecule from : 'C1C(Cl)CCCC' +197: [11:06:34] Explicit valence for atom # 1 F, 2, is greater than permitted +197: [11:06:34] ERROR: Could not sanitize molecule ending on line 21 +197: [11:06:34] ERROR: Explicit valence for atom # 1 F, 2, is greater than permitted +197: [11:06:34] ERROR: EOF hit while reading atoms +197: [11:06:34] ERROR: moving to the beginning of the next molecule +197: [11:06:34] Explicit valence for atom # 1 F, 2, is greater than permitted +197: [11:06:34] ERROR: Could not sanitize molecule ending on line 21 +197: [11:06:34] ERROR: Explicit valence for atom # 1 F, 2, is greater than permitted +197: [11:06:34] ERROR: EOF hit while reading atoms +197: [11:06:34] ERROR: moving to the beginning of the next molecule +197: ....[11:06:34] 197: 197: **** 197: Pre-condition Violation @@ -34621,7 +34581,7 @@ 197: 2# RDKit::RingInfo::numRings() const in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu//lib/libRDKitGraphMol.so.1 197: 3# boost::python::objects::caller_py_function_impl > >::operator()(_object*, _object*) in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so 197: 4# boost::python::objects::function::call(_object*, _object*) const in /lib/aarch64-linux-gnu/libboost_python313.so.1.83.0 -197: 5# 0x0000FFFF89EB2680 in /lib/aarch64-linux-gnu/libboost_python313.so.1.83.0 +197: 5# 0x0000FFFFACC52680 in /lib/aarch64-linux-gnu/libboost_python313.so.1.83.0 197: 6# boost::python::detail::exception_handler::operator()(boost::function0 const&) const in /lib/aarch64-linux-gnu/libboost_python313.so.1.83.0 197: 7# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdSLNParse.so 197: 8# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdChemReactions.so @@ -34632,17 +34592,17 @@ 197: 13# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdmolfiles.so 197: 14# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdCIPLabeler.so 197: 15# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so -197: 16# 0x0000FFFF8839C320 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so -197: 17# 0x0000FFFF8839C2B8 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so -197: 18# 0x0000FFFF8839C248 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so -197: 19# 0x0000FFFF8839C1E0 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so -197: 20# 0x0000FFFF8839C178 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so +197: 16# 0x0000FFFFAB13C320 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so +197: 17# 0x0000FFFFAB13C2B8 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so +197: 18# 0x0000FFFFAB13C248 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so +197: 19# 0x0000FFFFAB13C1E0 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so +197: 20# 0x0000FFFFAB13C178 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so 197: 21# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/rdBase.so 197: 22# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/rdBase.so 197: 23# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/rdBase.so 197: 24# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/rdBase.so 197: 25# boost::python::handle_exception_impl(boost::function0) in /lib/aarch64-linux-gnu/libboost_python313.so.1.83.0 -197: 26# 0x0000FFFF89EAF25C in /lib/aarch64-linux-gnu/libboost_python313.so.1.83.0 +197: 26# 0x0000FFFFACC4F25C in /lib/aarch64-linux-gnu/libboost_python313.so.1.83.0 197: 27# _PyObject_MakeTpCall in /usr/bin/python3 197: 28# _PyEval_EvalFrameDefault in /usr/bin/python3 197: 29# 0x000000000053D3B0 in /usr/bin/python3 @@ -34674,13 +34634,13 @@ 197: 55# 0x000000000065EE50 in /usr/bin/python3 197: 56# Py_RunMain in /usr/bin/python3 197: 57# Py_BytesMain in /usr/bin/python3 -197: 58# 0x0000FFFF8ABF229C in /lib/aarch64-linux-gnu/libc.so.6 +197: 58# 0x0000FFFFAD99229C in /lib/aarch64-linux-gnu/libc.so.6 197: 59# __libc_start_main in /lib/aarch64-linux-gnu/libc.so.6 197: 60# _start in /usr/bin/python3 197: ---------- 197: **** 197: -197: .............[02:19:39] +197: .............[11:06:34] 197: 197: **** 197: Range Error @@ -34694,7 +34654,7 @@ 197: 2# RDKit::ROMol::getAtomWithIdx(unsigned int) in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu//lib/libRDKitGraphMol.so.1 197: 3# boost::python::objects::caller_py_function_impl >, boost::mpl::vector3 > >::operator()(_object*, _object*) in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so 197: 4# boost::python::objects::function::call(_object*, _object*) const in /lib/aarch64-linux-gnu/libboost_python313.so.1.83.0 -197: 5# 0x0000FFFF89EB2680 in /lib/aarch64-linux-gnu/libboost_python313.so.1.83.0 +197: 5# 0x0000FFFFACC52680 in /lib/aarch64-linux-gnu/libboost_python313.so.1.83.0 197: 6# boost::python::detail::exception_handler::operator()(boost::function0 const&) const in /lib/aarch64-linux-gnu/libboost_python313.so.1.83.0 197: 7# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdSLNParse.so 197: 8# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdChemReactions.so @@ -34705,17 +34665,17 @@ 197: 13# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdmolfiles.so 197: 14# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdCIPLabeler.so 197: 15# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so -197: 16# 0x0000FFFF8839C320 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so -197: 17# 0x0000FFFF8839C2B8 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so -197: 18# 0x0000FFFF8839C248 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so -197: 19# 0x0000FFFF8839C1E0 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so -197: 20# 0x0000FFFF8839C178 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so +197: 16# 0x0000FFFFAB13C320 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so +197: 17# 0x0000FFFFAB13C2B8 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so +197: 18# 0x0000FFFFAB13C248 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so +197: 19# 0x0000FFFFAB13C1E0 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so +197: 20# 0x0000FFFFAB13C178 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so 197: 21# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/rdBase.so 197: 22# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/rdBase.so 197: 23# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/rdBase.so 197: 24# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/rdBase.so 197: 25# boost::python::handle_exception_impl(boost::function0) in /lib/aarch64-linux-gnu/libboost_python313.so.1.83.0 -197: 26# 0x0000FFFF89EAF25C in /lib/aarch64-linux-gnu/libboost_python313.so.1.83.0 +197: 26# 0x0000FFFFACC4F25C in /lib/aarch64-linux-gnu/libboost_python313.so.1.83.0 197: 27# _PyObject_MakeTpCall in /usr/bin/python3 197: 28# _PyEval_EvalFrameDefault in /usr/bin/python3 197: 29# 0x000000000053D3B0 in /usr/bin/python3 @@ -34747,33 +34707,148 @@ 197: 55# 0x000000000065EE50 in /usr/bin/python3 197: 56# Py_RunMain in /usr/bin/python3 197: 57# Py_BytesMain in /usr/bin/python3 -197: 58# 0x0000FFFF8ABF229C in /lib/aarch64-linux-gnu/libc.so.6 +197: 58# 0x0000FFFFAD99229C in /lib/aarch64-linux-gnu/libc.so.6 197: 59# __libc_start_main in /lib/aarch64-linux-gnu/libc.so.6 197: 60# _start in /usr/bin/python3 197: ---------- 197: **** 197: -197: ...[02:19:39] Can't kekulize mol. Unkekulized atoms: 0 1 2 3 4 -214: ........[02:19:39] Explicit valence for atom # 1 O, 3, is greater than permitted -197: ............................[02:19:39] SMILES Parse Error: unclosed ring for input: 'C1CC' +197: ...[11:06:34] Can't kekulize mol. Unkekulized atoms: 0 1 2 3 4 +221: ....... +221: ---------------------------------------------------------------------- +221: Ran 7 tests in 0.025s +221: +221: OK +210/238 Test #219: pyMolEnumerator ........................ Passed 0.49 sec +test 222 + Start 222: generalizedSubstructCatch + +222: Test command: /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/GeneralizedSubstruct/generalizedSubstructCatch +222: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/GeneralizedSubstruct +222: Test timeout computed to be: 1500 +211/238 Test #221: pyAbbreviations ........................ Passed 0.38 sec +test 223 + Start 223: pyGeneralizedSubstruct + +223: Test command: /usr/bin/python3 "/build/reproducible-path/rdkit-202503.1/Code/GraphMol/GeneralizedSubstruct/Wrap/testGeneralizedSubstruct.py" +223: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/GeneralizedSubstruct/Wrap +223: Test timeout computed to be: 1500 +197: ............................[11:06:34] SMILES Parse Error: unclosed ring for input: 'C1CC' 197: ......smi: CC1=C(n2cccc2[C@H](C)Cl)C(C)CCC1 |(2.679,0.4142,;1.3509,1.181,;0.0229,0.4141,;0.0229,-1.1195,;1.2645,-2.0302,;0.7901,-3.4813,;-0.7446,-3.4813,;-1.219,-2.0302,;-2.679,-1.5609,;-3.0039,-0.0556,;-3.8202,-2.595,;-1.3054,1.1809,;-2.6335,0.4141,;-1.3054,2.7145,;0.0229,3.4813,;1.3509,2.7146,),wD:8.9,2.11,a:2,&1:8| 197: 643 -197: ..[02:19:39] WARNING: not removing hydrogen atom without neighbors -197: [02:19:39] WARNING: not removing hydrogen atom with dummy atom neighbors -197: [02:19:39] WARNING: not removing hydrogen atom with wedged bond -197: [02:19:39] WARNING: not removing hydrogen atom without neighbors -197: [02:19:39] WARNING: not removing hydrogen atom with dummy atom neighbors +197: ..[11:06:34] WARNING: not removing hydrogen atom without neighbors +197: [11:06:34] WARNING: not removing hydrogen atom with dummy atom neighbors +197: [11:06:34] WARNING: not removing hydrogen atom with wedged bond +197: [11:06:34] WARNING: not removing hydrogen atom without neighbors +197: [11:06:34] WARNING: not removing hydrogen atom with dummy atom neighbors +197: ......[11:06:35] Explicit valence for atom # 1 F, 2, is greater than permitted +197: [11:06:35] Can't kekulize mol. Unkekulized atoms: 0 1 2 +197: .[11:06:35] Explicit valence for atom # 1 F, 2, is greater than permitted +197: [11:06:35] Explicit valence for atom # 1 F, 2, is greater than permitted +197: [11:06:35] Explicit valence for atom # 1 F, 2, is greater than permitted +197: [11:06:35] Explicit valence for atom # 1 F, 2, is greater than permitted +197: [11:06:35] Can't kekulize mol. Unkekulized atoms: 0 1 2 +197: [11:06:35] Can't kekulize mol. Unkekulized atoms: 0 1 2 +197: [11:06:35] Can't kekulize mol. Unkekulized atoms: 0 1 2 +197: ..........[11:06:35] SMARTS Parse Error: syntax error while parsing: CCC |$foo;;bar$| ourname +197: [11:06:35] SMARTS Parse Error: Failed parsing SMARTS 'CCC |$foo;;bar$| ourname' for input: 'CCC |$foo;;bar$| ourname' +197: .[11:06:35] SMILES Parse Error: syntax error while parsing: CCC |$foo;;bar$| ourname +197: [11:06:35] SMILES Parse Error: check for mistakes around position 4: +197: [11:06:35] CCC |$foo;;bar$| ourname +197: [11:06:35] ~~~^ +197: [11:06:35] SMILES Parse Error: Failed parsing SMILES 'CCC |$foo;;bar$| ourname' for input: 'CCC |$foo;;bar$| ourname' +197: ..[11:06:35] SMILES Parse Error: syntax error while parsing: error +197: [11:06:35] SMILES Parse Error: check for mistakes around position 1: +197: [11:06:35] error +197: [11:06:35] ^ +197: [11:06:35] SMILES Parse Error: Failed parsing SMILES 'error' for input: 'error' +197: [11:06:35] SMILES Parse Error: Failed parsing SMILES 'd' for input: 'd' +197: [11:06:35] SMARTS Parse Error: Failed parsing SMARTS 'error' for input: 'error' +197: [11:06:35] SMARTS Parse Error: Failed parsing SMARTS 'd' for input: 'd' +197: .........................[11:06:35] SMILES Parse Error: syntax error while parsing: garbage_0 +197: [11:06:35] SMILES Parse Error: check for mistakes around position 1: +197: [11:06:35] garbage_0 +197: [11:06:35] ^ +197: [11:06:35] SMILES Parse Error: Failed parsing SMILES 'garbage_0' for input: 'garbage_0' +197: [11:06:35] SMILES Parse Error: syntax error while parsing: garbage_2 +197: [11:06:35] SMILES Parse Error: check for mistakes around position 1: +197: [11:06:35] garbage_2 +197: [11:06:35] ^ +197: [11:06:35] SMILES Parse Error: Failed parsing SMILES 'garbage_2' for input: 'garbage_2' +197: [11:06:35] SMILES Parse Error: syntax error while parsing: garbage_4 +197: [11:06:35] SMILES Parse Error: check for mistakes around position 1: +197: [11:06:35] garbage_4 +197: [11:06:35] ^ +197: [11:06:35] SMILES Parse Error: Failed parsing SMILES 'garbage_4' for input: 'garbage_4' +222: Randomness seeded to: 740831844 +222: =============================================================================== +222: All tests passed (486 assertions in 10 test cases) +222: +212/238 Test #222: generalizedSubstructCatch .............. Passed 0.40 sec +test 224 + Start 224: testMolProcessing + +224: Test command: /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/MolProcessing/testMolProcessing +224: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/MolProcessing +224: Test timeout computed to be: 1500 +197: ............ +197: ---------------------------------------------------------------------- +197: Ran 279 tests in 7.176s +197: +197: OK +197: supplier: +197: supplier: +197: supplier: +213/238 Test #197: pyGraphMolWrap ......................... Passed 7.71 sec +test 225 + Start 225: pyMolProcessing + +225: Test command: /usr/bin/python3 "/build/reproducible-path/rdkit-202503.1/Code/GraphMol/MolProcessing/Wrap/testMolProcessing.py" +225: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/MolProcessing/Wrap +225: Test timeout computed to be: 1500 +214: ............[11:06:35] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +214: [11:06:35] Warning: ambiguous stereochemistry - opposing bonds have opposite wedging - at atom 1 ignored. +214: [11:06:35] Warning: ambiguous stereochemistry - opposing bonds have opposite wedging - at atom 1 ignored. +223: ....... +223: ---------------------------------------------------------------------- +223: Ran 7 tests in 0.283s +223: +223: OK +214: ........[11:06:35] Explicit valence for atom # 1 O, 3, is greater than permitted +214/238 Test #223: pyGeneralizedSubstruct ................. Passed 0.80 sec +test 226 + Start 226: testMIF + +226: Test command: /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/MolInteractionFields/testMIF +226: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/MolInteractionFields +226: Test timeout computed to be: 1500 +150: --------------------------------- +150: test getO3AForProbeConfs +150: +150: *********************************************************** +215/238 Test #150: testO3AAlign ........................... Passed 27.77 sec +test 227 + Start 227: pyMIF + +227: Test command: /usr/bin/python3 "/build/reproducible-path/rdkit-202503.1/Code/GraphMol/MolInteractionFields/Wrap/testMIF.py" +227: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/MolInteractionFields/Wrap +227: Test timeout computed to be: 1500 +225: .. +225: ---------------------------------------------------------------------- +225: Ran 2 tests in 0.193s +225: +225: OK 214: .. 214: ---------------------------------------------------------------------- -214: Ran 38 tests in 3.504s +214: Ran 38 tests in 3.590s 214: 214: OK 214: done -150: --------------------------------- -150: test getO3AForProbeConfs -150: -150: *********************************************************** -216/238 Test #150: testO3AAlign ........................... Passed 28.25 sec +226: Randomness seeded to: 3957813372 +226: =============================================================================== +226: All tests passed (27926 assertions in 8 test cases) +226: +216/238 Test #226: testMIF ................................ Passed 0.15 sec test 228 Start 228: testQuery @@ -34797,13 +34872,20 @@ 228: XOr 228: pointer and copy foo 228: Set2 -217/238 Test #228: testQuery .............................. Passed 0.01 sec +217/238 Test #225: pyMolProcessing ........................ Passed 0.49 sec +218/238 Test #228: testQuery .............................. Passed 0.01 sec test 229 Start 229: testBaseFeatures 229: Test command: /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/Features/testBaseFeatures 229: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/Features 229: Test timeout computed to be: 1500 +test 230 + Start 230: testMatCalc + +230: Test command: /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/DataManip/MetricMatrixCalc/testMatCalc +230: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/DataManip/MetricMatrixCalc +230: Test timeout computed to be: 1500 229: ------------------------------------- 229: Basics for ExplicitFeatures. 229: done @@ -34813,13 +34895,13 @@ 229: ------------------------------------- 229: ExplicitFeatures 2D, string type. 229: done -218/238 Test #229: testBaseFeatures ....................... Passed 0.01 sec -test 230 - Start 230: testMatCalc +219/238 Test #229: testBaseFeatures ....................... Passed 0.01 sec +test 231 + Start 231: pyMatCalc -230: Test command: /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/DataManip/MetricMatrixCalc/testMatCalc -230: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/DataManip/MetricMatrixCalc -230: Test timeout computed to be: 1500 +231: Test command: /usr/bin/python3 "/build/reproducible-path/rdkit-202503.1/Code/DataManip/MetricMatrixCalc/Wrap/testMatricCalc.py" +231: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/DataManip/MetricMatrixCalc/Wrap +231: Test timeout computed to be: 1500 230: 1.68022e+08 230: 1.73149e+08 230: 1.05549e+08 @@ -34865,26 +34947,19 @@ 230: 9.49496e+07 230: 2.25618e+08 230: 1.30219e+08 -219/238 Test #230: testMatCalc ............................ Passed 0.01 sec -test 231 - Start 231: pyMatCalc - -231: Test command: /usr/bin/python3 "/build/reproducible-path/rdkit-202503.1/Code/DataManip/MetricMatrixCalc/Wrap/testMatricCalc.py" -231: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/DataManip/MetricMatrixCalc/Wrap -231: Test timeout computed to be: 1500 -220/238 Test #214: pyMolStandardize ....................... Passed 3.91 sec +220/238 Test #230: testMatCalc ............................ Passed 0.01 sec test 232 Start 232: testSimDivPickers 232: Test command: /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/SimDivPickers/testSimDivPickers 232: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/SimDivPickers 232: Test timeout computed to be: 1500 -232: [02:19:39] ------------------------------------- -232: [02:19:39] Testing github issue 1421: MaxMinPicker picking non-existent element. -232: [02:19:39] Done -232: [02:19:39] ------------------------------------- -232: [02:19:39] Testing github issue 2245: MinMax Diversity picker seeding shows deterministic / non-random behaviour. -232: [02:19:39] Done +232: [11:06:35] ------------------------------------- +232: [11:06:35] Testing github issue 1421: MaxMinPicker picking non-existent element. +232: [11:06:35] Done +232: [11:06:35] ------------------------------------- +232: [11:06:35] Testing github issue 2245: MinMax Diversity picker seeding shows deterministic / non-random behaviour. +232: [11:06:35] Done 221/238 Test #232: testSimDivPickers ...................... Passed 0.01 sec test 233 Start 233: pickersTestsCatch @@ -34892,78 +34967,31 @@ 233: Test command: /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/SimDivPickers/pickersTestsCatch 233: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/SimDivPickers 233: Test timeout computed to be: 1500 -197: ......[02:19:39] Explicit valence for atom # 1 F, 2, is greater than permitted -197: [02:19:39] Can't kekulize mol. Unkekulized atoms: 0 1 2 -197: .[02:19:39] Explicit valence for atom # 1 F, 2, is greater than permitted -197: [02:19:39] Explicit valence for atom # 1 F, 2, is greater than permitted -197: [02:19:39] Explicit valence for atom # 1 F, 2, is greater than permitted -197: [02:19:39] Explicit valence for atom # 1 F, 2, is greater than permitted -197: [02:19:39] Can't kekulize mol. Unkekulized atoms: 0 1 2 -197: [02:19:39] Can't kekulize mol. Unkekulized atoms: 0 1 2 -197: [02:19:39] Can't kekulize mol. Unkekulized atoms: 0 1 2 -197: ..........[02:19:39] SMARTS Parse Error: syntax error while parsing: CCC |$foo;;bar$| ourname -197: [02:19:39] SMARTS Parse Error: Failed parsing SMARTS 'CCC |$foo;;bar$| ourname' for input: 'CCC |$foo;;bar$| ourname' -197: .[02:19:39] SMILES Parse Error: syntax error while parsing: CCC |$foo;;bar$| ourname -197: [02:19:39] SMILES Parse Error: check for mistakes around position 4: -197: [02:19:39] CCC |$foo;;bar$| ourname -197: [02:19:39] ~~~^ -197: [02:19:39] SMILES Parse Error: Failed parsing SMILES 'CCC |$foo;;bar$| ourname' for input: 'CCC |$foo;;bar$| ourname' -197: ..[02:19:39] SMILES Parse Error: syntax error while parsing: error -197: [02:19:39] SMILES Parse Error: check for mistakes around position 1: -197: [02:19:39] error -197: [02:19:39] ^ -197: [02:19:39] SMILES Parse Error: Failed parsing SMILES 'error' for input: 'error' -197: [02:19:39] SMILES Parse Error: Failed parsing SMILES 'd' for input: 'd' -197: [02:19:39] SMARTS Parse Error: Failed parsing SMARTS 'error' for input: 'error' -197: [02:19:39] SMARTS Parse Error: Failed parsing SMARTS 'd' for input: 'd' -233: Randomness seeded to: 2031090639 -233: =============================================================================== -233: All tests passed (21267 assertions in 1 test case) -233: -222/238 Test #233: pickersTestsCatch ...................... Passed 0.11 sec +222/238 Test #214: pyMolStandardize ....................... Passed 4.01 sec test 234 Start 234: pySimDivPickers 234: Test command: /usr/bin/python3 "/build/reproducible-path/rdkit-202503.1/Code/SimDivPickers/Wrap/testPickers.py" 234: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/SimDivPickers/Wrap 234: Test timeout computed to be: 1500 -197: .........................[02:19:39] SMILES Parse Error: syntax error while parsing: garbage_0 -197: [02:19:39] SMILES Parse Error: check for mistakes around position 1: -197: [02:19:39] garbage_0 -197: [02:19:39] ^ -197: [02:19:39] SMILES Parse Error: Failed parsing SMILES 'garbage_0' for input: 'garbage_0' -197: [02:19:39] SMILES Parse Error: syntax error while parsing: garbage_2 -197: [02:19:39] SMILES Parse Error: check for mistakes around position 1: -197: [02:19:39] garbage_2 -197: [02:19:39] ^ -197: [02:19:39] SMILES Parse Error: Failed parsing SMILES 'garbage_2' for input: 'garbage_2' -197: [02:19:39] SMILES Parse Error: syntax error while parsing: garbage_4 -197: [02:19:39] SMILES Parse Error: check for mistakes around position 1: -197: [02:19:39] garbage_4 -197: [02:19:39] ^ -197: [02:19:39] SMILES Parse Error: Failed parsing SMILES 'garbage_4' for input: 'garbage_4' -197: ............ -197: ---------------------------------------------------------------------- -197: Ran 279 tests in 7.972s -197: -197: OK -197: supplier: -197: supplier: -197: supplier: 227: ....... 227: ---------------------------------------------------------------------- -227: Ran 7 tests in 0.051s +227: Ran 7 tests in 0.042s 227: 227: OK +233: Randomness seeded to: 3177107768 +233: =============================================================================== +233: All tests passed (21267 assertions in 1 test case) +233: 227: Testing MIF wrapper -223/238 Test #227: pyMIF .................................. Passed 0.46 sec +223/238 Test #233: pickersTestsCatch ...................... Passed 0.13 sec test 235 Start 235: pyRanker 235: Test command: /usr/bin/python3 "/build/reproducible-path/rdkit-202503.1/Code/ML/InfoTheory/Wrap/testRanker.py" 235: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/ML/InfoTheory/Wrap 235: Test timeout computed to be: 1500 -224/238 Test #197: pyGraphMolWrap ......................... Passed 8.56 sec +224/238 Test #227: pyMIF .................................. Passed 0.31 sec test 236 Start 236: testChemicalFeatures @@ -34980,11 +35008,11 @@ 237: Test command: /usr/bin/python3 "/build/reproducible-path/rdkit-202503.1/Code/ChemicalFeatures/Wrap/testFeatures.py" 237: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/ChemicalFeatures/Wrap 237: Test timeout computed to be: 1500 -234: [02:19:39] the useCache argument is deprecated and ignored -234: ...[02:19:39] the useCache argument is deprecated and ignored -234: [02:19:39] the useCache argument is deprecated and ignored -234: .[02:19:39] the useCache argument is deprecated and ignored -235: ..[02:19:39] +234: [11:06:36] the useCache argument is deprecated and ignored +234: ...[11:06:36] the useCache argument is deprecated and ignored +234: [11:06:36] the useCache argument is deprecated and ignored +234: .[11:06:36] the useCache argument is deprecated and ignored +235: ..[11:06:36] 235: 235: **** 235: Invariant Violation @@ -34999,14 +35027,14 @@ 235: 3# RDInfoTheory::getTopNbits(RDInfoTheory::InfoBitRanker*, int) in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/ML/InfoTheory/rdInfoTheory.so 235: 4# boost::python::objects::caller_py_function_impl > >::operator()(_object*, _object*) in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/ML/InfoTheory/rdInfoTheory.so 235: 5# boost::python::objects::function::call(_object*, _object*) const in /lib/aarch64-linux-gnu/libboost_python313.so.1.83.0 -235: 6# 0x0000FFFFA7752680 in /lib/aarch64-linux-gnu/libboost_python313.so.1.83.0 +235: 6# 0x0000FFFFB6822680 in /lib/aarch64-linux-gnu/libboost_python313.so.1.83.0 235: 7# boost::python::detail::exception_handler::operator()(boost::function0 const&) const in /lib/aarch64-linux-gnu/libboost_python313.so.1.83.0 235: 8# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/rdBase.so 235: 9# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/rdBase.so 235: 10# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/rdBase.so 235: 11# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/rdBase.so 235: 12# boost::python::handle_exception_impl(boost::function0) in /lib/aarch64-linux-gnu/libboost_python313.so.1.83.0 -235: 13# 0x0000FFFFA774F25C in /lib/aarch64-linux-gnu/libboost_python313.so.1.83.0 +235: 13# 0x0000FFFFB681F25C in /lib/aarch64-linux-gnu/libboost_python313.so.1.83.0 235: 14# _PyObject_MakeTpCall in /usr/bin/python3 235: 15# _PyEval_EvalFrameDefault in /usr/bin/python3 235: 16# 0x000000000053D3B0 in /usr/bin/python3 @@ -35038,7 +35066,7 @@ 235: 42# 0x000000000065EE50 in /usr/bin/python3 235: 43# Py_RunMain in /usr/bin/python3 235: 44# Py_BytesMain in /usr/bin/python3 -235: 45# 0x0000FFFFA90B229C in /lib/aarch64-linux-gnu/libc.so.6 +235: 45# 0x0000FFFFB818229C in /lib/aarch64-linux-gnu/libc.so.6 235: 46# __libc_start_main in /lib/aarch64-linux-gnu/libc.so.6 235: 47# _start in /usr/bin/python3 235: ---------- @@ -35046,10 +35074,10 @@ 235: 235: ... 235: ---------------------------------------------------------------------- -235: Ran 5 tests in 0.014s +235: Ran 5 tests in 0.017s 235: 235: OK -226/238 Test #235: pyRanker ............................... Passed 0.30 sec +226/238 Test #235: pyRanker ............................... Passed 0.33 sec test 238 Start 238: pythonProjectTests @@ -35058,54 +35086,57 @@ 238: Test timeout computed to be: 1500 237: .. 237: ---------------------------------------------------------------------- -237: Ran 2 tests in 0.008s +237: Ran 2 tests in 0.001s 237: 237: OK 237: Testing ChemicalFeatures Wrapper code: -227/238 Test #237: pyFeatures ............................. Passed 0.35 sec +227/238 Test #237: pyFeatures ............................. Passed 0.39 sec 231: ..... 231: ---------------------------------------------------------------------- -231: Ran 5 tests in 0.401s +231: Ran 5 tests in 0.413s 231: 231: OK -228/238 Test #231: pyMatCalc .............................. Passed 0.76 sec -224: Randomness seeded to: 1571677508 +228/238 Test #231: pyMatCalc .............................. Passed 0.79 sec +147: [11:06:36] UFFTYPER: Unrecognized atom type: S_6+6 (0) +147: [11:06:36] UFFTYPER: Warning: hybridization set to SP3 for atom 0 +147: [11:06:36] UFFTYPER: Unrecognized charge state for atom: 0 +224: Randomness seeded to: 398660467 224: =============================================================================== 224: All tests passed (203 assertions in 1 test case) 224: -229/238 Test #224: testMolProcessing ...................... Passed 2.16 sec +229/238 Test #224: testMolProcessing ...................... Passed 1.70 sec 234: ....... 234: ---------------------------------------------------------------------- -234: Ran 11 tests in 0.692s +234: Ran 11 tests in 0.963s 234: 234: OK -230/238 Test #234: pySimDivPickers ........................ Passed 0.92 sec +230/238 Test #234: pySimDivPickers ........................ Passed 1.18 sec 238: ============================= test session starts ============================== 238: platform linux -- Python 3.13.6, pytest-8.3.5, pluggy-1.6.0 238: rootdir: /build/reproducible-path/rdkit-202503.1/Projects 238: configfile: pytest.ini 238: collected 12 items 238: -146: [02:19:44] done -212: [02:19:45] Explicit valence for atom # 0 Br, 1, is greater than permitted +212: [11:06:45] Explicit valence for atom # 0 Br, 1, is greater than permitted 212: =============================================================================== 212: All tests passed (38344 assertions in 51 test cases) 212: -231/238 Test #212: molStandardizeCatchTest ................ Passed 11.50 sec -146: [02:19:44] --------------------------------- -146: [02:19:44] test github issue 256: handling of zero-atom molecules +231/238 Test #212: molStandardizeCatchTest ................ Passed 15.43 sec +146: [11:06:46] done +146: [11:06:46] --------------------------------- +146: [11:06:46] test github issue 256: handling of zero-atom molecules 146: -146: [02:19:44] --------------------------------- -146: [02:19:44] test embedder callback function -146: [02:19:44] --------------------------------- -146: [02:19:44] test multi-threaded multi-conf embedding +146: [11:06:46] --------------------------------- +146: [11:06:46] test embedder callback function +146: [11:06:46] --------------------------------- +146: [11:06:46] test multi-threaded multi-conf embedding 146: -146: [02:19:46] --------------------------------- -146: [02:19:46] test github issue 563: Incorrect ring stereochemistry after embedding +146: [11:06:50] --------------------------------- +146: [11:06:50] test github issue 563: Incorrect ring stereochemistry after embedding 146: 146: CNC[C@H]1CC[C@H](C[NH3+])CC1 -146: [02:19:47] --------------------------------- -146: [02:19:47] test github issue 568: Incorrect stereochemistry after embedding +146: [11:06:51] --------------------------------- +146: [11:06:51] 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 @@ -35123,17 +35154,24 @@ 146: CC(=O)C[C@@]12CCC[C@H]1[C@@H]1CCC3=CC(=O)CC[C@@H]3[C@H]1CC2 146: O=C(O)[C@@H]1C[C@H]2C[C@@H](CCc3nn[nH]n3)CC[C@H]2CN1 146: COc1ccc2c(c1)OC[C@@H](N1CCC(O)(c3ccc(F)cc3)CC1)[C@H]2O +146: Oc1ccc2c(c1)OC[C@@H](N1CCC(Cc3ccccc3)CC1)[C@H]2O +146: Oc1ccc2c(c1)OC[C@H](N1CCC(O)(c3ccccc3)CC1)[C@@H]2O +146: CC(=O)c1ccc2c(c1)[C@@]13CCCC[C@H]1[C@@H](C2)N(CC1CC1)CC3 +146: CC(=O)O[C@@H]1CC[C@@H]2CN3CCc4cc5c(cc4[C@@H]3C[C@@H]2C1)OCO5 +238: DbCLI/UnitTestDbCLI.py ............ [100%] +238: +238: =============================== warnings summary =============================== +238: ../obj-aarch64-linux-gnu/rdkit/Chem/MolDb/Loader_sa.py:20 +238: /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/MolDb/Loader_sa.py:20: MovedIn20Warning: The ``declarative_base()`` function is now available as sqlalchemy.orm.declarative_base(). (deprecated since: 2.0) (Background on SQLAlchemy 2.0 at: https://sqlalche.me/e/b8d9) +238: decBase = declarative_base() +238: +238: -- Docs: https://docs.pytest.org/en/stable/how-to/capture-warnings.html +238: ======================== 12 passed, 1 warning in 25.74s ======================== 171: =============================================================================== 171: All tests passed (93 assertions in 5 test cases) 171: -146: Oc1ccc2c(c1)OC[C@@H](N1CCC(Cc3ccccc3)CC1)[C@H]2O -232/238 Test #171: testRascalCluster ...................... Passed 37.63 sec -5: [02:19:51] Finished: testMultipleTimes() -5: [02:19:51] -5: ----------------------------------------- -233/238 Test #5: testConcurrentQueue .................... Passed 48.76 sec -146: Oc1ccc2c(c1)OC[C@H](N1CCC(O)(c3ccccc3)CC1)[C@@H]2O -147: [02:19:52] Interrupted, cancelling conformer generation +232/238 Test #171: testRascalCluster ...................... Passed 50.10 sec +147: [11:07:02] 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] @@ -35166,23 +35204,12 @@ 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: CC(=O)c1ccc2c(c1)[C@@]13CCCC[C@H]1[C@@H](C2)N(CC1CC1)CC3 +233/238 Test #238: pythonProjectTests ..................... Passed 26.50 sec 147: =============================================================================== 147: All tests passed (12742 assertions in 21 test cases) 147: -234/238 Test #147: distGeomHelpersCatch ................... Passed 42.76 sec -146: CC(=O)O[C@@H]1CC[C@@H]2CN3CCc4cc5c(cc4[C@@H]3C[C@@H]2C1)OCO5 +234/238 Test #147: distGeomHelpersCatch ................... Passed 56.40 sec 146: COc1cc2c(cc1OC)[C@@H]1C[C@@H]3C[C@H](O)CC[C@@H]3CN1CC2 -238: DbCLI/UnitTestDbCLI.py ............ [100%] -238: -238: =============================== warnings summary =============================== -238: ../obj-aarch64-linux-gnu/rdkit/Chem/MolDb/Loader_sa.py:20 -238: /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/MolDb/Loader_sa.py:20: MovedIn20Warning: The ``declarative_base()`` function is now available as sqlalchemy.orm.declarative_base(). (deprecated since: 2.0) (Background on SQLAlchemy 2.0 at: https://sqlalche.me/e/b8d9) -238: decBase = declarative_base() -238: -238: -- Docs: https://docs.pytest.org/en/stable/how-to/capture-warnings.html -238: ======================== 12 passed, 1 warning in 13.68s ======================== -235/238 Test #238: pythonProjectTests ..................... Passed 14.20 sec 146: N#C[C@@H]1C[C@@H]2CN3CCc4cc5c(cc4[C@@H]3C[C@@H]2C[C@@H]1O)OCO5 146: COC(=O)[C@@H]1C[C@](C)(C(=O)O)NC(=O)N1 146: CC(=O)OC1=C(Sc2ccccc2)C[C@H]2Cc3cc4cccc(O)c4c(O)c3C(=O)[C@H]2C1 @@ -35190,52 +35217,56 @@ 146: C[C@H](C(N)=O)N1CC[C@@]23CCCC[C@@H]2[C@@H]1Cc1ccc(OCc2cccc(F)c2)cc13 146: CN1C(=O)CC[C@@]2(C)C1=CCc1cc(Cl)ccc12 146: Cc1nc(COc2ccc3c(c2)[C@@H](O)[C@@H](Cc2cccnc2)CO3)ccc1[N+](=O)[O-] -146: [02:19:59] Molecule does not have explicit Hs. Consider calling AddHs() -146: [02:19:56] --------------------------------- -146: [02:19:56] test github issue 696: Bad 1-4 bounds matrix elements in highly constrained system -146: [02:19:56] --------------------------------- -146: [02:19:56] More ChEMBL molecules failing bounds smoothing. -146: [02:19:56] --------------------------------- -146: [02:19:56] ugly conformations can be generated for highly constrained ring systems. -146: [02:19:56] --------------------------------- -146: [02:19:56] test embed parameters structure. -146: [02:19:56] --------------------------------- -146: [02:19:56] test github 1227: Hs being used in RMSD filtering. -146: [02:19:56] --------------------------------- -146: [02:19:56] Failure to embed larger aromatic rings. -146: [02:19:57] --------------------------------- -146: [02:19:57] Deterministic with large random seeds -146: [02:19:58] --------------------------------- -146: [02:19:58] Github #1990: seg fault after RemoveHs -146: [02:19:59] --------------------------------- -146: [02:19:59] Github #2246: Use coordMap when starting embedding from random coords -146: [02:19:59] --------------------------------- -146: [02:19:59] Providing a distance bounds matrix. -146: [02:19:59] --------------------------------- -146: [02:19:59] Disabling fragmentation. -146: [02:19:59] --------------------------------- -146: [02:19:59] Using symmetry in conformation pruning. -146: [02:19:59] --------------------------------- -146: [02:19:59] Force trans amides. -146: [02:19:59] --------------------------------- -146: [02:19:59] test missing Hs warning. -146: [02:19:59] --------------------------------- -146: [02:19:59] basic H bond support. -146: [02:19:59] ******************************************************* -236/238 Test #146: testDistGeomHelpers .................... Passed 49.87 sec +146: [11:07:11] Molecule does not have explicit Hs. Consider calling AddHs() +146: [11:07:06] --------------------------------- +146: [11:07:06] test github issue 696: Bad 1-4 bounds matrix elements in highly constrained system +146: [11:07:06] --------------------------------- +146: [11:07:06] More ChEMBL molecules failing bounds smoothing. +146: [11:07:06] --------------------------------- +146: [11:07:06] ugly conformations can be generated for highly constrained ring systems. +146: [11:07:06] --------------------------------- +146: [11:07:06] test embed parameters structure. +146: [11:07:06] --------------------------------- +146: [11:07:06] test github 1227: Hs being used in RMSD filtering. +146: [11:07:06] --------------------------------- +146: [11:07:06] Failure to embed larger aromatic rings. +146: [11:07:08] --------------------------------- +146: [11:07:08] Deterministic with large random seeds +146: [11:07:10] --------------------------------- +146: [11:07:10] Github #1990: seg fault after RemoveHs +146: [11:07:10] --------------------------------- +146: [11:07:10] Github #2246: Use coordMap when starting embedding from random coords +146: [11:07:11] --------------------------------- +146: [11:07:11] Providing a distance bounds matrix. +146: [11:07:11] --------------------------------- +146: [11:07:11] Disabling fragmentation. +146: [11:07:11] --------------------------------- +146: [11:07:11] Using symmetry in conformation pruning. +146: [11:07:11] --------------------------------- +146: [11:07:11] Force trans amides. +146: [11:07:11] --------------------------------- +146: [11:07:11] test missing Hs warning. +146: [11:07:11] --------------------------------- +146: [11:07:11] basic H bond support. +146: [11:07:12] ******************************************************* +235/238 Test #146: testDistGeomHelpers .................... Passed 65.67 sec 170: =============================================================================== 170: All tests passed (3590 assertions in 35 test cases) 170: -237/238 Test #170: testRascalMCES ......................... Passed 50.21 sec -174: Randomness seeded to: 3515037965 +236/238 Test #170: testRascalMCES ......................... Passed 67.38 sec +174: Randomness seeded to: 3121085058 174: =============================================================================== 174: All tests passed (28 assertions in 2 test cases) 174: -238/238 Test #174: testSynthonSpaceRascalSearch ........... Passed 62.55 sec +237/238 Test #174: testSynthonSpaceRascalSearch ........... Passed 91.18 sec +5: [11:07:53] Finished: testMultipleTimes() +5: [11:07:53] +5: ----------------------------------------- +238/238 Test #5: testConcurrentQueue .................... Passed 114.38 sec 100% tests passed, 0 tests failed out of 238 -Total Test time (real) = 76.25 sec +Total Test time (real) = 114.43 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 @@ -37897,17 +37928,17 @@ diversion by libc6 from: /lib/ld-linux-aarch64.so.1 dpkg-shlibdeps: warning: diversions involved - output may be incorrect diversion by libc6 to: /lib/ld-linux-aarch64.so.1.usr-is-merged -dpkg-shlibdeps: warning: debian/postgresql-17-rdkit/usr/lib/postgresql/17/lib/rdkit.so contains an unresolvable reference to symbol AggCheckCallContext: it's probably a plugin +dpkg-shlibdeps: warning: debian/postgresql-17-rdkit/usr/lib/postgresql/17/lib/rdkit.so contains an unresolvable reference to symbol MemoryContextRegisterResetCallback: 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_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 PyLong_FromLong used by debian/librdkit1t64/usr/lib/libRDKitRDBoost.so.1.2025.03.1 found in none of the libraries +dpkg-shlibdeps: warning: symbol PyExc_KeyError used by debian/librdkit1t64/usr/lib/libRDKitRDBoost.so.1.2025.03.1 found in none of the libraries +dpkg-shlibdeps: warning: symbol _Py_NoneStruct used by debian/librdkit1t64/usr/lib/libRDKitRDBoost.so.1.2025.03.1 found in none of the libraries dpkg-shlibdeps: warning: symbol PyExc_ValueError used by debian/librdkit1t64/usr/lib/libRDKitRDBoost.so.1.2025.03.1 found in none of the libraries -dpkg-shlibdeps: warning: symbol _Py_Dealloc used by debian/librdkit1t64/usr/lib/libRDKitRDBoost.so.1.2025.03.1 found in none of the libraries +dpkg-shlibdeps: warning: symbol PyExc_IndexError used by debian/librdkit1t64/usr/lib/libRDKitRDBoost.so.1.2025.03.1 found in none of the libraries +dpkg-shlibdeps: warning: symbol PyLong_FromUnsignedLong used by debian/librdkit1t64/usr/lib/libRDKitRDBoost.so.1.2025.03.1 found in none of the libraries +dpkg-shlibdeps: warning: symbol 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 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 PyErr_SetString used by debian/librdkit1t64/usr/lib/libRDKitRDBoost.so.1.2025.03.1 found in none of the libraries dpkg-shlibdeps: warning: symbol PyObject_CallFunction used by debian/librdkit1t64/usr/lib/libRDKitRDBoost.so.1.2025.03.1 found in none of the libraries dpkg-shlibdeps: warning: 2 other similar warnings have been skipped (use -v to see them all) dh_installdeb -O--buildsystem=cmake @@ -37919,15 +37950,15 @@ 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 'librdkit1t64' in '../librdkit1t64_202503.1-5_arm64.deb'. +dpkg-deb: building package 'librdkit1t64-dbgsym' in '../librdkit1t64-dbgsym_202503.1-5_arm64.deb'. +dpkg-deb: building package 'python3-rdkit-dbgsym' in '../python3-rdkit-dbgsym_202503.1-5_arm64.deb'. dpkg-deb: building package 'rdkit-doc' in '../rdkit-doc_202503.1-5_all.deb'. -dpkg-deb: building package 'python3-rdkit' in '../python3-rdkit_202503.1-5_arm64.deb'. -dpkg-deb: building package 'postgresql-17-rdkit-dbgsym' in '../postgresql-17-rdkit-dbgsym_202503.1-5_arm64.deb'. dpkg-deb: building package 'rdkit-data' in '../rdkit-data_202503.1-5_all.deb'. -dpkg-deb: building package 'python3-rdkit-dbgsym' in '../python3-rdkit-dbgsym_202503.1-5_arm64.deb'. -dpkg-deb: building package 'librdkit1t64-dbgsym' in '../librdkit1t64-dbgsym_202503.1-5_arm64.deb'. -dpkg-deb: building package 'librdkit-dev' in '../librdkit-dev_202503.1-5_arm64.deb'. +dpkg-deb: building package 'librdkit1t64' in '../librdkit1t64_202503.1-5_arm64.deb'. +dpkg-deb: building package 'python3-rdkit' in '../python3-rdkit_202503.1-5_arm64.deb'. dpkg-deb: building package 'postgresql-17-rdkit' in '../postgresql-17-rdkit_202503.1-5_arm64.deb'. +dpkg-deb: building package 'librdkit-dev' in '../librdkit-dev_202503.1-5_arm64.deb'. +dpkg-deb: building package 'postgresql-17-rdkit-dbgsym' in '../postgresql-17-rdkit-dbgsym_202503.1-5_arm64.deb'. dpkg-genbuildinfo --build=binary -O../rdkit_202503.1-5_arm64.buildinfo dpkg-genchanges --build=binary -O../rdkit_202503.1-5_arm64.changes dpkg-genchanges: info: binary-only upload (no source code included) @@ -37935,12 +37966,14 @@ 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/2894544/tmp/hooks/B01_cleanup starting +I: user script /srv/workspace/pbuilder/2894544/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/1886249 and its subdirectories -I: Current time: Tue Aug 19 02:23:59 -12 2025 -I: pbuilder-time-stamp: 1755613439 +I: removing directory /srv/workspace/pbuilder/2894544 and its subdirectories +I: Current time: Tue Sep 22 11:10:54 +14 2026 +I: pbuilder-time-stamp: 1790025054