Diff of the two buildlogs: -- --- b1/build.log 2025-01-16 00:46:34.090173521 +0000 +++ b2/build.log 2025-01-16 01:18:55.082457581 +0000 @@ -1,6 +1,6 @@ I: pbuilder: network access will be disabled during build -I: Current time: Wed Jan 15 12:27:52 -12 2025 -I: pbuilder-time-stamp: 1736987272 +I: Current time: Wed Feb 18 21:09:44 +14 2026 +I: pbuilder-time-stamp: 1771398584 I: Building the build Environment I: extracting base tarball [/var/cache/pbuilder/unstable-reproducible-base.tgz] I: copying local configuration @@ -34,52 +34,84 @@ dpkg-source: info: applying disable_python_test.patch I: Not using root during the build. I: Installing the build-deps -I: user script /srv/workspace/pbuilder/2869322/tmp/hooks/D02_print_environment starting +I: user script /srv/workspace/pbuilder/3933652/tmp/hooks/D01_modify_environment starting +debug: Running on codethink01-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 Feb 18 07:09 /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/3933652/tmp/hooks/D01_modify_environment finished +I: user script /srv/workspace/pbuilder/3933652/tmp/hooks/D02_print_environment starting I: set - BUILDDIR='/build/reproducible-path' - BUILDUSERGECOS='first user,first room,first work-phone,first home-phone,first other' - BUILDUSERNAME='pbuilder1' - BUILD_ARCH='arm64' - DEBIAN_FRONTEND='noninteractive' + BASH=/bin/sh + BASHOPTS=checkwinsize:cmdhist:complete_fullquote:extquote:force_fignore:globasciiranges:globskipdots:hostcomplete:interactive_comments:patsub_replacement:progcomp:promptvars:sourcepath + BASH_ALIASES=() + BASH_ARGC=() + BASH_ARGV=() + BASH_CMDS=() + BASH_LINENO=([0]="12" [1]="0") + BASH_LOADABLES_PATH=/usr/local/lib/bash:/usr/lib/bash:/opt/local/lib/bash:/usr/pkg/lib/bash:/opt/pkg/lib/bash:. + BASH_SOURCE=([0]="/tmp/hooks/D02_print_environment" [1]="/tmp/hooks/D02_print_environment") + BASH_VERSINFO=([0]="5" [1]="2" [2]="37" [3]="1" [4]="release" [5]="aarch64-unknown-linux-gnu") + BASH_VERSION='5.2.37(1)-release' + BUILDDIR=/build/reproducible-path + BUILDUSERGECOS='second user,second room,second work-phone,second home-phone,second other' + BUILDUSERNAME=pbuilder2 + BUILD_ARCH=arm64 + DEBIAN_FRONTEND=noninteractive DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=12 ' - DISTRIBUTION='unstable' - HOME='/root' - HOST_ARCH='arm64' + DIRSTACK=() + DISTRIBUTION=unstable + EUID=0 + FUNCNAME=([0]="Echo" [1]="main") + GROUPS=() + HOME=/root + HOSTNAME=i-capture-the-hostname + HOSTTYPE=aarch64 + HOST_ARCH=arm64 IFS=' ' - INVOCATION_ID='53fc479a14d140c3979529f715f3705c' - 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='2869322' - PS1='# ' - PS2='> ' + INVOCATION_ID=c6ee60b604054be99e5fde058ffa84cb + 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=3933652 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.aOzPix50/pbuilderrc_zcOi --distribution unstable --hookdir /etc/pbuilder/first-build-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/unstable-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/r-b-build.aOzPix50/b1 --logfile b1/build.log rdkit_202409.4-1.dsc' - SUDO_GID='109' - 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.aOzPix50/pbuilderrc_C434 --distribution unstable --hookdir /etc/pbuilder/rebuild-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/unstable-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/r-b-build.aOzPix50/b2 --logfile b2/build.log rdkit_202409.4-1.dsc' + SUDO_GID=109 + SUDO_UID=104 + SUDO_USER=jenkins + TERM=unknown + TZ=/usr/share/zoneinfo/Etc/GMT-14 + UID=0 + USER=root + _='I: set' + http_proxy=http://192.168.101.4:3128 I: uname -a - Linux codethink02-arm64 6.1.0-30-cloud-arm64 #1 SMP Debian 6.1.124-1 (2025-01-12) aarch64 GNU/Linux + Linux i-capture-the-hostname 6.1.0-30-cloud-arm64 #1 SMP Debian 6.1.124-1 (2025-01-12) aarch64 GNU/Linux I: ls -l /bin - lrwxrwxrwx 1 root root 7 Nov 22 14:40 /bin -> usr/bin -I: user script /srv/workspace/pbuilder/2869322/tmp/hooks/D02_print_environment finished + lrwxrwxrwx 1 root root 7 Nov 22 2024 /bin -> usr/bin +I: user script /srv/workspace/pbuilder/3933652/tmp/hooks/D02_print_environment finished -> Attempting to satisfy build-dependencies -> Creating pbuilder-satisfydepends-dummy package Package: pbuilder-satisfydepends-dummy @@ -575,7 +607,7 @@ Get: 373 http://deb.debian.org/debian unstable/main arm64 texlive-latex-recommended all 2024.20250114-1 [8760 kB] Get: 374 http://deb.debian.org/debian unstable/main arm64 texlive-pictures all 2024.20250114-1 [17.1 MB] Get: 375 http://deb.debian.org/debian unstable/main arm64 texlive-latex-extra all 2024.20250114-1 [24.7 MB] -Fetched 399 MB in 3s (124 MB/s) +Fetched 399 MB in 2s (233 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 ... 19964 files and directories currently installed.) @@ -1779,8 +1811,8 @@ Setting up tzdata (2024b-6) ... Current default time zone: 'Etc/UTC' -Local time is now: Thu Jan 16 00:28:50 UTC 2025. -Universal Time is now: Thu Jan 16 00:28:50 UTC 2025. +Local time is now: Wed Feb 18 07:11:11 UTC 2026. +Universal Time is now: Wed Feb 18 07:11:11 UTC 2026. Run 'dpkg-reconfigure tzdata' if you wish to change it. Setting up libboost-atomic1.83.0:arm64 (1.83.0-4) ... @@ -1941,11 +1973,6 @@ Setting up pandoc (3.1.11.1+ds-2) ... Setting up libfreetype6:arm64 (2.13.3+dfsg-1) ... Setting up ssl-cert (1.1.3) ... -hostname: Name or service not known -make-ssl-cert: Could not get FQDN, using 'codethink02-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) ... Setting up x11proto-core-dev (2024.1-1) ... Setting up shared-mime-info (2.4-5+b1) ... @@ -2177,7 +2204,11 @@ Building tag database... -> Finished parsing the build-deps I: Building the package -I: Running cd /build/reproducible-path/rdkit-202409.4/ && 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_202409.4-1_source.changes +I: user script /srv/workspace/pbuilder/3933652/tmp/hooks/A99_set_merged_usr starting +Not re-configuring usrmerge for unstable +I: user script /srv/workspace/pbuilder/3933652/tmp/hooks/A99_set_merged_usr finished +hostname: Name or service not known +I: Running cd /build/reproducible-path/rdkit-202409.4/ && 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_202409.4-1_source.changes dpkg-buildpackage: info: source package rdkit dpkg-buildpackage: info: source version 202409.4-1 dpkg-buildpackage: info: source distribution unstable @@ -2283,8 +2314,8 @@ -- Found Cairo: /usr/include/cairo -- Found Freetype: /usr/lib/aarch64-linux-gnu/libfreetype.so (found version "2.13.3") postgres: /usr/include/postgresql;/usr/include/postgresql/17/server --- Configuring done (3.6s) --- Generating done (1.0s) +-- Configuring done (5.2s) +-- Generating done (2.5s) CMake Warning: Manually-specified variables were not used by the project: @@ -2318,7 +2349,7 @@ -- Detecting CXX compile features - done -- Found PostgreSQL: /usr/lib/aarch64-linux-gnu/libpq.so (found version "17.2") postgres: /usr/include/postgresql;/usr/include/postgresql/17/server --- Configuring done (1.1s) +-- Configuring done (2.1s) -- Generating done (0.0s) -- Build files have been written to: /build/reproducible-path/rdkit-202409.4/Code/PgSQL/rdkit/build-17 make[1]: Leaving directory '/build/reproducible-path/rdkit-202409.4' @@ -2332,88 +2363,86 @@ make -f CMakeFiles/Makefile2 all make[3]: Entering directory '/build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu' make -f External/INCHI-API/CMakeFiles/inchi_support.dir/build.make External/INCHI-API/CMakeFiles/inchi_support.dir/depend -make -f Code/RDGeneral/CMakeFiles/RDGeneral.dir/build.make Code/RDGeneral/CMakeFiles/RDGeneral.dir/depend -make -f External/CoordGen/CMakeFiles/coordgen_support.dir/build.make External/CoordGen/CMakeFiles/coordgen_support.dir/depend -make -f External/RingFamilies/CMakeFiles/ringdecomposerlib_support.dir/build.make External/RingFamilies/CMakeFiles/ringdecomposerlib_support.dir/depend -make -f External/GA/CMakeFiles/ga.dir/build.make External/GA/CMakeFiles/ga.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu' +make -f 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-DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_BOOST_STACKTRACE -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.4/External -I/usr/include/python3.13 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202409.4/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/RDGeneral/CMakeFiles/RDGeneral.dir/LocaleSwitcher.cpp.o -MF CMakeFiles/RDGeneral.dir/LocaleSwitcher.cpp.o.d -o CMakeFiles/RDGeneral.dir/LocaleSwitcher.cpp.o -c /build/reproducible-path/rdkit-202409.4/Code/RDGeneral/LocaleSwitcher.cpp [ 1%] Building CXX object 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-D_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.1.2024.09.4 /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-202409.4/obj-aarch64-linux-gnu' -make -f Code/SimDivPickers/CMakeFiles/testSimDivPickers.dir/build.make Code/SimDivPickers/CMakeFiles/testSimDivPickers.dir/build -make[4]: Entering directory '/build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu' -[ 9%] Building CXX object Code/SimDivPickers/CMakeFiles/testSimDivPickers.dir/testPickers.cpp.o -cd /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/SimDivPickers && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.4/External -I/usr/include/python3.13 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202409.4/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/SimDivPickers/CMakeFiles/testSimDivPickers.dir/testPickers.cpp.o -MF CMakeFiles/testSimDivPickers.dir/testPickers.cpp.o.d -o CMakeFiles/testSimDivPickers.dir/testPickers.cpp.o -c /build/reproducible-path/rdkit-202409.4/Code/SimDivPickers/testPickers.cpp -[ 9%] Linking CXX executable testRDValue -cd /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/RDGeneral && /usr/bin/cmake -E cmake_link_script CMakeFiles/testRDValue.dir/link.txt --verbose=1 -/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/testRDValue.dir/link.d CMakeFiles/testRDValue.dir/testRDValue.cpp.o -o testRDValue ../../lib/libRDKitRDGeneral.so.1.2024.09.4 /usr/lib/aarch64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl +[ 7%] Built target logTestsCatch +[ 7%] Linking CXX shared library ../../lib/libRDKitCatalogs.so +cd /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/Catalogs && /usr/bin/cmake -E cmake_link_script CMakeFiles/Catalogs.dir/link.txt --verbose=1 +[ 8%] Linking CXX executable testMatrices +cd /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/Numerics && /usr/bin/cmake -E cmake_link_script CMakeFiles/testMatrices.dir/link.txt --verbose=1 +/usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC 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/usr/bin/cmake -E cmake_link_script CMakeFiles/testSimDivPickers.dir/link.txt --verbose=1 -/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/testSimDivPickers.dir/link.d CMakeFiles/testSimDivPickers.dir/testPickers.cpp.o -o testSimDivPickers ../../lib/libRDKitSimDivPickers.so.1.2024.09.4 ../../lib/libRDKithc.so.1.2024.09.4 ../../lib/libRDKitRDGeneral.so.1.2024.09.4 /usr/lib/aarch64-linux-gnu/libboost_system.so.1.83.0 /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-202409.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/testMatrices.dir/link.d CMakeFiles/testMatrices.dir/testMatrices.cpp.o -o testMatrices ../../lib/libRDKitRDGeneral.so.1.2024.09.4 /usr/lib/aarch64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl +[ 8%] Built target Catalogs make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu' -[ 9%] Built target testSimDivPickers -[ 9%] Linking CXX executable testDict -cd /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/RDGeneral && /usr/bin/cmake -E cmake_link_script CMakeFiles/testDict.dir/link.txt --verbose=1 -[ 9%] Linking CXX shared library ../../lib/libRDKitDataStructs.so +[ 8%] Built target testMatrices +[ 8%] Linking CXX shared library ../../lib/libRDKitDataStructs.so cd /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/DataStructs && /usr/bin/cmake -E cmake_link_script CMakeFiles/DataStructs.dir/link.txt --verbose=1 -/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/testDict.dir/link.d CMakeFiles/testDict.dir/testDict.cpp.o -o testDict ../../lib/libRDKitRDGeneral.so.1.2024.09.4 /usr/lib/aarch64-linux-gnu/libboost_system.so.1.83.0 /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-202409.4/obj-aarch64-linux-gnu' -[ 9%] Built target testDict /usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,--dependency-file=CMakeFiles/DataStructs.dir/link.d -Wl,-z,relro -Wl,-z,now -shared -Wl,-soname,libRDKitDataStructs.so.1 -o ../../lib/libRDKitDataStructs.so.1.2024.09.4 CMakeFiles/DataStructs.dir/BitVect.cpp.o CMakeFiles/DataStructs.dir/SparseBitVect.cpp.o CMakeFiles/DataStructs.dir/ExplicitBitVect.cpp.o CMakeFiles/DataStructs.dir/Utils.cpp.o CMakeFiles/DataStructs.dir/base64.cpp.o CMakeFiles/DataStructs.dir/BitOps.cpp.o CMakeFiles/DataStructs.dir/DiscreteDistMat.cpp.o CMakeFiles/DataStructs.dir/DiscreteValueVect.cpp.o CMakeFiles/DataStructs.dir/FPBReader.cpp.o CMakeFiles/DataStructs.dir/MultiFPBReader.cpp.o CMakeFiles/DataStructs.dir/RealValueVect.cpp.o ../../lib/libRDKitRDGeneral.so.1.2024.09.4 /usr/lib/aarch64-linux-gnu/libboost_system.so.1.83.0 /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-202409.4/obj-aarch64-linux-gnu/Code/DataStructs && /usr/bin/cmake -E cmake_symlink_library ../../lib/libRDKitDataStructs.so.1.2024.09.4 ../../lib/libRDKitDataStructs.so.1 ../../lib/libRDKitDataStructs.so make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu' -[ 9%] Built target DataStructs +[ 8%] Built target DataStructs make -f Code/Geometry/CMakeFiles/RDGeometryLib.dir/build.make Code/Geometry/CMakeFiles/RDGeometryLib.dir/depend -make -f Code/DataStructs/CMakeFiles/testDataStructs.dir/build.make Code/DataStructs/CMakeFiles/testDataStructs.dir/depend -make -f Code/DataStructs/CMakeFiles/testFPB.dir/build.make Code/DataStructs/CMakeFiles/testFPB.dir/depend -make -f Code/DataStructs/CMakeFiles/testMultiFPB.dir/build.make Code/DataStructs/CMakeFiles/testMultiFPB.dir/depend -make -f Code/DataStructs/CMakeFiles/catchDataStructs.dir/build.make Code/DataStructs/CMakeFiles/catchDataStructs.dir/depend -make -f Code/DataStructs/Wrap/CMakeFiles/cDataStructs.dir/build.make Code/DataStructs/Wrap/CMakeFiles/cDataStructs.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu' +make -f Code/DataStructs/CMakeFiles/testDataStructs.dir/build.make Code/DataStructs/CMakeFiles/testDataStructs.dir/depend cd /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202409.4 /build/reproducible-path/rdkit-202409.4/Code/Geometry /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/Geometry /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/Geometry/CMakeFiles/RDGeometryLib.dir/DependInfo.cmake "--color=" make[4]: Entering directory '/build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu' +make -f Code/DataStructs/CMakeFiles/testFPB.dir/build.make Code/DataStructs/CMakeFiles/testFPB.dir/depend cd /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202409.4 /build/reproducible-path/rdkit-202409.4/Code/DataStructs /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/DataStructs /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/DataStructs/CMakeFiles/testDataStructs.dir/DependInfo.cmake "--color=" make[4]: Entering directory '/build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu' +make 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Code/Geometry/CMakeFiles/RDGeometryLib.dir/build.make Code/Geometry/CMakeFiles/RDGeometryLib.dir/build cd /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202409.4 /build/reproducible-path/rdkit-202409.4/Code/DataStructs /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/DataStructs /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/DataStructs/CMakeFiles/testMultiFPB.dir/DependInfo.cmake "--color=" make[4]: Entering directory '/build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu' -cd /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202409.4 /build/reproducible-path/rdkit-202409.4/Code/DataStructs /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/DataStructs /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/DataStructs/CMakeFiles/catchDataStructs.dir/DependInfo.cmake "--color=" -make -f Code/SimDivPickers/CMakeFiles/pickersTestsCatch.dir/build.make Code/SimDivPickers/CMakeFiles/pickersTestsCatch.dir/depend -make[4]: Entering directory '/build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu' -cd /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202409.4 /build/reproducible-path/rdkit-202409.4/Code/DataStructs/Wrap /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/DataStructs/Wrap /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/DataStructs/Wrap/CMakeFiles/cDataStructs.dir/DependInfo.cmake "--color=" -make[4]: Entering directory '/build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu' -cd /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202409.4 /build/reproducible-path/rdkit-202409.4/Code/DataManip/MetricMatrixCalc/Wrap /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/DataManip/MetricMatrixCalc/Wrap /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/DataManip/MetricMatrixCalc/Wrap/CMakeFiles/rdMetricMatrixCalc.dir/DependInfo.cmake "--color=" -make[4]: Entering directory '/build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu' -cd /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202409.4 /build/reproducible-path/rdkit-202409.4/Code/SimDivPickers /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/SimDivPickers /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/SimDivPickers/CMakeFiles/pickersTestsCatch.dir/DependInfo.cmake "--color=" -make -f Code/SimDivPickers/Wrap/CMakeFiles/rdSimDivPickers.dir/build.make Code/SimDivPickers/Wrap/CMakeFiles/rdSimDivPickers.dir/depend -make -f Code/ML/InfoTheory/CMakeFiles/InfoTheory.dir/build.make Code/ML/InfoTheory/CMakeFiles/InfoTheory.dir/depend -make[4]: Entering directory '/build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu' -cd /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202409.4 /build/reproducible-path/rdkit-202409.4/Code/SimDivPickers/Wrap /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/SimDivPickers/Wrap 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Code/Geometry/CMakeFiles/RDGeometryLib.dir/point.cpp.o +cd /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/Geometry && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDGeometryLib_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_RDGEOMETRYLIB_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.4/External -I/usr/include/python3.13 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202409.4/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security 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testFPB +[ 12%] Building CXX object Code/DataStructs/Wrap/CMakeFiles/cDataStructs.dir/SparseIntVect.cpp.o +cd /build/reproducible-path/rdkit-202409.4/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_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-202409.4/External -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202409.4/Code -isystem /usr/include/python3.13 -isystem /usr/include/eigen3 -g -O2 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-E cmake_link_script CMakeFiles/Alignment.dir/link.txt --verbose=1 +/usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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.1.2024.09.4 CMakeFiles/Alignment.dir/AlignPoints.cpp.o ../../../lib/libRDKitRDGeometryLib.so.1.2024.09.4 ../../../lib/libRDKitDataStructs.so.1.2024.09.4 ../../../lib/libRDKitRDGeneral.so.1.2024.09.4 /usr/lib/aarch64-linux-gnu/libboost_system.so.1.83.0 /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-202409.4/obj-aarch64-linux-gnu/Code/Numerics/Alignment && /usr/bin/cmake -E cmake_symlink_library ../../../lib/libRDKitAlignment.so.1.2024.09.4 ../../../lib/libRDKitAlignment.so.1 ../../../lib/libRDKitAlignment.so make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu' -[ 15%] Built target testDataStructs +[ 15%] Built target Alignment make -f Code/Geometry/CMakeFiles/testRealValueGrid.dir/build.make Code/Geometry/CMakeFiles/testRealValueGrid.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu' cd /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202409.4 /build/reproducible-path/rdkit-202409.4/Code/Geometry /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/Geometry /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/Geometry/CMakeFiles/testRealValueGrid.dir/DependInfo.cmake "--color=" @@ -2916,19 +2947,6 @@ make[4]: Entering directory '/build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu' [ 15%] Building CXX object Code/Geometry/CMakeFiles/geometryTestsCatch.dir/catch_tests.cpp.o cd /build/reproducible-path/rdkit-202409.4/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_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.4/External -I/usr/include/python3.13 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202409.4/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/Geometry/CMakeFiles/geometryTestsCatch.dir/catch_tests.cpp.o -MF CMakeFiles/geometryTestsCatch.dir/catch_tests.cpp.o.d -o CMakeFiles/geometryTestsCatch.dir/catch_tests.cpp.o -c /build/reproducible-path/rdkit-202409.4/Code/Geometry/catch_tests.cpp -[ 15%] Building CXX object Code/SimDivPickers/Wrap/CMakeFiles/rdSimDivPickers.dir/HierarchicalClusterPicker.cpp.o -cd /build/reproducible-path/rdkit-202409.4/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 -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DrdSimDivPickers_EXPORTS -I/build/reproducible-path/rdkit-202409.4/External -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202409.4/Code -isystem /usr/include/python3.13 -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/SimDivPickers/Wrap/CMakeFiles/rdSimDivPickers.dir/HierarchicalClusterPicker.cpp.o -MF CMakeFiles/rdSimDivPickers.dir/HierarchicalClusterPicker.cpp.o.d -o CMakeFiles/rdSimDivPickers.dir/HierarchicalClusterPicker.cpp.o -c /build/reproducible-path/rdkit-202409.4/Code/SimDivPickers/Wrap/HierarchicalClusterPicker.cpp -[ 15%] Building CXX object Code/ML/InfoTheory/Wrap/CMakeFiles/rdInfoTheory.dir/rdInfoTheory.cpp.o -cd /build/reproducible-path/rdkit-202409.4/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 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Code/GraphMol/CMakeFiles/GraphMol.dir/QueryAtom.cpp.o -cd /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/GraphMol && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DGraphMol_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_GRAPHMOL_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.4/External -I/usr/include/python3.13 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202409.4/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/CMakeFiles/GraphMol.dir/QueryAtom.cpp.o -MF CMakeFiles/GraphMol.dir/QueryAtom.cpp.o.d -o CMakeFiles/GraphMol.dir/QueryAtom.cpp.o -c /build/reproducible-path/rdkit-202409.4/Code/GraphMol/QueryAtom.cpp -[ 15%] Linking CXX executable testTransforms -cd /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/Geometry && /usr/bin/cmake -E cmake_link_script CMakeFiles/testTransforms.dir/link.txt --verbose=1 -[ 15%] Building CXX object Code/GraphMol/CMakeFiles/GraphMol.dir/QueryBond.cpp.o -cd /build/reproducible-path/rdkit-202409.4/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 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/build/reproducible-path/rdkit-202409.4/Code/GraphMol/QueryBond.cpp -/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_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.1.2024.09.4 ../../lib/libRDKitDataStructs.so.1.2024.09.4 ../../lib/libRDKitRDGeneral.so.1.2024.09.4 /usr/lib/aarch64-linux-gnu/libboost_system.so.1.83.0 /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-202409.4/obj-aarch64-linux-gnu' -[ 15%] Built target testTransforms make -f Code/Geometry/Wrap/CMakeFiles/rdGeometry.dir/build.make Code/Geometry/Wrap/CMakeFiles/rdGeometry.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu' cd /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202409.4 /build/reproducible-path/rdkit-202409.4/Code/Geometry/Wrap /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/Geometry/Wrap /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/Geometry/Wrap/CMakeFiles/rdGeometry.dir/DependInfo.cmake "--color=" @@ -2937,11 +2955,11 @@ make[4]: Entering directory '/build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu' [ 15%] Building CXX object Code/Geometry/Wrap/CMakeFiles/rdGeometry.dir/Point.cpp.o cd /build/reproducible-path/rdkit-202409.4/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_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DrdGeometry_EXPORTS -I/build/reproducible-path/rdkit-202409.4/External -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202409.4/Code -isystem /usr/include/python3.13 -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -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-202409.4/Code/Geometry/Wrap/Point.cpp -[ 15%] Linking CXX executable testGrid -cd /build/reproducible-path/rdkit-202409.4/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-202409.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_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.1.2024.09.4 ../../lib/libRDKitDataStructs.so.1.2024.09.4 ../../lib/libRDKitRDGeneral.so.1.2024.09.4 /usr/lib/aarch64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl +[ 15%] Linking CXX shared module ../../../rdkit/SimDivFilters/rdSimDivPickers.so +cd /build/reproducible-path/rdkit-202409.4/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-202409.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -g -fwrapv -O2 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Built target rdSimDivPickers make -f Code/Numerics/CMakeFiles/testConrec.dir/build.make Code/Numerics/CMakeFiles/testConrec.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu' cd /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202409.4 /build/reproducible-path/rdkit-202409.4/Code/Numerics /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/Numerics /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/Numerics/CMakeFiles/testConrec.dir/DependInfo.cmake "--color=" @@ -2950,13 +2968,11 @@ make[4]: Entering directory '/build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu' [ 15%] Building CXX object Code/Numerics/CMakeFiles/testConrec.dir/testConrec.cpp.o cd /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/Numerics && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.4/External -I/usr/include/python3.13 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202409.4/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/Numerics/CMakeFiles/testConrec.dir/testConrec.cpp.o -MF CMakeFiles/testConrec.dir/testConrec.cpp.o.d -o CMakeFiles/testConrec.dir/testConrec.cpp.o -c /build/reproducible-path/rdkit-202409.4/Code/Numerics/testConrec.cpp -[ 15%] Linking CXX executable testRealValueGrid -cd /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/Geometry && /usr/bin/cmake -E cmake_link_script CMakeFiles/testRealValueGrid.dir/link.txt --verbose=1 -[ 15%] Linking CXX executable geometryTestsCatch -cd /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/Geometry && /usr/bin/cmake -E cmake_link_script CMakeFiles/geometryTestsCatch.dir/link.txt --verbose=1 -/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra 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CXX object Code/Numerics/Alignment/Wrap/CMakeFiles/rdAlignment.dir/rdAlignment.cpp.o cd /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/Numerics/Alignment/Wrap && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_NUMPY_DYN_LINK -DBOOST_NUMPY_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DrdAlignment_EXPORTS -I/build/reproducible-path/rdkit-202409.4/External -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202409.4/Code -isystem /usr/include/python3.13 -isystem /usr/include/eigen3 -g -O2 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-Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/Geometry/Wrap/CMakeFiles/rdGeometry.dir/UniformRealValueGrid3D.cpp.o -MF CMakeFiles/rdGeometry.dir/UniformRealValueGrid3D.cpp.o.d -o CMakeFiles/rdGeometry.dir/UniformRealValueGrid3D.cpp.o -c /build/reproducible-path/rdkit-202409.4/Code/Geometry/Wrap/UniformRealValueGrid3D.cpp [ 17%] Linking CXX shared library ../../lib/libRDKitChemicalFeatures.so cd /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/ChemicalFeatures && /usr/bin/cmake -E cmake_link_script CMakeFiles/ChemicalFeatures.dir/link.txt --verbose=1 /usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.4=. -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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Code/ChemicalFeatures/CMakeFiles/testChemicalFeatures.dir/testChemicalFeatures.cpp.o -MF CMakeFiles/testChemicalFeatures.dir/testChemicalFeatures.cpp.o.d -o CMakeFiles/testChemicalFeatures.dir/testChemicalFeatures.cpp.o -c /build/reproducible-path/rdkit-202409.4/Code/ChemicalFeatures/testChemicalFeatures.cpp -[ 17%] Linking CXX shared module ../../../rdkit/SimDivFilters/rdSimDivPickers.so -cd /build/reproducible-path/rdkit-202409.4/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-202409.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=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.1.2024.09.4 ../../../lib/libRDKitDataStructs.so.1.2024.09.4 ../../../lib/libRDKitRDBoost.so.1.2024.09.4 ../../../lib/libRDKithc.so.1.2024.09.4 /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.1.2024.09.4 /usr/lib/aarch64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl +[ 17%] Linking CXX executable testConrec +cd /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/Numerics && 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-I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202409.4/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-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-202409.4/Code/GraphMol/Bond.cpp [ 17%] Linking CXX shared module ../../../../rdkit/Numerics/rdAlignment.so cd /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/Numerics/Alignment/Wrap && /usr/bin/cmake -E cmake_link_script CMakeFiles/rdAlignment.dir/link.txt --verbose=1 /usr/bin/c++ -fPIC -g -O2 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-I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202409.4/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-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-202409.4/Code/GraphMol/MolOps.cpp +[ 17%] Linking CXX executable testChemicalFeatures +cd /build/reproducible-path/rdkit-202409.4/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-202409.4=. 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/build/reproducible-path/rdkit-202409.4/Code/GraphMol/FindRings.cpp: In function 'void RDKit::MolOps::findRingFamilies(const RDKit::ROMol&)': /build/reproducible-path/rdkit-202409.4/Code/GraphMol/FindRings.cpp:1342:36: warning: unused parameter 'mol' [-Wunused-parameter] 1342 | void findRingFamilies(const ROMol &mol) { | ~~~~~~~~~~~~~^~~ -/usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -g -fwrapv -O2 -Wl,--dependency-file=CMakeFiles/cDataStructs.dir/link.d -Wl,-z,relro -Wl,-z,now -shared -o ../../../rdkit/DataStructs/cDataStructs.so CMakeFiles/cDataStructs.dir/DataStructs.cpp.o CMakeFiles/cDataStructs.dir/DiscreteValueVect.cpp.o 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/build/reproducible-path/rdkit-202409.4/Code/GraphMol/QueryOps.cpp +[ 18%] Building CXX object Code/GraphMol/CMakeFiles/GraphMol.dir/MolPickler.cpp.o +cd /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/GraphMol && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DGraphMol_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_GRAPHMOL_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.4/External -I/usr/include/python3.13 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202409.4/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.4=. 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-DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.4/External -I/usr/include/python3.13 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202409.4/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-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/Kekulize.cpp.o -MF CMakeFiles/GraphMol.dir/Kekulize.cpp.o.d -o CMakeFiles/GraphMol.dir/Kekulize.cpp.o -c /build/reproducible-path/rdkit-202409.4/Code/GraphMol/Kekulize.cpp [ 18%] Building CXX object Code/GraphMol/CMakeFiles/GraphMol.dir/ConjugHybrid.cpp.o cd /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/GraphMol && 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-I/build/reproducible-path/rdkit-202409.4/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/CMakeFiles/GraphMol.dir/Matrices.cpp.o -MF CMakeFiles/GraphMol.dir/Matrices.cpp.o.d -o CMakeFiles/GraphMol.dir/Matrices.cpp.o -c /build/reproducible-path/rdkit-202409.4/Code/GraphMol/Matrices.cpp -/usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -shared -Wl,-O1 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/usr/lib/aarch64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl +make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu' +[ 19%] Built target cDataStructs [ 19%] Building CXX object Code/GraphMol/CMakeFiles/GraphMol.dir/RingInfo.cpp.o cd /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/GraphMol && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DGraphMol_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_GRAPHMOL_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.4/External -I/usr/include/python3.13 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202409.4/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-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-202409.4/Code/GraphMol/RingInfo.cpp [ 19%] Building CXX object Code/GraphMol/CMakeFiles/GraphMol.dir/Conformer.cpp.o @@ -3117,8 +3143,13 @@ cd /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/GraphMol && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB 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-isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-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-202409.4/Code/GraphMol/Resonance.cpp +[ 19%] Linking CXX shared module ../../../rdkit/rdBase.so +cd /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/RDBoost/Wrap && /usr/bin/cmake -E cmake_link_script CMakeFiles/rdBase.dir/link.txt --verbose=1 [ 19%] Building CXX object Code/GraphMol/CMakeFiles/GraphMol.dir/StereoGroup.cpp.o cd /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/GraphMol && /usr/bin/c++ 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/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-202409.4/obj-aarch64-linux-gnu' +[ 19%] Built target rdBase [ 20%] Building CXX object Code/GraphMol/CMakeFiles/GraphMol.dir/new_canon.cpp.o cd /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/GraphMol && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DGraphMol_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_GRAPHMOL_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.4/External -I/usr/include/python3.13 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202409.4/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-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/new_canon.cpp.o -MF CMakeFiles/GraphMol.dir/new_canon.cpp.o.d -o CMakeFiles/GraphMol.dir/new_canon.cpp.o -c /build/reproducible-path/rdkit-202409.4/Code/GraphMol/new_canon.cpp [ 20%] Building CXX object Code/GraphMol/CMakeFiles/GraphMol.dir/SubstanceGroup.cpp.o @@ -3143,1437 +3174,1411 @@ [ 20%] Built target GraphMol make -f Code/GraphMol/MolTransforms/CMakeFiles/MolTransforms.dir/build.make 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/build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/GraphMol/MolTransforms /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/GraphMol/MolTransforms/CMakeFiles/MolTransforms.dir/DependInfo.cmake "--color=" -make -f Code/GraphMol/CMakeFiles/tableTestsCatch.dir/build.make Code/GraphMol/CMakeFiles/tableTestsCatch.dir/depend -make -f Code/GraphMol/Subgraphs/CMakeFiles/Subgraphs.dir/build.make Code/GraphMol/Subgraphs/CMakeFiles/Subgraphs.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu' cd /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202409.4 /build/reproducible-path/rdkit-202409.4/Code/GraphMol/SmilesParse /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/GraphMol/SmilesParse 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-I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202409.4/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-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-202409.4/Code/GraphMol/SmilesParse/SmartsWrite.cpp +[ 21%] Building CXX object Code/GraphMol/Trajectory/CMakeFiles/Trajectory.dir/Trajectory.cpp.o +cd /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/GraphMol/Trajectory && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB 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/usr/include/python3.13 -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-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-202409.4/Code/GraphMol/Wrap/Queries.cpp -[ 23%] Linking CXX shared library ../../../lib/libRDKitTrajectory.so +[ 21%] Building CXX object Code/GraphMol/MolCatalog/CMakeFiles/MolCatalog.dir/MolCatalogEntry.cpp.o +cd /build/reproducible-path/rdkit-202409.4/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-202409.4/External -I/usr/include/python3.13 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202409.4/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-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/CMakeFiles/PartialCharges.dir/GasteigerParams.cpp.o -MF CMakeFiles/PartialCharges.dir/GasteigerParams.cpp.o.d -o CMakeFiles/PartialCharges.dir/GasteigerParams.cpp.o -c /build/reproducible-path/rdkit-202409.4/Code/GraphMol/PartialCharges/GasteigerParams.cpp +[ 21%] Linking CXX shared library ../../../lib/libRDKitTrajectory.so cd /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/GraphMol/Trajectory && /usr/bin/cmake -E cmake_link_script CMakeFiles/Trajectory.dir/link.txt --verbose=1 /usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,--dependency-file=CMakeFiles/Trajectory.dir/link.d -Wl,-z,relro -Wl,-z,now -shared -Wl,-soname,libRDKitTrajectory.so.1 -o ../../../lib/libRDKitTrajectory.so.1.2024.09.4 CMakeFiles/Trajectory.dir/Trajectory.cpp.o ../../../lib/libRDKitGraphMol.so.1.2024.09.4 ../../../lib/libRDKitRDGeometryLib.so.1.2024.09.4 ../../../lib/libRDKitDataStructs.so.1.2024.09.4 ../../../lib/libRDKitRDGeneral.so.1.2024.09.4 /usr/lib/aarch64-linux-gnu/libboost_system.so.1.83.0 /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-202409.4/obj-aarch64-linux-gnu/Code/GraphMol/Trajectory && /usr/bin/cmake -E cmake_symlink_library ../../../lib/libRDKitTrajectory.so.1.2024.09.4 ../../../lib/libRDKitTrajectory.so.1 ../../../lib/libRDKitTrajectory.so make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu' -[ 23%] Built target Trajectory -make -f Code/Numerics/Optimizer/CMakeFiles/Optimizer.dir/build.make Code/Numerics/Optimizer/CMakeFiles/Optimizer.dir/depend +[ 21%] Built target Trajectory +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-202409.4/obj-aarch64-linux-gnu' -cd /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202409.4 /build/reproducible-path/rdkit-202409.4/Code/Numerics/Optimizer 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object Code/GraphMol/Subgraphs/CMakeFiles/Subgraphs.dir/SubgraphUtils.cpp.o cd /build/reproducible-path/rdkit-202409.4/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_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-202409.4/External -I/build/reproducible-path/rdkit-202409.4/External/boost-numeric-bindings -I/usr/include/python3.13 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202409.4/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-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-202409.4/Code/GraphMol/Subgraphs/SubgraphUtils.cpp -[ 23%] Linking CXX shared library ../../../lib/libRDKitMolCatalog.so -cd /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/GraphMol/MolCatalog && /usr/bin/cmake -E cmake_link_script CMakeFiles/MolCatalog.dir/link.txt --verbose=1 -/usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.4=. -fstack-protector-strong -fstack-clash-protection -Wformat 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cmake_symlink_library ../../../lib/libRDKitMolCatalog.so.1.2024.09.4 ../../../lib/libRDKitMolCatalog.so.1 ../../../lib/libRDKitMolCatalog.so -make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu' -[ 23%] Built target MolCatalog -make -f Code/GraphMol/Wrap/CMakeFiles/rdtrajectory.dir/build.make Code/GraphMol/Wrap/CMakeFiles/rdtrajectory.dir/depend -make[4]: Entering directory '/build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu' -cd /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202409.4 /build/reproducible-path/rdkit-202409.4/Code/GraphMol/Wrap /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/GraphMol/Wrap /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/GraphMol/Wrap/CMakeFiles/rdtrajectory.dir/DependInfo.cmake "--color=" -make[4]: Leaving 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CMakeFiles/rdqueries.dir/rdqueries.cpp.o.d -o CMakeFiles/rdqueries.dir/rdqueries.cpp.o -c /build/reproducible-path/rdkit-202409.4/Code/GraphMol/Wrap/rdqueries.cpp [ 23%] Linking CXX shared library ../../../lib/libRDKitGenericGroups.so cd /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/GraphMol/GenericGroups && /usr/bin/cmake -E cmake_link_script CMakeFiles/GenericGroups.dir/link.txt --verbose=1 /usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,--dependency-file=CMakeFiles/GenericGroups.dir/link.d -Wl,-z,relro -Wl,-z,now -shared -Wl,-soname,libRDKitGenericGroups.so.1 -o ../../../lib/libRDKitGenericGroups.so.1.2024.09.4 CMakeFiles/GenericGroups.dir/GenericGroups.cpp.o ../../../lib/libRDKitGraphMol.so.1.2024.09.4 ../../../lib/libRDKitRDGeometryLib.so.1.2024.09.4 ../../../lib/libRDKitDataStructs.so.1.2024.09.4 ../../../lib/libRDKitRDGeneral.so.1.2024.09.4 /usr/lib/aarch64-linux-gnu/libboost_system.so.1.83.0 /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-202409.4/obj-aarch64-linux-gnu/Code/GraphMol/GenericGroups && /usr/bin/cmake -E cmake_symlink_library ../../../lib/libRDKitGenericGroups.so.1.2024.09.4 ../../../lib/libRDKitGenericGroups.so.1 ../../../lib/libRDKitGenericGroups.so make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu' +[ 23%] Building CXX object Code/GraphMol/CIPLabeler/CMakeFiles/CIPLabeler.dir/Edge.cpp.o +cd /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/GraphMol/CIPLabeler && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK 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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-202409.4/Code/GraphMol/CIPLabeler/Edge.cpp [ 23%] Built target GenericGroups -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-202409.4/obj-aarch64-linux-gnu' -cd /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202409.4 /build/reproducible-path/rdkit-202409.4/Code/GraphMol/PartialCharges/Wrap /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/GraphMol/PartialCharges/Wrap 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-DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DrdPartialCharges_EXPORTS -I/build/reproducible-path/rdkit-202409.4/External -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202409.4/Code -isystem /usr/include/python3.13 -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-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-202409.4/Code/GraphMol/PartialCharges/Wrap/rdPartialCharges.cpp -[ 23%] Linking CXX shared library ../../../lib/libRDKitMolTransforms.so -cd /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/GraphMol/MolTransforms && /usr/bin/cmake -E cmake_link_script CMakeFiles/MolTransforms.dir/link.txt --verbose=1 -/usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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.1.2024.09.4 CMakeFiles/MolTransforms.dir/MolTransforms.cpp.o ../../../lib/libRDKitGraphMol.so.1.2024.09.4 ../../../lib/libRDKitEigenSolvers.so.1.2024.09.4 ../../../lib/libRDKitRDGeometryLib.so.1.2024.09.4 ../../../lib/libRDKitDataStructs.so.1.2024.09.4 ../../../lib/libRDKitRDGeneral.so.1.2024.09.4 /usr/lib/aarch64-linux-gnu/libboost_system.so.1.83.0 /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-202409.4/obj-aarch64-linux-gnu/Code/GraphMol/MolTransforms && /usr/bin/cmake -E cmake_symlink_library ../../../lib/libRDKitMolTransforms.so.1.2024.09.4 ../../../lib/libRDKitMolTransforms.so.1 ../../../lib/libRDKitMolTransforms.so -make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu' -[ 23%] Built target MolTransforms -make -f Code/GraphMol/Substruct/CMakeFiles/SubstructMatch.dir/build.make Code/GraphMol/Substruct/CMakeFiles/SubstructMatch.dir/depend +make -f Code/GraphMol/Wrap/CMakeFiles/rdtrajectory.dir/build.make Code/GraphMol/Wrap/CMakeFiles/rdtrajectory.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu' -cd /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202409.4 /build/reproducible-path/rdkit-202409.4/Code/GraphMol/Substruct /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/GraphMol/Substruct /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/GraphMol/Substruct/CMakeFiles/SubstructMatch.dir/DependInfo.cmake "--color=" +cd /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202409.4 /build/reproducible-path/rdkit-202409.4/Code/GraphMol/Wrap /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu 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CMakeFiles/SubstructMatch.dir/SubstructMatch.cpp.o.d -o CMakeFiles/SubstructMatch.dir/SubstructMatch.cpp.o -c /build/reproducible-path/rdkit-202409.4/Code/GraphMol/Substruct/SubstructMatch.cpp -[ 23%] Linking CXX shared library ../../../lib/libRDKitOptimizer.so -cd /build/reproducible-path/rdkit-202409.4/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-202409.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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.1.2024.09.4 CMakeFiles/Optimizer.dir/BFGSOpt.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-202409.4/obj-aarch64-linux-gnu/Code/GraphMol/Substruct && /usr/bin/cmake -E cmake_symlink_library ../../../lib/libRDKitSubstructMatch.so.1.2024.09.4 ../../../lib/libRDKitSubstructMatch.so.1 ../../../lib/libRDKitSubstructMatch.so -make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu' -[ 31%] Built target SubstructMatch -[ 31%] Building CXX object Code/GraphMol/SmilesParse/CMakeFiles/SmilesParse.dir/SmartsWrite.cpp.o -cd /build/reproducible-path/rdkit-202409.4/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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/build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/GraphMol/SLNParse && /usr/bin/cmake -E cmake_symlink_library ../../../lib/libRDKitSLNParse.so.1.2024.09.4 ../../../lib/libRDKitSLNParse.so.1 ../../../lib/libRDKitSLNParse.so -make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu' -[ 31%] Built target SLNParse -[ 31%] Building CXX object Code/GraphMol/SmilesParse/CMakeFiles/SmilesParse.dir/CanonicalizeStereoGroups.cpp.o -cd /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/GraphMol/SmilesParse && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDKIT_SMILESPARSE_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DSmilesParse_EXPORTS -I/build/reproducible-path/rdkit-202409.4/External -I/usr/include/python3.13 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202409.4/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-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/CanonicalizeStereoGroups.cpp.o -MF CMakeFiles/SmilesParse.dir/CanonicalizeStereoGroups.cpp.o.d -o CMakeFiles/SmilesParse.dir/CanonicalizeStereoGroups.cpp.o -c /build/reproducible-path/rdkit-202409.4/Code/GraphMol/SmilesParse/CanonicalizeStereoGroups.cpp -[ 31%] Building CXX object Code/ForceField/CMakeFiles/ForceField.dir/MMFF/OopBend.cpp.o -cd /build/reproducible-path/rdkit-202409.4/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_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.4/External -I/usr/include/python3.13 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202409.4/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security 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-DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DSmilesParse_EXPORTS -I/build/reproducible-path/rdkit-202409.4/External -I/usr/include/python3.13 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202409.4/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/SmilesParse/CMakeFiles/SmilesParse.dir/smiles.tab.cpp.o -MF CMakeFiles/SmilesParse.dir/smiles.tab.cpp.o.d -o CMakeFiles/SmilesParse.dir/smiles.tab.cpp.o -c /build/reproducible-path/rdkit-202409.4/Code/GraphMol/SmilesParse/smiles.tab.cpp -/build/reproducible-path/rdkit-202409.4/Code/ForceField/MMFF/StretchBend.cpp: In function 'std::pair ForceFields::MMFF::Utils::calcStbnForceConstants(const ForceFields::MMFF::MMFFStbn*)': -/build/reproducible-path/rdkit-202409.4/Code/ForceField/MMFF/StretchBend.cpp:27:35: note: parameter passing for argument of type 'std::pair' when C++17 is enabled changed to match C++14 in GCC 10.1 - 27 | const MMFFStbn *mmffStbnParams) { - | ^ -[ 31%] Linking CXX shared module ../../../../rdkit/Chem/rdMolInterchange.so -cd /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/GraphMol/MolInterchange/Wrap && /usr/bin/cmake -E cmake_link_script CMakeFiles/rdMolInterchange.dir/link.txt --verbose=1 -/usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -shared -Wl,-O1 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Code/GraphMol/SLNParse/Wrap/CMakeFiles/rdSLNParse.dir/build.make Code/GraphMol/SLNParse/Wrap/CMakeFiles/rdSLNParse.dir/depend +[ 27%] Building CXX object Code/GraphMol/PartialCharges/Wrap/CMakeFiles/rdPartialCharges.dir/rdPartialCharges.cpp.o +cd /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/GraphMol/PartialCharges/Wrap && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_NUMPY_DYN_LINK -DBOOST_NUMPY_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DrdPartialCharges_EXPORTS -I/build/reproducible-path/rdkit-202409.4/External 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-DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DrdMolTransforms_EXPORTS -I/build/reproducible-path/rdkit-202409.4/External -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202409.4/Code -isystem /usr/include/python3.13 -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=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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-ffile-prefix-map=/build/reproducible-path/rdkit-202409.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-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-202409.4/Code/GraphMol/ShapeHelpers/ShapeUtils.cpp +[ 28%] Linking CXX shared library ../../../lib/libRDKitSmilesParse.so cd /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/GraphMol/SmilesParse && /usr/bin/cmake -E cmake_link_script CMakeFiles/SmilesParse.dir/link.txt --verbose=1 +make -f Code/GraphMol/MolCatalog/Wrap/CMakeFiles/rdMolCatalog.dir/build.make Code/GraphMol/MolCatalog/Wrap/CMakeFiles/rdMolCatalog.dir/depend +make[4]: 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-ffile-prefix-map=/build/reproducible-path/rdkit-202409.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/MolCatalog/Wrap/CMakeFiles/rdMolCatalog.dir/rdMolCatalog.cpp.o -MF CMakeFiles/rdMolCatalog.dir/rdMolCatalog.cpp.o.d -o CMakeFiles/rdMolCatalog.dir/rdMolCatalog.cpp.o -c /build/reproducible-path/rdkit-202409.4/Code/GraphMol/MolCatalog/Wrap/rdMolCatalog.cpp /usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=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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-ldl cd /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/GraphMol/SmilesParse && /usr/bin/cmake -E cmake_symlink_library ../../../lib/libRDKitSmilesParse.so.1.2024.09.4 ../../../lib/libRDKitSmilesParse.so.1 ../../../lib/libRDKitSmilesParse.so make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu' -[ 33%] Built target SmilesParse -make -f Code/GraphMol/MolAlign/CMakeFiles/MolAlign.dir/build.make Code/GraphMol/MolAlign/CMakeFiles/MolAlign.dir/depend -make -f Code/GraphMol/ForceFieldHelpers/CMakeFiles/ForceFieldHelpers.dir/build.make Code/GraphMol/ForceFieldHelpers/CMakeFiles/ForceFieldHelpers.dir/depend +[ 28%] Built target SmilesParse make -f Code/GraphMol/CMakeFiles/graphmolcpTest.dir/build.make Code/GraphMol/CMakeFiles/graphmolcpTest.dir/depend -make -f Code/GraphMol/CMakeFiles/graphmolqueryTest.dir/build.make Code/GraphMol/CMakeFiles/graphmolqueryTest.dir/depend -make -f Code/GraphMol/CMakeFiles/graphmolIterTest.dir/build.make 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-I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202409.4/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/GraphMol/CMakeFiles/graphmolcpTest.dir/cptest.cpp.o -MF CMakeFiles/graphmolcpTest.dir/cptest.cpp.o.d -o CMakeFiles/graphmolcpTest.dir/cptest.cpp.o -c /build/reproducible-path/rdkit-202409.4/Code/GraphMol/cptest.cpp +[ 28%] Linking CXX shared library ../../../lib/libRDKitOptimizer.so +cd /build/reproducible-path/rdkit-202409.4/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 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../../../lib/libRDKitEigenSolvers.so.1.2024.09.4 ../../../lib/libRDKitRDGeneral.so.1.2024.09.4 /usr/lib/aarch64-linux-gnu/libboost_system.so.1.83.0 /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-202409.4/obj-aarch64-linux-gnu/Code/GraphMol/ShapeHelpers && /usr/bin/cmake -E cmake_symlink_library ../../../lib/libRDKitShapeHelpers.so.1.2024.09.4 ../../../lib/libRDKitShapeHelpers.so.1 ../../../lib/libRDKitShapeHelpers.so make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu' -[ 34%] Built target moliteratorTestsCatch +[ 30%] Built target ShapeHelpers make -f Code/GraphMol/SmilesParse/CMakeFiles/v2smiTestCatch.dir/build.make Code/GraphMol/SmilesParse/CMakeFiles/v2smiTestCatch.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu' cd /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu && 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/build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/GraphMol/SmilesParse && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.4/External -I/usr/include/python3.13 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202409.4/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.4=. -fstack-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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-Wdate-time -D_FORTIFY_SOURCE=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/testSubgraphs1.dir/test1.cpp.o -MF CMakeFiles/testSubgraphs1.dir/test1.cpp.o.d -o CMakeFiles/testSubgraphs1.dir/test1.cpp.o -c /build/reproducible-path/rdkit-202409.4/Code/GraphMol/Subgraphs/test1.cpp -[ 34%] Linking CXX executable queryTestsCatch -cd /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/GraphMol && /usr/bin/cmake -E cmake_link_script CMakeFiles/queryTestsCatch.dir/link.txt --verbose=1 -/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/queryTestsCatch.dir/link.d CMakeFiles/queryTestsCatch.dir/catch_queries.cpp.o -o queryTestsCatch ../RDGeneral/librdkitCatch.a ../../lib/libRDKitSmilesParse.so.1.2024.09.4 ../../lib/libRDKitGraphMol.so.1.2024.09.4 /usr/lib/libCatch2.a ../../lib/libRDKitRDGeometryLib.so.1.2024.09.4 ../../lib/libRDKitDataStructs.so.1.2024.09.4 ../../lib/libRDKitRDGeneral.so.1.2024.09.4 /usr/lib/aarch64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl +[ 30%] Linking CXX shared library ../../../lib/libRDKitMolInterchange.so +cd /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/GraphMol/MolInterchange && /usr/bin/cmake -E cmake_link_script CMakeFiles/MolInterchange.dir/link.txt --verbose=1 +[ 30%] Linking CXX executable graphmolIterTest +cd /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/GraphMol && /usr/bin/cmake -E cmake_link_script CMakeFiles/graphmolIterTest.dir/link.txt --verbose=1 +/usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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.1.2024.09.4 CMakeFiles/MolInterchange.dir/Parser.cpp.o CMakeFiles/MolInterchange.dir/Writer.cpp.o ../../../lib/libRDKitGraphMol.so.1.2024.09.4 ../../../lib/libRDKitRDGeometryLib.so.1.2024.09.4 ../../../lib/libRDKitDataStructs.so.1.2024.09.4 ../../../lib/libRDKitRDGeneral.so.1.2024.09.4 /usr/lib/aarch64-linux-gnu/libboost_system.so.1.83.0 /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-202409.4/obj-aarch64-linux-gnu/Code/GraphMol/MolInterchange && /usr/bin/cmake -E cmake_symlink_library ../../../lib/libRDKitMolInterchange.so.1.2024.09.4 ../../../lib/libRDKitMolInterchange.so.1 ../../../lib/libRDKitMolInterchange.so make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu' -[ 34%] Built target queryTestsCatch +/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/graphmolIterTest.dir/link.d CMakeFiles/graphmolIterTest.dir/itertest.cpp.o -o graphmolIterTest ../../lib/libRDKitSmilesParse.so.1.2024.09.4 ../../lib/libRDKitGraphMol.so.1.2024.09.4 ../../lib/libRDKitRDGeometryLib.so.1.2024.09.4 ../../lib/libRDKitDataStructs.so.1.2024.09.4 ../../lib/libRDKitRDGeneral.so.1.2024.09.4 /usr/lib/aarch64-linux-gnu/libboost_system.so.1.83.0 /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-202409.4/obj-aarch64-linux-gnu' +[ 30%] Built target MolInterchange +[ 30%] Built target graphmolIterTest make -f Code/GraphMol/Subgraphs/CMakeFiles/testSubgraphs2.dir/build.make Code/GraphMol/Subgraphs/CMakeFiles/testSubgraphs2.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu' cd /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202409.4 /build/reproducible-path/rdkit-202409.4/Code/GraphMol/Subgraphs 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-I/build/reproducible-path/rdkit-202409.4/External -I/usr/include/python3.13 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202409.4/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-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/lex.yysln.cpp.o -MF CMakeFiles/SLNParse.dir/lex.yysln.cpp.o.d -o CMakeFiles/SLNParse.dir/lex.yysln.cpp.o -c /build/reproducible-path/rdkit-202409.4/Code/GraphMol/SLNParse/lex.yysln.cpp make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu' make -f Code/GraphMol/Subgraphs/CMakeFiles/testSubgraphs2.dir/build.make 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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 +[ 31%] Linking CXX shared library ../../../lib/libRDKitSubstructMatch.so +cd /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/GraphMol/Substruct && /usr/bin/cmake -E cmake_link_script CMakeFiles/SubstructMatch.dir/link.txt --verbose=1 +/usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,--dependency-file=CMakeFiles/SubstructMatch.dir/link.d -Wl,-z,relro -Wl,-z,now -shared -Wl,-soname,libRDKitSubstructMatch.so.1 -o ../../../lib/libRDKitSubstructMatch.so.1.2024.09.4 CMakeFiles/SubstructMatch.dir/SubstructMatch.cpp.o 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module ../../../../rdkit/Chem/rdMolTransforms.so +cd /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/GraphMol/MolTransforms/Wrap && /usr/bin/cmake -E cmake_link_script CMakeFiles/rdMolTransforms.dir/link.txt --verbose=1 +/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/queryTestsCatch.dir/link.d CMakeFiles/queryTestsCatch.dir/catch_queries.cpp.o -o queryTestsCatch ../RDGeneral/librdkitCatch.a ../../lib/libRDKitSmilesParse.so.1.2024.09.4 ../../lib/libRDKitGraphMol.so.1.2024.09.4 /usr/lib/libCatch2.a ../../lib/libRDKitRDGeometryLib.so.1.2024.09.4 ../../lib/libRDKitDataStructs.so.1.2024.09.4 ../../lib/libRDKitRDGeneral.so.1.2024.09.4 /usr/lib/aarch64-linux-gnu/libboost_system.so.1.83.0 /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-202409.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/smiTest2.dir/link.d CMakeFiles/smiTest2.dir/test2.cpp.o -o smiTest2 ../../../lib/libRDKitSmilesParse.so.1.2024.09.4 ../../../lib/libRDKitGraphMol.so.1.2024.09.4 ../../../lib/libRDKitRDGeometryLib.so.1.2024.09.4 ../../../lib/libRDKitDataStructs.so.1.2024.09.4 ../../../lib/libRDKitRDGeneral.so.1.2024.09.4 /usr/lib/aarch64-linux-gnu/libboost_system.so.1.83.0 /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-202409.4/obj-aarch64-linux-gnu' +make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu' +[ 31%] Built target queryTestsCatch make -f Code/GraphMol/FragCatalog/CMakeFiles/FragCatalog.dir/build.make Code/GraphMol/FragCatalog/CMakeFiles/FragCatalog.dir/depend +[ 31%] Built target smiTest2 make[4]: Entering directory '/build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu' +make -f Code/GraphMol/PartialCharges/CMakeFiles/testPartialCharges.dir/build.make Code/GraphMol/PartialCharges/CMakeFiles/testPartialCharges.dir/depend cd /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202409.4 /build/reproducible-path/rdkit-202409.4/Code/GraphMol/FragCatalog /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu 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-I/build/reproducible-path/rdkit-202409.4/Code -I/build/reproducible-path/rdkit-202409.4/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=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-202409.4/Code/GraphMol/Subgraphs/catch_tests.cpp -[ 34%] Linking CXX executable molbundleTestsCatch -cd /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/GraphMol && /usr/bin/cmake -E cmake_link_script CMakeFiles/molbundleTestsCatch.dir/link.txt --verbose=1 -/usr/bin/c++ -g -O2 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/usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202409.4 /build/reproducible-path/rdkit-202409.4/Code/GraphMol/PartialCharges /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/GraphMol/PartialCharges /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/GraphMol/PartialCharges/CMakeFiles/testPartialCharges.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu' -[ 34%] Built target molbundleTestsCatch -make -f Code/GraphMol/PartialCharges/CMakeFiles/testPartialCharges.dir/build.make Code/GraphMol/PartialCharges/CMakeFiles/testPartialCharges.dir/depend +make -f Code/GraphMol/FragCatalog/CMakeFiles/FragCatalog.dir/build.make Code/GraphMol/FragCatalog/CMakeFiles/FragCatalog.dir/build make[4]: Entering directory '/build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu' -cd 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Code/GraphMol/FragCatalog/CMakeFiles/FragCatalog.dir/FragCatalogUtils.cpp.o +cd /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/GraphMol/FragCatalog && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DFragCatalog_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_FRAGCATALOG_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.4/External -I/usr/include/python3.13 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202409.4/Code -I/build/reproducible-path/rdkit-202409.4/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 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-I/build/reproducible-path/rdkit-202409.4/Code -I/build/reproducible-path/rdkit-202409.4/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/Fingerprints/CMakeFiles/Fingerprints.dir/PatternFingerprints.cpp.o -MF CMakeFiles/Fingerprints.dir/PatternFingerprints.cpp.o.d -o CMakeFiles/Fingerprints.dir/PatternFingerprints.cpp.o -c /build/reproducible-path/rdkit-202409.4/Code/GraphMol/Fingerprints/PatternFingerprints.cpp -[ 35%] Linking CXX shared library ../../../lib/libRDKitMolAlign.so -cd /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/GraphMol/MolAlign && /usr/bin/cmake -E cmake_link_script 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../../../lib/libRDKitEigenSolvers.so.1.2024.09.4 ../../../lib/libRDKitGenericGroups.so.1.2024.09.4 ../../../lib/libRDKitGraphMol.so.1.2024.09.4 ../../../lib/libRDKitRDGeometryLib.so.1.2024.09.4 ../../../lib/libRDKitDataStructs.so.1.2024.09.4 ../../../lib/libRDKitRDGeneral.so.1.2024.09.4 /usr/lib/aarch64-linux-gnu/libboost_system.so.1.83.0 /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-202409.4/obj-aarch64-linux-gnu/Code/GraphMol/MolAlign && /usr/bin/cmake -E cmake_symlink_library ../../../lib/libRDKitMolAlign.so.1.2024.09.4 ../../../lib/libRDKitMolAlign.so.1 ../../../lib/libRDKitMolAlign.so +make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu' +[ 35%] Built target MolAlign make -f Code/GraphMol/ReducedGraphs/Wrap/CMakeFiles/rdReducedGraphs.dir/build.make Code/GraphMol/ReducedGraphs/Wrap/CMakeFiles/rdReducedGraphs.dir/depend make[4]: Entering 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-I/build/reproducible-path/rdkit-202409.4/External -I/usr/include/python3.13 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202409.4/Code -I/build/reproducible-path/rdkit-202409.4/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/Fingerprints/CMakeFiles/Fingerprints.dir/PatternFingerprints.cpp.o -MF CMakeFiles/Fingerprints.dir/PatternFingerprints.cpp.o.d -o CMakeFiles/Fingerprints.dir/PatternFingerprints.cpp.o -c /build/reproducible-path/rdkit-202409.4/Code/GraphMol/Fingerprints/PatternFingerprints.cpp +[ 35%] Building CXX object Code/ForceField/CMakeFiles/ForceField.dir/DistanceConstraint.cpp.o +cd /build/reproducible-path/rdkit-202409.4/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_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.4/External -I/usr/include/python3.13 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202409.4/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.4=. -fstack-protector-strong -fstack-clash-protection -Wformat 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/usr/lib/aarch64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl +make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu' +[ 35%] Built target testReducedGraphs +make -f Code/GraphMol/Depictor/CMakeFiles/Depictor.dir/build.make Code/GraphMol/Depictor/CMakeFiles/Depictor.dir/depend +make[4]: Entering directory '/build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu' +cd /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202409.4 /build/reproducible-path/rdkit-202409.4/Code/GraphMol/Depictor /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/GraphMol/Depictor /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/GraphMol/Depictor/CMakeFiles/Depictor.dir/DependInfo.cmake "--color=" +make[4]: Leaving directory 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-I/build/reproducible-path/rdkit-202409.4/External -I/usr/include/python3.13 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202409.4/Code -I/build/reproducible-path/rdkit-202409.4/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/FragCatalog/CMakeFiles/FragCatalog.dir/FragCatParams.cpp.o -MF CMakeFiles/FragCatalog.dir/FragCatParams.cpp.o.d -o CMakeFiles/FragCatalog.dir/FragCatParams.cpp.o -c /build/reproducible-path/rdkit-202409.4/Code/GraphMol/FragCatalog/FragCatParams.cpp +[ 37%] Linking CXX shared library ../../../lib/libRDKitMolChemicalFeatures.so cd 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CMakeFiles/FragCatalog.dir/FragCatGenerator.cpp.o CMakeFiles/FragCatalog.dir/FragCatalogEntry.cpp.o CMakeFiles/FragCatalog.dir/FragCatParams.cpp.o CMakeFiles/FragCatalog.dir/FragFPGenerator.cpp.o ../../../lib/libRDKitSubgraphs.so.1.2024.09.4 ../../../lib/libRDKitSubstructMatch.so.1.2024.09.4 ../../../lib/libRDKitSmilesParse.so.1.2024.09.4 ../../../lib/libRDKitCatalogs.so.1.2024.09.4 ../../../lib/libRDKitGenericGroups.so.1.2024.09.4 ../../../lib/libRDKitGraphMol.so.1.2024.09.4 ../../../lib/libRDKitRDGeometryLib.so.1.2024.09.4 ../../../lib/libRDKitDataStructs.so.1.2024.09.4 ../../../lib/libRDKitRDGeneral.so.1.2024.09.4 /usr/lib/aarch64-linux-gnu/libboost_system.so.1.83.0 /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-202409.4/obj-aarch64-linux-gnu/Code/GraphMol/FragCatalog && /usr/bin/cmake -E cmake_symlink_library ../../../lib/libRDKitFragCatalog.so.1.2024.09.4 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39%] Building CXX object Code/ForceField/CMakeFiles/ForceField.dir/UFF/BondStretch.cpp.o +cd /build/reproducible-path/rdkit-202409.4/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_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.4/External -I/usr/include/python3.13 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202409.4/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.4=. -fstack-protector-strong -fstack-clash-protection -Wformat 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../../../lib/libRDKitDepictor.so cd /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/GraphMol/Depictor && /usr/bin/cmake -E cmake_link_script CMakeFiles/Depictor.dir/link.txt --verbose=1 -/usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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.1.2024.09.4 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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-I/build/reproducible-path/rdkit-202409.4/External -I/usr/include/python3.13 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202409.4/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -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/DistViolationContrib.cpp.o -MF CMakeFiles/DistGeometry.dir/DistViolationContrib.cpp.o.d -o CMakeFiles/DistGeometry.dir/DistViolationContrib.cpp.o -c /build/reproducible-path/rdkit-202409.4/Code/DistGeom/DistViolationContrib.cpp -[ 43%] Building CXX object Code/GraphMol/Fingerprints/CMakeFiles/Fingerprints.dir/RDKitFPGenerator.cpp.o +[ 39%] Building CXX object External/INCHI-API/CMakeFiles/RDInchiLib.dir/inchi.cpp.o +cd /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/External/INCHI-API && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDInchiLib_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_RDINCHILIB_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_INCHI_SUPPORT -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.4/External -I/usr/include/python3.13 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202409.4/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT External/INCHI-API/CMakeFiles/RDInchiLib.dir/inchi.cpp.o -MF CMakeFiles/RDInchiLib.dir/inchi.cpp.o.d -o CMakeFiles/RDInchiLib.dir/inchi.cpp.o -c /build/reproducible-path/rdkit-202409.4/External/INCHI-API/inchi.cpp +[ 39%] Building CXX object Code/ForceField/CMakeFiles/ForceField.dir/UFF/Inversion.cpp.o +cd /build/reproducible-path/rdkit-202409.4/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_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.4/External -I/usr/include/python3.13 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202409.4/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -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/Inversion.cpp.o -MF CMakeFiles/ForceField.dir/UFF/Inversion.cpp.o.d -o CMakeFiles/ForceField.dir/UFF/Inversion.cpp.o -c /build/reproducible-path/rdkit-202409.4/Code/ForceField/UFF/Inversion.cpp +[ 39%] Building CXX object Code/GraphMol/Fingerprints/CMakeFiles/Fingerprints.dir/RDKitFPGenerator.cpp.o cd /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/GraphMol/Fingerprints && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DFingerprints_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_FINGERPRINTS_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.4/External -I/usr/include/python3.13 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202409.4/Code -I/build/reproducible-path/rdkit-202409.4/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-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-202409.4/Code/GraphMol/Fingerprints/RDKitFPGenerator.cpp -[ 43%] Building CXX object Code/GraphMol/Fingerprints/CMakeFiles/Fingerprints.dir/FingerprintUtil.cpp.o +[ 39%] Building CXX object Code/GraphMol/Fingerprints/CMakeFiles/Fingerprints.dir/FingerprintUtil.cpp.o cd /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/GraphMol/Fingerprints && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DFingerprints_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_FINGERPRINTS_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.4/External -I/usr/include/python3.13 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202409.4/Code -I/build/reproducible-path/rdkit-202409.4/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-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-202409.4/Code/GraphMol/Fingerprints/FingerprintUtil.cpp -[ 43%] Building CXX object Code/GraphMol/Fingerprints/CMakeFiles/Fingerprints.dir/TopologicalTorsionGenerator.cpp.o -cd /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/GraphMol/Fingerprints && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DFingerprints_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_FINGERPRINTS_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.4/External -I/usr/include/python3.13 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202409.4/Code -I/build/reproducible-path/rdkit-202409.4/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-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/TopologicalTorsionGenerator.cpp.o -MF CMakeFiles/Fingerprints.dir/TopologicalTorsionGenerator.cpp.o.d -o CMakeFiles/Fingerprints.dir/TopologicalTorsionGenerator.cpp.o -c /build/reproducible-path/rdkit-202409.4/Code/GraphMol/Fingerprints/TopologicalTorsionGenerator.cpp -[ 43%] Building CXX object Code/DistGeom/CMakeFiles/DistGeometry.dir/DistViolationContribs.cpp.o -cd /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/DistGeom && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DDistGeometry_EXPORTS -DRDKIT_DISTGEOMETRY_BUILD -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.4/External -I/usr/include/python3.13 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202409.4/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -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-202409.4/Code/DistGeom/DistViolationContribs.cpp -[ 43%] Linking CXX shared library ../../../lib/libRDKitFilterCatalog.so -cd /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/GraphMol/FilterCatalog && /usr/bin/cmake -E cmake_link_script CMakeFiles/FilterCatalog.dir/link.txt --verbose=1 -[ 43%] Building CXX object Code/DistGeom/CMakeFiles/DistGeometry.dir/ChiralViolationContrib.cpp.o -cd /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/DistGeom && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DDistGeometry_EXPORTS -DRDKIT_DISTGEOMETRY_BUILD -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.4/External -I/usr/include/python3.13 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202409.4/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 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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.1.2024.09.4 ../../../lib/libRDKitSubstructMatch.so.1.2024.09.4 ../../../lib/libRDKitSmilesParse.so.1.2024.09.4 ../../../lib/libRDKitCatalogs.so.1.2024.09.4 ../../../lib/libRDKitGenericGroups.so.1.2024.09.4 ../../../lib/libRDKitGraphMol.so.1.2024.09.4 ../../../lib/libRDKitRDGeometryLib.so.1.2024.09.4 ../../../lib/libRDKitDataStructs.so.1.2024.09.4 ../../../lib/libRDKitRDGeneral.so.1.2024.09.4 /usr/lib/aarch64-linux-gnu/libboost_system.so.1.83.0 /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-202409.4/obj-aarch64-linux-gnu/Code/GraphMol/FilterCatalog && /usr/bin/cmake -E cmake_symlink_library ../../../lib/libRDKitFilterCatalog.so.1.2024.09.4 ../../../lib/libRDKitFilterCatalog.so.1 ../../../lib/libRDKitFilterCatalog.so +[ 39%] Building CXX object Code/ForceField/CMakeFiles/ForceField.dir/UFF/Inversions.cpp.o +cd /build/reproducible-path/rdkit-202409.4/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_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.4/External -I/usr/include/python3.13 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202409.4/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -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-202409.4/Code/ForceField/UFF/Inversions.cpp +[ 39%] Linking CXX shared library ../../../lib/libRDKitFragCatalog.so +cd /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/GraphMol/FragCatalog && /usr/bin/cmake -E cmake_link_script CMakeFiles/FragCatalog.dir/link.txt --verbose=1 +/usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,--dependency-file=CMakeFiles/FragCatalog.dir/link.d -Wl,-z,relro -Wl,-z,now -shared -Wl,-soname,libRDKitFragCatalog.so.1 -o ../../../lib/libRDKitFragCatalog.so.1.2024.09.4 CMakeFiles/FragCatalog.dir/FragCatalogUtils.cpp.o CMakeFiles/FragCatalog.dir/FragCatGenerator.cpp.o CMakeFiles/FragCatalog.dir/FragCatalogEntry.cpp.o CMakeFiles/FragCatalog.dir/FragCatParams.cpp.o CMakeFiles/FragCatalog.dir/FragFPGenerator.cpp.o ../../../lib/libRDKitSubgraphs.so.1.2024.09.4 ../../../lib/libRDKitSubstructMatch.so.1.2024.09.4 ../../../lib/libRDKitSmilesParse.so.1.2024.09.4 ../../../lib/libRDKitCatalogs.so.1.2024.09.4 ../../../lib/libRDKitGenericGroups.so.1.2024.09.4 ../../../lib/libRDKitGraphMol.so.1.2024.09.4 ../../../lib/libRDKitRDGeometryLib.so.1.2024.09.4 ../../../lib/libRDKitDataStructs.so.1.2024.09.4 ../../../lib/libRDKitRDGeneral.so.1.2024.09.4 /usr/lib/aarch64-linux-gnu/libboost_system.so.1.83.0 /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-202409.4/obj-aarch64-linux-gnu/Code/GraphMol/FragCatalog && /usr/bin/cmake -E cmake_symlink_library ../../../lib/libRDKitFragCatalog.so.1.2024.09.4 ../../../lib/libRDKitFragCatalog.so.1 ../../../lib/libRDKitFragCatalog.so make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu' -[ 43%] Built target FilterCatalog -make -f Code/ForceField/Wrap/CMakeFiles/rdForceField.dir/build.make Code/ForceField/Wrap/CMakeFiles/rdForceField.dir/depend +[ 39%] Built target FragCatalog +make -f Code/GraphMol/ChemTransforms/CMakeFiles/ChemTransforms.dir/build.make Code/GraphMol/ChemTransforms/CMakeFiles/ChemTransforms.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu' -cd /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202409.4 /build/reproducible-path/rdkit-202409.4/Code/ForceField/Wrap /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/ForceField/Wrap /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/ForceField/Wrap/CMakeFiles/rdForceField.dir/DependInfo.cmake "--color=" +cd /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202409.4 /build/reproducible-path/rdkit-202409.4/Code/GraphMol/ChemTransforms /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/GraphMol/ChemTransforms 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-I/build/reproducible-path/rdkit-202409.4/External -I/usr/include/python3.13 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202409.4/Code -I/build/reproducible-path/rdkit-202409.4/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-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/TopologicalTorsionGenerator.cpp.o -MF CMakeFiles/Fingerprints.dir/TopologicalTorsionGenerator.cpp.o.d -o CMakeFiles/Fingerprints.dir/TopologicalTorsionGenerator.cpp.o -c /build/reproducible-path/rdkit-202409.4/Code/GraphMol/Fingerprints/TopologicalTorsionGenerator.cpp +[ 39%] Building CXX object 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+cd /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/External/INCHI-API && /usr/bin/cmake -E cmake_symlink_library ../../lib/libRDKitRDInchiLib.so.1.2024.09.4 ../../lib/libRDKitRDInchiLib.so.1 ../../lib/libRDKitRDInchiLib.so make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu' -make -f External/INCHI-API/CMakeFiles/RDInchiLib.dir/build.make External/INCHI-API/CMakeFiles/RDInchiLib.dir/build +[ 41%] Built target RDInchiLib +make -f External/INCHI-API/Wrap/CMakeFiles/rdinchi.dir/build.make External/INCHI-API/Wrap/CMakeFiles/rdinchi.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu' -[ 45%] Building CXX object External/INCHI-API/CMakeFiles/RDInchiLib.dir/inchi.cpp.o -cd /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/External/INCHI-API && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB 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Code/ForceField/CMakeFiles/ForceField.dir/MMFF/BondStretch.cpp.o +cd /build/reproducible-path/rdkit-202409.4/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_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.4/External -I/usr/include/python3.13 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202409.4/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security 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Code/ForceField/CMakeFiles/ForceField.dir/MMFF/OopBend.cpp.o +cd /build/reproducible-path/rdkit-202409.4/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_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.4/External -I/usr/include/python3.13 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202409.4/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -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-202409.4/Code/ForceField/MMFF/OopBend.cpp +[ 41%] Linking CXX shared library ../../../lib/libRDKitFingerprints.so cd /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/GraphMol/Fingerprints && /usr/bin/cmake -E cmake_link_script CMakeFiles/Fingerprints.dir/link.txt --verbose=1 /usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.4=. -fstack-protector-strong -fstack-clash-protection -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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Code/GraphMol/DistGeomHelpers/CMakeFiles/DistGeomHelpers.dir/BoundsMatrixBuilder.cpp.o -cd /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/GraphMol/DistGeomHelpers && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DDistGeomHelpers_EXPORTS -DRDKIT_DISTGEOMHELPERS_BUILD -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.4/External -I/usr/include/python3.13 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202409.4/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.4=. -fstack-protector-strong 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/usr/include/python3.13 -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/MolHash/Wrap/CMakeFiles/rdMolHash.dir/rdMolHash.cpp.o -MF CMakeFiles/rdMolHash.dir/rdMolHash.cpp.o.d -o CMakeFiles/rdMolHash.dir/rdMolHash.cpp.o -c /build/reproducible-path/rdkit-202409.4/Code/GraphMol/MolHash/Wrap/rdMolHash.cpp -[ 45%] Linking CXX shared module ../../../../rdkit/Chem/rdForceFieldHelpers.so -cd /build/reproducible-path/rdkit-202409.4/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 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CMakeFiles/DistGeomHelpers.dir/Embedder.cpp.o.d -o CMakeFiles/DistGeomHelpers.dir/Embedder.cpp.o -c /build/reproducible-path/rdkit-202409.4/Code/GraphMol/DistGeomHelpers/Embedder.cpp -[ 45%] Linking CXX shared library ../../../lib/libRDKitMolInteractionFields.so -cd /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/GraphMol/MolInteractionFields && /usr/bin/cmake -E cmake_link_script CMakeFiles/MolInteractionFields.dir/link.txt --verbose=1 -[ 45%] Linking CXX shared library ../../lib/libRDKitRDInchiLib.so -cd /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/External/INCHI-API && /usr/bin/cmake -E cmake_link_script CMakeFiles/RDInchiLib.dir/link.txt --verbose=1 -/usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function 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/usr/lib/aarch64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl -cd /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/GraphMol/MolInteractionFields && /usr/bin/cmake -E cmake_symlink_library ../../../lib/libRDKitMolInteractionFields.so.1.2024.09.4 ../../../lib/libRDKitMolInteractionFields.so.1 ../../../lib/libRDKitMolInteractionFields.so -make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu' -[ 45%] Built target MolInteractionFields -make -f Code/GraphMol/MolInteractionFields/Wrap/CMakeFiles/rdMIF.dir/build.make Code/GraphMol/MolInteractionFields/Wrap/CMakeFiles/rdMIF.dir/depend -make[4]: Entering directory '/build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu' -cd /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202409.4 /build/reproducible-path/rdkit-202409.4/Code/GraphMol/MolInteractionFields/Wrap 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'/build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu' -cd /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/External/INCHI-API && /usr/bin/cmake -E cmake_symlink_library ../../lib/libRDKitRDInchiLib.so.1.2024.09.4 ../../lib/libRDKitRDInchiLib.so.1 ../../lib/libRDKitRDInchiLib.so -[ 46%] Building CXX object Code/GraphMol/MolInteractionFields/Wrap/CMakeFiles/rdMIF.dir/rdMIF.cpp.o -cd /build/reproducible-path/rdkit-202409.4/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 -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DrdMIF_EXPORTS -I/build/reproducible-path/rdkit-202409.4/External -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202409.4/Code -isystem /usr/include/python3.13 -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-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-202409.4/Code/GraphMol/MolInteractionFields/Wrap/rdMIF.cpp -make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu' -[ 46%] Built target 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'/build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu' -[ 46%] Building CXX object External/INCHI-API/Wrap/CMakeFiles/rdinchi.dir/pyInchi.cpp.o -cd /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/External/INCHI-API/Wrap && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_NUMPY_DYN_LINK -DBOOST_NUMPY_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -Drdinchi_EXPORTS -I/build/reproducible-path/rdkit-202409.4/External -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202409.4/Code -isystem /usr/include/python3.13 -isystem 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cmake_link_script CMakeFiles/MolHash.dir/link.txt --verbose=1 +[ 44%] Linking CXX shared library ../../lib/libRDKitForceField.so +cd /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/ForceField && /usr/bin/cmake -E cmake_link_script CMakeFiles/ForceField.dir/link.txt --verbose=1 +/usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,--dependency-file=CMakeFiles/MolHash.dir/link.d -Wl,-z,relro -Wl,-z,now -shared -Wl,-soname,libRDKitMolHash.so.1 -o ../../../lib/libRDKitMolHash.so.1.2024.09.4 CMakeFiles/MolHash.dir/hashfunctions.cpp.o CMakeFiles/MolHash.dir/normalize.cpp.o ../../../lib/libRDKitDepictor.so.1.2024.09.4 /usr/lib/aarch64-linux-gnu/libcoordgen.so 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/usr/lib/aarch64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl +cd /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/ForceField && /usr/bin/cmake -E cmake_symlink_library ../../lib/libRDKitForceField.so.1.2024.09.4 ../../lib/libRDKitForceField.so.1 ../../lib/libRDKitForceField.so +make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu' +[ 44%] Built target ForceField +make -f Code/GraphMol/ForceFieldHelpers/CMakeFiles/ForceFieldHelpers.dir/build.make Code/GraphMol/ForceFieldHelpers/CMakeFiles/ForceFieldHelpers.dir/depend +make[4]: Entering directory '/build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu' +cd /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202409.4 /build/reproducible-path/rdkit-202409.4/Code/GraphMol/ForceFieldHelpers /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu 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Code/GraphMol/FileParsers/CMakeFiles/FileParsers.dir/TDTWriter.cpp.o -cd /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DFileParsers_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_FILEPARSERS_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.4/External -I/usr/include/python3.13 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202409.4/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.4=. -fstack-protector-strong -fstack-clash-protection -Wformat 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../../../../rdkit/Chem/rdFingerprintGenerator.so cd /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/GraphMol/Fingerprints/Wrap && /usr/bin/cmake -E cmake_link_script CMakeFiles/rdFingerprintGenerator.dir/link.txt --verbose=1 /usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=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/rdFingerprintGenerator.dir/link.d -Wl,-z,relro -Wl,-z,now -shared -o ../../../../rdkit/Chem/rdFingerprintGenerator.so CMakeFiles/rdFingerprintGenerator.dir/FingerprintGeneratorWrapper.cpp.o ../../../../lib/libRDKitFingerprints.so.1.2024.09.4 ../../../../lib/libRDKitRDBoost.so.1.2024.09.4 ../../../../lib/libRDKitSubgraphs.so.1.2024.09.4 ../../../../lib/libRDKitSubstructMatch.so.1.2024.09.4 ../../../../lib/libRDKitGenericGroups.so.1.2024.09.4 ../../../../lib/libRDKitSmilesParse.so.1.2024.09.4 ../../../../lib/libRDKitGraphMol.so.1.2024.09.4 ../../../../lib/libRDKitRDGeometryLib.so.1.2024.09.4 ../../../../lib/libRDKitDataStructs.so.1.2024.09.4 /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.1.2024.09.4 /usr/lib/aarch64-linux-gnu/libboost_system.so.1.83.0 /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-202409.4/obj-aarch64-linux-gnu' -[ 48%] Built target rdFingerprintGenerator -[ 48%] Building CXX object Code/GraphMol/FileParsers/CMakeFiles/FileParsers.dir/TplFileParser.cpp.o +[ 45%] Built target rdFingerprintGenerator +[ 45%] Building CXX object Code/GraphMol/ForceFieldHelpers/CMakeFiles/ForceFieldHelpers.dir/MMFF/Builder.cpp.o +cd /build/reproducible-path/rdkit-202409.4/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_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.4/External -I/usr/include/python3.13 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202409.4/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.4=. -fstack-protector-strong 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-I/build/reproducible-path/rdkit-202409.4/External -I/usr/include/python3.13 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202409.4/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-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-202409.4/Code/GraphMol/FileParsers/TplFileParser.cpp -[ 49%] Building CXX object Code/GraphMol/FileParsers/CMakeFiles/FileParsers.dir/TplFileWriter.cpp.o +[ 46%] Building CXX object Code/GraphMol/FileParsers/CMakeFiles/FileParsers.dir/TplFileWriter.cpp.o cd /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DFileParsers_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_FILEPARSERS_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.4/External -I/usr/include/python3.13 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202409.4/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.4=. -fstack-protector-strong -fstack-clash-protection -Wformat 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match C++14 in GCC 10.1 + 419 | MMFF::Utils::calcStbnForceConstants(&mmffStbnParams); + | ^ +[ 46%] Building CXX object Code/GraphMol/FileParsers/CMakeFiles/FileParsers.dir/PDBParser.cpp.o cd /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DFileParsers_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_FILEPARSERS_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.4/External -I/usr/include/python3.13 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202409.4/Code -isystem /usr/include/eigen3 -g -O2 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Code/GraphMol/FileParsers/CMakeFiles/FileParsers.dir/MultithreadedMolSupplier.cpp.o -MF CMakeFiles/FileParsers.dir/MultithreadedMolSupplier.cpp.o.d -o CMakeFiles/FileParsers.dir/MultithreadedMolSupplier.cpp.o -c /build/reproducible-path/rdkit-202409.4/Code/GraphMol/FileParsers/MultithreadedMolSupplier.cpp -[ 50%] Building CXX object Code/GraphMol/FileParsers/CMakeFiles/FileParsers.dir/MultithreadedSmilesMolSupplier.cpp.o +[ 47%] Building CXX object Code/GraphMol/FileParsers/CMakeFiles/FileParsers.dir/MultithreadedSmilesMolSupplier.cpp.o cd /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DFileParsers_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_FILEPARSERS_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT 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/usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -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-202409.4/Code/DistGeom/TriangleSmooth.cpp +[ 48%] Building CXX object Code/DistGeom/CMakeFiles/DistGeometry.dir/DistViolationContrib.cpp.o +cd /build/reproducible-path/rdkit-202409.4/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 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-I/build/reproducible-path/rdkit-202409.4/External -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202409.4/Code -isystem /usr/include/python3.13 -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/ForceField/Wrap/CMakeFiles/rdForceField.dir/ForceField.cpp.o -MF CMakeFiles/rdForceField.dir/ForceField.cpp.o.d -o CMakeFiles/rdForceField.dir/ForceField.cpp.o -c /build/reproducible-path/rdkit-202409.4/Code/ForceField/Wrap/ForceField.cpp +[ 49%] Building CXX object Code/DistGeom/CMakeFiles/DistGeometry.dir/DistViolationContribs.cpp.o +[ 49%] Building CXX object Code/DistGeom/CMakeFiles/DistGeometry.dir/ChiralViolationContrib.cpp.o +cd /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/DistGeom && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DDistGeometry_EXPORTS -DRDKIT_DISTGEOMETRY_BUILD -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.4/External -I/usr/include/python3.13 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202409.4/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 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-I/build/reproducible-path/rdkit-202409.4/External -I/usr/include/python3.13 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202409.4/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -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/ChiralViolationContrib.cpp.o -MF CMakeFiles/DistGeometry.dir/ChiralViolationContrib.cpp.o.d -o CMakeFiles/DistGeometry.dir/ChiralViolationContrib.cpp.o -c /build/reproducible-path/rdkit-202409.4/Code/DistGeom/ChiralViolationContrib.cpp +[ 49%] Building CXX object Code/DistGeom/CMakeFiles/DistGeometry.dir/ChiralViolationContribs.cpp.o +cd 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CMakeFiles/MolInteractionFields.dir/MIFDescriptors.cpp.o.d -o CMakeFiles/MolInteractionFields.dir/MIFDescriptors.cpp.o -c /build/reproducible-path/rdkit-202409.4/Code/GraphMol/MolInteractionFields/MIFDescriptors.cpp +[ 49%] Linking CXX shared library ../../lib/libRDKitDistGeometry.so +cd /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/DistGeom && /usr/bin/cmake -E cmake_link_script CMakeFiles/DistGeometry.dir/link.txt --verbose=1 +/usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,--dependency-file=CMakeFiles/DistGeometry.dir/link.d -Wl,-z,relro -Wl,-z,now -shared -Wl,-soname,libRDKitDistGeometry.so.1 -o ../../lib/libRDKitDistGeometry.so.1.2024.09.4 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/usr/lib/aarch64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl +cd /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/DistGeom && /usr/bin/cmake -E cmake_symlink_library ../../lib/libRDKitDistGeometry.so.1.2024.09.4 ../../lib/libRDKitDistGeometry.so.1 ../../lib/libRDKitDistGeometry.so +make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu' +[ 49%] Built target DistGeometry +make -f Code/GraphMol/DistGeomHelpers/CMakeFiles/DistGeomHelpers.dir/build.make Code/GraphMol/DistGeomHelpers/CMakeFiles/DistGeomHelpers.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu' -cd /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202409.4 /build/reproducible-path/rdkit-202409.4/Code/GraphMol /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu 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forceFieldHelpersCatch +cd /build/reproducible-path/rdkit-202409.4/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-202409.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/forceFieldHelpersCatch.dir/link.d CMakeFiles/forceFieldHelpersCatch.dir/catch_tests.cpp.o -o forceFieldHelpersCatch ../../RDGeneral/librdkitCatch.a ../../../lib/libRDKitForceFieldHelpers.so.1.2024.09.4 ../../../lib/libRDKitSmilesParse.so.1.2024.09.4 ../../../lib/libRDKitForceField.so.1.2024.09.4 /usr/lib/libCatch2.a ../../../lib/libRDKitOptimizer.so.1.2024.09.4 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/build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/GraphMol && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.4/External -I/usr/include/python3.13 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202409.4/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/GraphMol/CMakeFiles/graphmoltestPickler.dir/testPickler.cpp.o -MF CMakeFiles/graphmoltestPickler.dir/testPickler.cpp.o.d -o CMakeFiles/graphmoltestPickler.dir/testPickler.cpp.o -c /build/reproducible-path/rdkit-202409.4/Code/GraphMol/testPickler.cpp +[ 51%] Linking CXX shared library ../../../lib/libRDKitMolInteractionFields.so +cd /build/reproducible-path/rdkit-202409.4/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-202409.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=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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/build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/GraphMol/MolInteractionFields && /usr/bin/cmake -E cmake_symlink_library ../../../lib/libRDKitMolInteractionFields.so.1.2024.09.4 ../../../lib/libRDKitMolInteractionFields.so.1 ../../../lib/libRDKitMolInteractionFields.so +make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu' +[ 51%] Built target MolInteractionFields +make -f Code/GraphMol/CMakeFiles/graphmoltestPicklerGlobalSetting.dir/build.make Code/GraphMol/CMakeFiles/graphmoltestPicklerGlobalSetting.dir/depend +make[4]: Entering directory '/build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu' +cd /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202409.4 /build/reproducible-path/rdkit-202409.4/Code/GraphMol /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/GraphMol /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/GraphMol/CMakeFiles/graphmoltestPicklerGlobalSetting.dir/DependInfo.cmake "--color=" +make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu' make -f Code/GraphMol/CMakeFiles/graphmoltestPicklerGlobalSetting.dir/build.make Code/GraphMol/CMakeFiles/graphmoltestPicklerGlobalSetting.dir/build -make -f Code/GraphMol/CMakeFiles/hanoiTest.dir/build.make Code/GraphMol/CMakeFiles/hanoiTest.dir/build make[4]: Entering directory '/build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu' +[ 51%] Building CXX object Code/GraphMol/CMakeFiles/graphmoltestPicklerGlobalSetting.dir/testPicklerGlobalSettings.cpp.o +cd /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/GraphMol && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB 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CMakeFiles/graphmoltestPicklerGlobalSetting.dir/testPicklerGlobalSettings.cpp.o.d -o CMakeFiles/graphmoltestPicklerGlobalSetting.dir/testPicklerGlobalSettings.cpp.o -c /build/reproducible-path/rdkit-202409.4/Code/GraphMol/testPicklerGlobalSettings.cpp +[ 51%] Linking CXX shared module ../../../rdkit/ForceField/rdForceField.so +cd /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/ForceField/Wrap && /usr/bin/cmake -E cmake_link_script CMakeFiles/rdForceField.dir/link.txt --verbose=1 +make -f Code/GraphMol/CMakeFiles/hanoiTest.dir/build.make Code/GraphMol/CMakeFiles/hanoiTest.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu' +cd /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202409.4 /build/reproducible-path/rdkit-202409.4/Code/GraphMol /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/GraphMol /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/GraphMol/CMakeFiles/hanoiTest.dir/DependInfo.cmake "--color=" +make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu' +make -f Code/GraphMol/CMakeFiles/hanoiTest.dir/build.make Code/GraphMol/CMakeFiles/hanoiTest.dir/build make[4]: Entering directory '/build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu' -make -f Code/GraphMol/CMakeFiles/molBundleTest.dir/build.make Code/GraphMol/CMakeFiles/molBundleTest.dir/build +[ 51%] Building CXX object Code/GraphMol/CMakeFiles/hanoiTest.dir/hanoitest.cpp.o +cd /build/reproducible-path/rdkit-202409.4/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/libRDKitTrajectory.so.1.2024.09.4 ../../../lib/libRDKitGraphMol.so.1.2024.09.4 ../../../lib/libRDKitRDGeometryLib.so.1.2024.09.4 ../../../lib/libRDKitDataStructs.so.1.2024.09.4 /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.1.2024.09.4 /usr/lib/aarch64-linux-gnu/libboost_system.so.1.83.0 /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-202409.4/obj-aarch64-linux-gnu' +[ 51%] Built target rdForceField +make -f Code/GraphMol/CMakeFiles/resMolSupplierTest.dir/build.make Code/GraphMol/CMakeFiles/resMolSupplierTest.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu' +cd /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202409.4 /build/reproducible-path/rdkit-202409.4/Code/GraphMol /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/GraphMol /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/GraphMol/CMakeFiles/resMolSupplierTest.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu' make -f Code/GraphMol/CMakeFiles/resMolSupplierTest.dir/build.make Code/GraphMol/CMakeFiles/resMolSupplierTest.dir/build make[4]: Entering directory '/build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu' -[ 50%] Building CXX object Code/GraphMol/CMakeFiles/graphmolMolOpsTest.dir/molopstest.cpp.o +[ 51%] Building CXX object Code/GraphMol/CMakeFiles/resMolSupplierTest.dir/resMolSupplierTest.cpp.o +cd /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/GraphMol && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.4/External -I/usr/include/python3.13 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202409.4/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/GraphMol/CMakeFiles/resMolSupplierTest.dir/resMolSupplierTest.cpp.o -MF CMakeFiles/resMolSupplierTest.dir/resMolSupplierTest.cpp.o.d -o CMakeFiles/resMolSupplierTest.dir/resMolSupplierTest.cpp.o -c /build/reproducible-path/rdkit-202409.4/Code/GraphMol/resMolSupplierTest.cpp +[ 51%] Linking CXX shared module ../../../../rdkit/Chem/rdForceFieldHelpers.so +cd /build/reproducible-path/rdkit-202409.4/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-202409.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=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/rdForceFieldHelpers.dir/link.d -Wl,-z,relro -Wl,-z,now -shared -o ../../../../rdkit/Chem/rdForceFieldHelpers.so CMakeFiles/rdForceFieldHelpers.dir/rdForceFields.cpp.o ../../../../lib/libRDKitForceFieldHelpers.so.1.2024.09.4 ../../../../lib/libRDKitRDBoost.so.1.2024.09.4 ../../../../lib/libRDKitSmilesParse.so.1.2024.09.4 ../../../../lib/libRDKitSubstructMatch.so.1.2024.09.4 ../../../../lib/libRDKitGenericGroups.so.1.2024.09.4 ../../../../lib/libRDKitForceField.so.1.2024.09.4 ../../../../lib/libRDKitOptimizer.so.1.2024.09.4 ../../../../lib/libRDKitTrajectory.so.1.2024.09.4 ../../../../lib/libRDKitGraphMol.so.1.2024.09.4 ../../../../lib/libRDKitRDGeometryLib.so.1.2024.09.4 ../../../../lib/libRDKitDataStructs.so.1.2024.09.4 /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.1.2024.09.4 /usr/lib/aarch64-linux-gnu/libboost_system.so.1.83.0 /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-202409.4/obj-aarch64-linux-gnu' +make -f Code/GraphMol/CMakeFiles/molBundleTest.dir/build.make Code/GraphMol/CMakeFiles/molBundleTest.dir/depend +make[4]: Entering directory '/build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu' +cd /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202409.4 /build/reproducible-path/rdkit-202409.4/Code/GraphMol /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/GraphMol /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/GraphMol/CMakeFiles/molBundleTest.dir/DependInfo.cmake "--color=" +[ 51%] Built target rdForceFieldHelpers +make -f Code/GraphMol/CMakeFiles/testSGroup.dir/build.make Code/GraphMol/CMakeFiles/testSGroup.dir/depend +make[4]: Entering directory '/build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu' +cd /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202409.4 /build/reproducible-path/rdkit-202409.4/Code/GraphMol /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/GraphMol /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/GraphMol/CMakeFiles/testSGroup.dir/DependInfo.cmake "--color=" +make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu' +make -f Code/GraphMol/CMakeFiles/molBundleTest.dir/build.make Code/GraphMol/CMakeFiles/molBundleTest.dir/build +make[4]: Entering directory '/build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu' make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu' make -f Code/GraphMol/CMakeFiles/testSGroup.dir/build.make Code/GraphMol/CMakeFiles/testSGroup.dir/build -[ 50%] Building CXX object Code/ForceField/UFF/CMakeFiles/testUFFForceField.dir/testUFFForceField.cpp.o -[ 50%] Building CXX object External/CoordGen/CMakeFiles/testCoordGen.dir/test.cpp.o -[ 51%] Building CXX object Code/GraphMol/CMakeFiles/graphmolTest1.dir/test1.cpp.o -[ 51%] Building CXX object Code/ForceField/MMFF/CMakeFiles/testMMFFForceField.dir/testMMFFForceField.cpp.o -cd /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/GraphMol && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.4/External -I/usr/include/python3.13 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202409.4/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/GraphMol/CMakeFiles/graphmolMolOpsTest.dir/molopstest.cpp.o -MF CMakeFiles/graphmolMolOpsTest.dir/molopstest.cpp.o.d -o CMakeFiles/graphmolMolOpsTest.dir/molopstest.cpp.o -c /build/reproducible-path/rdkit-202409.4/Code/GraphMol/molopstest.cpp make[4]: Entering directory '/build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu' -[ 51%] Building CXX object Code/GraphMol/CMakeFiles/graphmoltestChirality.dir/testChirality.cpp.o -cd /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/ForceField/UFF && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.4/External -I/usr/include/python3.13 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202409.4/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/ForceField/UFF/CMakeFiles/testUFFForceField.dir/testUFFForceField.cpp.o -MF CMakeFiles/testUFFForceField.dir/testUFFForceField.cpp.o.d -o CMakeFiles/testUFFForceField.dir/testUFFForceField.cpp.o -c /build/reproducible-path/rdkit-202409.4/Code/ForceField/UFF/testUFFForceField.cpp -cd /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/External/CoordGen && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DIN_COORDGEN -DIN_MAEPARSER -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION 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Code/GraphMol/CMakeFiles/graphmolTestsCatch.dir/build.make Code/GraphMol/CMakeFiles/graphmolTestsCatch.dir/build make[4]: Entering directory '/build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu' -[ 52%] Building CXX object Code/GraphMol/CMakeFiles/graphmolTestsCatch.dir/catch_graphmol.cpp.o +[ 51%] Building CXX object Code/GraphMol/CMakeFiles/graphmolTestsCatch.dir/catch_graphmol.cpp.o cd /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/GraphMol && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.4/External -I/usr/include/python3.13 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202409.4/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/GraphMol/CMakeFiles/graphmolTestsCatch.dir/catch_graphmol.cpp.o -MF CMakeFiles/graphmolTestsCatch.dir/catch_graphmol.cpp.o.d -o CMakeFiles/graphmolTestsCatch.dir/catch_graphmol.cpp.o -c /build/reproducible-path/rdkit-202409.4/Code/GraphMol/catch_graphmol.cpp -[ 52%] Linking CXX executable graphmoltestPicklerGlobalSetting -cd /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/GraphMol && /usr/bin/cmake -E cmake_link_script CMakeFiles/graphmoltestPicklerGlobalSetting.dir/link.txt 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../../lib/libRDKitDataStructs.so.1.2024.09.4 ../../lib/libRDKitRDGeneral.so.1.2024.09.4 -ldl /usr/lib/aarch64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_iostreams.so.1.83.0 /usr/lib/aarch64-linux-gnu/libmaeparser.so make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu' -[ 52%] Built target graphmoltestPicklerGlobalSetting +[ 52%] Built target testCoordGen make -f Code/GraphMol/CMakeFiles/graphmolOrganometallicsCatch.dir/build.make Code/GraphMol/CMakeFiles/graphmolOrganometallicsCatch.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu' cd /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202409.4 /build/reproducible-path/rdkit-202409.4/Code/GraphMol /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/GraphMol /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/GraphMol/CMakeFiles/graphmolOrganometallicsCatch.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu' make -f Code/GraphMol/CMakeFiles/graphmolOrganometallicsCatch.dir/build.make Code/GraphMol/CMakeFiles/graphmolOrganometallicsCatch.dir/build make[4]: Entering directory '/build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu' -/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/hanoiTest.dir/link.d 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'/build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu' [ 52%] Building CXX object Code/GraphMol/CMakeFiles/graphmolOrganometallicsCatch.dir/catch_organometallics.cpp.o cd /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/GraphMol && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.4/External -I/usr/include/python3.13 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202409.4/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/GraphMol/CMakeFiles/graphmolOrganometallicsCatch.dir/catch_organometallics.cpp.o -MF CMakeFiles/graphmolOrganometallicsCatch.dir/catch_organometallics.cpp.o.d -o CMakeFiles/graphmolOrganometallicsCatch.dir/catch_organometallics.cpp.o -c /build/reproducible-path/rdkit-202409.4/Code/GraphMol/catch_organometallics.cpp -[ 52%] Built target hanoiTest +[ 52%] Linking CXX executable test-valgrind +cd /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/GraphMol && /usr/bin/cmake -E cmake_link_script CMakeFiles/test-valgrind.dir/link.txt --verbose=1 +/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.4=. -fstack-protector-strong -fstack-clash-protection -Wformat 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../../lib/libRDKitGenericGroups.so.1.2024.09.4 ../../lib/libRDKitGraphMol.so.1.2024.09.4 ../../lib/libRDKitRDGeometryLib.so.1.2024.09.4 ../../lib/libRDKitDataStructs.so.1.2024.09.4 ../../lib/libRDKitRDGeneral.so.1.2024.09.4 /usr/lib/aarch64-linux-gnu/libboost_system.so.1.83.0 /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 graphmoltestPicklerGlobalSetting +cd /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/GraphMol && /usr/bin/cmake -E cmake_link_script CMakeFiles/graphmoltestPicklerGlobalSetting.dir/link.txt --verbose=1 +/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function 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../../lib/libRDKitDataStructs.so.1.2024.09.4 ../../lib/libRDKitRDGeneral.so.1.2024.09.4 /usr/lib/aarch64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl /usr/lib/aarch64-linux-gnu/libmaeparser.so +[ 53%] Linking CXX executable graphmolAdjustQueryCatch +cd /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/GraphMol && /usr/bin/cmake -E cmake_link_script CMakeFiles/graphmolAdjustQueryCatch.dir/link.txt --verbose=1 +/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/graphmolAdjustQueryCatch.dir/link.d 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-I/usr/include/python3.13 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202409.4/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=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-202409.4/Code/GraphMol/Depictor/catch_tests.cpp -[ 54%] Linking CXX executable graphmoltestChirality -cd /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/GraphMol && /usr/bin/cmake -E cmake_link_script CMakeFiles/graphmoltestChirality.dir/link.txt --verbose=1 -[ 54%] Linking CXX executable canonTestsCatch -cd /build/reproducible-path/rdkit-202409.4/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-202409.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_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.1.2024.09.4 ../../lib/libRDKitChemTransforms.so.1.2024.09.4 ../../lib/libRDKitDepictor.so.1.2024.09.4 /usr/lib/aarch64-linux-gnu/libcoordgen.so ../../lib/libRDKitMolAlign.so.1.2024.09.4 ../../lib/libRDKitSmilesParse.so.1.2024.09.4 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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-202409.4/obj-aarch64-linux-gnu' -[ 54%] Built target graphmoltestChirality +[ 53%] Building CXX object Code/GraphMol/Depictor/CMakeFiles/depictorCatch.dir/catch_tests.cpp.o +cd /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/GraphMol/Depictor && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DIN_COORDGEN -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.4/External -I/usr/include/python3.13 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202409.4/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=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-202409.4/Code/GraphMol/Depictor/catch_tests.cpp +[ 53%] Built target canonTestsCatch 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-202409.4/obj-aarch64-linux-gnu' cd 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../../lib/libRDKitRDGeneral.so.1.2024.09.4 /usr/lib/aarch64-linux-gnu/libboost_system.so.1.83.0 /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-202409.4/obj-aarch64-linux-gnu' -[ 54%] Built target canonTestsCatch +[ 53%] Built target graphmoltestPickler make -f Code/GraphMol/FileParsers/CMakeFiles/testAtropisomers.dir/build.make Code/GraphMol/FileParsers/CMakeFiles/testAtropisomers.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu' cd /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202409.4 /build/reproducible-path/rdkit-202409.4/Code/GraphMol/FileParsers /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu 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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-202409.4/obj-aarch64-linux-gnu' -[ 55%] Built target nontetrahedralCatch +[ 54%] Built target nontetrahedralCatch make -f Code/GraphMol/FileParsers/CMakeFiles/testMolSupplier.dir/build.make Code/GraphMol/FileParsers/CMakeFiles/testMolSupplier.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu' cd /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202409.4 /build/reproducible-path/rdkit-202409.4/Code/GraphMol/FileParsers /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers 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/usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/GraphMol/FileParsers/CMakeFiles/testMolWriter.dir/testMolWriter.cpp.o -MF CMakeFiles/testMolWriter.dir/testMolWriter.cpp.o.d -o CMakeFiles/testMolWriter.dir/testMolWriter.cpp.o -c /build/reproducible-path/rdkit-202409.4/Code/GraphMol/FileParsers/testMolWriter.cpp -[ 55%] Linking CXX executable testGeneralFileReader -cd /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers && /usr/bin/cmake -E cmake_link_script CMakeFiles/testGeneralFileReader.dir/link.txt --verbose=1 -/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.4=. -fstack-protector-strong 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../../../lib/libRDKitGraphMol.so.1.2024.09.4 ../../../lib/libRDKitRDGeometryLib.so.1.2024.09.4 ../../../lib/libRDKitDataStructs.so.1.2024.09.4 ../../../lib/libRDKitRDGeneral.so.1.2024.09.4 -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 +[ 54%] Linking CXX executable testMultithreadedMolSupplier +cd /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers && /usr/bin/cmake -E cmake_link_script CMakeFiles/testMultithreadedMolSupplier.dir/link.txt --verbose=1 +/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=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/libRDKitRDGeometryLib.so.1.2024.09.4 ../../../lib/libRDKitDataStructs.so.1.2024.09.4 ../../../lib/libRDKitRDGeneral.so.1.2024.09.4 -ldl /usr/lib/aarch64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_iostreams.so.1.83.0 make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu' -[ 55%] Built target testGeneralFileReader +[ 54%] Built target testMultithreadedMolSupplier make -f Code/GraphMol/FileParsers/CMakeFiles/testTplParser.dir/build.make Code/GraphMol/FileParsers/CMakeFiles/testTplParser.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu' cd /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202409.4 /build/reproducible-path/rdkit-202409.4/Code/GraphMol/FileParsers /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/CMakeFiles/testTplParser.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu' make -f Code/GraphMol/FileParsers/CMakeFiles/testTplParser.dir/build.make Code/GraphMol/FileParsers/CMakeFiles/testTplParser.dir/build make[4]: Entering directory '/build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu' -[ 55%] Building CXX object Code/GraphMol/FileParsers/CMakeFiles/testTplParser.dir/testTpls.cpp.o +[ 54%] Building CXX object Code/GraphMol/FileParsers/CMakeFiles/testTplParser.dir/testTpls.cpp.o cd /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.4/External -I/usr/include/python3.13 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202409.4/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/GraphMol/FileParsers/CMakeFiles/testTplParser.dir/testTpls.cpp.o -MF CMakeFiles/testTplParser.dir/testTpls.cpp.o.d -o CMakeFiles/testTplParser.dir/testTpls.cpp.o -c /build/reproducible-path/rdkit-202409.4/Code/GraphMol/FileParsers/testTpls.cpp -[ 55%] Building CXX object Code/GraphMol/ChemReactions/CMakeFiles/ChemReactions.dir/ReactionPickler.cpp.o -cd /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/GraphMol/ChemReactions && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DChemReactions_EXPORTS -DRDKIT_CHEMREACTIONS_BUILD -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.4/External -I/usr/include/python3.13 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202409.4/Code -I/build/reproducible-path/rdkit-202409.4/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-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-202409.4/Code/GraphMol/ChemReactions/ReactionPickler.cpp -[ 55%] Linking CXX executable testMultithreadedMolSupplier -cd /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers && /usr/bin/cmake 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../../../lib/libRDKitMolTransforms.so.1.2024.09.4 ../../../lib/libRDKitEigenSolvers.so.1.2024.09.4 ../../../lib/libRDKitAlignment.so.1.2024.09.4 /usr/lib/aarch64-linux-gnu/libmaeparser.so ../../../lib/libRDKitSmilesParse.so.1.2024.09.4 ../../../lib/libRDKitSubgraphs.so.1.2024.09.4 ../../../lib/libRDKitSubstructMatch.so.1.2024.09.4 ../../../lib/libRDKitGenericGroups.so.1.2024.09.4 ../../../lib/libRDKitGraphMol.so.1.2024.09.4 ../../../lib/libRDKitRDGeometryLib.so.1.2024.09.4 ../../../lib/libRDKitDataStructs.so.1.2024.09.4 ../../../lib/libRDKitRDGeneral.so.1.2024.09.4 -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 +[ 54%] Linking CXX executable testGeneralFileReader +cd /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers && /usr/bin/cmake -E cmake_link_script CMakeFiles/testGeneralFileReader.dir/link.txt --verbose=1 +/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/testGeneralFileReader.dir/link.d CMakeFiles/testGeneralFileReader.dir/testGeneralFileReader.cpp.o -o testGeneralFileReader ../../../lib/libRDKitFileParsers.so.1.2024.09.4 ../../../lib/libRDKitRDStreams.so.1.2024.09.4 ../../../lib/libRDKitChemTransforms.so.1.2024.09.4 ../../../lib/libRDKitDepictor.so.1.2024.09.4 /usr/lib/aarch64-linux-gnu/libcoordgen.so ../../../lib/libRDKitMolAlign.so.1.2024.09.4 ../../../lib/libRDKitMolTransforms.so.1.2024.09.4 ../../../lib/libRDKitEigenSolvers.so.1.2024.09.4 ../../../lib/libRDKitAlignment.so.1.2024.09.4 ../../../lib/libRDKitSmilesParse.so.1.2024.09.4 ../../../lib/libRDKitSubstructMatch.so.1.2024.09.4 ../../../lib/libRDKitGenericGroups.so.1.2024.09.4 ../../../lib/libRDKitGraphMol.so.1.2024.09.4 ../../../lib/libRDKitRDGeometryLib.so.1.2024.09.4 ../../../lib/libRDKitDataStructs.so.1.2024.09.4 ../../../lib/libRDKitRDGeneral.so.1.2024.09.4 -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-202409.4/obj-aarch64-linux-gnu' -[ 55%] Built target testMultithreadedMolSupplier +[ 54%] Built target testGeneralFileReader make -f Code/GraphMol/FileParsers/CMakeFiles/testMol2ToMol.dir/build.make Code/GraphMol/FileParsers/CMakeFiles/testMol2ToMol.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu' cd /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202409.4 /build/reproducible-path/rdkit-202409.4/Code/GraphMol/FileParsers /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/CMakeFiles/testMol2ToMol.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu' make -f Code/GraphMol/FileParsers/CMakeFiles/testMol2ToMol.dir/build.make Code/GraphMol/FileParsers/CMakeFiles/testMol2ToMol.dir/build make[4]: Entering directory '/build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu' -[ 55%] Building CXX object Code/GraphMol/FileParsers/CMakeFiles/testMol2ToMol.dir/testMol2ToMol.cpp.o +[ 54%] Building CXX object Code/GraphMol/FileParsers/CMakeFiles/testMol2ToMol.dir/testMol2ToMol.cpp.o cd /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.4/External -I/usr/include/python3.13 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202409.4/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/GraphMol/FileParsers/CMakeFiles/testMol2ToMol.dir/testMol2ToMol.cpp.o -MF CMakeFiles/testMol2ToMol.dir/testMol2ToMol.cpp.o.d -o CMakeFiles/testMol2ToMol.dir/testMol2ToMol.cpp.o -c /build/reproducible-path/rdkit-202409.4/Code/GraphMol/FileParsers/testMol2ToMol.cpp -[ 55%] Linking CXX executable graphmolTestsCatch -cd /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/GraphMol && /usr/bin/cmake -E cmake_link_script CMakeFiles/graphmolTestsCatch.dir/link.txt --verbose=1 -/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_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.1.2024.09.4 /usr/lib/libCatch2.a ../../lib/libRDKitChemTransforms.so.1.2024.09.4 ../../lib/libRDKitDepictor.so.1.2024.09.4 /usr/lib/aarch64-linux-gnu/libcoordgen.so ../../lib/libRDKitMolAlign.so.1.2024.09.4 ../../lib/libRDKitSubstructMatch.so.1.2024.09.4 ../../lib/libRDKitGenericGroups.so.1.2024.09.4 ../../lib/libRDKitSmilesParse.so.1.2024.09.4 ../../lib/libRDKitMolTransforms.so.1.2024.09.4 ../../lib/libRDKitGraphMol.so.1.2024.09.4 ../../lib/libRDKitEigenSolvers.so.1.2024.09.4 ../../lib/libRDKitAlignment.so.1.2024.09.4 ../../lib/libRDKitRDGeometryLib.so.1.2024.09.4 ../../lib/libRDKitDataStructs.so.1.2024.09.4 ../../lib/libRDKitRDGeneral.so.1.2024.09.4 /usr/lib/aarch64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl /usr/lib/aarch64-linux-gnu/libmaeparser.so +[ 54%] Building CXX object Code/GraphMol/ChemReactions/CMakeFiles/ChemReactions.dir/ReactionPickler.cpp.o +cd /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/GraphMol/ChemReactions && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DChemReactions_EXPORTS -DRDKIT_CHEMREACTIONS_BUILD -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.4/External -I/usr/include/python3.13 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202409.4/Code -I/build/reproducible-path/rdkit-202409.4/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-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-202409.4/Code/GraphMol/ChemReactions/ReactionPickler.cpp +[ 54%] Linking CXX executable testTplParser +cd /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers && /usr/bin/cmake -E cmake_link_script CMakeFiles/testTplParser.dir/link.txt --verbose=1 +/usr/bin/c++ -g -O2 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../../../lib/libRDKitGraphMol.so.1.2024.09.4 ../../../lib/libRDKitRDGeometryLib.so.1.2024.09.4 ../../../lib/libRDKitDataStructs.so.1.2024.09.4 ../../../lib/libRDKitRDGeneral.so.1.2024.09.4 /usr/lib/aarch64-linux-gnu/libboost_system.so.1.83.0 /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-202409.4/obj-aarch64-linux-gnu' -[ 55%] Built target graphmolTestsCatch +[ 54%] Built target testTplParser make -f Code/GraphMol/FileParsers/CMakeFiles/testSequence.dir/build.make Code/GraphMol/FileParsers/CMakeFiles/testSequence.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu' cd /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202409.4 /build/reproducible-path/rdkit-202409.4/Code/GraphMol/FileParsers /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/CMakeFiles/testSequence.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu' make -f Code/GraphMol/FileParsers/CMakeFiles/testSequence.dir/build.make Code/GraphMol/FileParsers/CMakeFiles/testSequence.dir/build make[4]: Entering directory '/build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu' -[ 55%] Building CXX object Code/GraphMol/FileParsers/CMakeFiles/testSequence.dir/testSequence.cpp.o +[ 54%] Building CXX object Code/GraphMol/FileParsers/CMakeFiles/testSequence.dir/testSequence.cpp.o cd /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.4/External -I/usr/include/python3.13 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202409.4/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/GraphMol/FileParsers/CMakeFiles/testSequence.dir/testSequence.cpp.o -MF CMakeFiles/testSequence.dir/testSequence.cpp.o.d -o CMakeFiles/testSequence.dir/testSequence.cpp.o -c /build/reproducible-path/rdkit-202409.4/Code/GraphMol/FileParsers/testSequence.cpp -[ 55%] Linking CXX executable testTplParser -cd /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers && /usr/bin/cmake -E cmake_link_script CMakeFiles/testTplParser.dir/link.txt --verbose=1 -/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/testTplParser.dir/link.d CMakeFiles/testTplParser.dir/testTpls.cpp.o -o testTplParser 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../../../lib/libRDKitAlignment.so.1.2024.09.4 ../../../lib/libRDKitSmilesParse.so.1.2024.09.4 ../../../lib/libRDKitSubstructMatch.so.1.2024.09.4 ../../../lib/libRDKitGenericGroups.so.1.2024.09.4 ../../../lib/libRDKitGraphMol.so.1.2024.09.4 ../../../lib/libRDKitRDGeometryLib.so.1.2024.09.4 ../../../lib/libRDKitDataStructs.so.1.2024.09.4 ../../../lib/libRDKitRDGeneral.so.1.2024.09.4 /usr/lib/aarch64-linux-gnu/libboost_system.so.1.83.0 /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-202409.4/obj-aarch64-linux-gnu' -[ 55%] Built target testTplParser +[ 54%] Built target testMol2ToMol make -f Code/GraphMol/FileParsers/CMakeFiles/testExtendedStereoParsing.dir/build.make Code/GraphMol/FileParsers/CMakeFiles/testExtendedStereoParsing.dir/depend make[4]: Entering directory 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Code/GraphMol/FileParsers/CMakeFiles/testExtendedStereoParsing.dir/testExtendedStereoParsing.cpp.o +[ 54%] Building CXX object Code/GraphMol/FileParsers/CMakeFiles/testExtendedStereoParsing.dir/testExtendedStereoParsing.cpp.o cd /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.4/External -I/usr/include/python3.13 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202409.4/Code -isystem /usr/include/eigen3 -g -O2 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-fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/testMol2ToMol.dir/link.d CMakeFiles/testMol2ToMol.dir/testMol2ToMol.cpp.o -o testMol2ToMol ../../../lib/libRDKitFileParsers.so.1.2024.09.4 ../../../lib/libRDKitChemTransforms.so.1.2024.09.4 ../../../lib/libRDKitDepictor.so.1.2024.09.4 /usr/lib/aarch64-linux-gnu/libcoordgen.so ../../../lib/libRDKitMolAlign.so.1.2024.09.4 ../../../lib/libRDKitMolTransforms.so.1.2024.09.4 ../../../lib/libRDKitEigenSolvers.so.1.2024.09.4 ../../../lib/libRDKitAlignment.so.1.2024.09.4 ../../../lib/libRDKitSmilesParse.so.1.2024.09.4 ../../../lib/libRDKitSubstructMatch.so.1.2024.09.4 ../../../lib/libRDKitGenericGroups.so.1.2024.09.4 ../../../lib/libRDKitGraphMol.so.1.2024.09.4 ../../../lib/libRDKitRDGeometryLib.so.1.2024.09.4 ../../../lib/libRDKitDataStructs.so.1.2024.09.4 ../../../lib/libRDKitRDGeneral.so.1.2024.09.4 /usr/lib/aarch64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl /usr/lib/aarch64-linux-gnu/libmaeparser.so +[ 54%] Linking CXX executable graphmolTestsCatch +cd /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/GraphMol && /usr/bin/cmake -E cmake_link_script CMakeFiles/graphmolTestsCatch.dir/link.txt --verbose=1 +/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_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.1.2024.09.4 /usr/lib/libCatch2.a ../../lib/libRDKitChemTransforms.so.1.2024.09.4 ../../lib/libRDKitDepictor.so.1.2024.09.4 /usr/lib/aarch64-linux-gnu/libcoordgen.so ../../lib/libRDKitMolAlign.so.1.2024.09.4 ../../lib/libRDKitSubstructMatch.so.1.2024.09.4 ../../lib/libRDKitGenericGroups.so.1.2024.09.4 ../../lib/libRDKitSmilesParse.so.1.2024.09.4 ../../lib/libRDKitMolTransforms.so.1.2024.09.4 ../../lib/libRDKitGraphMol.so.1.2024.09.4 ../../lib/libRDKitEigenSolvers.so.1.2024.09.4 ../../lib/libRDKitAlignment.so.1.2024.09.4 ../../lib/libRDKitRDGeometryLib.so.1.2024.09.4 ../../lib/libRDKitDataStructs.so.1.2024.09.4 ../../lib/libRDKitRDGeneral.so.1.2024.09.4 /usr/lib/aarch64-linux-gnu/libboost_system.so.1.83.0 /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-202409.4/obj-aarch64-linux-gnu' -[ 55%] Built target testMol2ToMol +[ 54%] Built target graphmolTestsCatch make -f Code/GraphMol/FileParsers/CMakeFiles/fileParsersCatchTest.dir/build.make Code/GraphMol/FileParsers/CMakeFiles/fileParsersCatchTest.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu' cd /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202409.4 /build/reproducible-path/rdkit-202409.4/Code/GraphMol/FileParsers /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers 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-DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.4/External -I/usr/include/python3.13 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202409.4/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/GraphMol/FileParsers/CMakeFiles/fileParsersCatchTest.dir/file_parsers_catch.cpp.o -MF CMakeFiles/fileParsersCatchTest.dir/file_parsers_catch.cpp.o.d -o 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-I/build/reproducible-path/rdkit-202409.4/External -I/usr/include/python3.13 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202409.4/Code -I/build/reproducible-path/rdkit-202409.4/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/ChemReactions/CMakeFiles/ChemReactions.dir/ReactionWriter.cpp.o -MF CMakeFiles/ChemReactions.dir/ReactionWriter.cpp.o.d -o CMakeFiles/ChemReactions.dir/ReactionWriter.cpp.o -c /build/reproducible-path/rdkit-202409.4/Code/GraphMol/ChemReactions/ReactionWriter.cpp -[ 55%] Linking CXX executable testSequence +[ 54%] Linking CXX executable testSequence cd 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Code/GraphMol/FileParsers/CMakeFiles/testPropertyLists.dir/testPropertyLists.cpp.o cd /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.4/External -I/usr/include/python3.13 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202409.4/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security 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/build/reproducible-path/rdkit-202409.4/Code/GraphMol/FileParsers/molfile_stereo_catch.cpp -[ 55%] Linking CXX executable chiralityTestsCatch -cd /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/GraphMol && /usr/bin/cmake -E cmake_link_script CMakeFiles/chiralityTestsCatch.dir/link.txt --verbose=1 -/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/chiralityTestsCatch.dir/link.d CMakeFiles/chiralityTestsCatch.dir/catch_chirality.cpp.o -o chiralityTestsCatch ../RDGeneral/librdkitCatch.a ../../lib/libRDKitCIPLabeler.so.1.2024.09.4 ../../lib/libRDKitFileParsers.so.1.2024.09.4 /usr/lib/libCatch2.a 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Code/GraphMol/FileParsers/CMakeFiles/connectTheDotsTest.dir/connectTheDots_catch.cpp.o cd /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.4/External -I/usr/include/python3.13 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202409.4/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security 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'/build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu' -[ 55%] Built target testMolSupplier +[ 54%] Built target testMolWriter 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-202409.4/obj-aarch64-linux-gnu' -[ 55%] Building CXX object Code/GraphMol/ChemReactions/CMakeFiles/ChemReactions.dir/ReactionDepict.cpp.o cd /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202409.4 /build/reproducible-path/rdkit-202409.4/Code/GraphMol/FileParsers /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/CMakeFiles/v2MolSuppliers.dir/DependInfo.cmake "--color=" -cd 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/build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/GraphMol && /usr/bin/cmake -E cmake_link_script CMakeFiles/chiralityTestsCatch.dir/link.txt --verbose=1 +/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/chiralityTestsCatch.dir/link.d CMakeFiles/chiralityTestsCatch.dir/catch_chirality.cpp.o -o chiralityTestsCatch ../RDGeneral/librdkitCatch.a ../../lib/libRDKitCIPLabeler.so.1.2024.09.4 ../../lib/libRDKitFileParsers.so.1.2024.09.4 /usr/lib/libCatch2.a ../../lib/libRDKitChemTransforms.so.1.2024.09.4 ../../lib/libRDKitDepictor.so.1.2024.09.4 /usr/lib/aarch64-linux-gnu/libcoordgen.so ../../lib/libRDKitMolAlign.so.1.2024.09.4 ../../lib/libRDKitSmilesParse.so.1.2024.09.4 ../../lib/libRDKitMolTransforms.so.1.2024.09.4 ../../lib/libRDKitEigenSolvers.so.1.2024.09.4 ../../lib/libRDKitAlignment.so.1.2024.09.4 ../../lib/libRDKitSubstructMatch.so.1.2024.09.4 ../../lib/libRDKitGenericGroups.so.1.2024.09.4 ../../lib/libRDKitGraphMol.so.1.2024.09.4 ../../lib/libRDKitRDGeometryLib.so.1.2024.09.4 ../../lib/libRDKitDataStructs.so.1.2024.09.4 ../../lib/libRDKitRDGeneral.so.1.2024.09.4 /usr/lib/aarch64-linux-gnu/libboost_system.so.1.83.0 /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-202409.4/obj-aarch64-linux-gnu' -[ 55%] Built target testMolWriter +[ 54%] Built target chiralityTestsCatch make -f Code/GraphMol/FileParsers/CMakeFiles/v2FileParsersCatchTest.dir/build.make Code/GraphMol/FileParsers/CMakeFiles/v2FileParsersCatchTest.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu' cd /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202409.4 /build/reproducible-path/rdkit-202409.4/Code/GraphMol/FileParsers /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/CMakeFiles/v2FileParsersCatchTest.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu' make -f Code/GraphMol/FileParsers/CMakeFiles/v2FileParsersCatchTest.dir/build.make Code/GraphMol/FileParsers/CMakeFiles/v2FileParsersCatchTest.dir/build make[4]: Entering directory '/build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu' -[ 55%] Building CXX object Code/GraphMol/FileParsers/CMakeFiles/v2FileParsersCatchTest.dir/v2_file_parsers_catch.cpp.o +[ 54%] Building CXX object Code/GraphMol/FileParsers/CMakeFiles/v2FileParsersCatchTest.dir/v2_file_parsers_catch.cpp.o cd /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.4/External -I/usr/include/python3.13 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202409.4/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=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-202409.4/Code/GraphMol/FileParsers/v2_file_parsers_catch.cpp -[ 55%] Linking CXX executable smiTestCatch +[ 54%] Linking CXX executable smiTestCatch cd /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/GraphMol/SmilesParse && /usr/bin/cmake -E cmake_link_script CMakeFiles/smiTestCatch.dir/link.txt --verbose=1 +[ 54%] Building CXX object Code/GraphMol/ChemReactions/CMakeFiles/ChemReactions.dir/ReactionDepict.cpp.o +cd /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/GraphMol/ChemReactions && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DChemReactions_EXPORTS -DRDKIT_CHEMREACTIONS_BUILD -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.4/External -I/usr/include/python3.13 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202409.4/Code -I/build/reproducible-path/rdkit-202409.4/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 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-Wl,--dependency-file=CMakeFiles/smiTestCatch.dir/link.d CMakeFiles/smiTestCatch.dir/catch_tests.cpp.o -o smiTestCatch ../../RDGeneral/librdkitCatch.a ../../../lib/libRDKitFileParsers.so.1.2024.09.4 /usr/lib/libCatch2.a ../../../lib/libRDKitChemTransforms.so.1.2024.09.4 ../../../lib/libRDKitDepictor.so.1.2024.09.4 /usr/lib/aarch64-linux-gnu/libcoordgen.so ../../../lib/libRDKitMolAlign.so.1.2024.09.4 ../../../lib/libRDKitSmilesParse.so.1.2024.09.4 ../../../lib/libRDKitMolTransforms.so.1.2024.09.4 ../../../lib/libRDKitEigenSolvers.so.1.2024.09.4 ../../../lib/libRDKitAlignment.so.1.2024.09.4 ../../../lib/libRDKitSubstructMatch.so.1.2024.09.4 ../../../lib/libRDKitGenericGroups.so.1.2024.09.4 ../../../lib/libRDKitGraphMol.so.1.2024.09.4 ../../../lib/libRDKitRDGeometryLib.so.1.2024.09.4 ../../../lib/libRDKitDataStructs.so.1.2024.09.4 ../../../lib/libRDKitRDGeneral.so.1.2024.09.4 /usr/lib/aarch64-linux-gnu/libboost_system.so.1.83.0 /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-202409.4/obj-aarch64-linux-gnu' -[ 55%] Built target smiTestCatch +[ 54%] Built target smiTestCatch 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-202409.4/obj-aarch64-linux-gnu' cd /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202409.4 /build/reproducible-path/rdkit-202409.4/Code/GraphMol/FileParsers /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers 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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-202409.4/Code/GraphMol/FileParsers/multithreaded_supplier_catch.cpp -[ 55%] Building CXX object Code/GraphMol/ChemReactions/CMakeFiles/ChemReactions.dir/ReactionFingerprints.cpp.o -cd /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/GraphMol/ChemReactions && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DChemReactions_EXPORTS -DRDKIT_CHEMREACTIONS_BUILD -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.4/External -I/usr/include/python3.13 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202409.4/Code -I/build/reproducible-path/rdkit-202409.4/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/ChemReactions/CMakeFiles/ChemReactions.dir/ReactionFingerprints.cpp.o -MF CMakeFiles/ChemReactions.dir/ReactionFingerprints.cpp.o.d -o CMakeFiles/ChemReactions.dir/ReactionFingerprints.cpp.o -c /build/reproducible-path/rdkit-202409.4/Code/GraphMol/ChemReactions/ReactionFingerprints.cpp -[ 55%] Linking CXX executable connectTheDotsTest +[ 54%] Linking CXX executable connectTheDotsTest cd /build/reproducible-path/rdkit-202409.4/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-202409.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_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.1.2024.09.4 /usr/lib/libCatch2.a 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connectTheDotsTest +[ 54%] Built target connectTheDotsTest make -f Code/GraphMol/Substruct/CMakeFiles/testSubstructMatch.dir/build.make Code/GraphMol/Substruct/CMakeFiles/testSubstructMatch.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu' cd /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202409.4 /build/reproducible-path/rdkit-202409.4/Code/GraphMol/Substruct /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/GraphMol/Substruct /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/GraphMol/Substruct/CMakeFiles/testSubstructMatch.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu' make -f Code/GraphMol/Substruct/CMakeFiles/testSubstructMatch.dir/build.make 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-I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202409.4/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=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-202409.4/Code/GraphMol/Substruct/test1.cpp -[ 55%] Linking CXX executable XYZFileParserCatchTest +[ 54%] Linking CXX executable XYZFileParserCatchTest cd /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers && /usr/bin/cmake -E cmake_link_script CMakeFiles/XYZFileParserCatchTest.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/XYZFileParserCatchTest.dir/link.d CMakeFiles/XYZFileParserCatchTest.dir/XYZFileParserCatchTest.cpp.o -o XYZFileParserCatchTest ../../RDGeneral/librdkitCatch.a ../../../lib/libRDKitFileParsers.so.1.2024.09.4 /usr/lib/libCatch2.a ../../../lib/libRDKitChemTransforms.so.1.2024.09.4 ../../../lib/libRDKitDepictor.so.1.2024.09.4 /usr/lib/aarch64-linux-gnu/libcoordgen.so ../../../lib/libRDKitMolAlign.so.1.2024.09.4 ../../../lib/libRDKitMolTransforms.so.1.2024.09.4 ../../../lib/libRDKitEigenSolvers.so.1.2024.09.4 ../../../lib/libRDKitAlignment.so.1.2024.09.4 ../../../lib/libRDKitSmilesParse.so.1.2024.09.4 ../../../lib/libRDKitSubstructMatch.so.1.2024.09.4 ../../../lib/libRDKitGenericGroups.so.1.2024.09.4 ../../../lib/libRDKitGraphMol.so.1.2024.09.4 ../../../lib/libRDKitRDGeometryLib.so.1.2024.09.4 ../../../lib/libRDKitDataStructs.so.1.2024.09.4 ../../../lib/libRDKitRDGeneral.so.1.2024.09.4 /usr/lib/aarch64-linux-gnu/libboost_system.so.1.83.0 /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-202409.4/obj-aarch64-linux-gnu' -[ 55%] Built target XYZFileParserCatchTest +[ 54%] Built target XYZFileParserCatchTest make -f Code/GraphMol/Substruct/CMakeFiles/substructTestCatch.dir/build.make Code/GraphMol/Substruct/CMakeFiles/substructTestCatch.dir/depend make[4]: Entering directory 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55%] Linking CXX executable graphmolMolOpsTest +cd /build/reproducible-path/rdkit-202409.4/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-202409.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_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.1.2024.09.4 ../../lib/libRDKitChemTransforms.so.1.2024.09.4 ../../lib/libRDKitDepictor.so.1.2024.09.4 /usr/lib/aarch64-linux-gnu/libcoordgen.so ../../lib/libRDKitMolAlign.so.1.2024.09.4 ../../lib/libRDKitSubstructMatch.so.1.2024.09.4 ../../lib/libRDKitGenericGroups.so.1.2024.09.4 ../../lib/libRDKitSmilesParse.so.1.2024.09.4 ../../lib/libRDKitMolTransforms.so.1.2024.09.4 ../../lib/libRDKitGraphMol.so.1.2024.09.4 ../../lib/libRDKitEigenSolvers.so.1.2024.09.4 ../../lib/libRDKitAlignment.so.1.2024.09.4 ../../lib/libRDKitRDGeometryLib.so.1.2024.09.4 ../../lib/libRDKitDataStructs.so.1.2024.09.4 ../../lib/libRDKitRDGeneral.so.1.2024.09.4 /usr/lib/aarch64-linux-gnu/libboost_system.so.1.83.0 /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-202409.4/obj-aarch64-linux-gnu' -[ 57%] Built target molfileStereoCatchTest +[ 55%] Built target graphmolMolOpsTest make -f Code/GraphMol/FilterCatalog/CMakeFiles/filterCatalogTest.dir/build.make Code/GraphMol/FilterCatalog/CMakeFiles/filterCatalogTest.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu' cd /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202409.4 /build/reproducible-path/rdkit-202409.4/Code/GraphMol/FilterCatalog /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/GraphMol/FilterCatalog /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/GraphMol/FilterCatalog/CMakeFiles/filterCatalogTest.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu' make -f Code/GraphMol/FilterCatalog/CMakeFiles/filterCatalogTest.dir/build.make Code/GraphMol/FilterCatalog/CMakeFiles/filterCatalogTest.dir/build make[4]: Entering directory '/build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu' -[ 57%] Building CXX object Code/GraphMol/FilterCatalog/CMakeFiles/filterCatalogTest.dir/filtercatalogtest.cpp.o +[ 55%] Building CXX object Code/GraphMol/FilterCatalog/CMakeFiles/filterCatalogTest.dir/filtercatalogtest.cpp.o cd /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/GraphMol/FilterCatalog && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.4/External -I/usr/include/python3.13 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202409.4/Code -I/build/reproducible-path/rdkit-202409.4/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/GraphMol/FilterCatalog/CMakeFiles/filterCatalogTest.dir/filtercatalogtest.cpp.o -MF CMakeFiles/filterCatalogTest.dir/filtercatalogtest.cpp.o.d -o CMakeFiles/filterCatalogTest.dir/filtercatalogtest.cpp.o -c /build/reproducible-path/rdkit-202409.4/Code/GraphMol/FilterCatalog/filtercatalogtest.cpp -[ 57%] Linking CXX executable multithreadedSupplierCatchTest -cd /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers && /usr/bin/cmake -E cmake_link_script CMakeFiles/multithreadedSupplierCatchTest.dir/link.txt --verbose=1 -/usr/bin/c++ -g -O2 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../../../lib/libRDKitSmilesParse.so.1.2024.09.4 ../../../lib/libRDKitSubstructMatch.so.1.2024.09.4 ../../../lib/libRDKitGenericGroups.so.1.2024.09.4 ../../../lib/libRDKitGraphMol.so.1.2024.09.4 ../../../lib/libRDKitRDGeometryLib.so.1.2024.09.4 ../../../lib/libRDKitDataStructs.so.1.2024.09.4 ../../../lib/libRDKitRDGeneral.so.1.2024.09.4 /usr/lib/aarch64-linux-gnu/libboost_system.so.1.83.0 /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 +[ 56%] Linking CXX executable molfileStereoCatchTest +cd /build/reproducible-path/rdkit-202409.4/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-202409.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_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.1.2024.09.4 ../../../lib/libRDKitCIPLabeler.so.1.2024.09.4 ../../../lib/libRDKitSubgraphs.so.1.2024.09.4 /usr/lib/libCatch2.a ../../../lib/libRDKitChemTransforms.so.1.2024.09.4 ../../../lib/libRDKitDepictor.so.1.2024.09.4 /usr/lib/aarch64-linux-gnu/libcoordgen.so ../../../lib/libRDKitMolAlign.so.1.2024.09.4 ../../../lib/libRDKitMolTransforms.so.1.2024.09.4 ../../../lib/libRDKitEigenSolvers.so.1.2024.09.4 ../../../lib/libRDKitAlignment.so.1.2024.09.4 ../../../lib/libRDKitSmilesParse.so.1.2024.09.4 ../../../lib/libRDKitSubstructMatch.so.1.2024.09.4 ../../../lib/libRDKitGenericGroups.so.1.2024.09.4 /usr/lib/aarch64-linux-gnu/libmaeparser.so ../../../lib/libRDKitGraphMol.so.1.2024.09.4 ../../../lib/libRDKitRDGeometryLib.so.1.2024.09.4 ../../../lib/libRDKitDataStructs.so.1.2024.09.4 ../../../lib/libRDKitRDGeneral.so.1.2024.09.4 /usr/lib/aarch64-linux-gnu/libboost_system.so.1.83.0 /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-202409.4/obj-aarch64-linux-gnu' -[ 57%] Built target multithreadedSupplierCatchTest +[ 56%] Built target molfileStereoCatchTest make -f Code/GraphMol/FragCatalog/CMakeFiles/testFragCatalog.dir/build.make Code/GraphMol/FragCatalog/CMakeFiles/testFragCatalog.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu' cd /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202409.4 /build/reproducible-path/rdkit-202409.4/Code/GraphMol/FragCatalog /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/GraphMol/FragCatalog /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/GraphMol/FragCatalog/CMakeFiles/testFragCatalog.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu' make -f Code/GraphMol/FragCatalog/CMakeFiles/testFragCatalog.dir/build.make Code/GraphMol/FragCatalog/CMakeFiles/testFragCatalog.dir/build make[4]: Entering directory '/build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu' -[ 57%] Building CXX object Code/GraphMol/FragCatalog/CMakeFiles/testFragCatalog.dir/test1.cpp.o +[ 56%] Building CXX object Code/GraphMol/FragCatalog/CMakeFiles/testFragCatalog.dir/test1.cpp.o cd /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/GraphMol/FragCatalog && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.4/External -I/usr/include/python3.13 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202409.4/Code -I/build/reproducible-path/rdkit-202409.4/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/GraphMol/FragCatalog/CMakeFiles/testFragCatalog.dir/test1.cpp.o -MF CMakeFiles/testFragCatalog.dir/test1.cpp.o.d -o CMakeFiles/testFragCatalog.dir/test1.cpp.o -c /build/reproducible-path/rdkit-202409.4/Code/GraphMol/FragCatalog/test1.cpp -[ 57%] Linking CXX executable graphmolMolOpsTest -cd /build/reproducible-path/rdkit-202409.4/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-202409.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_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.1.2024.09.4 ../../lib/libRDKitChemTransforms.so.1.2024.09.4 ../../lib/libRDKitDepictor.so.1.2024.09.4 /usr/lib/aarch64-linux-gnu/libcoordgen.so ../../lib/libRDKitMolAlign.so.1.2024.09.4 ../../lib/libRDKitSubstructMatch.so.1.2024.09.4 ../../lib/libRDKitGenericGroups.so.1.2024.09.4 ../../lib/libRDKitSmilesParse.so.1.2024.09.4 ../../lib/libRDKitMolTransforms.so.1.2024.09.4 ../../lib/libRDKitGraphMol.so.1.2024.09.4 ../../lib/libRDKitEigenSolvers.so.1.2024.09.4 ../../lib/libRDKitAlignment.so.1.2024.09.4 ../../lib/libRDKitRDGeometryLib.so.1.2024.09.4 ../../lib/libRDKitDataStructs.so.1.2024.09.4 ../../lib/libRDKitRDGeneral.so.1.2024.09.4 /usr/lib/aarch64-linux-gnu/libboost_system.so.1.83.0 /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 +[ 56%] Linking CXX executable cdxmlParserCatchTest +cd /build/reproducible-path/rdkit-202409.4/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-202409.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_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.1.2024.09.4 /usr/lib/libCatch2.a ../../../lib/libRDKitChemTransforms.so.1.2024.09.4 ../../../lib/libRDKitDepictor.so.1.2024.09.4 /usr/lib/aarch64-linux-gnu/libcoordgen.so ../../../lib/libRDKitMolAlign.so.1.2024.09.4 ../../../lib/libRDKitMolTransforms.so.1.2024.09.4 ../../../lib/libRDKitEigenSolvers.so.1.2024.09.4 ../../../lib/libRDKitAlignment.so.1.2024.09.4 ../../../lib/libRDKitSmilesParse.so.1.2024.09.4 ../../../lib/libRDKitSubstructMatch.so.1.2024.09.4 ../../../lib/libRDKitGenericGroups.so.1.2024.09.4 ../../../lib/libRDKitGraphMol.so.1.2024.09.4 ../../../lib/libRDKitRDGeometryLib.so.1.2024.09.4 ../../../lib/libRDKitDataStructs.so.1.2024.09.4 ../../../lib/libRDKitRDGeneral.so.1.2024.09.4 /usr/lib/aarch64-linux-gnu/libboost_system.so.1.83.0 /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-202409.4/obj-aarch64-linux-gnu' -[ 57%] Built target graphmolMolOpsTest +[ 56%] Built target cdxmlParserCatchTest 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-202409.4/obj-aarch64-linux-gnu' cd /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202409.4 /build/reproducible-path/rdkit-202409.4/Code/GraphMol/FragCatalog/Wrap /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/GraphMol/FragCatalog/Wrap /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/GraphMol/FragCatalog/Wrap/CMakeFiles/rdfragcatalog.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu' make -f Code/GraphMol/FragCatalog/Wrap/CMakeFiles/rdfragcatalog.dir/build.make Code/GraphMol/FragCatalog/Wrap/CMakeFiles/rdfragcatalog.dir/build make[4]: Entering directory '/build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu' -[ 57%] Building CXX object Code/GraphMol/FragCatalog/Wrap/CMakeFiles/rdfragcatalog.dir/rdfragcatalog.cpp.o +[ 56%] Building CXX object Code/GraphMol/FragCatalog/Wrap/CMakeFiles/rdfragcatalog.dir/rdfragcatalog.cpp.o cd /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/GraphMol/FragCatalog/Wrap && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_NUMPY_DYN_LINK -DBOOST_NUMPY_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -Drdfragcatalog_EXPORTS -I/build/reproducible-path/rdkit-202409.4/External -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202409.4/Code -I/build/reproducible-path/rdkit-202409.4/External/boost-numeric-bindings -isystem /usr/include/python3.13 -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/FragCatalog/Wrap/CMakeFiles/rdfragcatalog.dir/rdfragcatalog.cpp.o -MF CMakeFiles/rdfragcatalog.dir/rdfragcatalog.cpp.o.d -o CMakeFiles/rdfragcatalog.dir/rdfragcatalog.cpp.o -c /build/reproducible-path/rdkit-202409.4/Code/GraphMol/FragCatalog/Wrap/rdfragcatalog.cpp -[ 58%] Building CXX object Code/GraphMol/ChemReactions/CMakeFiles/ChemReactions.dir/ReactionUtils.cpp.o -cd 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Code/GraphMol/ChemReactions/CMakeFiles/ChemReactions.dir/ReactionRunner.cpp.o +cd /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/GraphMol/ChemReactions && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DChemReactions_EXPORTS -DRDKIT_CHEMREACTIONS_BUILD -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.4/External -I/usr/include/python3.13 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202409.4/Code -I/build/reproducible-path/rdkit-202409.4/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 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Code/GraphMol/ForceFieldHelpers/MMFF/CMakeFiles/testMMFFForceFieldHelpers.dir/build.make Code/GraphMol/ForceFieldHelpers/MMFF/CMakeFiles/testMMFFForceFieldHelpers.dir/build make -f Code/GraphMol/ForceFieldHelpers/MMFF/CMakeFiles/testMMFFForceFieldHelpersMultiThread.dir/build.make Code/GraphMol/ForceFieldHelpers/MMFF/CMakeFiles/testMMFFForceFieldHelpersMultiThread.dir/build make[4]: Entering directory '/build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu' -make[4]: Entering directory '/build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu' -[ 59%] Building CXX object Code/GraphMol/ForceFieldHelpers/MMFF/CMakeFiles/testMMFFForceFieldHelpers.dir/testMMFFHelpers.cpp.o -[ 59%] Building CXX object Code/GraphMol/ForceFieldHelpers/MMFF/CMakeFiles/testMMFFForceFieldHelpersMultiThread.dir/testMultiThread.cpp.o +[ 58%] Building CXX object Code/GraphMol/ForceFieldHelpers/MMFF/CMakeFiles/testMMFFForceFieldHelpersMultiThread.dir/testMultiThread.cpp.o cd 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-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-202409.4/Code/GraphMol/ForceFieldHelpers/MMFF/testMultiThread.cpp -cd /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/GraphMol/ForceFieldHelpers/MMFF && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.4/External -I/usr/include/python3.13 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202409.4/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=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-202409.4/Code/GraphMol/ForceFieldHelpers/MMFF/testMMFFHelpers.cpp -[ 59%] Linking CXX executable testMolTransforms -cd /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/GraphMol/MolTransforms && /usr/bin/cmake -E cmake_link_script CMakeFiles/testMolTransforms.dir/link.txt --verbose=1 -[ 59%] Linking CXX executable molTransformsTestCatch -/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_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.1.2024.09.4 ../../../lib/libRDKitChemTransforms.so.1.2024.09.4 ../../../lib/libRDKitDepictor.so.1.2024.09.4 /usr/lib/aarch64-linux-gnu/libcoordgen.so ../../../lib/libRDKitMolAlign.so.1.2024.09.4 ../../../lib/libRDKitMolTransforms.so.1.2024.09.4 ../../../lib/libRDKitEigenSolvers.so.1.2024.09.4 ../../../lib/libRDKitSmilesParse.so.1.2024.09.4 ../../../lib/libRDKitAlignment.so.1.2024.09.4 ../../../lib/libRDKitSubstructMatch.so.1.2024.09.4 ../../../lib/libRDKitGenericGroups.so.1.2024.09.4 ../../../lib/libRDKitGraphMol.so.1.2024.09.4 ../../../lib/libRDKitRDGeometryLib.so.1.2024.09.4 ../../../lib/libRDKitDataStructs.so.1.2024.09.4 ../../../lib/libRDKitRDGeneral.so.1.2024.09.4 /usr/lib/aarch64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl /usr/lib/aarch64-linux-gnu/libmaeparser.so +[ 58%] Linking CXX executable molTransformsTestCatch cd /build/reproducible-path/rdkit-202409.4/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-202409.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_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.1.2024.09.4 /usr/lib/libCatch2.a ../../../lib/libRDKitChemTransforms.so.1.2024.09.4 ../../../lib/libRDKitDepictor.so.1.2024.09.4 /usr/lib/aarch64-linux-gnu/libcoordgen.so ../../../lib/libRDKitMolAlign.so.1.2024.09.4 ../../../lib/libRDKitMolTransforms.so.1.2024.09.4 ../../../lib/libRDKitEigenSolvers.so.1.2024.09.4 ../../../lib/libRDKitAlignment.so.1.2024.09.4 ../../../lib/libRDKitSmilesParse.so.1.2024.09.4 ../../../lib/libRDKitSubstructMatch.so.1.2024.09.4 ../../../lib/libRDKitGenericGroups.so.1.2024.09.4 ../../../lib/libRDKitGraphMol.so.1.2024.09.4 ../../../lib/libRDKitRDGeometryLib.so.1.2024.09.4 ../../../lib/libRDKitDataStructs.so.1.2024.09.4 ../../../lib/libRDKitRDGeneral.so.1.2024.09.4 /usr/lib/aarch64-linux-gnu/libboost_system.so.1.83.0 /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-202409.4/obj-aarch64-linux-gnu' -[ 59%] Built target testMolTransforms +[ 58%] Built target molTransformsTestCatch make -f Code/GraphMol/ForceFieldHelpers/UFF/CMakeFiles/testUFFForceFieldHelpers.dir/build.make Code/GraphMol/ForceFieldHelpers/UFF/CMakeFiles/testUFFForceFieldHelpers.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu' cd /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202409.4 /build/reproducible-path/rdkit-202409.4/Code/GraphMol/ForceFieldHelpers/UFF /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/GraphMol/ForceFieldHelpers/UFF /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/GraphMol/ForceFieldHelpers/UFF/CMakeFiles/testUFFForceFieldHelpers.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu' make -f Code/GraphMol/ForceFieldHelpers/UFF/CMakeFiles/testUFFForceFieldHelpers.dir/build.make Code/GraphMol/ForceFieldHelpers/UFF/CMakeFiles/testUFFForceFieldHelpers.dir/build make[4]: Entering directory '/build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu' -[ 59%] Building CXX object Code/GraphMol/ForceFieldHelpers/UFF/CMakeFiles/testUFFForceFieldHelpers.dir/testUFFHelpers.cpp.o +[ 58%] Building CXX object Code/GraphMol/ForceFieldHelpers/UFF/CMakeFiles/testUFFForceFieldHelpers.dir/testUFFHelpers.cpp.o cd /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/GraphMol/ForceFieldHelpers/UFF && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.4/External -I/usr/include/python3.13 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202409.4/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=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-202409.4/Code/GraphMol/ForceFieldHelpers/UFF/testUFFHelpers.cpp -/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_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.1.2024.09.4 /usr/lib/libCatch2.a ../../../lib/libRDKitChemTransforms.so.1.2024.09.4 ../../../lib/libRDKitDepictor.so.1.2024.09.4 /usr/lib/aarch64-linux-gnu/libcoordgen.so ../../../lib/libRDKitMolAlign.so.1.2024.09.4 ../../../lib/libRDKitMolTransforms.so.1.2024.09.4 ../../../lib/libRDKitEigenSolvers.so.1.2024.09.4 ../../../lib/libRDKitAlignment.so.1.2024.09.4 ../../../lib/libRDKitSmilesParse.so.1.2024.09.4 ../../../lib/libRDKitSubstructMatch.so.1.2024.09.4 ../../../lib/libRDKitGenericGroups.so.1.2024.09.4 ../../../lib/libRDKitGraphMol.so.1.2024.09.4 ../../../lib/libRDKitRDGeometryLib.so.1.2024.09.4 ../../../lib/libRDKitDataStructs.so.1.2024.09.4 ../../../lib/libRDKitRDGeneral.so.1.2024.09.4 /usr/lib/aarch64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl /usr/lib/aarch64-linux-gnu/libmaeparser.so +[ 58%] Linking CXX executable testMolTransforms +cd /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/GraphMol/MolTransforms && /usr/bin/cmake -E cmake_link_script CMakeFiles/testMolTransforms.dir/link.txt --verbose=1 +[ 58%] Building CXX object Code/GraphMol/FragCatalog/Wrap/CMakeFiles/rdfragcatalog.dir/FragCatGenerator.cpp.o +cd /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/GraphMol/FragCatalog/Wrap && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_NUMPY_DYN_LINK -DBOOST_NUMPY_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -Drdfragcatalog_EXPORTS -I/build/reproducible-path/rdkit-202409.4/External -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202409.4/Code -I/build/reproducible-path/rdkit-202409.4/External/boost-numeric-bindings -isystem /usr/include/python3.13 -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-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-202409.4/Code/GraphMol/FragCatalog/Wrap/FragCatGenerator.cpp +/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_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.1.2024.09.4 ../../../lib/libRDKitChemTransforms.so.1.2024.09.4 ../../../lib/libRDKitDepictor.so.1.2024.09.4 /usr/lib/aarch64-linux-gnu/libcoordgen.so ../../../lib/libRDKitMolAlign.so.1.2024.09.4 ../../../lib/libRDKitMolTransforms.so.1.2024.09.4 ../../../lib/libRDKitEigenSolvers.so.1.2024.09.4 ../../../lib/libRDKitSmilesParse.so.1.2024.09.4 ../../../lib/libRDKitAlignment.so.1.2024.09.4 ../../../lib/libRDKitSubstructMatch.so.1.2024.09.4 ../../../lib/libRDKitGenericGroups.so.1.2024.09.4 ../../../lib/libRDKitGraphMol.so.1.2024.09.4 ../../../lib/libRDKitRDGeometryLib.so.1.2024.09.4 ../../../lib/libRDKitDataStructs.so.1.2024.09.4 ../../../lib/libRDKitRDGeneral.so.1.2024.09.4 /usr/lib/aarch64-linux-gnu/libboost_system.so.1.83.0 /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-202409.4/obj-aarch64-linux-gnu' -[ 59%] Built target molTransformsTestCatch +[ 58%] Built target testMolTransforms make -f Code/GraphMol/ForceFieldHelpers/CrystalFF/CMakeFiles/testCrystalForceField.dir/build.make Code/GraphMol/ForceFieldHelpers/CrystalFF/CMakeFiles/testCrystalForceField.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu' cd /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202409.4 /build/reproducible-path/rdkit-202409.4/Code/GraphMol/ForceFieldHelpers/CrystalFF /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/GraphMol/ForceFieldHelpers/CrystalFF /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/GraphMol/ForceFieldHelpers/CrystalFF/CMakeFiles/testCrystalForceField.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu' make -f Code/GraphMol/ForceFieldHelpers/CrystalFF/CMakeFiles/testCrystalForceField.dir/build.make Code/GraphMol/ForceFieldHelpers/CrystalFF/CMakeFiles/testCrystalForceField.dir/build make[4]: Entering directory '/build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu' -[ 59%] Building CXX object Code/GraphMol/ForceFieldHelpers/CrystalFF/CMakeFiles/testCrystalForceField.dir/testCrystalFF.cpp.o +[ 58%] Building CXX object Code/GraphMol/ForceFieldHelpers/CrystalFF/CMakeFiles/testCrystalForceField.dir/testCrystalFF.cpp.o cd /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/GraphMol/ForceFieldHelpers/CrystalFF && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.4/External -I/usr/include/python3.13 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Code/GraphMol/DistGeomHelpers/CMakeFiles/testDistGeomHelpers.dir/testDgeomHelpers.cpp.o cd /build/reproducible-path/rdkit-202409.4/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 -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.4/External -I/usr/include/python3.13 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202409.4/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security 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-I/build/reproducible-path/rdkit-202409.4/External -I/usr/include/python3.13 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202409.4/Code -I/build/reproducible-path/rdkit-202409.4/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-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/MolDescriptors.cpp.o -MF CMakeFiles/Descriptors.dir/MolDescriptors.cpp.o.d -o CMakeFiles/Descriptors.dir/MolDescriptors.cpp.o -c /build/reproducible-path/rdkit-202409.4/Code/GraphMol/Descriptors/MolDescriptors.cpp -[ 61%] Linking CXX executable testFingerprintGenerators -cd 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-I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202409.4/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/GraphMol/MolAlign/CMakeFiles/molAlignCatchTest.dir/catch_tests.cpp.o -MF CMakeFiles/molAlignCatchTest.dir/catch_tests.cpp.o.d -o CMakeFiles/molAlignCatchTest.dir/catch_tests.cpp.o -c /build/reproducible-path/rdkit-202409.4/Code/GraphMol/MolAlign/catch_tests.cpp -[ 61%] Linking CXX executable testCrystalForceField -cd /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/GraphMol/ForceFieldHelpers/CrystalFF && /usr/bin/cmake -E cmake_link_script CMakeFiles/testCrystalForceField.dir/link.txt --verbose=1 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../../../../lib/libRDKitMolAlign.so.1.2024.09.4 ../../../../lib/libRDKitMolTransforms.so.1.2024.09.4 ../../../../lib/libRDKitEigenSolvers.so.1.2024.09.4 ../../../../lib/libRDKitSmilesParse.so.1.2024.09.4 ../../../../lib/libRDKitSubstructMatch.so.1.2024.09.4 ../../../../lib/libRDKitGenericGroups.so.1.2024.09.4 ../../../../lib/libRDKitAlignment.so.1.2024.09.4 ../../../../lib/libRDKitGraphMol.so.1.2024.09.4 ../../../../lib/libRDKitRDGeometryLib.so.1.2024.09.4 ../../../../lib/libRDKitDataStructs.so.1.2024.09.4 ../../../../lib/libRDKitRDGeneral.so.1.2024.09.4 /usr/lib/aarch64-linux-gnu/libboost_system.so.1.83.0 /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 +[ 60%] Building CXX object Code/GraphMol/Descriptors/CMakeFiles/Descriptors.dir/MolSurf.cpp.o +cd /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/GraphMol/Descriptors && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DDescriptors_EXPORTS -DRDKIT_DESCRIPTORS_BUILD -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.4/External -I/usr/include/python3.13 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202409.4/Code -I/build/reproducible-path/rdkit-202409.4/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/Descriptors/CMakeFiles/Descriptors.dir/MolSurf.cpp.o -MF CMakeFiles/Descriptors.dir/MolSurf.cpp.o.d -o CMakeFiles/Descriptors.dir/MolSurf.cpp.o -c /build/reproducible-path/rdkit-202409.4/Code/GraphMol/Descriptors/MolSurf.cpp +[ 61%] Linking CXX executable testMMFFForceFieldHelpers +cd /build/reproducible-path/rdkit-202409.4/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-202409.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/testMMFFForceFieldHelpers.dir/link.d CMakeFiles/testMMFFForceFieldHelpers.dir/testMMFFHelpers.cpp.o -o testMMFFForceFieldHelpers ../../../../lib/libRDKitDistGeomHelpers.so.1.2024.09.4 ../../../../lib/libRDKitFileParsers.so.1.2024.09.4 ../../../../lib/libRDKitDistGeometry.so.1.2024.09.4 ../../../../lib/libRDKitForceFieldHelpers.so.1.2024.09.4 ../../../../lib/libRDKitForceField.so.1.2024.09.4 ../../../../lib/libRDKitOptimizer.so.1.2024.09.4 ../../../../lib/libRDKitTrajectory.so.1.2024.09.4 ../../../../lib/libRDKitChemTransforms.so.1.2024.09.4 ../../../../lib/libRDKitDepictor.so.1.2024.09.4 ../../../../lib/libRDKitMolAlign.so.1.2024.09.4 ../../../../lib/libRDKitMolTransforms.so.1.2024.09.4 ../../../../lib/libRDKitEigenSolvers.so.1.2024.09.4 ../../../../lib/libRDKitSmilesParse.so.1.2024.09.4 ../../../../lib/libRDKitSubstructMatch.so.1.2024.09.4 ../../../../lib/libRDKitGenericGroups.so.1.2024.09.4 ../../../../lib/libRDKitAlignment.so.1.2024.09.4 ../../../../lib/libRDKitGraphMol.so.1.2024.09.4 ../../../../lib/libRDKitRDGeometryLib.so.1.2024.09.4 ../../../../lib/libRDKitDataStructs.so.1.2024.09.4 ../../../../lib/libRDKitRDGeneral.so.1.2024.09.4 /usr/lib/aarch64-linux-gnu/libboost_system.so.1.83.0 /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-202409.4/obj-aarch64-linux-gnu' -[ 61%] Built target testCrystalForceField +[ 61%] Built target testMMFFForceFieldHelpers make -f Code/GraphMol/MolChemicalFeatures/CMakeFiles/testFeatures.dir/build.make Code/GraphMol/MolChemicalFeatures/CMakeFiles/testFeatures.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu' cd /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202409.4 /build/reproducible-path/rdkit-202409.4/Code/GraphMol/MolChemicalFeatures /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/GraphMol/MolChemicalFeatures /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/GraphMol/MolChemicalFeatures/CMakeFiles/testFeatures.dir/DependInfo.cmake "--color=" +[ 61%] Building CXX object Code/GraphMol/FragCatalog/Wrap/CMakeFiles/rdfragcatalog.dir/FragFPGenerator.cpp.o +cd /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/GraphMol/FragCatalog/Wrap && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_NUMPY_DYN_LINK -DBOOST_NUMPY_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -Drdfragcatalog_EXPORTS -I/build/reproducible-path/rdkit-202409.4/External -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202409.4/Code -I/build/reproducible-path/rdkit-202409.4/External/boost-numeric-bindings -isystem /usr/include/python3.13 -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/FragCatalog/Wrap/CMakeFiles/rdfragcatalog.dir/FragFPGenerator.cpp.o -MF CMakeFiles/rdfragcatalog.dir/FragFPGenerator.cpp.o.d -o CMakeFiles/rdfragcatalog.dir/FragFPGenerator.cpp.o -c /build/reproducible-path/rdkit-202409.4/Code/GraphMol/FragCatalog/Wrap/FragFPGenerator.cpp make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu' make -f Code/GraphMol/MolChemicalFeatures/CMakeFiles/testFeatures.dir/build.make Code/GraphMol/MolChemicalFeatures/CMakeFiles/testFeatures.dir/build make[4]: Entering directory '/build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu' @@ -5346,8 +5355,6 @@ cd /build/reproducible-path/rdkit-202409.4/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 -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.4/External -I/usr/include/python3.13 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202409.4/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=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/MolChemicalFeatures/CMakeFiles/testFeatures.dir/testFeatures.cpp.o -MF CMakeFiles/testFeatures.dir/testFeatures.cpp.o.d -o CMakeFiles/testFeatures.dir/testFeatures.cpp.o -c /build/reproducible-path/rdkit-202409.4/Code/GraphMol/MolChemicalFeatures/testFeatures.cpp [ 61%] Linking CXX executable testFingerprints cd /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/GraphMol/Fingerprints && /usr/bin/cmake -E cmake_link_script CMakeFiles/testFingerprints.dir/link.txt --verbose=1 -[ 61%] Building CXX object Code/GraphMol/FragCatalog/Wrap/CMakeFiles/rdfragcatalog.dir/FragFPGenerator.cpp.o -cd /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/GraphMol/FragCatalog/Wrap && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_NUMPY_DYN_LINK -DBOOST_NUMPY_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -Drdfragcatalog_EXPORTS -I/build/reproducible-path/rdkit-202409.4/External -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202409.4/Code -I/build/reproducible-path/rdkit-202409.4/External/boost-numeric-bindings -isystem /usr/include/python3.13 -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/FragCatalog/Wrap/CMakeFiles/rdfragcatalog.dir/FragFPGenerator.cpp.o -MF CMakeFiles/rdfragcatalog.dir/FragFPGenerator.cpp.o.d -o CMakeFiles/rdfragcatalog.dir/FragFPGenerator.cpp.o -c /build/reproducible-path/rdkit-202409.4/Code/GraphMol/FragCatalog/Wrap/FragFPGenerator.cpp /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_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.1.2024.09.4 ../../../lib/libRDKitFileParsers.so.1.2024.09.4 ../../../lib/libRDKitSubgraphs.so.1.2024.09.4 ../../../lib/libRDKitChemTransforms.so.1.2024.09.4 ../../../lib/libRDKitDepictor.so.1.2024.09.4 /usr/lib/aarch64-linux-gnu/libcoordgen.so ../../../lib/libRDKitMolAlign.so.1.2024.09.4 ../../../lib/libRDKitSubstructMatch.so.1.2024.09.4 ../../../lib/libRDKitGenericGroups.so.1.2024.09.4 ../../../lib/libRDKitSmilesParse.so.1.2024.09.4 ../../../lib/libRDKitMolTransforms.so.1.2024.09.4 ../../../lib/libRDKitGraphMol.so.1.2024.09.4 ../../../lib/libRDKitEigenSolvers.so.1.2024.09.4 ../../../lib/libRDKitAlignment.so.1.2024.09.4 ../../../lib/libRDKitRDGeometryLib.so.1.2024.09.4 ../../../lib/libRDKitDataStructs.so.1.2024.09.4 ../../../lib/libRDKitRDGeneral.so.1.2024.09.4 /usr/lib/aarch64-linux-gnu/libboost_system.so.1.83.0 /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-202409.4/obj-aarch64-linux-gnu' [ 61%] Built target testFingerprints @@ -5359,227 +5366,237 @@ make[4]: Entering directory '/build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu' [ 61%] Building CXX object Code/GraphMol/ShapeHelpers/CMakeFiles/testShapeHelpers.dir/testShapeHelpers.cpp.o cd /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/GraphMol/ShapeHelpers && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.4/External -I/usr/include/python3.13 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202409.4/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/GraphMol/ShapeHelpers/CMakeFiles/testShapeHelpers.dir/testShapeHelpers.cpp.o -MF CMakeFiles/testShapeHelpers.dir/testShapeHelpers.cpp.o.d -o CMakeFiles/testShapeHelpers.dir/testShapeHelpers.cpp.o -c /build/reproducible-path/rdkit-202409.4/Code/GraphMol/ShapeHelpers/testShapeHelpers.cpp -[ 61%] Building CXX object Code/GraphMol/ChemReactions/CMakeFiles/ChemReactions.dir/SanitizeRxn.cpp.o -cd /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/GraphMol/ChemReactions && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DChemReactions_EXPORTS -DRDKIT_CHEMREACTIONS_BUILD -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.4/External -I/usr/include/python3.13 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202409.4/Code -I/build/reproducible-path/rdkit-202409.4/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/ChemReactions/CMakeFiles/ChemReactions.dir/SanitizeRxn.cpp.o -MF CMakeFiles/ChemReactions.dir/SanitizeRxn.cpp.o.d -o CMakeFiles/ChemReactions.dir/SanitizeRxn.cpp.o -c 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-DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.4/External -I/usr/include/python3.13 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202409.4/Code -I/build/reproducible-path/rdkit-202409.4/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/Descriptors/CMakeFiles/Descriptors.dir/MolSurf.cpp.o -MF CMakeFiles/Descriptors.dir/MolSurf.cpp.o.d -o CMakeFiles/Descriptors.dir/MolSurf.cpp.o -c /build/reproducible-path/rdkit-202409.4/Code/GraphMol/Descriptors/MolSurf.cpp -/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/testMMFFForceFieldHelpers.dir/link.d CMakeFiles/testMMFFForceFieldHelpers.dir/testMMFFHelpers.cpp.o -o testMMFFForceFieldHelpers ../../../../lib/libRDKitDistGeomHelpers.so.1.2024.09.4 ../../../../lib/libRDKitFileParsers.so.1.2024.09.4 ../../../../lib/libRDKitDistGeometry.so.1.2024.09.4 ../../../../lib/libRDKitForceFieldHelpers.so.1.2024.09.4 ../../../../lib/libRDKitForceField.so.1.2024.09.4 ../../../../lib/libRDKitOptimizer.so.1.2024.09.4 ../../../../lib/libRDKitTrajectory.so.1.2024.09.4 ../../../../lib/libRDKitChemTransforms.so.1.2024.09.4 ../../../../lib/libRDKitDepictor.so.1.2024.09.4 ../../../../lib/libRDKitMolAlign.so.1.2024.09.4 ../../../../lib/libRDKitMolTransforms.so.1.2024.09.4 ../../../../lib/libRDKitEigenSolvers.so.1.2024.09.4 ../../../../lib/libRDKitSmilesParse.so.1.2024.09.4 ../../../../lib/libRDKitSubstructMatch.so.1.2024.09.4 ../../../../lib/libRDKitGenericGroups.so.1.2024.09.4 ../../../../lib/libRDKitAlignment.so.1.2024.09.4 ../../../../lib/libRDKitGraphMol.so.1.2024.09.4 ../../../../lib/libRDKitRDGeometryLib.so.1.2024.09.4 ../../../../lib/libRDKitDataStructs.so.1.2024.09.4 ../../../../lib/libRDKitRDGeneral.so.1.2024.09.4 /usr/lib/aarch64-linux-gnu/libboost_system.so.1.83.0 /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 +[ 62%] Linking CXX executable testFingerprintGenerators +cd /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/GraphMol/Fingerprints && /usr/bin/cmake -E cmake_link_script 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Building CXX object Code/GraphMol/MolCatalog/CMakeFiles/testMolCatalog.dir/test1.cpp.o cd /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/GraphMol/MolCatalog && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.4/External -I/usr/include/python3.13 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202409.4/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security 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-Wl,-z,now -Wl,--dependency-file=CMakeFiles/testMolAlign.dir/link.d CMakeFiles/testMolAlign.dir/testMolAlign.cpp.o -o testMolAlign ../../../lib/libRDKitFileParsers.so.1.2024.09.4 ../../../lib/libRDKitDistGeomHelpers.so.1.2024.09.4 ../../../lib/libRDKitChemTransforms.so.1.2024.09.4 ../../../lib/libRDKitDepictor.so.1.2024.09.4 /usr/lib/aarch64-linux-gnu/libcoordgen.so /usr/lib/aarch64-linux-gnu/libmaeparser.so ../../../lib/libRDKitMolAlign.so.1.2024.09.4 ../../../lib/libRDKitMolTransforms.so.1.2024.09.4 ../../../lib/libRDKitAlignment.so.1.2024.09.4 ../../../lib/libRDKitDistGeometry.so.1.2024.09.4 ../../../lib/libRDKitForceFieldHelpers.so.1.2024.09.4 ../../../lib/libRDKitSmilesParse.so.1.2024.09.4 ../../../lib/libRDKitSubstructMatch.so.1.2024.09.4 ../../../lib/libRDKitGenericGroups.so.1.2024.09.4 ../../../lib/libRDKitEigenSolvers.so.1.2024.09.4 ../../../lib/libRDKitForceField.so.1.2024.09.4 ../../../lib/libRDKitOptimizer.so.1.2024.09.4 ../../../lib/libRDKitTrajectory.so.1.2024.09.4 ../../../lib/libRDKitGraphMol.so.1.2024.09.4 ../../../lib/libRDKitRDGeometryLib.so.1.2024.09.4 ../../../lib/libRDKitDataStructs.so.1.2024.09.4 ../../../lib/libRDKitRDGeneral.so.1.2024.09.4 /usr/lib/aarch64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl +[ 62%] Building CXX object Code/GraphMol/ChemReactions/CMakeFiles/ChemReactions.dir/SanitizeRxn.cpp.o +cd /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/GraphMol/ChemReactions && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DChemReactions_EXPORTS -DRDKIT_CHEMREACTIONS_BUILD -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.4/External -I/usr/include/python3.13 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202409.4/Code -I/build/reproducible-path/rdkit-202409.4/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/ChemReactions/CMakeFiles/ChemReactions.dir/SanitizeRxn.cpp.o -MF CMakeFiles/ChemReactions.dir/SanitizeRxn.cpp.o.d -o CMakeFiles/ChemReactions.dir/SanitizeRxn.cpp.o -c /build/reproducible-path/rdkit-202409.4/Code/GraphMol/ChemReactions/SanitizeRxn.cpp +[ 62%] Linking CXX executable testUFFForceFieldHelpers +cd /build/reproducible-path/rdkit-202409.4/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-202409.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_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.1.2024.09.4 ../../../../lib/libRDKitFileParsers.so.1.2024.09.4 ../../../../lib/libRDKitDistGeometry.so.1.2024.09.4 ../../../../lib/libRDKitForceFieldHelpers.so.1.2024.09.4 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/usr/lib/aarch64-linux-gnu/libcoordgen.so /usr/lib/aarch64-linux-gnu/libmaeparser.so make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu' -[ 63%] Built target testMolAlign +[ 62%] Built target testUFFForceFieldHelpers 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-202409.4/obj-aarch64-linux-gnu' cd /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202409.4 /build/reproducible-path/rdkit-202409.4/Code/GraphMol/FMCS /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/GraphMol/FMCS /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/GraphMol/FMCS/CMakeFiles/FMCS.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu' make -f Code/GraphMol/FMCS/CMakeFiles/FMCS.dir/build.make Code/GraphMol/FMCS/CMakeFiles/FMCS.dir/build make[4]: Entering directory '/build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu' -[ 63%] Building CXX object Code/GraphMol/FMCS/CMakeFiles/FMCS.dir/FMCS.cpp.o +[ 62%] Building CXX object Code/GraphMol/FMCS/CMakeFiles/FMCS.dir/FMCS.cpp.o cd /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/GraphMol/FMCS && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DFMCS_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_FMCS_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.4/External -I/usr/include/python3.13 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202409.4/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-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-202409.4/Code/GraphMol/FMCS/FMCS.cpp -[ 63%] Linking CXX executable testShapeHelpers -cd /build/reproducible-path/rdkit-202409.4/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 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../../../lib/libRDKitEigenSolvers.so.1.2024.09.4 ../../../lib/libRDKitGraphMol.so.1.2024.09.4 ../../../lib/libRDKitRDGeometryLib.so.1.2024.09.4 ../../../lib/libRDKitDataStructs.so.1.2024.09.4 ../../../lib/libRDKitRDGeneral.so.1.2024.09.4 /usr/lib/aarch64-linux-gnu/libboost_system.so.1.83.0 /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 +[ 62%] Linking CXX executable molAlignCatchTest +cd /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/GraphMol/MolAlign && /usr/bin/cmake -E cmake_link_script CMakeFiles/molAlignCatchTest.dir/link.txt --verbose=1 +[ 62%] Linking CXX shared module ../../../../rdkit/Chem/rdfragcatalog.so +cd /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/GraphMol/FragCatalog/Wrap && /usr/bin/cmake -E cmake_link_script CMakeFiles/rdfragcatalog.dir/link.txt --verbose=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 make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu' -[ 63%] Built target testShapeHelpers +[ 62%] Built target rdfragcatalog make -f Code/GraphMol/MolHash/CMakeFiles/molHashCatchTest.dir/build.make Code/GraphMol/MolHash/CMakeFiles/molHashCatchTest.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu' +/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_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 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-Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/GraphMol/MolHash/CMakeFiles/molHashCatchTest.dir/catch_tests.cpp.o -MF CMakeFiles/molHashCatchTest.dir/catch_tests.cpp.o.d -o CMakeFiles/molHashCatchTest.dir/catch_tests.cpp.o -c /build/reproducible-path/rdkit-202409.4/Code/GraphMol/MolHash/catch_tests.cpp -[ 63%] Linking CXX executable molAlignCatchTest -cd /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/GraphMol/MolAlign && /usr/bin/cmake -E cmake_link_script CMakeFiles/molAlignCatchTest.dir/link.txt --verbose=1 -[ 63%] Linking CXX shared module ../../../../rdkit/Chem/rdfragcatalog.so -cd /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/GraphMol/FragCatalog/Wrap && /usr/bin/cmake -E cmake_link_script CMakeFiles/rdfragcatalog.dir/link.txt --verbose=1 -/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security 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make[4]: Entering directory '/build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu' +make[4]: Entering directory '/build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu' cd /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202409.4 /build/reproducible-path/rdkit-202409.4/Code/GraphMol/MMPA /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/GraphMol/MMPA /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/GraphMol/MMPA/CMakeFiles/MMPA.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu' make -f Code/GraphMol/MMPA/CMakeFiles/MMPA.dir/build.make Code/GraphMol/MMPA/CMakeFiles/MMPA.dir/build make[4]: Entering directory '/build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu' -[ 63%] Building CXX object Code/GraphMol/MMPA/CMakeFiles/MMPA.dir/MMPA.cpp.o +[ 62%] Building CXX object Code/GraphMol/MolHash/CMakeFiles/molHashCatchTest.dir/catch_tests.cpp.o +cd /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/GraphMol/MolHash && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.4/External -I/usr/include/python3.13 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202409.4/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.4=. -fstack-protector-strong 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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/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/testShapeHelpers.dir/link.d CMakeFiles/testShapeHelpers.dir/testShapeHelpers.cpp.o -o testShapeHelpers ../../../lib/libRDKitShapeHelpers.so.1.2024.09.4 ../../../lib/libRDKitFileParsers.so.1.2024.09.4 ../../../lib/libRDKitChemTransforms.so.1.2024.09.4 ../../../lib/libRDKitDepictor.so.1.2024.09.4 ../../../lib/libRDKitMolAlign.so.1.2024.09.4 ../../../lib/libRDKitAlignment.so.1.2024.09.4 ../../../lib/libRDKitSmilesParse.so.1.2024.09.4 ../../../lib/libRDKitSubstructMatch.so.1.2024.09.4 ../../../lib/libRDKitGenericGroups.so.1.2024.09.4 ../../../lib/libRDKitMolTransforms.so.1.2024.09.4 ../../../lib/libRDKitEigenSolvers.so.1.2024.09.4 ../../../lib/libRDKitGraphMol.so.1.2024.09.4 ../../../lib/libRDKitRDGeometryLib.so.1.2024.09.4 ../../../lib/libRDKitDataStructs.so.1.2024.09.4 ../../../lib/libRDKitRDGeneral.so.1.2024.09.4 /usr/lib/aarch64-linux-gnu/libboost_system.so.1.83.0 /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-202409.4/obj-aarch64-linux-gnu' -[ 63%] Built target rdfragcatalog +[ 62%] Building CXX object Code/GraphMol/Descriptors/CMakeFiles/Descriptors.dir/Lipinski.cpp.o +cd /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/GraphMol/Descriptors && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DDescriptors_EXPORTS -DRDKIT_DESCRIPTORS_BUILD -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.4/External -I/usr/include/python3.13 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202409.4/Code -I/build/reproducible-path/rdkit-202409.4/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/Descriptors/CMakeFiles/Descriptors.dir/Lipinski.cpp.o -MF CMakeFiles/Descriptors.dir/Lipinski.cpp.o.d -o CMakeFiles/Descriptors.dir/Lipinski.cpp.o -c /build/reproducible-path/rdkit-202409.4/Code/GraphMol/Descriptors/Lipinski.cpp +[ 62%] Built target testShapeHelpers make -f Code/GraphMol/RascalMCES/CMakeFiles/RascalMCES.dir/build.make Code/GraphMol/RascalMCES/CMakeFiles/RascalMCES.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu' cd /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202409.4 /build/reproducible-path/rdkit-202409.4/Code/GraphMol/RascalMCES /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/GraphMol/RascalMCES 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-DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DRascalMCES_EXPORTS -I/build/reproducible-path/rdkit-202409.4/External -I/usr/include/python3.13 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202409.4/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-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-202409.4/Code/GraphMol/RascalMCES/RascalMCES.cpp -[ 63%] Linking CXX executable testUFFForceFieldHelpers -cd /build/reproducible-path/rdkit-202409.4/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-202409.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_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.1.2024.09.4 ../../../../lib/libRDKitFileParsers.so.1.2024.09.4 ../../../../lib/libRDKitDistGeometry.so.1.2024.09.4 ../../../../lib/libRDKitForceFieldHelpers.so.1.2024.09.4 ../../../../lib/libRDKitForceField.so.1.2024.09.4 ../../../../lib/libRDKitOptimizer.so.1.2024.09.4 ../../../../lib/libRDKitTrajectory.so.1.2024.09.4 ../../../../lib/libRDKitChemTransforms.so.1.2024.09.4 ../../../../lib/libRDKitDepictor.so.1.2024.09.4 ../../../../lib/libRDKitMolAlign.so.1.2024.09.4 ../../../../lib/libRDKitMolTransforms.so.1.2024.09.4 ../../../../lib/libRDKitEigenSolvers.so.1.2024.09.4 ../../../../lib/libRDKitSmilesParse.so.1.2024.09.4 ../../../../lib/libRDKitSubstructMatch.so.1.2024.09.4 ../../../../lib/libRDKitGenericGroups.so.1.2024.09.4 ../../../../lib/libRDKitAlignment.so.1.2024.09.4 ../../../../lib/libRDKitGraphMol.so.1.2024.09.4 ../../../../lib/libRDKitRDGeometryLib.so.1.2024.09.4 ../../../../lib/libRDKitDataStructs.so.1.2024.09.4 ../../../../lib/libRDKitRDGeneral.so.1.2024.09.4 /usr/lib/aarch64-linux-gnu/libboost_system.so.1.83.0 /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 +[ 62%] Linking CXX executable testMolCatalog +cd /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/GraphMol/MolCatalog && /usr/bin/cmake -E cmake_link_script CMakeFiles/testMolCatalog.dir/link.txt --verbose=1 +[ 62%] Linking CXX executable testMolAlign +cd /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/GraphMol/MolAlign && /usr/bin/cmake -E cmake_link_script CMakeFiles/testMolAlign.dir/link.txt --verbose=1 +/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/testMolCatalog.dir/link.d CMakeFiles/testMolCatalog.dir/test1.cpp.o -o testMolCatalog ../../../lib/libRDKitMolCatalog.so.1.2024.09.4 ../../../lib/libRDKitFileParsers.so.1.2024.09.4 ../../../lib/libRDKitCatalogs.so.1.2024.09.4 ../../../lib/libRDKitChemTransforms.so.1.2024.09.4 ../../../lib/libRDKitDepictor.so.1.2024.09.4 /usr/lib/aarch64-linux-gnu/libcoordgen.so ../../../lib/libRDKitMolAlign.so.1.2024.09.4 ../../../lib/libRDKitSmilesParse.so.1.2024.09.4 ../../../lib/libRDKitMolTransforms.so.1.2024.09.4 ../../../lib/libRDKitEigenSolvers.so.1.2024.09.4 ../../../lib/libRDKitAlignment.so.1.2024.09.4 ../../../lib/libRDKitSubstructMatch.so.1.2024.09.4 ../../../lib/libRDKitGenericGroups.so.1.2024.09.4 ../../../lib/libRDKitGraphMol.so.1.2024.09.4 ../../../lib/libRDKitRDGeometryLib.so.1.2024.09.4 ../../../lib/libRDKitDataStructs.so.1.2024.09.4 ../../../lib/libRDKitRDGeneral.so.1.2024.09.4 /usr/lib/aarch64-linux-gnu/libboost_system.so.1.83.0 /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-202409.4/obj-aarch64-linux-gnu' -[ 63%] Building CXX object Code/GraphMol/ChemReactions/CMakeFiles/ChemReactions.dir/PNGParser.cpp.o -cd /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/GraphMol/ChemReactions && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DChemReactions_EXPORTS -DRDKIT_CHEMREACTIONS_BUILD -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.4/External -I/usr/include/python3.13 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202409.4/Code -I/build/reproducible-path/rdkit-202409.4/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-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-202409.4/Code/GraphMol/ChemReactions/PNGParser.cpp -[ 63%] Built target testUFFForceFieldHelpers +[ 62%] Built target testMolCatalog 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-202409.4/obj-aarch64-linux-gnu' cd /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202409.4 /build/reproducible-path/rdkit-202409.4/Code/GraphMol/SynthonSpaceSearch /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/GraphMol/SynthonSpaceSearch /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/GraphMol/SynthonSpaceSearch/CMakeFiles/SynthonSpaceSearch.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu' make -f Code/GraphMol/SynthonSpaceSearch/CMakeFiles/SynthonSpaceSearch.dir/build.make 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-DRDK_USE_STRICT_ROTOR_DEFINITION -DSynthonSpaceSearch_EXPORTS -I/build/reproducible-path/rdkit-202409.4/External -I/usr/include/python3.13 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202409.4/Code -I/build/reproducible-path/rdkit-202409.4/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-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-202409.4/Code/GraphMol/SynthonSpaceSearch/SynthonSpaceSearch_details.cpp -[ 63%] Linking CXX executable testMolCatalog -cd /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/GraphMol/MolCatalog && /usr/bin/cmake -E cmake_link_script CMakeFiles/testMolCatalog.dir/link.txt --verbose=1 -/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/testMolCatalog.dir/link.d CMakeFiles/testMolCatalog.dir/test1.cpp.o -o testMolCatalog ../../../lib/libRDKitMolCatalog.so.1.2024.09.4 ../../../lib/libRDKitFileParsers.so.1.2024.09.4 ../../../lib/libRDKitCatalogs.so.1.2024.09.4 ../../../lib/libRDKitChemTransforms.so.1.2024.09.4 ../../../lib/libRDKitDepictor.so.1.2024.09.4 /usr/lib/aarch64-linux-gnu/libcoordgen.so ../../../lib/libRDKitMolAlign.so.1.2024.09.4 ../../../lib/libRDKitSmilesParse.so.1.2024.09.4 ../../../lib/libRDKitMolTransforms.so.1.2024.09.4 ../../../lib/libRDKitEigenSolvers.so.1.2024.09.4 ../../../lib/libRDKitAlignment.so.1.2024.09.4 ../../../lib/libRDKitSubstructMatch.so.1.2024.09.4 ../../../lib/libRDKitGenericGroups.so.1.2024.09.4 ../../../lib/libRDKitGraphMol.so.1.2024.09.4 ../../../lib/libRDKitRDGeometryLib.so.1.2024.09.4 ../../../lib/libRDKitDataStructs.so.1.2024.09.4 ../../../lib/libRDKitRDGeneral.so.1.2024.09.4 /usr/lib/aarch64-linux-gnu/libboost_system.so.1.83.0 /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-202409.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security 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../../../lib/libRDKitEigenSolvers.so.1.2024.09.4 ../../../lib/libRDKitForceField.so.1.2024.09.4 ../../../lib/libRDKitOptimizer.so.1.2024.09.4 ../../../lib/libRDKitTrajectory.so.1.2024.09.4 ../../../lib/libRDKitGraphMol.so.1.2024.09.4 ../../../lib/libRDKitRDGeometryLib.so.1.2024.09.4 ../../../lib/libRDKitDataStructs.so.1.2024.09.4 ../../../lib/libRDKitRDGeneral.so.1.2024.09.4 /usr/lib/aarch64-linux-gnu/libboost_system.so.1.83.0 /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-202409.4/obj-aarch64-linux-gnu' -[ 63%] Built target testMolCatalog +[ 62%] Built target testMolAlign 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-202409.4/obj-aarch64-linux-gnu' cd 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-I/usr/include/python3.13 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202409.4/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/FMCS/CMakeFiles/FMCS.dir/Seed.cpp.o -MF CMakeFiles/FMCS.dir/Seed.cpp.o.d -o CMakeFiles/FMCS.dir/Seed.cpp.o -c /build/reproducible-path/rdkit-202409.4/Code/GraphMol/FMCS/Seed.cpp -[ 63%] Linking CXX shared library ../../../lib/libRDKitMMPA.so +[ 62%] Building CXX object Code/GraphMol/Descriptors/CMakeFiles/Descriptors.dir/ConnectivityDescriptors.cpp.o +cd /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/GraphMol/Descriptors && /usr/bin/c++ 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-D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/Descriptors/CMakeFiles/Descriptors.dir/ConnectivityDescriptors.cpp.o -MF CMakeFiles/Descriptors.dir/ConnectivityDescriptors.cpp.o.d -o CMakeFiles/Descriptors.dir/ConnectivityDescriptors.cpp.o -c /build/reproducible-path/rdkit-202409.4/Code/GraphMol/Descriptors/ConnectivityDescriptors.cpp +[ 62%] Linking CXX shared library ../../../lib/libRDKitMMPA.so cd /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/GraphMol/MMPA && /usr/bin/cmake -E cmake_link_script CMakeFiles/MMPA.dir/link.txt --verbose=1 +[ 62%] Linking CXX executable trajectoryTest +cd /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/GraphMol/Trajectory && /usr/bin/cmake -E cmake_link_script CMakeFiles/trajectoryTest.dir/link.txt --verbose=1 /usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.4=. -fstack-protector-strong 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CMakeFiles/rdMMPA.dir/rdMMPA.cpp.o.d -o CMakeFiles/rdMMPA.dir/rdMMPA.cpp.o -c /build/reproducible-path/rdkit-202409.4/Code/GraphMol/MMPA/Wrap/rdMMPA.cpp -[ 64%] Linking CXX executable molInterchangeTest1 -cd /build/reproducible-path/rdkit-202409.4/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-202409.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_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.1.2024.09.4 ../../../lib/libRDKitFileParsers.so.1.2024.09.4 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molInterchangeTest1 -[ 64%] Building CXX object Code/GraphMol/Descriptors/CMakeFiles/Descriptors.dir/MQN.cpp.o -cd /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/GraphMol/Descriptors && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DDescriptors_EXPORTS -DRDKIT_DESCRIPTORS_BUILD -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.4/External -I/usr/include/python3.13 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202409.4/Code -I/build/reproducible-path/rdkit-202409.4/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 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/build/reproducible-path/rdkit-202409.4/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-202409.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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.1.2024.09.4 CMakeFiles/MolProcessing.dir/MolProcessing.cpp.o ../../../lib/libRDKitFileParsers.so.1.2024.09.4 ../../../lib/libRDKitFingerprints.so.1.2024.09.4 ../../../lib/libRDKitRDStreams.so.1.2024.09.4 ../../../lib/libRDKitChemTransforms.so.1.2024.09.4 ../../../lib/libRDKitDepictor.so.1.2024.09.4 /usr/lib/aarch64-linux-gnu/libcoordgen.so ../../../lib/libRDKitMolAlign.so.1.2024.09.4 ../../../lib/libRDKitMolTransforms.so.1.2024.09.4 ../../../lib/libRDKitEigenSolvers.so.1.2024.09.4 ../../../lib/libRDKitAlignment.so.1.2024.09.4 /usr/lib/aarch64-linux-gnu/libmaeparser.so ../../../lib/libRDKitSmilesParse.so.1.2024.09.4 ../../../lib/libRDKitSubgraphs.so.1.2024.09.4 ../../../lib/libRDKitSubstructMatch.so.1.2024.09.4 ../../../lib/libRDKitGenericGroups.so.1.2024.09.4 ../../../lib/libRDKitGraphMol.so.1.2024.09.4 ../../../lib/libRDKitRDGeometryLib.so.1.2024.09.4 ../../../lib/libRDKitDataStructs.so.1.2024.09.4 ../../../lib/libRDKitRDGeneral.so.1.2024.09.4 -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-202409.4/obj-aarch64-linux-gnu/Code/GraphMol/MolProcessing && /usr/bin/cmake -E cmake_symlink_library 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-I/build/reproducible-path/rdkit-202409.4/External -I/usr/include/python3.13 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202409.4/Code -I/build/reproducible-path/rdkit-202409.4/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=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/MolProcessing/CMakeFiles/testMolProcessing.dir/processing_tests.cpp.o -MF CMakeFiles/testMolProcessing.dir/processing_tests.cpp.o.d -o CMakeFiles/testMolProcessing.dir/processing_tests.cpp.o -c /build/reproducible-path/rdkit-202409.4/Code/GraphMol/MolProcessing/processing_tests.cpp -[ 65%] Building CXX object Code/GraphMol/Descriptors/CMakeFiles/Descriptors.dir/Data3Ddescriptors.cpp.o -cd /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/GraphMol/Descriptors && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DDescriptors_EXPORTS -DRDKIT_DESCRIPTORS_BUILD -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.4/External -I/usr/include/python3.13 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202409.4/Code -I/build/reproducible-path/rdkit-202409.4/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 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-DRascalMCES_EXPORTS -I/build/reproducible-path/rdkit-202409.4/External -I/usr/include/python3.13 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202409.4/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-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-202409.4/Code/GraphMol/RascalMCES/RascalCluster.cpp +[ 65%] Linking CXX executable testAbbreviations +cd /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/GraphMol/Abbreviations && /usr/bin/cmake -E cmake_link_script CMakeFiles/testAbbreviations.dir/link.txt --verbose=1 +/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/testAbbreviations.dir/link.d CMakeFiles/testAbbreviations.dir/catch_tests.cpp.o -o testAbbreviations ../../RDGeneral/librdkitCatch.a ../../../lib/libRDKitAbbreviations.so.1.2024.09.4 ../../../lib/libRDKitFileParsers.so.1.2024.09.4 /usr/lib/libCatch2.a ../../../lib/libRDKitChemTransforms.so.1.2024.09.4 ../../../lib/libRDKitDepictor.so.1.2024.09.4 /usr/lib/aarch64-linux-gnu/libcoordgen.so ../../../lib/libRDKitMolAlign.so.1.2024.09.4 ../../../lib/libRDKitSmilesParse.so.1.2024.09.4 ../../../lib/libRDKitSubstructMatch.so.1.2024.09.4 ../../../lib/libRDKitGenericGroups.so.1.2024.09.4 ../../../lib/libRDKitMolTransforms.so.1.2024.09.4 ../../../lib/libRDKitGraphMol.so.1.2024.09.4 ../../../lib/libRDKitEigenSolvers.so.1.2024.09.4 ../../../lib/libRDKitAlignment.so.1.2024.09.4 ../../../lib/libRDKitRDGeometryLib.so.1.2024.09.4 ../../../lib/libRDKitDataStructs.so.1.2024.09.4 ../../../lib/libRDKitRDGeneral.so.1.2024.09.4 /usr/lib/aarch64-linux-gnu/libboost_system.so.1.83.0 /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-202409.4/obj-aarch64-linux-gnu' -[ 65%] Built target testMMPA +[ 65%] Built target testAbbreviations 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-202409.4/obj-aarch64-linux-gnu' cd /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202409.4 /build/reproducible-path/rdkit-202409.4/Code/GraphMol/MolProcessing/Wrap /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/GraphMol/MolProcessing/Wrap /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/GraphMol/MolProcessing/Wrap/CMakeFiles/rdMolProcessing.dir/DependInfo.cmake "--color=" @@ -5607,181 +5624,191 @@ make[4]: Entering directory '/build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu' [ 65%] Building CXX object Code/GraphMol/MolProcessing/Wrap/CMakeFiles/rdMolProcessing.dir/rdMolProcessing.cpp.o cd /build/reproducible-path/rdkit-202409.4/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_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-202409.4/External -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202409.4/Code -I/build/reproducible-path/rdkit-202409.4/External/boost-numeric-bindings -isystem /usr/include/python3.13 -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard 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-DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.4/External -I/usr/include/python3.13 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202409.4/Code -I/build/reproducible-path/rdkit-202409.4/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-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/MolData3Ddescriptors.cpp.o -MF CMakeFiles/Descriptors.dir/MolData3Ddescriptors.cpp.o.d -o 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-I/build/reproducible-path/rdkit-202409.4/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-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-202409.4/Code/GraphMol/ChemReactions/Enumerate/EvenSamplePairs.cpp -[ 69%] Linking CXX shared library ../../../lib/libRDKitFMCS.so +[ 67%] Linking CXX shared library ../../../lib/libRDKitFMCS.so cd /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/GraphMol/FMCS && 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-DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.4/External -I/usr/include/python3.13 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202409.4/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=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-202409.4/Code/GraphMol/FMCS/testFMCS_Unit.cpp -[ 69%] Linking CXX shared library ../../../lib/libRDKitSynthonSpaceSearch.so -cd /build/reproducible-path/rdkit-202409.4/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-202409.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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.1.2024.09.4 CMakeFiles/SynthonSpaceSearch.dir/SynthonSpaceSearch_details.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 /usr/lib/aarch64-linux-gnu/libmaeparser.so cd /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/GraphMol/RascalMCES && /usr/bin/cmake -E cmake_symlink_library ../../../lib/libRDKitRascalMCES.so.1.2024.09.4 ../../../lib/libRDKitRascalMCES.so.1 ../../../lib/libRDKitRascalMCES.so make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu' -[ 71%] Built target RascalMCES +[ 70%] Built target RascalMCES +make -f Code/GraphMol/ChemReactions/CMakeFiles/rxnTestCatch.dir/build.make Code/GraphMol/ChemReactions/CMakeFiles/rxnTestCatch.dir/depend +make[4]: Entering directory '/build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu' +cd /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" 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make[4]: Entering directory '/build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu' cd /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202409.4 /build/reproducible-path/rdkit-202409.4/Code/GraphMol/MolDraw2D /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/GraphMol/MolDraw2D /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/GraphMol/MolDraw2D/CMakeFiles/MolDraw2D.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu' make -f Code/GraphMol/MolDraw2D/CMakeFiles/MolDraw2D.dir/build.make Code/GraphMol/MolDraw2D/CMakeFiles/MolDraw2D.dir/build make[4]: Entering directory '/build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu' -[ 71%] Building CXX object Code/GraphMol/MolDraw2D/CMakeFiles/MolDraw2D.dir/MolDraw2D.cpp.o +[ 72%] Building CXX object Code/GraphMol/MolDraw2D/CMakeFiles/MolDraw2D.dir/MolDraw2D.cpp.o cd /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/GraphMol/MolDraw2D && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DMolDraw2D_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_MOLDRAW2D_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_CAIRO_SUPPORT -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_FREETYPE_SUPPORT -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.4/External -I/usr/include/freetype2 -I/usr/include/python3.13 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202409.4/Code -I/build/reproducible-path/rdkit-202409.4/External/boost-numeric-bindings -isystem /usr/include/eigen3 -isystem /usr/include/cairo -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-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-202409.4/Code/GraphMol/MolDraw2D/MolDraw2D.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-202409.4/Code/RDGeneral/Dict.h:19, - from /build/reproducible-path/rdkit-202409.4/Code/GraphMol/QueryOps.h:16, - from /build/reproducible-path/rdkit-202409.4/Code/GraphMol/MolDraw2D/MolDraw2D.cpp:16: -/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-202409.4/Code/GraphMol/MolDraw2D/MolDraw2D.cpp:771:42: required from here - 771 | auto new_mins = getAtomCoords(make_pair(x_min, y_min)); - | ~~~~~~~~~^~~~~~~~~~~~~~ -/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) - | ^~~~~~~~~ -[ 71%] Linking CXX 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-I/build/reproducible-path/rdkit-202409.4/External -I/usr/include/python3.13 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202409.4/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=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-202409.4/Code/GraphMol/RascalMCES/mces_catch.cpp -/usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security 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-DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.4/External -I/usr/include/python3.13 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202409.4/Code -I/build/reproducible-path/rdkit-202409.4/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/MarvinParse/CMakeFiles/MarvinParser.dir/MarvinDefs.cpp.o -MF CMakeFiles/MarvinParser.dir/MarvinDefs.cpp.o.d -o CMakeFiles/MarvinParser.dir/MarvinDefs.cpp.o -c /build/reproducible-path/rdkit-202409.4/Code/GraphMol/MarvinParse/MarvinDefs.cpp +[ 73%] Linking CXX executable testEnumeration +cd /build/reproducible-path/rdkit-202409.4/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 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/testEnumeration.dir/link.d CMakeFiles/testEnumeration.dir/Enumerate/testEnumerate.cpp.o -o testEnumeration ../../../lib/libRDKitChemReactions.so.1.2024.09.4 ../../../lib/libRDKitFilterCatalog.so.1.2024.09.4 ../../../lib/libRDKitCatalogs.so.1.2024.09.4 ../../../lib/libRDKitFingerprints.so.1.2024.09.4 ../../../lib/libRDKitSubgraphs.so.1.2024.09.4 ../../../lib/libRDKitFileParsers.so.1.2024.09.4 /usr/lib/aarch64-linux-gnu/libmaeparser.so ../../../lib/libRDKitChemTransforms.so.1.2024.09.4 ../../../lib/libRDKitDepictor.so.1.2024.09.4 /usr/lib/aarch64-linux-gnu/libcoordgen.so ../../../lib/libRDKitMolAlign.so.1.2024.09.4 ../../../lib/libRDKitMolTransforms.so.1.2024.09.4 ../../../lib/libRDKitEigenSolvers.so.1.2024.09.4 ../../../lib/libRDKitAlignment.so.1.2024.09.4 ../../../lib/libRDKitSubstructMatch.so.1.2024.09.4 ../../../lib/libRDKitGenericGroups.so.1.2024.09.4 ../../../lib/libRDKitSmilesParse.so.1.2024.09.4 ../../../lib/libRDKitGraphMol.so.1.2024.09.4 ../../../lib/libRDKitRDGeometryLib.so.1.2024.09.4 ../../../lib/libRDKitDataStructs.so.1.2024.09.4 ../../../lib/libRDKitRDGeneral.so.1.2024.09.4 /usr/lib/aarch64-linux-gnu/libboost_system.so.1.83.0 /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-202409.4/obj-aarch64-linux-gnu' -[ 71%] Built target 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-I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202409.4/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=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-202409.4/Code/GraphMol/RascalMCES/mces_cluster_catch.cpp -[ 72%] Linking CXX shared module ../../../../rdkit/Chem/rdFMCS.so -cd /build/reproducible-path/rdkit-202409.4/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-202409.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=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.1.2024.09.4 ../../../../lib/libRDKitRDBoost.so.1.2024.09.4 ../../../../lib/libRDKitFileParsers.so.1.2024.09.4 /usr/lib/aarch64-linux-gnu/libmaeparser.so ../../../../lib/libRDKitChemTransforms.so.1.2024.09.4 ../../../../lib/libRDKitDepictor.so.1.2024.09.4 /usr/lib/aarch64-linux-gnu/libcoordgen.so ../../../../lib/libRDKitMolAlign.so.1.2024.09.4 ../../../../lib/libRDKitMolTransforms.so.1.2024.09.4 ../../../../lib/libRDKitEigenSolvers.so.1.2024.09.4 ../../../../lib/libRDKitAlignment.so.1.2024.09.4 ../../../../lib/libRDKitSmilesParse.so.1.2024.09.4 ../../../../lib/libRDKitSubstructMatch.so.1.2024.09.4 ../../../../lib/libRDKitGenericGroups.so.1.2024.09.4 ../../../../lib/libRDKitGraphMol.so.1.2024.09.4 ../../../../lib/libRDKitRDGeometryLib.so.1.2024.09.4 ../../../../lib/libRDKitDataStructs.so.1.2024.09.4 /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.1.2024.09.4 /usr/lib/aarch64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl +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-202409.4/Code/RDGeneral/Dict.h:19, + from /build/reproducible-path/rdkit-202409.4/Code/GraphMol/QueryOps.h:16, + from /build/reproducible-path/rdkit-202409.4/Code/GraphMol/MolDraw2D/MolDraw2D.cpp:16: +/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-202409.4/Code/GraphMol/MolDraw2D/MolDraw2D.cpp:771:42: required from here + 771 | auto new_mins = getAtomCoords(make_pair(x_min, y_min)); + | ~~~~~~~~~^~~~~~~~~~~~~~ +/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) + | ^~~~~~~~~ +[ 73%] Building CXX object Code/GraphMol/MolStandardize/CMakeFiles/MolStandardize.dir/Normalize.cpp.o +cd /build/reproducible-path/rdkit-202409.4/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_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.4/External -I/usr/include/python3.13 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202409.4/Code -I/build/reproducible-path/rdkit-202409.4/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-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-202409.4/Code/GraphMol/MolStandardize/Normalize.cpp +[ 73%] Linking CXX executable testRascalCluster +cd /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/GraphMol/RascalMCES && /usr/bin/cmake -E cmake_link_script CMakeFiles/testRascalCluster.dir/link.txt --verbose=1 +/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/testRascalCluster.dir/link.d CMakeFiles/testRascalCluster.dir/mces_cluster_catch.cpp.o -o testRascalCluster ../../RDGeneral/librdkitCatch.a ../../../lib/libRDKitRascalMCES.so.1.2024.09.4 /usr/lib/libCatch2.a ../../../lib/libRDKitFileParsers.so.1.2024.09.4 /usr/lib/aarch64-linux-gnu/libmaeparser.so ../../../lib/libRDKitChemTransforms.so.1.2024.09.4 ../../../lib/libRDKitDepictor.so.1.2024.09.4 /usr/lib/aarch64-linux-gnu/libcoordgen.so ../../../lib/libRDKitMolAlign.so.1.2024.09.4 ../../../lib/libRDKitSmilesParse.so.1.2024.09.4 ../../../lib/libRDKitMolTransforms.so.1.2024.09.4 ../../../lib/libRDKitEigenSolvers.so.1.2024.09.4 ../../../lib/libRDKitAlignment.so.1.2024.09.4 ../../../lib/libRDKitSubstructMatch.so.1.2024.09.4 ../../../lib/libRDKitGenericGroups.so.1.2024.09.4 ../../../lib/libRDKitGraphMol.so.1.2024.09.4 ../../../lib/libRDKitRDGeometryLib.so.1.2024.09.4 ../../../lib/libRDKitDataStructs.so.1.2024.09.4 ../../../lib/libRDKitRDGeneral.so.1.2024.09.4 /usr/lib/aarch64-linux-gnu/libboost_system.so.1.83.0 /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-202409.4/obj-aarch64-linux-gnu' -[ 72%] Built target rdFMCS +[ 73%] Built target testRascalCluster 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-202409.4/obj-aarch64-linux-gnu' cd /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202409.4 /build/reproducible-path/rdkit-202409.4/Code/GraphMol/RascalMCES/Wrap /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/GraphMol/RascalMCES/Wrap /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/GraphMol/RascalMCES/Wrap/CMakeFiles/rdRascalMCES.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu' make -f Code/GraphMol/RascalMCES/Wrap/CMakeFiles/rdRascalMCES.dir/build.make Code/GraphMol/RascalMCES/Wrap/CMakeFiles/rdRascalMCES.dir/build make[4]: Entering directory '/build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu' -[ 72%] Building CXX object Code/GraphMol/RascalMCES/Wrap/CMakeFiles/rdRascalMCES.dir/rdRascalMCES.cpp.o +[ 73%] Building CXX object Code/GraphMol/RascalMCES/Wrap/CMakeFiles/rdRascalMCES.dir/rdRascalMCES.cpp.o cd /build/reproducible-path/rdkit-202409.4/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_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-202409.4/External -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202409.4/Code -isystem /usr/include/python3.13 -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-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-202409.4/Code/GraphMol/RascalMCES/Wrap/rdRascalMCES.cpp -[ 73%] Linking CXX executable testEnumeration -cd /build/reproducible-path/rdkit-202409.4/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 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated 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-I/build/reproducible-path/rdkit-202409.4/External -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202409.4/Code -I/build/reproducible-path/rdkit-202409.4/External/boost-numeric-bindings -isystem /usr/include/python3.13 -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/Wrap/CMakeFiles/rdmolfiles.dir/ForwardSDMolSupplier.cpp.o -MF CMakeFiles/rdmolfiles.dir/ForwardSDMolSupplier.cpp.o.d -o CMakeFiles/rdmolfiles.dir/ForwardSDMolSupplier.cpp.o -c /build/reproducible-path/rdkit-202409.4/Code/GraphMol/Wrap/ForwardSDMolSupplier.cpp +[ 79%] Linking CXX shared library ../../../lib/libRDKitMolEnumerator.so +cd /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/GraphMol/MolEnumerator && /usr/bin/cmake -E cmake_link_script CMakeFiles/MolEnumerator.dir/link.txt --verbose=1 +/usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,--dependency-file=CMakeFiles/MolEnumerator.dir/link.d -Wl,-z,relro -Wl,-z,now -shared -Wl,-soname,libRDKitMolEnumerator.so.1 -o ../../../lib/libRDKitMolEnumerator.so.1.2024.09.4 CMakeFiles/MolEnumerator.dir/MolEnumerator.cpp.o CMakeFiles/MolEnumerator.dir/PositionVariation.cpp.o CMakeFiles/MolEnumerator.dir/LinkNode.cpp.o CMakeFiles/MolEnumerator.dir/RepeatUnit.cpp.o ../../../lib/libRDKitChemReactions.so.1.2024.09.4 ../../../lib/libRDKitFileParsers.so.1.2024.09.4 /usr/lib/aarch64-linux-gnu/libmaeparser.so ../../../lib/libRDKitChemTransforms.so.1.2024.09.4 ../../../lib/libRDKitDepictor.so.1.2024.09.4 /usr/lib/aarch64-linux-gnu/libcoordgen.so ../../../lib/libRDKitMolAlign.so.1.2024.09.4 ../../../lib/libRDKitMolTransforms.so.1.2024.09.4 ../../../lib/libRDKitEigenSolvers.so.1.2024.09.4 ../../../lib/libRDKitAlignment.so.1.2024.09.4 ../../../lib/libRDKitFilterCatalog.so.1.2024.09.4 ../../../lib/libRDKitCatalogs.so.1.2024.09.4 ../../../lib/libRDKitFingerprints.so.1.2024.09.4 ../../../lib/libRDKitSubstructMatch.so.1.2024.09.4 ../../../lib/libRDKitGenericGroups.so.1.2024.09.4 ../../../lib/libRDKitSmilesParse.so.1.2024.09.4 ../../../lib/libRDKitSubgraphs.so.1.2024.09.4 ../../../lib/libRDKitGraphMol.so.1.2024.09.4 ../../../lib/libRDKitRDGeometryLib.so.1.2024.09.4 ../../../lib/libRDKitDataStructs.so.1.2024.09.4 ../../../lib/libRDKitRDGeneral.so.1.2024.09.4 /usr/lib/aarch64-linux-gnu/libboost_system.so.1.83.0 /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-202409.4/obj-aarch64-linux-gnu/Code/GraphMol/MolEnumerator && /usr/bin/cmake -E cmake_symlink_library ../../../lib/libRDKitMolEnumerator.so.1.2024.09.4 ../../../lib/libRDKitMolEnumerator.so.1 ../../../lib/libRDKitMolEnumerator.so make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu' -[ 74%] Built target testATF +[ 79%] Built target MolEnumerator make -f Code/GraphMol/Descriptors/CMakeFiles/testEEM.dir/build.make Code/GraphMol/Descriptors/CMakeFiles/testEEM.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu' cd /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202409.4 /build/reproducible-path/rdkit-202409.4/Code/GraphMol/Descriptors /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/GraphMol/Descriptors /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/GraphMol/Descriptors/CMakeFiles/testEEM.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu' make -f Code/GraphMol/Descriptors/CMakeFiles/testEEM.dir/build.make Code/GraphMol/Descriptors/CMakeFiles/testEEM.dir/build make[4]: Entering directory '/build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu' -[ 74%] Building CXX object Code/GraphMol/Descriptors/CMakeFiles/testEEM.dir/testEEM.cpp.o +[ 79%] Building CXX object Code/GraphMol/Descriptors/CMakeFiles/testEEM.dir/testEEM.cpp.o cd /build/reproducible-path/rdkit-202409.4/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_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.4/External -I/usr/include/python3.13 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202409.4/Code -I/build/reproducible-path/rdkit-202409.4/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=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-202409.4/Code/GraphMol/Descriptors/testEEM.cpp -[ 74%] Linking CXX executable testAUTOCORR2D -cd /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/GraphMol/Descriptors && /usr/bin/cmake -E cmake_link_script CMakeFiles/testAUTOCORR2D.dir/link.txt --verbose=1 -/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/testAUTOCORR2D.dir/link.d CMakeFiles/testAUTOCORR2D.dir/testAUTOCORR2D.cpp.o -o testAUTOCORR2D ../../../lib/libRDKitDescriptors.so.1.2024.09.4 ../../../lib/libRDKitPartialCharges.so.1.2024.09.4 ../../../lib/libRDKitFileParsers.so.1.2024.09.4 ../../../lib/libRDKitChemTransforms.so.1.2024.09.4 ../../../lib/libRDKitDepictor.so.1.2024.09.4 /usr/lib/aarch64-linux-gnu/libcoordgen.so ../../../lib/libRDKitMolAlign.so.1.2024.09.4 ../../../lib/libRDKitSmilesParse.so.1.2024.09.4 ../../../lib/libRDKitAlignment.so.1.2024.09.4 /usr/lib/aarch64-linux-gnu/libmaeparser.so ../../../lib/libRDKitSubgraphs.so.1.2024.09.4 ../../../lib/libRDKitSubstructMatch.so.1.2024.09.4 ../../../lib/libRDKitGenericGroups.so.1.2024.09.4 ../../../lib/libRDKitMolTransforms.so.1.2024.09.4 ../../../lib/libRDKitGraphMol.so.1.2024.09.4 ../../../lib/libRDKitRDGeometryLib.so.1.2024.09.4 ../../../lib/libRDKitDataStructs.so.1.2024.09.4 ../../../lib/libRDKitEigenSolvers.so.1.2024.09.4 ../../../lib/libRDKitRDGeneral.so.1.2024.09.4 /usr/lib/aarch64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl +[ 79%] Building CXX object Code/GraphMol/MolDraw2D/CMakeFiles/MolDraw2D.dir/DrawText.cpp.o +cd /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/GraphMol/MolDraw2D && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DMolDraw2D_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_MOLDRAW2D_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_CAIRO_SUPPORT -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_FREETYPE_SUPPORT -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.4/External -I/usr/include/freetype2 -I/usr/include/python3.13 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202409.4/Code -I/build/reproducible-path/rdkit-202409.4/External/boost-numeric-bindings -isystem /usr/include/eigen3 -isystem /usr/include/cairo -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-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/DrawText.cpp.o -MF CMakeFiles/MolDraw2D.dir/DrawText.cpp.o.d -o CMakeFiles/MolDraw2D.dir/DrawText.cpp.o -c /build/reproducible-path/rdkit-202409.4/Code/GraphMol/MolDraw2D/DrawText.cpp +In file included from /usr/include/boost/shared_ptr.hpp:17, + from /usr/include/boost/python/converter/shared_ptr_to_python.hpp:12, + from /usr/include/boost/python/converter/arg_to_python.hpp:15, + from /usr/include/boost/python/call.hpp:15, + from /usr/include/boost/python/object_core.hpp:14, + from /usr/include/boost/python/args.hpp:22, + from /usr/include/boost/python.hpp:11, + from /build/reproducible-path/rdkit-202409.4/Code/GraphMol/ChemReactions/Wrap/Enumerate.cpp:32: +In copy constructor 'boost::shared_ptr::shared_ptr(const boost::shared_ptr&) [with T = RDKit::ROMol]', + inlined from 'std::vector > > RDKit::ConvertToVect(T) [with T = boost::python::tuple]' at /build/reproducible-path/rdkit-202409.4/Code/GraphMol/ChemReactions/Wrap/Enumerate.cpp:55:25: +/usr/include/boost/smart_ptr/shared_ptr.hpp:459:66: warning: '*(const boost::shared_ptr*)((char*)& + offsetof(boost::python::extract >,boost::python::extract >::.boost::python::converter::extract_rvalue >::m_data.boost::python::converter::rvalue_from_python_data >::.boost::python::converter::rvalue_from_python_storage >::storage)).boost::shared_ptr::px' may be used uninitialized [-Wmaybe-uninitialized] + 459 | shared_ptr( shared_ptr const & r ) BOOST_SP_NOEXCEPT : px( r.px ), pn( r.pn ) + | ~~^~ +/build/reproducible-path/rdkit-202409.4/Code/GraphMol/ChemReactions/Wrap/Enumerate.cpp: In function 'std::vector > > RDKit::ConvertToVect(T) [with T = boost::python::tuple]': +/build/reproducible-path/rdkit-202409.4/Code/GraphMol/ChemReactions/Wrap/Enumerate.cpp:55:39: note: '' declared here + 55 | RDKit::ROMOL_SPTR mol = python::extract(bbs[i][j]); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +In file included from /usr/include/boost/smart_ptr/shared_ptr.hpp:18: +In copy constructor 'boost::detail::shared_count::shared_count(const boost::detail::shared_count&)', + inlined from 'boost::shared_ptr::shared_ptr(const boost::shared_ptr&) [with T = RDKit::ROMol]' at /usr/include/boost/smart_ptr/shared_ptr.hpp:459:72, + inlined from 'std::vector > > RDKit::ConvertToVect(T) [with T = boost::python::tuple]' at /build/reproducible-path/rdkit-202409.4/Code/GraphMol/ChemReactions/Wrap/Enumerate.cpp:55:25: +/usr/include/boost/smart_ptr/detail/shared_count.hpp:438:67: warning: '((const boost::detail::shared_count*)((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)))[1].boost::detail::shared_count::pi_' may be used uninitialized [-Wmaybe-uninitialized] + 438 | shared_count(shared_count const & r) BOOST_SP_NOEXCEPT: pi_(r.pi_) + | ~~^~~ +/build/reproducible-path/rdkit-202409.4/Code/GraphMol/ChemReactions/Wrap/Enumerate.cpp: In function 'std::vector > > RDKit::ConvertToVect(T) [with T = boost::python::tuple]': +/build/reproducible-path/rdkit-202409.4/Code/GraphMol/ChemReactions/Wrap/Enumerate.cpp:55:39: note: '' declared here + 55 | RDKit::ROMOL_SPTR mol = python::extract(bbs[i][j]); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +In copy constructor 'boost::shared_ptr::shared_ptr(const boost::shared_ptr&) [with T = RDKit::ROMol]', + inlined from 'std::vector > > RDKit::ConvertToVect(T) [with T = boost::python::list]' at /build/reproducible-path/rdkit-202409.4/Code/GraphMol/ChemReactions/Wrap/Enumerate.cpp:55:25: +/usr/include/boost/smart_ptr/shared_ptr.hpp:459:66: warning: '*(const boost::shared_ptr*)((char*)& + offsetof(boost::python::extract >,boost::python::extract >::.boost::python::converter::extract_rvalue >::m_data.boost::python::converter::rvalue_from_python_data >::.boost::python::converter::rvalue_from_python_storage >::storage)).boost::shared_ptr::px' may be used uninitialized [-Wmaybe-uninitialized] + 459 | shared_ptr( shared_ptr const & r ) BOOST_SP_NOEXCEPT : px( r.px ), pn( r.pn ) + | ~~^~ +/build/reproducible-path/rdkit-202409.4/Code/GraphMol/ChemReactions/Wrap/Enumerate.cpp: In function 'std::vector > > RDKit::ConvertToVect(T) [with T = boost::python::list]': +/build/reproducible-path/rdkit-202409.4/Code/GraphMol/ChemReactions/Wrap/Enumerate.cpp:55:39: note: '' declared here + 55 | RDKit::ROMOL_SPTR mol = python::extract(bbs[i][j]); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +In copy constructor 'boost::detail::shared_count::shared_count(const boost::detail::shared_count&)', + inlined from 'boost::shared_ptr::shared_ptr(const boost::shared_ptr&) [with T = RDKit::ROMol]' at /usr/include/boost/smart_ptr/shared_ptr.hpp:459:72, + inlined from 'std::vector > > RDKit::ConvertToVect(T) [with T = boost::python::list]' at /build/reproducible-path/rdkit-202409.4/Code/GraphMol/ChemReactions/Wrap/Enumerate.cpp:55:25: +/usr/include/boost/smart_ptr/detail/shared_count.hpp:438:67: warning: '((const boost::detail::shared_count*)((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)))[1].boost::detail::shared_count::pi_' may be used uninitialized [-Wmaybe-uninitialized] + 438 | shared_count(shared_count const & r) BOOST_SP_NOEXCEPT: pi_(r.pi_) + | ~~^~~ +/build/reproducible-path/rdkit-202409.4/Code/GraphMol/ChemReactions/Wrap/Enumerate.cpp: In function 'std::vector > > RDKit::ConvertToVect(T) [with T = boost::python::list]': +/build/reproducible-path/rdkit-202409.4/Code/GraphMol/ChemReactions/Wrap/Enumerate.cpp:55:39: note: '' declared here + 55 | RDKit::ROMOL_SPTR mol = python::extract(bbs[i][j]); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +[ 79%] Linking CXX executable testATF +cd /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/GraphMol/Descriptors && /usr/bin/cmake -E cmake_link_script CMakeFiles/testATF.dir/link.txt --verbose=1 +/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro 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../../../lib/libRDKitRDGeneral.so.1.2024.09.4 /usr/lib/aarch64-linux-gnu/libboost_system.so.1.83.0 /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-202409.4/obj-aarch64-linux-gnu' -[ 74%] Built target testAUTOCORR2D +[ 79%] Built target testATF make -f Code/GraphMol/Descriptors/CMakeFiles/testPBF.dir/build.make Code/GraphMol/Descriptors/CMakeFiles/testPBF.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu' cd /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202409.4 /build/reproducible-path/rdkit-202409.4/Code/GraphMol/Descriptors /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/GraphMol/Descriptors 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-DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.4/External -I/usr/include/python3.13 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202409.4/Code -I/build/reproducible-path/rdkit-202409.4/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=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/testPBF.dir/testPBF.cpp.o -MF CMakeFiles/testPBF.dir/testPBF.cpp.o.d -o CMakeFiles/testPBF.dir/testPBF.cpp.o -c /build/reproducible-path/rdkit-202409.4/Code/GraphMol/Descriptors/testPBF.cpp -[ 74%] Building CXX object Code/GraphMol/MarvinParse/CMakeFiles/MarvinParser.dir/MarvinDefs.cpp.o -cd /build/reproducible-path/rdkit-202409.4/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_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.4/External -I/usr/include/python3.13 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202409.4/Code -I/build/reproducible-path/rdkit-202409.4/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/MarvinParse/CMakeFiles/MarvinParser.dir/MarvinDefs.cpp.o -MF CMakeFiles/MarvinParser.dir/MarvinDefs.cpp.o.d -o CMakeFiles/MarvinParser.dir/MarvinDefs.cpp.o -c /build/reproducible-path/rdkit-202409.4/Code/GraphMol/MarvinParse/MarvinDefs.cpp -[ 74%] Building CXX object Code/GraphMol/MolEnumerator/CMakeFiles/MolEnumerator.dir/LinkNode.cpp.o -cd /build/reproducible-path/rdkit-202409.4/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_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.4/External -I/usr/include/python3.13 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202409.4/Code -I/build/reproducible-path/rdkit-202409.4/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-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-202409.4/Code/GraphMol/MolEnumerator/LinkNode.cpp -[ 74%] Linking CXX executable testBCUT +In file included from /usr/include/c++/14/vector:62, + from /build/reproducible-path/rdkit-202409.4/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]', + inlined from '_OI std::__copy_move_a2(_II, _II, _OI) [with bool _IsMove = false; _II = int*; _OI = int*]' at /usr/include/c++/14/bits/stl_algobase.h:521:30, + inlined from '_OI std::__copy_move_a1(_II, _II, _OI) [with bool _IsMove = false; _II = int*; _OI = int*]' at /usr/include/c++/14/bits/stl_algobase.h:548:42, + inlined from '_OI std::__copy_move_a(_II, _II, _OI) [with bool _IsMove = false; _II = __gnu_cxx::__normal_iterator >; _OI = int*]' at /usr/include/c++/14/bits/stl_algobase.h:555:31, + inlined from '_OI std::copy(_II, _II, _OI) [with _II = __gnu_cxx::__normal_iterator >; _OI = int*]' at /usr/include/c++/14/bits/stl_algobase.h:651:7, + inlined from 'static _ForwardIterator std::__uninitialized_copy::__uninit_copy(_InputIterator, _InputIterator, _ForwardIterator) [with _InputIterator = __gnu_cxx::__normal_iterator >; _ForwardIterator = int*]' at /usr/include/c++/14/bits/stl_uninitialized.h:147:27, + inlined from '_ForwardIterator std::uninitialized_copy(_InputIterator, _InputIterator, _ForwardIterator) [with _InputIterator = __gnu_cxx::__normal_iterator >; _ForwardIterator = int*]' at /usr/include/c++/14/bits/stl_uninitialized.h:185:15, + inlined from '_ForwardIterator std::__uninitialized_copy_a(_InputIterator, _InputIterator, _ForwardIterator, allocator<_Tp>&) [with _InputIterator = __gnu_cxx::__normal_iterator >; _ForwardIterator = int*; _Tp = int]' at /usr/include/c++/14/bits/stl_uninitialized.h:373:37, + inlined from 'void std::vector<_Tp, _Alloc>::_M_range_insert(iterator, _ForwardIterator, _ForwardIterator, std::forward_iterator_tag) [with _ForwardIterator = __gnu_cxx::__normal_iterator >; _Tp = int; _Alloc = std::allocator]' at /usr/include/c++/14/bits/vector.tcc:1022:38, + inlined from 'std::vector<_Tp, _Alloc>::iterator std::vector<_Tp, _Alloc>::insert(const_iterator, _InputIterator, _InputIterator) [with _InputIterator = __gnu_cxx::__normal_iterator >; = void; _Tp = int; _Alloc = std::allocator]' at /usr/include/c++/14/bits/stl_vector.h:1488:19, + inlined from 'void RDKit::MolDraw2D_detail::DrawMolMCHLasso::extractAtomColourLists(std::vector&, std::vector >&, std::vector >&) const' at /build/reproducible-path/rdkit-202409.4/Code/GraphMol/MolDraw2D/DrawMolMCHLasso.cpp:115:32: +/usr/include/c++/14/bits/stl_algobase.h:452:30: warning: 'void* __builtin_memmove(void*, const void*, long unsigned int)' writing between 5 and 9223372036854775804 bytes into a region of size 0 overflows the destination [-Wstringop-overflow=] + 452 | __builtin_memmove(__result, __first, sizeof(_Tp) * _Num); + | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +In file included from /usr/include/aarch64-linux-gnu/c++/14/bits/c++allocator.h:33, + from /usr/include/c++/14/bits/allocator.h:46, + from /usr/include/c++/14/vector:63: +In member function '_Tp* std::__new_allocator<_Tp>::allocate(size_type, const void*) [with _Tp = int]', + inlined from 'static _Tp* std::allocator_traits >::allocate(allocator_type&, size_type) [with _Tp = int]' at /usr/include/c++/14/bits/alloc_traits.h:515:28, + inlined from 'std::_Vector_base<_Tp, _Alloc>::pointer std::_Vector_base<_Tp, _Alloc>::_M_allocate(std::size_t) [with _Tp = int; _Alloc = std::allocator]' at /usr/include/c++/14/bits/stl_vector.h:380:33, + inlined from 'void std::vector<_Tp, _Alloc>::_M_range_insert(iterator, _ForwardIterator, _ForwardIterator, std::forward_iterator_tag) [with _ForwardIterator = __gnu_cxx::__normal_iterator >; _Tp = int; _Alloc = std::allocator]' at /usr/include/c++/14/bits/vector.tcc:1013:40, + inlined from 'std::vector<_Tp, _Alloc>::iterator std::vector<_Tp, _Alloc>::insert(const_iterator, _InputIterator, _InputIterator) [with _InputIterator = __gnu_cxx::__normal_iterator >; = void; _Tp = int; _Alloc = std::allocator]' at /usr/include/c++/14/bits/stl_vector.h:1488:19, + inlined from 'void RDKit::MolDraw2D_detail::DrawMolMCHLasso::extractAtomColourLists(std::vector&, std::vector >&, std::vector >&) const' at /build/reproducible-path/rdkit-202409.4/Code/GraphMol/MolDraw2D/DrawMolMCHLasso.cpp:115:32: +/usr/include/c++/14/bits/new_allocator.h:151:55: note: at offset [-9223372036854775808, -1] into destination object of size [4, 9223372036854775804] allocated by 'operator new' + 151 | return static_cast<_Tp*>(_GLIBCXX_OPERATOR_NEW(__n * sizeof(_Tp))); + | ^ +[ 79%] Building CXX object Code/GraphMol/MolDraw2D/CMakeFiles/MolDraw2D.dir/DrawTextNotFT.cpp.o +cd /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/GraphMol/MolDraw2D && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DMolDraw2D_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_MOLDRAW2D_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_CAIRO_SUPPORT -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_FREETYPE_SUPPORT -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.4/External -I/usr/include/freetype2 -I/usr/include/python3.13 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202409.4/Code -I/build/reproducible-path/rdkit-202409.4/External/boost-numeric-bindings -isystem /usr/include/eigen3 -isystem /usr/include/cairo -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-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-202409.4/Code/GraphMol/MolDraw2D/DrawTextNotFT.cpp +[ 79%] Linking CXX executable testBCUT cd /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/GraphMol/Descriptors && /usr/bin/cmake -E cmake_link_script CMakeFiles/testBCUT.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/testBCUT.dir/link.d CMakeFiles/testBCUT.dir/testBCUT.cpp.o -o testBCUT ../../../lib/libRDKitDescriptors.so.1.2024.09.4 ../../../lib/libRDKitPartialCharges.so.1.2024.09.4 ../../../lib/libRDKitFileParsers.so.1.2024.09.4 ../../../lib/libRDKitChemTransforms.so.1.2024.09.4 ../../../lib/libRDKitDepictor.so.1.2024.09.4 /usr/lib/aarch64-linux-gnu/libcoordgen.so ../../../lib/libRDKitMolAlign.so.1.2024.09.4 ../../../lib/libRDKitSmilesParse.so.1.2024.09.4 ../../../lib/libRDKitAlignment.so.1.2024.09.4 /usr/lib/aarch64-linux-gnu/libmaeparser.so ../../../lib/libRDKitSubgraphs.so.1.2024.09.4 ../../../lib/libRDKitSubstructMatch.so.1.2024.09.4 ../../../lib/libRDKitGenericGroups.so.1.2024.09.4 ../../../lib/libRDKitMolTransforms.so.1.2024.09.4 ../../../lib/libRDKitGraphMol.so.1.2024.09.4 ../../../lib/libRDKitRDGeometryLib.so.1.2024.09.4 ../../../lib/libRDKitDataStructs.so.1.2024.09.4 ../../../lib/libRDKitEigenSolvers.so.1.2024.09.4 ../../../lib/libRDKitRDGeneral.so.1.2024.09.4 /usr/lib/aarch64-linux-gnu/libboost_system.so.1.83.0 /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-202409.4/obj-aarch64-linux-gnu' -[ 74%] Built target testBCUT +[ 79%] Built target testBCUT make -f Code/GraphMol/Descriptors/CMakeFiles/testRDFcustom.dir/build.make Code/GraphMol/Descriptors/CMakeFiles/testRDFcustom.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu' cd 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-I/build/reproducible-path/rdkit-202409.4/External -I/usr/include/python3.13 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202409.4/Code -I/build/reproducible-path/rdkit-202409.4/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-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/Charge.cpp.o -MF CMakeFiles/MolStandardize.dir/Charge.cpp.o.d -o CMakeFiles/MolStandardize.dir/Charge.cpp.o -c /build/reproducible-path/rdkit-202409.4/Code/GraphMol/MolStandardize/Charge.cpp -[ 76%] Linking CXX executable testEEM -cd 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../../../lib/libRDKitSmilesParse.so.1.2024.09.4 ../../../lib/libRDKitAlignment.so.1.2024.09.4 /usr/lib/aarch64-linux-gnu/libmaeparser.so ../../../lib/libRDKitSubgraphs.so.1.2024.09.4 ../../../lib/libRDKitSubstructMatch.so.1.2024.09.4 ../../../lib/libRDKitGenericGroups.so.1.2024.09.4 ../../../lib/libRDKitMolTransforms.so.1.2024.09.4 ../../../lib/libRDKitGraphMol.so.1.2024.09.4 ../../../lib/libRDKitRDGeometryLib.so.1.2024.09.4 ../../../lib/libRDKitDataStructs.so.1.2024.09.4 ../../../lib/libRDKitEigenSolvers.so.1.2024.09.4 ../../../lib/libRDKitRDGeneral.so.1.2024.09.4 /usr/lib/aarch64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl +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-202409.4/Code/GraphMol/MolDraw2D/DrawText.h:19, + from /build/reproducible-path/rdkit-202409.4/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-202409.4/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) + | ^~~~~~~~~ +[ 80%] Building CXX object 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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-202409.4/obj-aarch64-linux-gnu' -[ 79%] Built target testAUTOCORR3D +[ 83%] Built target testAUTOCORR3D make -f Code/GraphMol/Deprotect/Wrap/CMakeFiles/rdDeprotect.dir/build.make Code/GraphMol/Deprotect/Wrap/CMakeFiles/rdDeprotect.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu' cd /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202409.4 /build/reproducible-path/rdkit-202409.4/Code/GraphMol/Deprotect/Wrap /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/GraphMol/Deprotect/Wrap 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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-202409.4/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) - | ^~~~~~~~~ -[ 84%] Building CXX object Code/GraphMol/MolStandardize/CMakeFiles/MolStandardize.dir/TransformCatalog/TransformCatalogUtils.cpp.o -cd 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../../../lib/libRDKitSubstructMatch.so.1.2024.09.4 ../../../lib/libRDKitGenericGroups.so.1.2024.09.4 ../../../lib/libRDKitGraphMol.so.1.2024.09.4 ../../../lib/libRDKitRDGeometryLib.so.1.2024.09.4 ../../../lib/libRDKitDataStructs.so.1.2024.09.4 ../../../lib/libRDKitRDGeneral.so.1.2024.09.4 /usr/lib/aarch64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl +[ 83%] Linking CXX executable testCoulombMat +cd /build/reproducible-path/rdkit-202409.4/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-202409.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function 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../../../lib/libRDKitRDGeneral.so.1.2024.09.4 /usr/lib/aarch64-linux-gnu/libboost_system.so.1.83.0 /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-202409.4/obj-aarch64-linux-gnu' -[ 84%] Built target testMrvToMol -make -f Code/GraphMol/Wrap/CMakeFiles/rdmolfiles.dir/build.make Code/GraphMol/Wrap/CMakeFiles/rdmolfiles.dir/depend -make[4]: Entering directory '/build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu' -cd /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202409.4 /build/reproducible-path/rdkit-202409.4/Code/GraphMol/Wrap /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/GraphMol/Wrap 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/usr/lib/aarch64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl -make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu' -[ 84%] Built target cxsmilesTest -[ 84%] Building CXX object Code/GraphMol/Wrap/CMakeFiles/rdmolfiles.dir/ForwardSDMolSupplier.cpp.o -cd /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/GraphMol/Wrap && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_NUMPY_DYN_LINK -DBOOST_NUMPY_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -Drdmolfiles_EXPORTS -I/build/reproducible-path/rdkit-202409.4/External -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202409.4/Code -I/build/reproducible-path/rdkit-202409.4/External/boost-numeric-bindings -isystem /usr/include/python3.13 -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/Wrap/CMakeFiles/rdmolfiles.dir/ForwardSDMolSupplier.cpp.o -MF CMakeFiles/rdmolfiles.dir/ForwardSDMolSupplier.cpp.o.d -o CMakeFiles/rdmolfiles.dir/ForwardSDMolSupplier.cpp.o -c /build/reproducible-path/rdkit-202409.4/Code/GraphMol/Wrap/ForwardSDMolSupplier.cpp -[ 84%] Linking CXX shared module ../../../../rdkit/Chem/rdMolDescriptors.so -cd 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Code/GraphMol/MolStandardize/CMakeFiles/MolStandardize.dir/TautomerCatalog/TautomerCatalogUtils.cpp.o -MF CMakeFiles/MolStandardize.dir/TautomerCatalog/TautomerCatalogUtils.cpp.o.d -o CMakeFiles/MolStandardize.dir/TautomerCatalog/TautomerCatalogUtils.cpp.o -c /build/reproducible-path/rdkit-202409.4/Code/GraphMol/MolStandardize/TautomerCatalog/TautomerCatalogUtils.cpp -[ 84%] Linking CXX executable testO3AAlign -cd /build/reproducible-path/rdkit-202409.4/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-202409.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=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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../../../../rdkit/Chem/rdMolAlign.so -cd /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/GraphMol/MolAlign/Wrap && /usr/bin/cmake -E cmake_link_script CMakeFiles/rdMolAlign.dir/link.txt --verbose=1 -/usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=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/rdMolAlign.dir/link.d -Wl,-z,relro -Wl,-z,now -shared -o ../../../../rdkit/Chem/rdMolAlign.so CMakeFiles/rdMolAlign.dir/rdMolAlign.cpp.o ../../../../lib/libRDKitO3AAlign.so.1.2024.09.4 ../../../../lib/libRDKitRDBoost.so.1.2024.09.4 ../../../../lib/libRDKitDescriptors.so.1.2024.09.4 ../../../../lib/libRDKitPartialCharges.so.1.2024.09.4 ../../../../lib/libRDKitFileParsers.so.1.2024.09.4 ../../../../lib/libRDKitChemTransforms.so.1.2024.09.4 ../../../../lib/libRDKitDepictor.so.1.2024.09.4 ../../../../lib/libRDKitMolAlign.so.1.2024.09.4 ../../../../lib/libRDKitAlignment.so.1.2024.09.4 ../../../../lib/libRDKitMolTransforms.so.1.2024.09.4 ../../../../lib/libRDKitEigenSolvers.so.1.2024.09.4 /usr/lib/aarch64-linux-gnu/libcoordgen.so /usr/lib/aarch64-linux-gnu/libmaeparser.so ../../../../lib/libRDKitSubgraphs.so.1.2024.09.4 ../../../../lib/libRDKitForceFieldHelpers.so.1.2024.09.4 ../../../../lib/libRDKitSmilesParse.so.1.2024.09.4 ../../../../lib/libRDKitSubstructMatch.so.1.2024.09.4 ../../../../lib/libRDKitGenericGroups.so.1.2024.09.4 ../../../../lib/libRDKitForceField.so.1.2024.09.4 ../../../../lib/libRDKitOptimizer.so.1.2024.09.4 ../../../../lib/libRDKitTrajectory.so.1.2024.09.4 ../../../../lib/libRDKitGraphMol.so.1.2024.09.4 ../../../../lib/libRDKitRDGeometryLib.so.1.2024.09.4 ../../../../lib/libRDKitDataStructs.so.1.2024.09.4 /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.1.2024.09.4 /usr/lib/aarch64-linux-gnu/libboost_system.so.1.83.0 /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-202409.4/obj-aarch64-linux-gnu' -[ 85%] Built target rdMolAlign -[ 85%] Building CXX object Code/GraphMol/MolDraw2D/CMakeFiles/MolDraw2D.dir/DrawMolMCHCircleAndLine.cpp.o -cd /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/GraphMol/MolDraw2D && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DMolDraw2D_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_MOLDRAW2D_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_CAIRO_SUPPORT -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_FREETYPE_SUPPORT -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.4/External -I/usr/include/freetype2 -I/usr/include/python3.13 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202409.4/Code -I/build/reproducible-path/rdkit-202409.4/External/boost-numeric-bindings -isystem /usr/include/eigen3 -isystem /usr/include/cairo -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-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-202409.4/Code/GraphMol/MolDraw2D/DrawMolMCHCircleAndLine.cpp -[ 85%] Building CXX object Code/GraphMol/MolDraw2D/CMakeFiles/MolDraw2D.dir/DrawMolMCHLasso.cpp.o -cd /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/GraphMol/MolDraw2D && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DMolDraw2D_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_MOLDRAW2D_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_CAIRO_SUPPORT -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_FREETYPE_SUPPORT -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.4/External -I/usr/include/freetype2 -I/usr/include/python3.13 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202409.4/Code -I/build/reproducible-path/rdkit-202409.4/External/boost-numeric-bindings -isystem /usr/include/eigen3 -isystem /usr/include/cairo -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-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/DrawMolMCHLasso.cpp.o -MF CMakeFiles/MolDraw2D.dir/DrawMolMCHLasso.cpp.o.d -o CMakeFiles/MolDraw2D.dir/DrawMolMCHLasso.cpp.o -c /build/reproducible-path/rdkit-202409.4/Code/GraphMol/MolDraw2D/DrawMolMCHLasso.cpp -In file included from /usr/include/boost/shared_ptr.hpp:17, - from /usr/include/boost/python/converter/shared_ptr_to_python.hpp:12, - from /usr/include/boost/python/converter/arg_to_python.hpp:15, - from /usr/include/boost/python/call.hpp:15, - from /usr/include/boost/python/object_core.hpp:14, - from /usr/include/boost/python/args.hpp:22, - from /usr/include/boost/python.hpp:11, - from /build/reproducible-path/rdkit-202409.4/Code/GraphMol/ChemReactions/Wrap/Enumerate.cpp:32: -In copy constructor 'boost::shared_ptr::shared_ptr(const boost::shared_ptr&) [with T = RDKit::ROMol]', - inlined from 'std::vector > > RDKit::ConvertToVect(T) [with T = boost::python::tuple]' at /build/reproducible-path/rdkit-202409.4/Code/GraphMol/ChemReactions/Wrap/Enumerate.cpp:55:25: -/usr/include/boost/smart_ptr/shared_ptr.hpp:459:66: warning: '*(const boost::shared_ptr*)((char*)& + offsetof(boost::python::extract >,boost::python::extract >::.boost::python::converter::extract_rvalue >::m_data.boost::python::converter::rvalue_from_python_data >::.boost::python::converter::rvalue_from_python_storage >::storage)).boost::shared_ptr::px' may be used uninitialized [-Wmaybe-uninitialized] - 459 | shared_ptr( shared_ptr const & r ) BOOST_SP_NOEXCEPT : px( r.px ), pn( r.pn ) - | ~~^~ -/build/reproducible-path/rdkit-202409.4/Code/GraphMol/ChemReactions/Wrap/Enumerate.cpp: In function 'std::vector > > RDKit::ConvertToVect(T) [with T = boost::python::tuple]': -/build/reproducible-path/rdkit-202409.4/Code/GraphMol/ChemReactions/Wrap/Enumerate.cpp:55:39: note: '' declared here - 55 | RDKit::ROMOL_SPTR mol = python::extract(bbs[i][j]); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -In file included from /usr/include/boost/smart_ptr/shared_ptr.hpp:18: -In copy constructor 'boost::detail::shared_count::shared_count(const boost::detail::shared_count&)', - inlined from 'boost::shared_ptr::shared_ptr(const boost::shared_ptr&) [with T = RDKit::ROMol]' at /usr/include/boost/smart_ptr/shared_ptr.hpp:459:72, - inlined from 'std::vector > > RDKit::ConvertToVect(T) [with T = boost::python::tuple]' at /build/reproducible-path/rdkit-202409.4/Code/GraphMol/ChemReactions/Wrap/Enumerate.cpp:55:25: -/usr/include/boost/smart_ptr/detail/shared_count.hpp:438:67: warning: '((const boost::detail::shared_count*)((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)))[1].boost::detail::shared_count::pi_' may be used uninitialized [-Wmaybe-uninitialized] - 438 | shared_count(shared_count const & r) BOOST_SP_NOEXCEPT: pi_(r.pi_) - | ~~^~~ -/build/reproducible-path/rdkit-202409.4/Code/GraphMol/ChemReactions/Wrap/Enumerate.cpp: In function 'std::vector > > RDKit::ConvertToVect(T) [with T = boost::python::tuple]': -/build/reproducible-path/rdkit-202409.4/Code/GraphMol/ChemReactions/Wrap/Enumerate.cpp:55:39: note: '' declared here - 55 | RDKit::ROMOL_SPTR mol = python::extract(bbs[i][j]); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -In copy constructor 'boost::shared_ptr::shared_ptr(const boost::shared_ptr&) [with T = RDKit::ROMol]', - inlined from 'std::vector > > RDKit::ConvertToVect(T) [with T = boost::python::list]' at /build/reproducible-path/rdkit-202409.4/Code/GraphMol/ChemReactions/Wrap/Enumerate.cpp:55:25: -/usr/include/boost/smart_ptr/shared_ptr.hpp:459:66: warning: '*(const boost::shared_ptr*)((char*)& + offsetof(boost::python::extract >,boost::python::extract >::.boost::python::converter::extract_rvalue >::m_data.boost::python::converter::rvalue_from_python_data >::.boost::python::converter::rvalue_from_python_storage >::storage)).boost::shared_ptr::px' may be used uninitialized [-Wmaybe-uninitialized] - 459 | shared_ptr( shared_ptr const & r ) BOOST_SP_NOEXCEPT : px( r.px ), pn( r.pn ) - | ~~^~ -/build/reproducible-path/rdkit-202409.4/Code/GraphMol/ChemReactions/Wrap/Enumerate.cpp: In function 'std::vector > > RDKit::ConvertToVect(T) [with T = boost::python::list]': -/build/reproducible-path/rdkit-202409.4/Code/GraphMol/ChemReactions/Wrap/Enumerate.cpp:55:39: note: '' declared here - 55 | RDKit::ROMOL_SPTR mol = python::extract(bbs[i][j]); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -In copy constructor 'boost::detail::shared_count::shared_count(const boost::detail::shared_count&)', - inlined from 'boost::shared_ptr::shared_ptr(const boost::shared_ptr&) [with T = RDKit::ROMol]' at /usr/include/boost/smart_ptr/shared_ptr.hpp:459:72, - inlined from 'std::vector > > RDKit::ConvertToVect(T) [with T = boost::python::list]' at /build/reproducible-path/rdkit-202409.4/Code/GraphMol/ChemReactions/Wrap/Enumerate.cpp:55:25: -/usr/include/boost/smart_ptr/detail/shared_count.hpp:438:67: warning: '((const boost::detail::shared_count*)((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)))[1].boost::detail::shared_count::pi_' may be used uninitialized [-Wmaybe-uninitialized] - 438 | shared_count(shared_count const & r) BOOST_SP_NOEXCEPT: pi_(r.pi_) - | ~~^~~ -/build/reproducible-path/rdkit-202409.4/Code/GraphMol/ChemReactions/Wrap/Enumerate.cpp: In function 'std::vector > > RDKit::ConvertToVect(T) [with T = boost::python::list]': -/build/reproducible-path/rdkit-202409.4/Code/GraphMol/ChemReactions/Wrap/Enumerate.cpp:55:39: note: '' declared here - 55 | RDKit::ROMOL_SPTR mol = python::extract(bbs[i][j]); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -[ 85%] Building CXX object Code/GraphMol/Wrap/CMakeFiles/rdmolfiles.dir/SDMolSupplier.cpp.o -cd /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/GraphMol/Wrap && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK 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-D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/Wrap/CMakeFiles/rdmolfiles.dir/SDMolSupplier.cpp.o -MF CMakeFiles/rdmolfiles.dir/SDMolSupplier.cpp.o.d -o CMakeFiles/rdmolfiles.dir/SDMolSupplier.cpp.o -c /build/reproducible-path/rdkit-202409.4/Code/GraphMol/Wrap/SDMolSupplier.cpp -[ 85%] Building CXX object Code/GraphMol/CIPLabeler/CMakeFiles/testCIPLabeler.dir/CIPMol.cpp.o -cd /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/GraphMol/CIPLabeler && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_CIPLABELER_BUILD -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.4/External -I/usr/include/python3.13 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202409.4/Code -I/build/reproducible-path/rdkit-202409.4/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=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-202409.4/Code/GraphMol/CIPLabeler/CIPMol.cpp -[ 85%] Building CXX object Code/GraphMol/MolDraw2D/CMakeFiles/MolDraw2D.dir/DrawShape.cpp.o -cd /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/GraphMol/MolDraw2D && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DMolDraw2D_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_MOLDRAW2D_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_CAIRO_SUPPORT -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_FREETYPE_SUPPORT -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.4/External -I/usr/include/freetype2 -I/usr/include/python3.13 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202409.4/Code -I/build/reproducible-path/rdkit-202409.4/External/boost-numeric-bindings -isystem /usr/include/eigen3 -isystem /usr/include/cairo -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-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-202409.4/Code/GraphMol/MolDraw2D/DrawShape.cpp -[ 85%] Building CXX object Code/GraphMol/MolDraw2D/CMakeFiles/MolDraw2D.dir/DrawText.cpp.o -cd /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/GraphMol/MolDraw2D && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DMolDraw2D_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_MOLDRAW2D_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_CAIRO_SUPPORT -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_FREETYPE_SUPPORT -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.4/External -I/usr/include/freetype2 -I/usr/include/python3.13 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202409.4/Code -I/build/reproducible-path/rdkit-202409.4/External/boost-numeric-bindings -isystem /usr/include/eigen3 -isystem /usr/include/cairo -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function 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CMakeFiles/MolStandardize.dir/Normalize.cpp.o CMakeFiles/MolStandardize.dir/Validate.cpp.o CMakeFiles/MolStandardize.dir/Charge.cpp.o CMakeFiles/MolStandardize.dir/Tautomer.cpp.o CMakeFiles/MolStandardize.dir/Fragment.cpp.o CMakeFiles/MolStandardize.dir/FragmentCatalog/FragmentCatalogEntry.cpp.o CMakeFiles/MolStandardize.dir/FragmentCatalog/FragmentCatalogParams.cpp.o CMakeFiles/MolStandardize.dir/FragmentCatalog/FragmentCatalogUtils.cpp.o CMakeFiles/MolStandardize.dir/AcidBaseCatalog/AcidBaseCatalogEntry.cpp.o CMakeFiles/MolStandardize.dir/AcidBaseCatalog/AcidBaseCatalogParams.cpp.o CMakeFiles/MolStandardize.dir/AcidBaseCatalog/AcidBaseCatalogUtils.cpp.o CMakeFiles/MolStandardize.dir/TransformCatalog/TransformCatalogEntry.cpp.o CMakeFiles/MolStandardize.dir/TransformCatalog/TransformCatalogParams.cpp.o CMakeFiles/MolStandardize.dir/TransformCatalog/TransformCatalogUtils.cpp.o CMakeFiles/MolStandardize.dir/TautomerCatalog/TautomerCatalogEntry.cpp.o CMakeFiles/MolStandardize.dir/TautomerCatalog/TautomerCatalogParams.cpp.o CMakeFiles/MolStandardize.dir/TautomerCatalog/TautomerCatalogUtils.cpp.o ../../../lib/libRDKitChemReactions.so.1.2024.09.4 ../../../lib/libRDKitFilterCatalog.so.1.2024.09.4 ../../../lib/libRDKitCatalogs.so.1.2024.09.4 ../../../lib/libRDKitFingerprints.so.1.2024.09.4 ../../../lib/libRDKitSubgraphs.so.1.2024.09.4 ../../../lib/libRDKitFileParsers.so.1.2024.09.4 ../../../lib/libRDKitChemTransforms.so.1.2024.09.4 ../../../lib/libRDKitDepictor.so.1.2024.09.4 /usr/lib/aarch64-linux-gnu/libcoordgen.so ../../../lib/libRDKitMolAlign.so.1.2024.09.4 ../../../lib/libRDKitSmilesParse.so.1.2024.09.4 ../../../lib/libRDKitSubstructMatch.so.1.2024.09.4 ../../../lib/libRDKitMolTransforms.so.1.2024.09.4 ../../../lib/libRDKitEigenSolvers.so.1.2024.09.4 ../../../lib/libRDKitAlignment.so.1.2024.09.4 ../../../lib/libRDKitGenericGroups.so.1.2024.09.4 ../../../lib/libRDKitGraphMol.so.1.2024.09.4 ../../../lib/libRDKitRDGeometryLib.so.1.2024.09.4 ../../../lib/libRDKitDataStructs.so.1.2024.09.4 ../../../lib/libRDKitRDGeneral.so.1.2024.09.4 /usr/lib/aarch64-linux-gnu/libboost_system.so.1.83.0 /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-202409.4/obj-aarch64-linux-gnu/Code/GraphMol/MolStandardize && /usr/bin/cmake -E cmake_symlink_library ../../../lib/libRDKitMolStandardize.so.1.2024.09.4 ../../../lib/libRDKitMolStandardize.so.1 ../../../lib/libRDKitMolStandardize.so -make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu' -[ 85%] Built target MolStandardize -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-202409.4/obj-aarch64-linux-gnu' -cd 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-Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/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-202409.4/Code/GraphMol/TautomerQuery/TautomerQuery.cpp -[ 86%] Building CXX object Code/GraphMol/Wrap/CMakeFiles/rdmolfiles.dir/TDTMolSupplier.cpp.o -cd /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/GraphMol/Wrap && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_NUMPY_DYN_LINK -DBOOST_NUMPY_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD 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CMakeFiles/rdmolfiles.dir/TDTMolSupplier.cpp.o.d -o CMakeFiles/rdmolfiles.dir/TDTMolSupplier.cpp.o -c /build/reproducible-path/rdkit-202409.4/Code/GraphMol/Wrap/TDTMolSupplier.cpp -[ 86%] Building CXX object Code/GraphMol/MolDraw2D/CMakeFiles/MolDraw2D.dir/DrawTextNotFT.cpp.o -cd /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/GraphMol/MolDraw2D && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DMolDraw2D_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_MOLDRAW2D_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_CAIRO_SUPPORT -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_FREETYPE_SUPPORT -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.4/External -I/usr/include/freetype2 -I/usr/include/python3.13 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202409.4/Code -I/build/reproducible-path/rdkit-202409.4/External/boost-numeric-bindings -isystem /usr/include/eigen3 -isystem /usr/include/cairo -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-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-202409.4/Code/GraphMol/MolDraw2D/DrawTextNotFT.cpp -[ 86%] Building CXX object Code/GraphMol/Wrap/CMakeFiles/rdmolfiles.dir/SmilesMolSupplier.cpp.o -cd /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/GraphMol/Wrap && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_NUMPY_DYN_LINK -DBOOST_NUMPY_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -Drdmolfiles_EXPORTS -I/build/reproducible-path/rdkit-202409.4/External -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202409.4/Code -I/build/reproducible-path/rdkit-202409.4/External/boost-numeric-bindings -isystem /usr/include/python3.13 -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-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/SmilesMolSupplier.cpp.o -MF CMakeFiles/rdmolfiles.dir/SmilesMolSupplier.cpp.o.d -o CMakeFiles/rdmolfiles.dir/SmilesMolSupplier.cpp.o -c /build/reproducible-path/rdkit-202409.4/Code/GraphMol/Wrap/SmilesMolSupplier.cpp -In file included from /usr/include/c++/14/vector:62, - from /build/reproducible-path/rdkit-202409.4/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]', - inlined from '_OI std::__copy_move_a2(_II, _II, _OI) [with bool _IsMove = false; _II = int*; _OI = int*]' at /usr/include/c++/14/bits/stl_algobase.h:521:30, - inlined from '_OI std::__copy_move_a1(_II, _II, _OI) [with bool _IsMove = false; _II = int*; _OI = int*]' at /usr/include/c++/14/bits/stl_algobase.h:548:42, - inlined from '_OI std::__copy_move_a(_II, _II, _OI) [with bool _IsMove = false; _II = __gnu_cxx::__normal_iterator >; _OI = int*]' at /usr/include/c++/14/bits/stl_algobase.h:555:31, - inlined from '_OI std::copy(_II, _II, _OI) [with _II = __gnu_cxx::__normal_iterator >; _OI = int*]' at /usr/include/c++/14/bits/stl_algobase.h:651:7, - inlined from 'static _ForwardIterator std::__uninitialized_copy::__uninit_copy(_InputIterator, _InputIterator, _ForwardIterator) [with _InputIterator = __gnu_cxx::__normal_iterator >; _ForwardIterator = int*]' at /usr/include/c++/14/bits/stl_uninitialized.h:147:27, - inlined from '_ForwardIterator std::uninitialized_copy(_InputIterator, _InputIterator, _ForwardIterator) [with _InputIterator = __gnu_cxx::__normal_iterator >; _ForwardIterator = int*]' at /usr/include/c++/14/bits/stl_uninitialized.h:185:15, - inlined from '_ForwardIterator std::__uninitialized_copy_a(_InputIterator, _InputIterator, _ForwardIterator, allocator<_Tp>&) [with _InputIterator = __gnu_cxx::__normal_iterator >; _ForwardIterator = int*; _Tp = int]' at /usr/include/c++/14/bits/stl_uninitialized.h:373:37, - inlined from 'void std::vector<_Tp, _Alloc>::_M_range_insert(iterator, _ForwardIterator, _ForwardIterator, std::forward_iterator_tag) [with _ForwardIterator = __gnu_cxx::__normal_iterator >; _Tp = int; _Alloc = std::allocator]' at /usr/include/c++/14/bits/vector.tcc:1022:38, - inlined from 'std::vector<_Tp, _Alloc>::iterator std::vector<_Tp, _Alloc>::insert(const_iterator, _InputIterator, _InputIterator) [with _InputIterator = __gnu_cxx::__normal_iterator >; = void; _Tp = int; _Alloc = std::allocator]' at /usr/include/c++/14/bits/stl_vector.h:1488:19, - inlined from 'void RDKit::MolDraw2D_detail::DrawMolMCHLasso::extractAtomColourLists(std::vector&, std::vector >&, std::vector >&) const' at /build/reproducible-path/rdkit-202409.4/Code/GraphMol/MolDraw2D/DrawMolMCHLasso.cpp:115:32: -/usr/include/c++/14/bits/stl_algobase.h:452:30: warning: 'void* __builtin_memmove(void*, const void*, long unsigned int)' writing between 5 and 9223372036854775804 bytes into a region of size 0 overflows the destination [-Wstringop-overflow=] - 452 | __builtin_memmove(__result, __first, sizeof(_Tp) * _Num); - | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -In file included from /usr/include/aarch64-linux-gnu/c++/14/bits/c++allocator.h:33, - from /usr/include/c++/14/bits/allocator.h:46, - from /usr/include/c++/14/vector:63: -In member function '_Tp* std::__new_allocator<_Tp>::allocate(size_type, const void*) [with _Tp = int]', - inlined from 'static _Tp* std::allocator_traits >::allocate(allocator_type&, size_type) [with _Tp = int]' at /usr/include/c++/14/bits/alloc_traits.h:515:28, - inlined from 'std::_Vector_base<_Tp, _Alloc>::pointer std::_Vector_base<_Tp, _Alloc>::_M_allocate(std::size_t) [with _Tp = int; _Alloc = std::allocator]' at /usr/include/c++/14/bits/stl_vector.h:380:33, - inlined from 'void std::vector<_Tp, _Alloc>::_M_range_insert(iterator, _ForwardIterator, _ForwardIterator, std::forward_iterator_tag) [with _ForwardIterator = __gnu_cxx::__normal_iterator >; _Tp = int; _Alloc = std::allocator]' at /usr/include/c++/14/bits/vector.tcc:1013:40, - inlined from 'std::vector<_Tp, _Alloc>::iterator std::vector<_Tp, _Alloc>::insert(const_iterator, _InputIterator, _InputIterator) [with _InputIterator = __gnu_cxx::__normal_iterator >; = void; _Tp = int; _Alloc = std::allocator]' at /usr/include/c++/14/bits/stl_vector.h:1488:19, - inlined from 'void RDKit::MolDraw2D_detail::DrawMolMCHLasso::extractAtomColourLists(std::vector&, std::vector >&, std::vector >&) const' at /build/reproducible-path/rdkit-202409.4/Code/GraphMol/MolDraw2D/DrawMolMCHLasso.cpp:115:32: -/usr/include/c++/14/bits/new_allocator.h:151:55: note: at offset [-9223372036854775808, -1] into destination object of size [4, 9223372036854775804] allocated by 'operator new' - 151 | return static_cast<_Tp*>(_GLIBCXX_OPERATOR_NEW(__n * sizeof(_Tp))); - | ^ -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-202409.4/Code/GraphMol/MolDraw2D/DrawText.h:19, - from /build/reproducible-path/rdkit-202409.4/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-202409.4/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) - | ^~~~~~~~~ -[ 86%] Building CXX object Code/GraphMol/CIPLabeler/CMakeFiles/testCIPLabeler.dir/CIPLabeler.cpp.o -cd /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/GraphMol/CIPLabeler && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_CIPLABELER_BUILD -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.4/External -I/usr/include/python3.13 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202409.4/Code -I/build/reproducible-path/rdkit-202409.4/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=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-202409.4/Code/GraphMol/CIPLabeler/CIPLabeler.cpp -[ 86%] Building CXX object Code/GraphMol/Wrap/CMakeFiles/rdchem.dir/Table.cpp.o -cd 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-I/usr/include/python3.13 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202409.4/Code -I/build/reproducible-path/rdkit-202409.4/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=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-202409.4/Code/GraphMol/CIPLabeler/Mancude.cpp -[ 87%] Linking CXX shared library ../../../lib/libRDKitTautomerQuery.so -cd /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/GraphMol/TautomerQuery && /usr/bin/cmake 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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 -MD -MT Code/GraphMol/MolStandardize/CMakeFiles/molStandardizeTest.dir/test1.cpp.o -MF CMakeFiles/molStandardizeTest.dir/test1.cpp.o.d -o CMakeFiles/molStandardizeTest.dir/test1.cpp.o -c /build/reproducible-path/rdkit-202409.4/Code/GraphMol/MolStandardize/test1.cpp -[ 87%] Building CXX object Code/GraphMol/MolDraw2D/CMakeFiles/MolDraw2D.dir/DrawTextFTJS.cpp.o -cd /build/reproducible-path/rdkit-202409.4/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 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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 -MD -MT Code/GraphMol/CIPLabeler/CMakeFiles/testCIPLabeler.dir/configs/Configuration.cpp.o -MF CMakeFiles/testCIPLabeler.dir/configs/Configuration.cpp.o.d -o CMakeFiles/testCIPLabeler.dir/configs/Configuration.cpp.o -c /build/reproducible-path/rdkit-202409.4/Code/GraphMol/CIPLabeler/configs/Configuration.cpp -[ 88%] Linking CXX executable molNormalizeTest -cd /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/GraphMol/MolStandardize && /usr/bin/cmake -E cmake_link_script CMakeFiles/molNormalizeTest.dir/link.txt --verbose=1 -/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security 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atomprops) { + | ^ +[ 84%] Building CXX object Code/GraphMol/Deprotect/Wrap/CMakeFiles/rdDeprotect.dir/DeprotectWrap.cpp.o +cd /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/GraphMol/Deprotect/Wrap && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_NUMPY_DYN_LINK -DBOOST_NUMPY_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DEPROTECT_BUILD -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DrdDeprotect_EXPORTS -I/build/reproducible-path/rdkit-202409.4/External -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202409.4/Code 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-I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202409.4/Code -I/build/reproducible-path/rdkit-202409.4/External/boost-numeric-bindings -isystem /usr/include/python3.13 -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-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-202409.4/Code/GraphMol/Wrap/MultithreadedSDMolSupplier.cpp +[ 84%] Linking CXX executable molNormalizeTest +cd /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/GraphMol/MolStandardize && /usr/bin/cmake -E cmake_link_script CMakeFiles/molNormalizeTest.dir/link.txt --verbose=1 +/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/molNormalizeTest.dir/link.d CMakeFiles/molNormalizeTest.dir/testNormalize.cpp.o -o molNormalizeTest ../../../lib/libRDKitMolStandardize.so.1.2024.09.4 ../../../lib/libRDKitChemReactions.so.1.2024.09.4 ../../../lib/libRDKitFilterCatalog.so.1.2024.09.4 ../../../lib/libRDKitCatalogs.so.1.2024.09.4 ../../../lib/libRDKitFingerprints.so.1.2024.09.4 ../../../lib/libRDKitSubgraphs.so.1.2024.09.4 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-I/build/reproducible-path/rdkit-202409.4/External -I/usr/include/python3.13 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202409.4/Code -I/build/reproducible-path/rdkit-202409.4/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/GraphMol/MolStandardize/CMakeFiles/molTautomerTest.dir/testTautomer.cpp.o -MF CMakeFiles/molTautomerTest.dir/testTautomer.cpp.o.d -o CMakeFiles/molTautomerTest.dir/testTautomer.cpp.o -c /build/reproducible-path/rdkit-202409.4/Code/GraphMol/MolStandardize/testTautomer.cpp -[ 89%] Linking CXX executable molStandardizeTest -cd 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../../../lib/libRDKitEigenSolvers.so.1.2024.09.4 ../../../lib/libRDKitAlignment.so.1.2024.09.4 ../../../lib/libRDKitSubstructMatch.so.1.2024.09.4 ../../../lib/libRDKitGenericGroups.so.1.2024.09.4 ../../../lib/libRDKitSmilesParse.so.1.2024.09.4 ../../../lib/libRDKitGraphMol.so.1.2024.09.4 ../../../lib/libRDKitRDGeometryLib.so.1.2024.09.4 ../../../lib/libRDKitDataStructs.so.1.2024.09.4 ../../../lib/libRDKitRDGeneral.so.1.2024.09.4 /usr/lib/aarch64-linux-gnu/libboost_system.so.1.83.0 /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-202409.4/obj-aarch64-linux-gnu' -[ 89%] Built target molStandardizeTest +[ 84%] Built target deprotectTest make -f Code/GraphMol/MolStandardize/CMakeFiles/molStandardizeSmallTest.dir/build.make Code/GraphMol/MolStandardize/CMakeFiles/molStandardizeSmallTest.dir/depend make[4]: Entering directory 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Code/GraphMol/MolStandardize/CMakeFiles/molStandardizeSmallTest.dir/test2.cpp.o +[ 85%] Linking CXX shared library ../../../lib/libRDKitO3AAlign.so +cd /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/GraphMol/MolAlign && /usr/bin/cmake -E cmake_link_script CMakeFiles/O3AAlign.dir/link.txt --verbose=1 +[ 85%] Building CXX object Code/GraphMol/MolStandardize/CMakeFiles/molStandardizeSmallTest.dir/test2.cpp.o cd /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/GraphMol/MolStandardize && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.4/External -I/usr/include/python3.13 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202409.4/Code -I/build/reproducible-path/rdkit-202409.4/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/GraphMol/MolStandardize/CMakeFiles/molStandardizeSmallTest.dir/test2.cpp.o -MF CMakeFiles/molStandardizeSmallTest.dir/test2.cpp.o.d -o CMakeFiles/molStandardizeSmallTest.dir/test2.cpp.o -c /build/reproducible-path/rdkit-202409.4/Code/GraphMol/MolStandardize/test2.cpp -[ 89%] 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 -MD -MT Code/GraphMol/CIPLabeler/CMakeFiles/testCIPLabeler.dir/configs/Tetrahedral.cpp.o -MF CMakeFiles/testCIPLabeler.dir/configs/Tetrahedral.cpp.o.d -o CMakeFiles/testCIPLabeler.dir/configs/Tetrahedral.cpp.o -c /build/reproducible-path/rdkit-202409.4/Code/GraphMol/CIPLabeler/configs/Tetrahedral.cpp -[ 89%] Building CXX object Code/GraphMol/CIPLabeler/CMakeFiles/testCIPLabeler.dir/configs/AtropisomerBond.cpp.o -cd /build/reproducible-path/rdkit-202409.4/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 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-isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=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-202409.4/Code/GraphMol/CIPLabeler/rules/Rule3.cpp -[ 91%] Linking CXX executable molValidateTest -cd /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/GraphMol/MolStandardize && /usr/bin/cmake -E cmake_link_script CMakeFiles/molValidateTest.dir/link.txt --verbose=1 -/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.4=. -fstack-protector-strong -fstack-clash-protection 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-Wextra -fPIC -std=gnu++17 -MD -MT Code/GraphMol/CIPLabeler/CMakeFiles/testCIPLabeler.dir/rules/Rule4a.cpp.o -MF CMakeFiles/testCIPLabeler.dir/rules/Rule4a.cpp.o.d -o CMakeFiles/testCIPLabeler.dir/rules/Rule4a.cpp.o -c /build/reproducible-path/rdkit-202409.4/Code/GraphMol/CIPLabeler/rules/Rule4a.cpp -[ 91%] Linking CXX executable molChargeTest -cd /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/GraphMol/MolStandardize && /usr/bin/cmake -E cmake_link_script CMakeFiles/molChargeTest.dir/link.txt --verbose=1 -[ 91%] Building CXX object Code/GraphMol/CIPLabeler/CMakeFiles/testCIPLabeler.dir/rules/Rule4b.cpp.o -cd /build/reproducible-path/rdkit-202409.4/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 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/usr/lib/aarch64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl +[ 86%] Linking CXX executable molStandardizeSmallTest +cd /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/GraphMol/MolStandardize && /usr/bin/cmake -E cmake_link_script CMakeFiles/molStandardizeSmallTest.dir/link.txt --verbose=1 +/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/molStandardizeSmallTest.dir/link.d CMakeFiles/molStandardizeSmallTest.dir/test2.cpp.o -o molStandardizeSmallTest ../../../lib/libRDKitMolStandardize.so.1.2024.09.4 ../../../lib/libRDKitChemReactions.so.1.2024.09.4 ../../../lib/libRDKitFilterCatalog.so.1.2024.09.4 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/usr/lib/aarch64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu' -[ 92%] Built target rdChemReactions -make -f Code/GraphMol/TautomerQuery/CMakeFiles/tautomerQueryTestCatch.dir/build.make Code/GraphMol/TautomerQuery/CMakeFiles/tautomerQueryTestCatch.dir/depend +[ 86%] Built target molStandardizeSmallTest +make -f Code/GraphMol/MolEnumerator/CMakeFiles/testMolEnumerator.dir/build.make Code/GraphMol/MolEnumerator/CMakeFiles/testMolEnumerator.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu' -cd /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202409.4 /build/reproducible-path/rdkit-202409.4/Code/GraphMol/TautomerQuery /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu 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-ffile-prefix-map=/build/reproducible-path/rdkit-202409.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/MolStandardize/Wrap/CMakeFiles/rdMolStandardize.dir/Validate.cpp.o -MF CMakeFiles/rdMolStandardize.dir/Validate.cpp.o.d -o CMakeFiles/rdMolStandardize.dir/Validate.cpp.o -c /build/reproducible-path/rdkit-202409.4/Code/GraphMol/MolStandardize/Wrap/Validate.cpp -[ 92%] Linking CXX shared library ../../../lib/libRDKitScaffoldNetwork.so -cd /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/GraphMol/ScaffoldNetwork && /usr/bin/cmake -E cmake_link_script CMakeFiles/ScaffoldNetwork.dir/link.txt --verbose=1 -/usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.4=. -fstack-protector-strong 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CMakeFiles/rdmolfiles.dir/SmilesMolSupplier.cpp.o.d -o CMakeFiles/rdmolfiles.dir/SmilesMolSupplier.cpp.o -c /build/reproducible-path/rdkit-202409.4/Code/GraphMol/Wrap/SmilesMolSupplier.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-202409.4/Code/RDGeneral/Invariant.h:17, + from /build/reproducible-path/rdkit-202409.4/Code/Numerics/Matrix.h:14, + from /build/reproducible-path/rdkit-202409.4/Code/Numerics/SquareMatrix.h:14, + from /build/reproducible-path/rdkit-202409.4/Code/Geometry/Transform3D.h:16, + from /build/reproducible-path/rdkit-202409.4/Code/GraphMol/MolAlign/AlignMolecules.h:14, + from /build/reproducible-path/rdkit-202409.4/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-202409.4/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) + | ^~~~~~~~~ +[ 89%] Linking CXX executable molStandardizePipelineTest +cd /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/GraphMol/MolStandardize && /usr/bin/cmake -E cmake_link_script CMakeFiles/molStandardizePipelineTest.dir/link.txt --verbose=1 +/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/molStandardizePipelineTest.dir/link.d CMakeFiles/molStandardizePipelineTest.dir/testPipeline.cpp.o -o molStandardizePipelineTest ../../RDGeneral/librdkitCatch.a ../../../lib/libRDKitMolStandardize.so.1.2024.09.4 /usr/lib/libCatch2.a ../../../lib/libRDKitChemReactions.so.1.2024.09.4 ../../../lib/libRDKitFilterCatalog.so.1.2024.09.4 ../../../lib/libRDKitCatalogs.so.1.2024.09.4 ../../../lib/libRDKitFingerprints.so.1.2024.09.4 ../../../lib/libRDKitSubgraphs.so.1.2024.09.4 ../../../lib/libRDKitFileParsers.so.1.2024.09.4 /usr/lib/aarch64-linux-gnu/libmaeparser.so ../../../lib/libRDKitChemTransforms.so.1.2024.09.4 ../../../lib/libRDKitDepictor.so.1.2024.09.4 /usr/lib/aarch64-linux-gnu/libcoordgen.so ../../../lib/libRDKitMolAlign.so.1.2024.09.4 ../../../lib/libRDKitMolTransforms.so.1.2024.09.4 ../../../lib/libRDKitEigenSolvers.so.1.2024.09.4 ../../../lib/libRDKitAlignment.so.1.2024.09.4 ../../../lib/libRDKitSmilesParse.so.1.2024.09.4 ../../../lib/libRDKitSubstructMatch.so.1.2024.09.4 ../../../lib/libRDKitGenericGroups.so.1.2024.09.4 ../../../lib/libRDKitGraphMol.so.1.2024.09.4 ../../../lib/libRDKitRDGeometryLib.so.1.2024.09.4 ../../../lib/libRDKitDataStructs.so.1.2024.09.4 ../../../lib/libRDKitRDGeneral.so.1.2024.09.4 /usr/lib/aarch64-linux-gnu/libboost_system.so.1.83.0 /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-202409.4/obj-aarch64-linux-gnu' -[ 92%] Built target ScaffoldNetwork +[ 89%] Built target molStandardizePipelineTest make -f Code/GraphMol/MolDraw2D/CMakeFiles/moldraw2DTestCatch.dir/build.make Code/GraphMol/MolDraw2D/CMakeFiles/moldraw2DTestCatch.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu' cd /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202409.4 /build/reproducible-path/rdkit-202409.4/Code/GraphMol/MolDraw2D /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/GraphMol/MolDraw2D /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/GraphMol/MolDraw2D/CMakeFiles/moldraw2DTestCatch.dir/DependInfo.cmake "--color=" -[ 92%] Linking CXX executable tautomerQueryTestCatch make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu' make -f Code/GraphMol/MolDraw2D/CMakeFiles/moldraw2DTestCatch.dir/build.make Code/GraphMol/MolDraw2D/CMakeFiles/moldraw2DTestCatch.dir/build -cd /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/GraphMol/TautomerQuery && /usr/bin/cmake -E cmake_link_script CMakeFiles/tautomerQueryTestCatch.dir/link.txt --verbose=1 make[4]: Entering directory '/build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu' -[ 92%] Building CXX object Code/GraphMol/MolDraw2D/CMakeFiles/moldraw2DTestCatch.dir/catch_tests.cpp.o +[ 89%] Building CXX object Code/GraphMol/MolDraw2D/CMakeFiles/moldraw2DTestCatch.dir/catch_tests.cpp.o cd /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/GraphMol/MolDraw2D && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_CAIRO_SUPPORT -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_FREETYPE_SUPPORT -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.4/External -I/usr/include/python3.13 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202409.4/Code -I/usr/include/freetype2 -I/build/reproducible-path/rdkit-202409.4/External/boost-numeric-bindings -isystem /usr/include/eigen3 -isystem /usr/include/cairo -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/GraphMol/MolDraw2D/CMakeFiles/moldraw2DTestCatch.dir/catch_tests.cpp.o -MF CMakeFiles/moldraw2DTestCatch.dir/catch_tests.cpp.o.d -o CMakeFiles/moldraw2DTestCatch.dir/catch_tests.cpp.o -c 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../../../lib/libRDKitFileParsers.so.1.2024.09.4 /usr/lib/aarch64-linux-gnu/libmaeparser.so ../../../lib/libRDKitChemTransforms.so.1.2024.09.4 ../../../lib/libRDKitDepictor.so.1.2024.09.4 /usr/lib/aarch64-linux-gnu/libcoordgen.so ../../../lib/libRDKitMolAlign.so.1.2024.09.4 ../../../lib/libRDKitMolTransforms.so.1.2024.09.4 ../../../lib/libRDKitEigenSolvers.so.1.2024.09.4 ../../../lib/libRDKitAlignment.so.1.2024.09.4 ../../../lib/libRDKitSmilesParse.so.1.2024.09.4 ../../../lib/libRDKitSubstructMatch.so.1.2024.09.4 ../../../lib/libRDKitGenericGroups.so.1.2024.09.4 ../../../lib/libRDKitGraphMol.so.1.2024.09.4 ../../../lib/libRDKitRDGeometryLib.so.1.2024.09.4 ../../../lib/libRDKitDataStructs.so.1.2024.09.4 ../../../lib/libRDKitRDGeneral.so.1.2024.09.4 /usr/lib/aarch64-linux-gnu/libboost_system.so.1.83.0 /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 shared module ../../../../rdkit/Chem/rdMolEnumerator.so +cd /build/reproducible-path/rdkit-202409.4/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-202409.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=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.1.2024.09.4 ../../../../lib/libRDKitRDBoost.so.1.2024.09.4 ../../../../lib/libRDKitChemReactions.so.1.2024.09.4 ../../../../lib/libRDKitFileParsers.so.1.2024.09.4 /usr/lib/aarch64-linux-gnu/libmaeparser.so ../../../../lib/libRDKitFilterCatalog.so.1.2024.09.4 ../../../../lib/libRDKitCatalogs.so.1.2024.09.4 ../../../../lib/libRDKitFingerprints.so.1.2024.09.4 ../../../../lib/libRDKitSubgraphs.so.1.2024.09.4 ../../../../lib/libRDKitChemTransforms.so.1.2024.09.4 ../../../../lib/libRDKitDepictor.so.1.2024.09.4 /usr/lib/aarch64-linux-gnu/libcoordgen.so ../../../../lib/libRDKitMolAlign.so.1.2024.09.4 ../../../../lib/libRDKitMolTransforms.so.1.2024.09.4 ../../../../lib/libRDKitEigenSolvers.so.1.2024.09.4 ../../../../lib/libRDKitAlignment.so.1.2024.09.4 ../../../../lib/libRDKitSmilesParse.so.1.2024.09.4 ../../../../lib/libRDKitSubstructMatch.so.1.2024.09.4 ../../../../lib/libRDKitGenericGroups.so.1.2024.09.4 ../../../../lib/libRDKitGraphMol.so.1.2024.09.4 ../../../../lib/libRDKitRDGeometryLib.so.1.2024.09.4 ../../../../lib/libRDKitDataStructs.so.1.2024.09.4 /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.1.2024.09.4 /usr/lib/aarch64-linux-gnu/libboost_system.so.1.83.0 /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-202409.4/obj-aarch64-linux-gnu' -[ 92%] Built target tautomerQueryTestCatch +[ 90%] Built target rdMolEnumerator make -f Code/GraphMol/MolDraw2D/CMakeFiles/moldraw2DRxnTest1.dir/build.make Code/GraphMol/MolDraw2D/CMakeFiles/moldraw2DRxnTest1.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu' cd /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202409.4 /build/reproducible-path/rdkit-202409.4/Code/GraphMol/MolDraw2D /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/GraphMol/MolDraw2D /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/GraphMol/MolDraw2D/CMakeFiles/moldraw2DRxnTest1.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu' make -f Code/GraphMol/MolDraw2D/CMakeFiles/moldraw2DRxnTest1.dir/build.make Code/GraphMol/MolDraw2D/CMakeFiles/moldraw2DRxnTest1.dir/build make[4]: Entering directory '/build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu' -[ 92%] Building CXX object Code/GraphMol/MolDraw2D/CMakeFiles/moldraw2DRxnTest1.dir/rxn_test1.cpp.o +[ 90%] Building CXX object Code/GraphMol/MolDraw2D/CMakeFiles/moldraw2DRxnTest1.dir/rxn_test1.cpp.o cd /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/GraphMol/MolDraw2D && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_CAIRO_SUPPORT -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_FREETYPE_SUPPORT -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.4/External -I/usr/include/freetype2 -I/usr/include/python3.13 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202409.4/Code -I/build/reproducible-path/rdkit-202409.4/External/boost-numeric-bindings -isystem /usr/include/eigen3 -isystem /usr/include/cairo -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/GraphMol/MolDraw2D/CMakeFiles/moldraw2DRxnTest1.dir/rxn_test1.cpp.o -MF CMakeFiles/moldraw2DRxnTest1.dir/rxn_test1.cpp.o.d -o CMakeFiles/moldraw2DRxnTest1.dir/rxn_test1.cpp.o -c /build/reproducible-path/rdkit-202409.4/Code/GraphMol/MolDraw2D/rxn_test1.cpp +[ 90%] Linking CXX shared library ../../../lib/libRDKitTautomerQuery.so +cd /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/GraphMol/TautomerQuery && /usr/bin/cmake -E cmake_link_script CMakeFiles/TautomerQuery.dir/link.txt --verbose=1 +/usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,--dependency-file=CMakeFiles/TautomerQuery.dir/link.d -Wl,-z,relro -Wl,-z,now -shared -Wl,-soname,libRDKitTautomerQuery.so.1 -o ../../../lib/libRDKitTautomerQuery.so.1.2024.09.4 CMakeFiles/TautomerQuery.dir/TautomerQuery.cpp.o ../../../lib/libRDKitMolStandardize.so.1.2024.09.4 ../../../lib/libRDKitChemReactions.so.1.2024.09.4 ../../../lib/libRDKitFilterCatalog.so.1.2024.09.4 ../../../lib/libRDKitCatalogs.so.1.2024.09.4 ../../../lib/libRDKitFingerprints.so.1.2024.09.4 ../../../lib/libRDKitSubgraphs.so.1.2024.09.4 ../../../lib/libRDKitFileParsers.so.1.2024.09.4 /usr/lib/aarch64-linux-gnu/libmaeparser.so ../../../lib/libRDKitChemTransforms.so.1.2024.09.4 ../../../lib/libRDKitDepictor.so.1.2024.09.4 /usr/lib/aarch64-linux-gnu/libcoordgen.so ../../../lib/libRDKitMolAlign.so.1.2024.09.4 ../../../lib/libRDKitMolTransforms.so.1.2024.09.4 ../../../lib/libRDKitEigenSolvers.so.1.2024.09.4 ../../../lib/libRDKitAlignment.so.1.2024.09.4 ../../../lib/libRDKitSmilesParse.so.1.2024.09.4 ../../../lib/libRDKitSubstructMatch.so.1.2024.09.4 ../../../lib/libRDKitGenericGroups.so.1.2024.09.4 ../../../lib/libRDKitGraphMol.so.1.2024.09.4 ../../../lib/libRDKitRDGeometryLib.so.1.2024.09.4 ../../../lib/libRDKitDataStructs.so.1.2024.09.4 ../../../lib/libRDKitRDGeneral.so.1.2024.09.4 /usr/lib/aarch64-linux-gnu/libboost_system.so.1.83.0 /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-202409.4/obj-aarch64-linux-gnu/Code/GraphMol/TautomerQuery && /usr/bin/cmake -E cmake_symlink_library ../../../lib/libRDKitTautomerQuery.so.1.2024.09.4 ../../../lib/libRDKitTautomerQuery.so.1 ../../../lib/libRDKitTautomerQuery.so +make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu' +[ 90%] Built target TautomerQuery +[ 90%] Building CXX object Code/GraphMol/Wrap/CMakeFiles/rdchem.dir/Bond.cpp.o +cd 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../../../lib/libRDKitChemTransforms.so.1.2024.09.4 ../../../lib/libRDKitDepictor.so.1.2024.09.4 /usr/lib/aarch64-linux-gnu/libcoordgen.so ../../../lib/libRDKitMolAlign.so.1.2024.09.4 ../../../lib/libRDKitMolTransforms.so.1.2024.09.4 ../../../lib/libRDKitEigenSolvers.so.1.2024.09.4 ../../../lib/libRDKitAlignment.so.1.2024.09.4 ../../../lib/libRDKitSmilesParse.so.1.2024.09.4 ../../../lib/libRDKitSubstructMatch.so.1.2024.09.4 ../../../lib/libRDKitGenericGroups.so.1.2024.09.4 ../../../lib/libRDKitGraphMol.so.1.2024.09.4 ../../../lib/libRDKitRDGeometryLib.so.1.2024.09.4 ../../../lib/libRDKitDataStructs.so.1.2024.09.4 ../../../lib/libRDKitRDGeneral.so.1.2024.09.4 /usr/lib/aarch64-linux-gnu/libboost_system.so.1.83.0 /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-202409.4/obj-aarch64-linux-gnu' -[ 95%] Built target testScaffoldNetwork +[ 95%] Built target tautomerQueryTestCatch make -f Code/GraphMol/GeneralizedSubstruct/CMakeFiles/generalizedSubstructCatch.dir/build.make Code/GraphMol/GeneralizedSubstruct/CMakeFiles/generalizedSubstructCatch.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu' cd /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202409.4 /build/reproducible-path/rdkit-202409.4/Code/GraphMol/GeneralizedSubstruct /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/GraphMol/GeneralizedSubstruct /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/GraphMol/GeneralizedSubstruct/CMakeFiles/generalizedSubstructCatch.dir/DependInfo.cmake "--color=" @@ -6955,11 +6945,17 @@ make[4]: Entering directory '/build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu' [ 95%] Building CXX object Code/GraphMol/GeneralizedSubstruct/CMakeFiles/generalizedSubstructCatch.dir/catch_tests.cpp.o cd /build/reproducible-path/rdkit-202409.4/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_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.4/External -I/usr/include/python3.13 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202409.4/Code -I/build/reproducible-path/rdkit-202409.4/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=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/GeneralizedSubstruct/CMakeFiles/generalizedSubstructCatch.dir/catch_tests.cpp.o -MF CMakeFiles/generalizedSubstructCatch.dir/catch_tests.cpp.o.d -o CMakeFiles/generalizedSubstructCatch.dir/catch_tests.cpp.o -c /build/reproducible-path/rdkit-202409.4/Code/GraphMol/GeneralizedSubstruct/catch_tests.cpp -[ 95%] Linking CXX executable moldraw2DTest1 -cd /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/GraphMol/MolDraw2D && /usr/bin/cmake -E cmake_link_script CMakeFiles/moldraw2DTest1.dir/link.txt --verbose=1 -/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security 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../../../lib/libRDKitSubstructMatch.so.1.2024.09.4 ../../../lib/libRDKitGenericGroups.so.1.2024.09.4 ../../../lib/libRDKitSubgraphs.so.1.2024.09.4 ../../../lib/libRDKitGraphMol.so.1.2024.09.4 ../../../lib/libRDKitRDGeometryLib.so.1.2024.09.4 ../../../lib/libRDKitDataStructs.so.1.2024.09.4 ../../../lib/libRDKitEigenSolvers.so.1.2024.09.4 ../../../lib/libRDKitRDGeneral.so.1.2024.09.4 /usr/lib/aarch64-linux-gnu/libboost_system.so.1.83.0 /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 +[ 95%] Building CXX object Code/GraphMol/CIPLabeler/CMakeFiles/testCIPLabeler.dir/rules/Rule4b.cpp.o +cd /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/GraphMol/CIPLabeler && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK 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Code/GraphMol/CIPLabeler/CMakeFiles/testCIPLabeler.dir/rules/Rule4b.cpp.o -MF CMakeFiles/testCIPLabeler.dir/rules/Rule4b.cpp.o.d -o CMakeFiles/testCIPLabeler.dir/rules/Rule4b.cpp.o -c /build/reproducible-path/rdkit-202409.4/Code/GraphMol/CIPLabeler/rules/Rule4b.cpp +[ 95%] Building CXX object Code/GraphMol/Wrap/CMakeFiles/rdmolfiles.dir/PDBWriter.cpp.o +cd /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/GraphMol/Wrap && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_NUMPY_DYN_LINK -DBOOST_NUMPY_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -Drdmolfiles_EXPORTS -I/build/reproducible-path/rdkit-202409.4/External -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202409.4/Code -I/build/reproducible-path/rdkit-202409.4/External/boost-numeric-bindings -isystem /usr/include/python3.13 -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/Wrap/CMakeFiles/rdmolfiles.dir/PDBWriter.cpp.o -MF CMakeFiles/rdmolfiles.dir/PDBWriter.cpp.o.d -o CMakeFiles/rdmolfiles.dir/PDBWriter.cpp.o -c /build/reproducible-path/rdkit-202409.4/Code/GraphMol/Wrap/PDBWriter.cpp +[ 95%] Building CXX object Code/GraphMol/Wrap/CMakeFiles/rdchem.dir/MonomerInfo.cpp.o +cd /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/GraphMol/Wrap && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_NUMPY_DYN_LINK -DBOOST_NUMPY_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -Drdchem_EXPORTS -I/build/reproducible-path/rdkit-202409.4/External -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202409.4/Code -I/build/reproducible-path/rdkit-202409.4/External/boost-numeric-bindings -isystem /usr/include/python3.13 -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/Wrap/CMakeFiles/rdchem.dir/MonomerInfo.cpp.o -MF CMakeFiles/rdchem.dir/MonomerInfo.cpp.o.d -o CMakeFiles/rdchem.dir/MonomerInfo.cpp.o -c /build/reproducible-path/rdkit-202409.4/Code/GraphMol/Wrap/MonomerInfo.cpp +[ 95%] Linking CXX shared module ../../../../rdkit/Chem/rdTautomerQuery.so +cd /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/GraphMol/TautomerQuery/Wrap && /usr/bin/cmake -E cmake_link_script CMakeFiles/rdTautomerQuery.dir/link.txt --verbose=1 +/usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=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.1.2024.09.4 ../../../../lib/libRDKitRDBoost.so.1.2024.09.4 ../../../../lib/libRDKitMolStandardize.so.1.2024.09.4 ../../../../lib/libRDKitChemReactions.so.1.2024.09.4 ../../../../lib/libRDKitFilterCatalog.so.1.2024.09.4 ../../../../lib/libRDKitCatalogs.so.1.2024.09.4 ../../../../lib/libRDKitFingerprints.so.1.2024.09.4 ../../../../lib/libRDKitSubgraphs.so.1.2024.09.4 ../../../../lib/libRDKitFileParsers.so.1.2024.09.4 /usr/lib/aarch64-linux-gnu/libmaeparser.so ../../../../lib/libRDKitChemTransforms.so.1.2024.09.4 ../../../../lib/libRDKitDepictor.so.1.2024.09.4 /usr/lib/aarch64-linux-gnu/libcoordgen.so ../../../../lib/libRDKitMolAlign.so.1.2024.09.4 ../../../../lib/libRDKitMolTransforms.so.1.2024.09.4 ../../../../lib/libRDKitEigenSolvers.so.1.2024.09.4 ../../../../lib/libRDKitAlignment.so.1.2024.09.4 ../../../../lib/libRDKitSmilesParse.so.1.2024.09.4 ../../../../lib/libRDKitSubstructMatch.so.1.2024.09.4 ../../../../lib/libRDKitGenericGroups.so.1.2024.09.4 ../../../../lib/libRDKitGraphMol.so.1.2024.09.4 ../../../../lib/libRDKitRDGeometryLib.so.1.2024.09.4 ../../../../lib/libRDKitDataStructs.so.1.2024.09.4 /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.1.2024.09.4 /usr/lib/aarch64-linux-gnu/libboost_system.so.1.83.0 /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-202409.4/obj-aarch64-linux-gnu' -[ 95%] Built target moldraw2DTest1 +[ 95%] Built target rdTautomerQuery 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-202409.4/obj-aarch64-linux-gnu' cd /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202409.4 /build/reproducible-path/rdkit-202409.4/Code/GraphMol/GeneralizedSubstruct/Wrap /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/GraphMol/GeneralizedSubstruct/Wrap /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/GraphMol/GeneralizedSubstruct/Wrap/CMakeFiles/rdGeneralizedSubstruct.dir/DependInfo.cmake "--color=" @@ -6968,78 +6964,50 @@ make[4]: Entering directory '/build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu' [ 95%] Building CXX object Code/GraphMol/GeneralizedSubstruct/Wrap/CMakeFiles/rdGeneralizedSubstruct.dir/rdGeneralizedSubstruct.cpp.o cd /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/GraphMol/GeneralizedSubstruct/Wrap && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_NUMPY_DYN_LINK -DBOOST_NUMPY_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DrdGeneralizedSubstruct_EXPORTS -I/build/reproducible-path/rdkit-202409.4/External -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202409.4/Code -I/build/reproducible-path/rdkit-202409.4/External/boost-numeric-bindings -isystem /usr/include/python3.13 -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/GeneralizedSubstruct/Wrap/CMakeFiles/rdGeneralizedSubstruct.dir/rdGeneralizedSubstruct.cpp.o -MF CMakeFiles/rdGeneralizedSubstruct.dir/rdGeneralizedSubstruct.cpp.o.d -o CMakeFiles/rdGeneralizedSubstruct.dir/rdGeneralizedSubstruct.cpp.o -c /build/reproducible-path/rdkit-202409.4/Code/GraphMol/GeneralizedSubstruct/Wrap/rdGeneralizedSubstruct.cpp -[ 96%] Linking CXX shared module ../../../../rdkit/Chem/Scaffolds/rdScaffoldNetwork.so -cd 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-ffile-prefix-map=/build/reproducible-path/rdkit-202409.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-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-202409.4/Code/PgSQL/rdkit/cache.c -[ 96%] Building C object Code/PgSQL/rdkit/CMakeFiles/rdkit.dir/guc.c.o -cd /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/PgSQL/rdkit && /usr/bin/cc -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKITVER=\"007600\" -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_CAIRO_SUPPORT -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_FREETYPE_SUPPORT -DRDK_BUILD_INCHI_SUPPORT -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_MOLINTERCHANGE_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_TOOLKIT_VERSION=\"2024.09.4\" -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -Drdkit_EXPORTS -I/build/reproducible-path/rdkit-202409.4/External -I/build/reproducible-path/rdkit-202409.4/Code -I/usr/include/postgresql -I/usr/include/postgresql/17/server -I/usr/include/python3.13 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202409.4/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-202409.4=. -fstack-protector-strong -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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-DRDK_USE_STRICT_ROTOR_DEFINITION -Drdkit_EXPORTS -I/build/reproducible-path/rdkit-202409.4/External -I/build/reproducible-path/rdkit-202409.4/Code -I/usr/include/postgresql -I/usr/include/postgresql/17/server -I/usr/include/python3.13 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202409.4/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-202409.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -fPIC -fPIC -MD -MT Code/PgSQL/rdkit/CMakeFiles/rdkit.dir/low_gist.c.o -MF CMakeFiles/rdkit.dir/low_gist.c.o.d -o CMakeFiles/rdkit.dir/low_gist.c.o -c /build/reproducible-path/rdkit-202409.4/Code/PgSQL/rdkit/low_gist.c -[ 96%] Building C object Code/PgSQL/rdkit/CMakeFiles/rdkit.dir/mol_op.c.o -cd /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/PgSQL/rdkit && /usr/bin/cc -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKITVER=\"007600\" -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_CAIRO_SUPPORT -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_FREETYPE_SUPPORT -DRDK_BUILD_INCHI_SUPPORT -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_MOLINTERCHANGE_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_TOOLKIT_VERSION=\"2024.09.4\" -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -Drdkit_EXPORTS -I/build/reproducible-path/rdkit-202409.4/External -I/build/reproducible-path/rdkit-202409.4/Code -I/usr/include/postgresql -I/usr/include/postgresql/17/server -I/usr/include/python3.13 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202409.4/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-202409.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -fPIC -fPIC -MD -MT Code/PgSQL/rdkit/CMakeFiles/rdkit.dir/mol_op.c.o -MF CMakeFiles/rdkit.dir/mol_op.c.o.d -o CMakeFiles/rdkit.dir/mol_op.c.o -c /build/reproducible-path/rdkit-202409.4/Code/PgSQL/rdkit/mol_op.c -[ 96%] Building C object Code/PgSQL/rdkit/CMakeFiles/rdkit.dir/rdkit_gist.c.o -cd /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/PgSQL/rdkit && /usr/bin/cc 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-isystem /usr/include/cairo -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/rdkit-202409.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-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-202409.4/Code/PgSQL/rdkit/rdkit_gist.c -[ 96%] Building C object Code/PgSQL/rdkit/CMakeFiles/rdkit.dir/bfp_gist.c.o -cd /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/PgSQL/rdkit && /usr/bin/cc -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKITVER=\"007600\" -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_CAIRO_SUPPORT -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_FREETYPE_SUPPORT -DRDK_BUILD_INCHI_SUPPORT -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_MOLINTERCHANGE_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_TOOLKIT_VERSION=\"2024.09.4\" -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -Drdkit_EXPORTS -I/build/reproducible-path/rdkit-202409.4/External -I/build/reproducible-path/rdkit-202409.4/Code -I/usr/include/postgresql -I/usr/include/postgresql/17/server -I/usr/include/python3.13 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202409.4/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-202409.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security 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-DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_TOOLKIT_VERSION=\"2024.09.4\" -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -Drdkit_EXPORTS -I/build/reproducible-path/rdkit-202409.4/External -I/build/reproducible-path/rdkit-202409.4/Code -I/usr/include/postgresql -I/usr/include/postgresql/17/server -I/usr/include/python3.13 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202409.4/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-202409.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-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-202409.4/Code/PgSQL/rdkit/bfp_gin.c -[ 97%] Building C object Code/PgSQL/rdkit/CMakeFiles/rdkit.dir/bitstring.c.o -cd /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/PgSQL/rdkit && /usr/bin/cc -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKITVER=\"007600\" -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_CAIRO_SUPPORT -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_FREETYPE_SUPPORT -DRDK_BUILD_INCHI_SUPPORT -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_MOLINTERCHANGE_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_TOOLKIT_VERSION=\"2024.09.4\" -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -Drdkit_EXPORTS -I/build/reproducible-path/rdkit-202409.4/External -I/build/reproducible-path/rdkit-202409.4/Code -I/usr/include/postgresql -I/usr/include/postgresql/17/server -I/usr/include/python3.13 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202409.4/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-202409.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -fPIC -fPIC -MD -MT Code/PgSQL/rdkit/CMakeFiles/rdkit.dir/bitstring.c.o -MF CMakeFiles/rdkit.dir/bitstring.c.o.d -o CMakeFiles/rdkit.dir/bitstring.c.o -c /build/reproducible-path/rdkit-202409.4/Code/PgSQL/rdkit/bitstring.c -[ 97%] Building C object Code/PgSQL/rdkit/CMakeFiles/rdkit.dir/rdkit_io.c.o -cd /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/PgSQL/rdkit && /usr/bin/cc -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKITVER=\"007600\" -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_CAIRO_SUPPORT -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_FREETYPE_SUPPORT -DRDK_BUILD_INCHI_SUPPORT -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_MOLINTERCHANGE_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_TOOLKIT_VERSION=\"2024.09.4\" -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -Drdkit_EXPORTS -I/build/reproducible-path/rdkit-202409.4/External -I/build/reproducible-path/rdkit-202409.4/Code -I/usr/include/postgresql -I/usr/include/postgresql/17/server -I/usr/include/python3.13 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202409.4/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-202409.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-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-202409.4/Code/PgSQL/rdkit/rdkit_io.c -[ 97%] Building C object Code/PgSQL/rdkit/CMakeFiles/rdkit.dir/rxn_op.c.o -cd /build/reproducible-path/rdkit-202409.4/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 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../../../lib/libRDKitRDGeneral.so.1.2024.09.4 -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 +[ 95%] Building CXX object Code/GraphMol/RGroupDecomposition/CMakeFiles/RGroupDecomposition.dir/RGroupCore.cpp.o +cd /build/reproducible-path/rdkit-202409.4/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_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-202409.4/External -I/usr/include/python3.13 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202409.4/Code -I/build/reproducible-path/rdkit-202409.4/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-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-202409.4/Code/GraphMol/RGroupDecomposition/RGroupCore.cpp +[ 95%] Linking CXX shared module ../../../../rdkit/Chem/rdGeneralizedSubstruct.so 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-I/build/reproducible-path/rdkit-202409.4/Code -I/usr/include/postgresql -I/usr/include/postgresql/17/server -I/usr/include/python3.13 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202409.4/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-202409.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-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-202409.4/Code/PgSQL/rdkit/bfp_gin.c +[ 97%] Building C object Code/PgSQL/rdkit/CMakeFiles/rdkit.dir/bitstring.c.o +cd /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/PgSQL/rdkit && /usr/bin/cc -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKITVER=\"007600\" -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_CAIRO_SUPPORT -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_FREETYPE_SUPPORT -DRDK_BUILD_INCHI_SUPPORT -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_MOLINTERCHANGE_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_TOOLKIT_VERSION=\"2024.09.4\" -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -Drdkit_EXPORTS -I/build/reproducible-path/rdkit-202409.4/External -I/build/reproducible-path/rdkit-202409.4/Code -I/usr/include/postgresql -I/usr/include/postgresql/17/server -I/usr/include/python3.13 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202409.4/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-202409.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -fPIC -fPIC -MD -MT Code/PgSQL/rdkit/CMakeFiles/rdkit.dir/bitstring.c.o -MF CMakeFiles/rdkit.dir/bitstring.c.o.d -o CMakeFiles/rdkit.dir/bitstring.c.o -c /build/reproducible-path/rdkit-202409.4/Code/PgSQL/rdkit/bitstring.c [ 97%] Linking CXX shared library ../../../lib/libRDKitSubstructLibrary.so cd /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/GraphMol/SubstructLibrary && /usr/bin/cmake -E cmake_link_script CMakeFiles/SubstructLibrary.dir/link.txt --verbose=1 +[ 97%] Building C object Code/PgSQL/rdkit/CMakeFiles/rdkit.dir/rdkit_io.c.o +cd /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/PgSQL/rdkit && /usr/bin/cc -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKITVER=\"007600\" -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_CAIRO_SUPPORT -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_FREETYPE_SUPPORT -DRDK_BUILD_INCHI_SUPPORT -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_MOLINTERCHANGE_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_TOOLKIT_VERSION=\"2024.09.4\" -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -Drdkit_EXPORTS -I/build/reproducible-path/rdkit-202409.4/External -I/build/reproducible-path/rdkit-202409.4/Code -I/usr/include/postgresql -I/usr/include/postgresql/17/server -I/usr/include/python3.13 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202409.4/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-202409.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-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-202409.4/Code/PgSQL/rdkit/rdkit_io.c /usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,--dependency-file=CMakeFiles/SubstructLibrary.dir/link.d -Wl,-z,relro -Wl,-z,now -shared -Wl,-soname,libRDKitSubstructLibrary.so.1 -o ../../../lib/libRDKitSubstructLibrary.so.1.2024.09.4 CMakeFiles/SubstructLibrary.dir/SubstructLibrary.cpp.o CMakeFiles/SubstructLibrary.dir/PatternFactory.cpp.o ../../../lib/libRDKitGeneralizedSubstruct.so.1.2024.09.4 ../../../lib/libRDKitTautomerQuery.so.1.2024.09.4 ../../../lib/libRDKitMolStandardize.so.1.2024.09.4 ../../../lib/libRDKitMolEnumerator.so.1.2024.09.4 ../../../lib/libRDKitChemReactions.so.1.2024.09.4 ../../../lib/libRDKitFingerprints.so.1.2024.09.4 ../../../lib/libRDKitFilterCatalog.so.1.2024.09.4 ../../../lib/libRDKitCatalogs.so.1.2024.09.4 ../../../lib/libRDKitSubgraphs.so.1.2024.09.4 ../../../lib/libRDKitFileParsers.so.1.2024.09.4 ../../../lib/libRDKitChemTransforms.so.1.2024.09.4 ../../../lib/libRDKitDepictor.so.1.2024.09.4 /usr/lib/aarch64-linux-gnu/libcoordgen.so ../../../lib/libRDKitMolAlign.so.1.2024.09.4 ../../../lib/libRDKitSubstructMatch.so.1.2024.09.4 ../../../lib/libRDKitGenericGroups.so.1.2024.09.4 ../../../lib/libRDKitSmilesParse.so.1.2024.09.4 ../../../lib/libRDKitMolTransforms.so.1.2024.09.4 ../../../lib/libRDKitGraphMol.so.1.2024.09.4 ../../../lib/libRDKitEigenSolvers.so.1.2024.09.4 ../../../lib/libRDKitAlignment.so.1.2024.09.4 ../../../lib/libRDKitRDGeometryLib.so.1.2024.09.4 ../../../lib/libRDKitDataStructs.so.1.2024.09.4 ../../../lib/libRDKitRDGeneral.so.1.2024.09.4 /usr/lib/aarch64-linux-gnu/libboost_system.so.1.83.0 /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-202409.4/obj-aarch64-linux-gnu/Code/GraphMol/SubstructLibrary && /usr/bin/cmake -E cmake_symlink_library ../../../lib/libRDKitSubstructLibrary.so.1.2024.09.4 ../../../lib/libRDKitSubstructLibrary.so.1 ../../../lib/libRDKitSubstructLibrary.so make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu' [ 97%] Built target SubstructLibrary make -f Code/GraphMol/SynthonSpaceSearch/CMakeFiles/testSynthonSpaceSubstructureSearch.dir/build.make Code/GraphMol/SynthonSpaceSearch/CMakeFiles/testSynthonSpaceSubstructureSearch.dir/depend -make -f Code/GraphMol/SynthonSpaceSearch/CMakeFiles/testSynthonSpaceFingerprintSearch.dir/build.make Code/GraphMol/SynthonSpaceSearch/CMakeFiles/testSynthonSpaceFingerprintSearch.dir/depend -make -f Code/GraphMol/SubstructLibrary/CMakeFiles/substructLibraryTest.dir/build.make Code/GraphMol/SubstructLibrary/CMakeFiles/substructLibraryTest.dir/depend -make -f Code/GraphMol/SubstructLibrary/CMakeFiles/substructLibraryCatchTest.dir/build.make Code/GraphMol/SubstructLibrary/CMakeFiles/substructLibraryCatchTest.dir/depend -make -f 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/build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/GraphMol/SubstructLibrary/CMakeFiles/substructLibraryCatchTest.dir/DependInfo.cmake "--color=" +[ 98%] Building CXX object Code/GraphMol/SynthonSpaceSearch/CMakeFiles/testSynthonSpaceSubstructureSearch.dir/substructure_search_catch_tests.cpp.o +cd /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/GraphMol/SynthonSpaceSearch && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.4/External -I/usr/include/python3.13 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202409.4/Code -I/build/reproducible-path/rdkit-202409.4/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=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-202409.4/Code/GraphMol/SynthonSpaceSearch/substructure_search_catch_tests.cpp +[ 98%] Building C object Code/PgSQL/rdkit/CMakeFiles/rdkit.dir/rxn_op.c.o +cd /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/PgSQL/rdkit && /usr/bin/cc -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKITVER=\"007600\" -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_CAIRO_SUPPORT -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_FREETYPE_SUPPORT -DRDK_BUILD_INCHI_SUPPORT -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_MOLINTERCHANGE_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_TOOLKIT_VERSION=\"2024.09.4\" -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -Drdkit_EXPORTS -I/build/reproducible-path/rdkit-202409.4/External -I/build/reproducible-path/rdkit-202409.4/Code -I/usr/include/postgresql -I/usr/include/postgresql/17/server -I/usr/include/python3.13 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202409.4/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-202409.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-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-202409.4/Code/PgSQL/rdkit/rxn_op.c +[ 98%] Building C object Code/PgSQL/rdkit/CMakeFiles/rdkit.dir/sfp_op.c.o +cd /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/PgSQL/rdkit && /usr/bin/cc -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKITVER=\"007600\" -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_CAIRO_SUPPORT -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_FREETYPE_SUPPORT -DRDK_BUILD_INCHI_SUPPORT -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_MOLINTERCHANGE_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_TOOLKIT_VERSION=\"2024.09.4\" -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -Drdkit_EXPORTS -I/build/reproducible-path/rdkit-202409.4/External -I/build/reproducible-path/rdkit-202409.4/Code -I/usr/include/postgresql -I/usr/include/postgresql/17/server -I/usr/include/python3.13 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202409.4/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-202409.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-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-202409.4/Code/PgSQL/rdkit/sfp_op.c +make -f Code/GraphMol/SynthonSpaceSearch/CMakeFiles/testSynthonSpaceFingerprintSearch.dir/build.make Code/GraphMol/SynthonSpaceSearch/CMakeFiles/testSynthonSpaceFingerprintSearch.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu' -cd /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202409.4 /build/reproducible-path/rdkit-202409.4/Code/GraphMol/SubstructLibrary/Wrap /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/GraphMol/SubstructLibrary/Wrap /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/GraphMol/SubstructLibrary/Wrap/CMakeFiles/rdSubstructLibrary.dir/DependInfo.cmake "--color=" -make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu' +cd /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202409.4 /build/reproducible-path/rdkit-202409.4/Code/GraphMol/SynthonSpaceSearch /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/GraphMol/SynthonSpaceSearch 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Code/GraphMol/SynthonSpaceSearch/CMakeFiles/testSynthonSpaceFingerprintSearch.dir/fingerprint_search_catch_tests.cpp.o -MF CMakeFiles/testSynthonSpaceFingerprintSearch.dir/fingerprint_search_catch_tests.cpp.o.d -o CMakeFiles/testSynthonSpaceFingerprintSearch.dir/fingerprint_search_catch_tests.cpp.o -c /build/reproducible-path/rdkit-202409.4/Code/GraphMol/SynthonSpaceSearch/fingerprint_search_catch_tests.cpp +make -f Code/GraphMol/SubstructLibrary/CMakeFiles/substructLibraryTest.dir/build.make Code/GraphMol/SubstructLibrary/CMakeFiles/substructLibraryTest.dir/depend +make[4]: Entering directory '/build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu' +cd /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202409.4 /build/reproducible-path/rdkit-202409.4/Code/GraphMol/SubstructLibrary /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu 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-I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202409.4/Code -I/build/reproducible-path/rdkit-202409.4/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/GraphMol/SubstructLibrary/CMakeFiles/substructLibraryTest.dir/substructLibraryTest.cpp.o -MF CMakeFiles/substructLibraryTest.dir/substructLibraryTest.cpp.o.d -o CMakeFiles/substructLibraryTest.dir/substructLibraryTest.cpp.o -c /build/reproducible-path/rdkit-202409.4/Code/GraphMol/SubstructLibrary/substructLibraryTest.cpp +make -f Code/GraphMol/SubstructLibrary/CMakeFiles/substructLibraryCatchTest.dir/build.make 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CMakeFiles/RGroupDecomposition.dir/RGroupGa.cpp.o ../../../lib/libRDKitFMCS.so.1.2024.09.4 ../../../lib/libRDKitga.so.1.2024.09.4 ../../../lib/libRDKitMolEnumerator.so.1.2024.09.4 ../../../lib/libRDKitTautomerQuery.so.1.2024.09.4 ../../../lib/libRDKitMolStandardize.so.1.2024.09.4 ../../../lib/libRDKitChemReactions.so.1.2024.09.4 ../../../lib/libRDKitFingerprints.so.1.2024.09.4 ../../../lib/libRDKitFileParsers.so.1.2024.09.4 ../../../lib/libRDKitChemTransforms.so.1.2024.09.4 ../../../lib/libRDKitDepictor.so.1.2024.09.4 /usr/lib/aarch64-linux-gnu/libcoordgen.so ../../../lib/libRDKitMolAlign.so.1.2024.09.4 ../../../lib/libRDKitMolTransforms.so.1.2024.09.4 ../../../lib/libRDKitEigenSolvers.so.1.2024.09.4 ../../../lib/libRDKitAlignment.so.1.2024.09.4 /usr/lib/aarch64-linux-gnu/libmaeparser.so ../../../lib/libRDKitFilterCatalog.so.1.2024.09.4 ../../../lib/libRDKitSubstructMatch.so.1.2024.09.4 ../../../lib/libRDKitGenericGroups.so.1.2024.09.4 ../../../lib/libRDKitSmilesParse.so.1.2024.09.4 ../../../lib/libRDKitSubgraphs.so.1.2024.09.4 ../../../lib/libRDKitGraphMol.so.1.2024.09.4 ../../../lib/libRDKitRDGeometryLib.so.1.2024.09.4 ../../../lib/libRDKitDataStructs.so.1.2024.09.4 ../../../lib/libRDKitCatalogs.so.1.2024.09.4 ../../../lib/libRDKitRDGeneral.so.1.2024.09.4 /usr/lib/aarch64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl @@ -7137,75 +7170,63 @@ make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu' [ 99%] Built target RGroupDecomposition make -f Code/GraphMol/RGroupDecomposition/CMakeFiles/testRGroupDecomp.dir/build.make Code/GraphMol/RGroupDecomposition/CMakeFiles/testRGroupDecomp.dir/depend +make[4]: Entering directory '/build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu' make -f Code/GraphMol/RGroupDecomposition/CMakeFiles/testRGroupDecompInternals.dir/build.make 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CMakeFiles/rdchem.dir/Chirality.cpp.o ../../../lib/libRDKitMarvinParser.so.1.2024.09.4 ../../../lib/libRDKitRDBoost.so.1.2024.09.4 ../../../lib/libRDKitChemReactions.so.1.2024.09.4 ../../../lib/libRDKitFilterCatalog.so.1.2024.09.4 ../../../lib/libRDKitCatalogs.so.1.2024.09.4 ../../../lib/libRDKitFingerprints.so.1.2024.09.4 ../../../lib/libRDKitSubgraphs.so.1.2024.09.4 ../../../lib/libRDKitFileParsers.so.1.2024.09.4 ../../../lib/libRDKitChemTransforms.so.1.2024.09.4 ../../../lib/libRDKitDepictor.so.1.2024.09.4 /usr/lib/aarch64-linux-gnu/libcoordgen.so ../../../lib/libRDKitMolAlign.so.1.2024.09.4 ../../../lib/libRDKitSmilesParse.so.1.2024.09.4 ../../../lib/libRDKitSubstructMatch.so.1.2024.09.4 ../../../lib/libRDKitMolTransforms.so.1.2024.09.4 ../../../lib/libRDKitEigenSolvers.so.1.2024.09.4 ../../../lib/libRDKitAlignment.so.1.2024.09.4 ../../../lib/libRDKitGenericGroups.so.1.2024.09.4 ../../../lib/libRDKitGraphMol.so.1.2024.09.4 ../../../lib/libRDKitRDGeometryLib.so.1.2024.09.4 ../../../lib/libRDKitDataStructs.so.1.2024.09.4 /usr/lib/aarch64-linux-gnu/libmaeparser.so /usr/lib/aarch64-linux-gnu/libboost_numpy313.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_python313.so.1.83.0 ../../../lib/libRDKitRDGeneral.so.1.2024.09.4 /usr/lib/aarch64-linux-gnu/libboost_system.so.1.83.0 /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]: Entering directory '/build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu' +make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu' +[ 99%] Built target rdchem +[ 99%] Building CXX object Code/GraphMol/RGroupDecomposition/Wrap/CMakeFiles/rdRGroupDecomposition.dir/rdRGroupComposition.cpp.o +cd /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/GraphMol/RGroupDecomposition/Wrap && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_NUMPY_DYN_LINK -DBOOST_NUMPY_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DrdRGroupDecomposition_EXPORTS -I/build/reproducible-path/rdkit-202409.4/External -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202409.4/Code -I/build/reproducible-path/rdkit-202409.4/External/boost-numeric-bindings -isystem /usr/include/python3.13 -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-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/Wrap/CMakeFiles/rdRGroupDecomposition.dir/rdRGroupComposition.cpp.o -MF CMakeFiles/rdRGroupDecomposition.dir/rdRGroupComposition.cpp.o.d -o CMakeFiles/rdRGroupDecomposition.dir/rdRGroupComposition.cpp.o -c /build/reproducible-path/rdkit-202409.4/Code/GraphMol/RGroupDecomposition/Wrap/rdRGroupComposition.cpp [ 99%] Linking CXX executable testSynthonSpaceFingerprintSearch cd /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/GraphMol/SynthonSpaceSearch && /usr/bin/cmake -E cmake_link_script CMakeFiles/testSynthonSpaceFingerprintSearch.dir/link.txt --verbose=1 -[ 99%] Linking CXX executable testRGroupDecompInternals -cd /build/reproducible-path/rdkit-202409.4/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-202409.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/testSynthonSpaceFingerprintSearch.dir/link.d CMakeFiles/testSynthonSpaceFingerprintSearch.dir/fingerprint_search_catch_tests.cpp.o -o testSynthonSpaceFingerprintSearch ../../RDGeneral/librdkitCatch.a ../../../lib/libRDKitSubstructLibrary.so.1.2024.09.4 ../../../lib/libRDKitSynthonSpaceSearch.so.1.2024.09.4 /usr/lib/libCatch2.a ../../../lib/libRDKitGeneralizedSubstruct.so.1.2024.09.4 ../../../lib/libRDKitMolEnumerator.so.1.2024.09.4 ../../../lib/libRDKitTautomerQuery.so.1.2024.09.4 ../../../lib/libRDKitMolStandardize.so.1.2024.09.4 ../../../lib/libRDKitChemReactions.so.1.2024.09.4 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/usr/lib/aarch64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu' [ 99%] Built target testSynthonSpaceFingerprintSearch -[ 99%] Linking CXX executable gaExample -cd /build/reproducible-path/rdkit-202409.4/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-202409.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/testRGroupDecompInternals.dir/link.d CMakeFiles/testRGroupDecompInternals.dir/testRGroupInternals.cpp.o -o testRGroupDecompInternals ../../../lib/libRDKitRGroupDecomposition.so.1.2024.09.4 ../../../lib/libRDKitFMCS.so.1.2024.09.4 ../../../lib/libRDKitga.so.1.2024.09.4 ../../../lib/libRDKitMolEnumerator.so.1.2024.09.4 ../../../lib/libRDKitTautomerQuery.so.1.2024.09.4 ../../../lib/libRDKitMolStandardize.so.1.2024.09.4 ../../../lib/libRDKitChemReactions.so.1.2024.09.4 ../../../lib/libRDKitFingerprints.so.1.2024.09.4 ../../../lib/libRDKitFileParsers.so.1.2024.09.4 ../../../lib/libRDKitChemTransforms.so.1.2024.09.4 ../../../lib/libRDKitDepictor.so.1.2024.09.4 /usr/lib/aarch64-linux-gnu/libcoordgen.so ../../../lib/libRDKitMolAlign.so.1.2024.09.4 ../../../lib/libRDKitMolTransforms.so.1.2024.09.4 ../../../lib/libRDKitEigenSolvers.so.1.2024.09.4 ../../../lib/libRDKitAlignment.so.1.2024.09.4 /usr/lib/aarch64-linux-gnu/libmaeparser.so ../../../lib/libRDKitFilterCatalog.so.1.2024.09.4 ../../../lib/libRDKitSubstructMatch.so.1.2024.09.4 ../../../lib/libRDKitGenericGroups.so.1.2024.09.4 ../../../lib/libRDKitSmilesParse.so.1.2024.09.4 ../../../lib/libRDKitSubgraphs.so.1.2024.09.4 ../../../lib/libRDKitGraphMol.so.1.2024.09.4 ../../../lib/libRDKitRDGeometryLib.so.1.2024.09.4 ../../../lib/libRDKitDataStructs.so.1.2024.09.4 ../../../lib/libRDKitCatalogs.so.1.2024.09.4 ../../../lib/libRDKitRDGeneral.so.1.2024.09.4 /usr/lib/aarch64-linux-gnu/libboost_system.so.1.83.0 /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-202409.4/obj-aarch64-linux-gnu' -[ 99%] Built target testRGroupDecompInternals -/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_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.1.2024.09.4 /usr/lib/aarch64-linux-gnu/libboost_program_options.so.1.83.0 ../../../lib/libRDKitFMCS.so.1.2024.09.4 ../../../lib/libRDKitga.so.1.2024.09.4 ../../../lib/libRDKitMolEnumerator.so.1.2024.09.4 ../../../lib/libRDKitTautomerQuery.so.1.2024.09.4 ../../../lib/libRDKitMolStandardize.so.1.2024.09.4 ../../../lib/libRDKitChemReactions.so.1.2024.09.4 ../../../lib/libRDKitFingerprints.so.1.2024.09.4 ../../../lib/libRDKitFileParsers.so.1.2024.09.4 ../../../lib/libRDKitChemTransforms.so.1.2024.09.4 ../../../lib/libRDKitDepictor.so.1.2024.09.4 /usr/lib/aarch64-linux-gnu/libcoordgen.so ../../../lib/libRDKitMolAlign.so.1.2024.09.4 ../../../lib/libRDKitMolTransforms.so.1.2024.09.4 ../../../lib/libRDKitEigenSolvers.so.1.2024.09.4 ../../../lib/libRDKitAlignment.so.1.2024.09.4 /usr/lib/aarch64-linux-gnu/libmaeparser.so 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CMakeFiles/substructLibraryTest.dir/link.txt --verbose=1 -/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_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.1.2024.09.4 ../../../lib/libRDKitGeneralizedSubstruct.so.1.2024.09.4 ../../../lib/libRDKitTautomerQuery.so.1.2024.09.4 ../../../lib/libRDKitMolStandardize.so.1.2024.09.4 ../../../lib/libRDKitMolEnumerator.so.1.2024.09.4 ../../../lib/libRDKitChemReactions.so.1.2024.09.4 ../../../lib/libRDKitFileParsers.so.1.2024.09.4 /usr/lib/aarch64-linux-gnu/libmaeparser.so ../../../lib/libRDKitFilterCatalog.so.1.2024.09.4 ../../../lib/libRDKitChemTransforms.so.1.2024.09.4 ../../../lib/libRDKitDepictor.so.1.2024.09.4 /usr/lib/aarch64-linux-gnu/libcoordgen.so ../../../lib/libRDKitMolAlign.so.1.2024.09.4 ../../../lib/libRDKitMolTransforms.so.1.2024.09.4 ../../../lib/libRDKitEigenSolvers.so.1.2024.09.4 ../../../lib/libRDKitAlignment.so.1.2024.09.4 ../../../lib/libRDKitFingerprints.so.1.2024.09.4 ../../../lib/libRDKitSmilesParse.so.1.2024.09.4 ../../../lib/libRDKitSubstructMatch.so.1.2024.09.4 ../../../lib/libRDKitGenericGroups.so.1.2024.09.4 ../../../lib/libRDKitSubgraphs.so.1.2024.09.4 ../../../lib/libRDKitGraphMol.so.1.2024.09.4 ../../../lib/libRDKitRDGeometryLib.so.1.2024.09.4 ../../../lib/libRDKitCatalogs.so.1.2024.09.4 ../../../lib/libRDKitDataStructs.so.1.2024.09.4 ../../../lib/libRDKitRDGeneral.so.1.2024.09.4 /usr/lib/aarch64-linux-gnu/libboost_system.so.1.83.0 /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-202409.4/obj-aarch64-linux-gnu' [ 99%] Linking CXX executable substructLibraryCatchTest cd /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/GraphMol/SubstructLibrary && /usr/bin/cmake -E cmake_link_script CMakeFiles/substructLibraryCatchTest.dir/link.txt --verbose=1 -[ 99%] Built target substructLibraryTest +[ 99%] Linking CXX executable substructLibraryTest +cd /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/GraphMol/SubstructLibrary && /usr/bin/cmake -E cmake_link_script CMakeFiles/substructLibraryTest.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function 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../../../lib/libRDKitAlignment.so.1.2024.09.4 ../../../lib/libRDKitFilterCatalog.so.1.2024.09.4 ../../../lib/libRDKitFingerprints.so.1.2024.09.4 ../../../lib/libRDKitSubgraphs.so.1.2024.09.4 ../../../lib/libRDKitSubstructMatch.so.1.2024.09.4 ../../../lib/libRDKitGenericGroups.so.1.2024.09.4 ../../../lib/libRDKitSmilesParse.so.1.2024.09.4 ../../../lib/libRDKitGraphMol.so.1.2024.09.4 ../../../lib/libRDKitRDGeometryLib.so.1.2024.09.4 ../../../lib/libRDKitCatalogs.so.1.2024.09.4 ../../../lib/libRDKitDataStructs.so.1.2024.09.4 ../../../lib/libRDKitRDGeneral.so.1.2024.09.4 /usr/lib/aarch64-linux-gnu/libboost_system.so.1.83.0 /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-202409.4/obj-aarch64-linux-gnu' [ 99%] Built target substructLibraryCatchTest +/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_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.1.2024.09.4 ../../../lib/libRDKitGeneralizedSubstruct.so.1.2024.09.4 ../../../lib/libRDKitTautomerQuery.so.1.2024.09.4 ../../../lib/libRDKitMolStandardize.so.1.2024.09.4 ../../../lib/libRDKitMolEnumerator.so.1.2024.09.4 ../../../lib/libRDKitChemReactions.so.1.2024.09.4 ../../../lib/libRDKitFileParsers.so.1.2024.09.4 /usr/lib/aarch64-linux-gnu/libmaeparser.so ../../../lib/libRDKitFilterCatalog.so.1.2024.09.4 ../../../lib/libRDKitChemTransforms.so.1.2024.09.4 ../../../lib/libRDKitDepictor.so.1.2024.09.4 /usr/lib/aarch64-linux-gnu/libcoordgen.so ../../../lib/libRDKitMolAlign.so.1.2024.09.4 ../../../lib/libRDKitMolTransforms.so.1.2024.09.4 ../../../lib/libRDKitEigenSolvers.so.1.2024.09.4 ../../../lib/libRDKitAlignment.so.1.2024.09.4 ../../../lib/libRDKitFingerprints.so.1.2024.09.4 ../../../lib/libRDKitSmilesParse.so.1.2024.09.4 ../../../lib/libRDKitSubstructMatch.so.1.2024.09.4 ../../../lib/libRDKitGenericGroups.so.1.2024.09.4 ../../../lib/libRDKitSubgraphs.so.1.2024.09.4 ../../../lib/libRDKitGraphMol.so.1.2024.09.4 ../../../lib/libRDKitRDGeometryLib.so.1.2024.09.4 ../../../lib/libRDKitCatalogs.so.1.2024.09.4 ../../../lib/libRDKitDataStructs.so.1.2024.09.4 ../../../lib/libRDKitRDGeneral.so.1.2024.09.4 /usr/lib/aarch64-linux-gnu/libboost_system.so.1.83.0 /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-202409.4/obj-aarch64-linux-gnu' +[ 99%] Built target substructLibraryTest [ 99%] Linking CXX executable testSynthonSpaceSubstructureSearch cd /build/reproducible-path/rdkit-202409.4/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_2()': @@ -7213,6 +7234,16 @@ /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_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.1.2024.09.4 ../../../lib/libRDKitSynthonSpaceSearch.so.1.2024.09.4 /usr/lib/libCatch2.a ../../../lib/libRDKitGeneralizedSubstruct.so.1.2024.09.4 ../../../lib/libRDKitMolEnumerator.so.1.2024.09.4 ../../../lib/libRDKitTautomerQuery.so.1.2024.09.4 ../../../lib/libRDKitMolStandardize.so.1.2024.09.4 ../../../lib/libRDKitChemReactions.so.1.2024.09.4 ../../../lib/libRDKitFilterCatalog.so.1.2024.09.4 ../../../lib/libRDKitCatalogs.so.1.2024.09.4 ../../../lib/libRDKitFingerprints.so.1.2024.09.4 ../../../lib/libRDKitSubgraphs.so.1.2024.09.4 ../../../lib/libRDKitFileParsers.so.1.2024.09.4 /usr/lib/aarch64-linux-gnu/libmaeparser.so ../../../lib/libRDKitChemTransforms.so.1.2024.09.4 ../../../lib/libRDKitDepictor.so.1.2024.09.4 /usr/lib/aarch64-linux-gnu/libcoordgen.so ../../../lib/libRDKitMolAlign.so.1.2024.09.4 ../../../lib/libRDKitSubstructMatch.so.1.2024.09.4 ../../../lib/libRDKitGenericGroups.so.1.2024.09.4 ../../../lib/libRDKitSmilesParse.so.1.2024.09.4 ../../../lib/libRDKitMolTransforms.so.1.2024.09.4 ../../../lib/libRDKitGraphMol.so.1.2024.09.4 ../../../lib/libRDKitEigenSolvers.so.1.2024.09.4 ../../../lib/libRDKitAlignment.so.1.2024.09.4 ../../../lib/libRDKitRDGeometryLib.so.1.2024.09.4 ../../../lib/libRDKitDataStructs.so.1.2024.09.4 ../../../lib/libRDKitRDGeneral.so.1.2024.09.4 /usr/lib/aarch64-linux-gnu/libboost_system.so.1.83.0 /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-202409.4/obj-aarch64-linux-gnu' [ 99%] Built target testSynthonSpaceSubstructureSearch +[ 99%] Linking CXX executable gaExample +cd /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/GraphMol/RGroupDecomposition && /usr/bin/cmake -E cmake_link_script CMakeFiles/gaExample.dir/link.txt --verbose=1 +[ 99%] Linking CXX executable testRGroupDecompInternals +cd /build/reproducible-path/rdkit-202409.4/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-202409.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_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.1.2024.09.4 /usr/lib/aarch64-linux-gnu/libboost_program_options.so.1.83.0 ../../../lib/libRDKitFMCS.so.1.2024.09.4 ../../../lib/libRDKitga.so.1.2024.09.4 ../../../lib/libRDKitMolEnumerator.so.1.2024.09.4 ../../../lib/libRDKitTautomerQuery.so.1.2024.09.4 ../../../lib/libRDKitMolStandardize.so.1.2024.09.4 ../../../lib/libRDKitChemReactions.so.1.2024.09.4 ../../../lib/libRDKitFingerprints.so.1.2024.09.4 ../../../lib/libRDKitFileParsers.so.1.2024.09.4 ../../../lib/libRDKitChemTransforms.so.1.2024.09.4 ../../../lib/libRDKitDepictor.so.1.2024.09.4 /usr/lib/aarch64-linux-gnu/libcoordgen.so ../../../lib/libRDKitMolAlign.so.1.2024.09.4 ../../../lib/libRDKitMolTransforms.so.1.2024.09.4 ../../../lib/libRDKitEigenSolvers.so.1.2024.09.4 ../../../lib/libRDKitAlignment.so.1.2024.09.4 /usr/lib/aarch64-linux-gnu/libmaeparser.so ../../../lib/libRDKitFilterCatalog.so.1.2024.09.4 ../../../lib/libRDKitSubstructMatch.so.1.2024.09.4 ../../../lib/libRDKitGenericGroups.so.1.2024.09.4 ../../../lib/libRDKitSmilesParse.so.1.2024.09.4 ../../../lib/libRDKitSubgraphs.so.1.2024.09.4 ../../../lib/libRDKitGraphMol.so.1.2024.09.4 ../../../lib/libRDKitRDGeometryLib.so.1.2024.09.4 ../../../lib/libRDKitDataStructs.so.1.2024.09.4 ../../../lib/libRDKitCatalogs.so.1.2024.09.4 ../../../lib/libRDKitRDGeneral.so.1.2024.09.4 /usr/lib/aarch64-linux-gnu/libboost_system.so.1.83.0 /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-202409.4/obj-aarch64-linux-gnu' +[ 99%] Built target gaExample +/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/testRGroupDecompInternals.dir/link.d CMakeFiles/testRGroupDecompInternals.dir/testRGroupInternals.cpp.o -o testRGroupDecompInternals ../../../lib/libRDKitRGroupDecomposition.so.1.2024.09.4 ../../../lib/libRDKitFMCS.so.1.2024.09.4 ../../../lib/libRDKitga.so.1.2024.09.4 ../../../lib/libRDKitMolEnumerator.so.1.2024.09.4 ../../../lib/libRDKitTautomerQuery.so.1.2024.09.4 ../../../lib/libRDKitMolStandardize.so.1.2024.09.4 ../../../lib/libRDKitChemReactions.so.1.2024.09.4 ../../../lib/libRDKitFingerprints.so.1.2024.09.4 ../../../lib/libRDKitFileParsers.so.1.2024.09.4 ../../../lib/libRDKitChemTransforms.so.1.2024.09.4 ../../../lib/libRDKitDepictor.so.1.2024.09.4 /usr/lib/aarch64-linux-gnu/libcoordgen.so ../../../lib/libRDKitMolAlign.so.1.2024.09.4 ../../../lib/libRDKitMolTransforms.so.1.2024.09.4 ../../../lib/libRDKitEigenSolvers.so.1.2024.09.4 ../../../lib/libRDKitAlignment.so.1.2024.09.4 /usr/lib/aarch64-linux-gnu/libmaeparser.so ../../../lib/libRDKitFilterCatalog.so.1.2024.09.4 ../../../lib/libRDKitSubstructMatch.so.1.2024.09.4 ../../../lib/libRDKitGenericGroups.so.1.2024.09.4 ../../../lib/libRDKitSmilesParse.so.1.2024.09.4 ../../../lib/libRDKitSubgraphs.so.1.2024.09.4 ../../../lib/libRDKitGraphMol.so.1.2024.09.4 ../../../lib/libRDKitRDGeometryLib.so.1.2024.09.4 ../../../lib/libRDKitDataStructs.so.1.2024.09.4 ../../../lib/libRDKitCatalogs.so.1.2024.09.4 ../../../lib/libRDKitRDGeneral.so.1.2024.09.4 /usr/lib/aarch64-linux-gnu/libboost_system.so.1.83.0 /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-202409.4/obj-aarch64-linux-gnu' +[ 99%] Built target testRGroupDecompInternals [ 99%] Linking CXX shared module ../../../../rdkit/Chem/rdRGroupDecomposition.so cd /build/reproducible-path/rdkit-202409.4/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-202409.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=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.1.2024.09.4 ../../../../lib/libRDKitRDBoost.so.1.2024.09.4 ../../../../lib/libRDKitFMCS.so.1.2024.09.4 ../../../../lib/libRDKitga.so.1.2024.09.4 ../../../../lib/libRDKitMolEnumerator.so.1.2024.09.4 ../../../../lib/libRDKitTautomerQuery.so.1.2024.09.4 ../../../../lib/libRDKitMolStandardize.so.1.2024.09.4 ../../../../lib/libRDKitChemReactions.so.1.2024.09.4 ../../../../lib/libRDKitFingerprints.so.1.2024.09.4 ../../../../lib/libRDKitFileParsers.so.1.2024.09.4 ../../../../lib/libRDKitChemTransforms.so.1.2024.09.4 ../../../../lib/libRDKitDepictor.so.1.2024.09.4 /usr/lib/aarch64-linux-gnu/libcoordgen.so ../../../../lib/libRDKitMolAlign.so.1.2024.09.4 ../../../../lib/libRDKitMolTransforms.so.1.2024.09.4 ../../../../lib/libRDKitEigenSolvers.so.1.2024.09.4 ../../../../lib/libRDKitAlignment.so.1.2024.09.4 /usr/lib/aarch64-linux-gnu/libmaeparser.so ../../../../lib/libRDKitFilterCatalog.so.1.2024.09.4 ../../../../lib/libRDKitSubstructMatch.so.1.2024.09.4 ../../../../lib/libRDKitGenericGroups.so.1.2024.09.4 ../../../../lib/libRDKitSmilesParse.so.1.2024.09.4 ../../../../lib/libRDKitSubgraphs.so.1.2024.09.4 ../../../../lib/libRDKitGraphMol.so.1.2024.09.4 ../../../../lib/libRDKitRDGeometryLib.so.1.2024.09.4 ../../../../lib/libRDKitDataStructs.so.1.2024.09.4 ../../../../lib/libRDKitCatalogs.so.1.2024.09.4 /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.1.2024.09.4 /usr/lib/aarch64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl @@ -7223,16 +7254,16 @@ /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_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.1.2024.09.4 /usr/lib/libCatch2.a ../../../lib/libRDKitFMCS.so.1.2024.09.4 ../../../lib/libRDKitga.so.1.2024.09.4 ../../../lib/libRDKitMolEnumerator.so.1.2024.09.4 ../../../lib/libRDKitTautomerQuery.so.1.2024.09.4 ../../../lib/libRDKitMolStandardize.so.1.2024.09.4 ../../../lib/libRDKitChemReactions.so.1.2024.09.4 ../../../lib/libRDKitFingerprints.so.1.2024.09.4 ../../../lib/libRDKitFileParsers.so.1.2024.09.4 ../../../lib/libRDKitChemTransforms.so.1.2024.09.4 ../../../lib/libRDKitDepictor.so.1.2024.09.4 /usr/lib/aarch64-linux-gnu/libcoordgen.so ../../../lib/libRDKitMolAlign.so.1.2024.09.4 ../../../lib/libRDKitMolTransforms.so.1.2024.09.4 ../../../lib/libRDKitEigenSolvers.so.1.2024.09.4 ../../../lib/libRDKitAlignment.so.1.2024.09.4 /usr/lib/aarch64-linux-gnu/libmaeparser.so ../../../lib/libRDKitFilterCatalog.so.1.2024.09.4 ../../../lib/libRDKitSubstructMatch.so.1.2024.09.4 ../../../lib/libRDKitGenericGroups.so.1.2024.09.4 ../../../lib/libRDKitSmilesParse.so.1.2024.09.4 ../../../lib/libRDKitSubgraphs.so.1.2024.09.4 ../../../lib/libRDKitGraphMol.so.1.2024.09.4 ../../../lib/libRDKitRDGeometryLib.so.1.2024.09.4 ../../../lib/libRDKitDataStructs.so.1.2024.09.4 ../../../lib/libRDKitCatalogs.so.1.2024.09.4 ../../../lib/libRDKitRDGeneral.so.1.2024.09.4 /usr/lib/aarch64-linux-gnu/libboost_system.so.1.83.0 /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-202409.4/obj-aarch64-linux-gnu' [ 99%] Built target rgroupCatchTests -[ 99%] Linking CXX executable testRGroupDecomp -cd /build/reproducible-path/rdkit-202409.4/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-202409.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_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.1.2024.09.4 ../../../lib/libRDKitFMCS.so.1.2024.09.4 ../../../lib/libRDKitga.so.1.2024.09.4 ../../../lib/libRDKitMolEnumerator.so.1.2024.09.4 ../../../lib/libRDKitTautomerQuery.so.1.2024.09.4 ../../../lib/libRDKitMolStandardize.so.1.2024.09.4 ../../../lib/libRDKitChemReactions.so.1.2024.09.4 ../../../lib/libRDKitFingerprints.so.1.2024.09.4 ../../../lib/libRDKitFileParsers.so.1.2024.09.4 ../../../lib/libRDKitChemTransforms.so.1.2024.09.4 ../../../lib/libRDKitDepictor.so.1.2024.09.4 /usr/lib/aarch64-linux-gnu/libcoordgen.so ../../../lib/libRDKitMolAlign.so.1.2024.09.4 ../../../lib/libRDKitMolTransforms.so.1.2024.09.4 ../../../lib/libRDKitEigenSolvers.so.1.2024.09.4 ../../../lib/libRDKitAlignment.so.1.2024.09.4 /usr/lib/aarch64-linux-gnu/libmaeparser.so ../../../lib/libRDKitFilterCatalog.so.1.2024.09.4 ../../../lib/libRDKitSubstructMatch.so.1.2024.09.4 ../../../lib/libRDKitGenericGroups.so.1.2024.09.4 ../../../lib/libRDKitSmilesParse.so.1.2024.09.4 ../../../lib/libRDKitSubgraphs.so.1.2024.09.4 ../../../lib/libRDKitGraphMol.so.1.2024.09.4 ../../../lib/libRDKitRDGeometryLib.so.1.2024.09.4 ../../../lib/libRDKitDataStructs.so.1.2024.09.4 ../../../lib/libRDKitCatalogs.so.1.2024.09.4 ../../../lib/libRDKitRDGeneral.so.1.2024.09.4 /usr/lib/aarch64-linux-gnu/libboost_system.so.1.83.0 /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-202409.4/obj-aarch64-linux-gnu' -[ 99%] Built target testRGroupDecomp [100%] Linking CXX shared module ../../../../rdkit/Chem/rdSubstructLibrary.so cd /build/reproducible-path/rdkit-202409.4/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-202409.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=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.1.2024.09.4 ../../../../lib/libRDKitRDBoost.so.1.2024.09.4 ../../../../lib/libRDKitGeneralizedSubstruct.so.1.2024.09.4 ../../../../lib/libRDKitMolEnumerator.so.1.2024.09.4 ../../../../lib/libRDKitTautomerQuery.so.1.2024.09.4 ../../../../lib/libRDKitMolStandardize.so.1.2024.09.4 ../../../../lib/libRDKitChemReactions.so.1.2024.09.4 ../../../../lib/libRDKitFileParsers.so.1.2024.09.4 /usr/lib/aarch64-linux-gnu/libmaeparser.so ../../../../lib/libRDKitFilterCatalog.so.1.2024.09.4 ../../../../lib/libRDKitChemTransforms.so.1.2024.09.4 ../../../../lib/libRDKitDepictor.so.1.2024.09.4 /usr/lib/aarch64-linux-gnu/libcoordgen.so ../../../../lib/libRDKitMolAlign.so.1.2024.09.4 ../../../../lib/libRDKitMolTransforms.so.1.2024.09.4 ../../../../lib/libRDKitEigenSolvers.so.1.2024.09.4 ../../../../lib/libRDKitAlignment.so.1.2024.09.4 ../../../../lib/libRDKitFingerprints.so.1.2024.09.4 ../../../../lib/libRDKitSubgraphs.so.1.2024.09.4 ../../../../lib/libRDKitSubstructMatch.so.1.2024.09.4 ../../../../lib/libRDKitGenericGroups.so.1.2024.09.4 ../../../../lib/libRDKitSmilesParse.so.1.2024.09.4 ../../../../lib/libRDKitGraphMol.so.1.2024.09.4 ../../../../lib/libRDKitRDGeometryLib.so.1.2024.09.4 ../../../../lib/libRDKitCatalogs.so.1.2024.09.4 ../../../../lib/libRDKitDataStructs.so.1.2024.09.4 /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.1.2024.09.4 /usr/lib/aarch64-linux-gnu/libboost_system.so.1.83.0 /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-202409.4/obj-aarch64-linux-gnu' [100%] Built target rdSubstructLibrary +[100%] Linking CXX executable testRGroupDecomp +cd /build/reproducible-path/rdkit-202409.4/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-202409.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_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.1.2024.09.4 ../../../lib/libRDKitFMCS.so.1.2024.09.4 ../../../lib/libRDKitga.so.1.2024.09.4 ../../../lib/libRDKitMolEnumerator.so.1.2024.09.4 ../../../lib/libRDKitTautomerQuery.so.1.2024.09.4 ../../../lib/libRDKitMolStandardize.so.1.2024.09.4 ../../../lib/libRDKitChemReactions.so.1.2024.09.4 ../../../lib/libRDKitFingerprints.so.1.2024.09.4 ../../../lib/libRDKitFileParsers.so.1.2024.09.4 ../../../lib/libRDKitChemTransforms.so.1.2024.09.4 ../../../lib/libRDKitDepictor.so.1.2024.09.4 /usr/lib/aarch64-linux-gnu/libcoordgen.so ../../../lib/libRDKitMolAlign.so.1.2024.09.4 ../../../lib/libRDKitMolTransforms.so.1.2024.09.4 ../../../lib/libRDKitEigenSolvers.so.1.2024.09.4 ../../../lib/libRDKitAlignment.so.1.2024.09.4 /usr/lib/aarch64-linux-gnu/libmaeparser.so ../../../lib/libRDKitFilterCatalog.so.1.2024.09.4 ../../../lib/libRDKitSubstructMatch.so.1.2024.09.4 ../../../lib/libRDKitGenericGroups.so.1.2024.09.4 ../../../lib/libRDKitSmilesParse.so.1.2024.09.4 ../../../lib/libRDKitSubgraphs.so.1.2024.09.4 ../../../lib/libRDKitGraphMol.so.1.2024.09.4 ../../../lib/libRDKitRDGeometryLib.so.1.2024.09.4 ../../../lib/libRDKitDataStructs.so.1.2024.09.4 ../../../lib/libRDKitCatalogs.so.1.2024.09.4 ../../../lib/libRDKitRDGeneral.so.1.2024.09.4 /usr/lib/aarch64-linux-gnu/libboost_system.so.1.83.0 /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-202409.4/obj-aarch64-linux-gnu' +[100%] Built target testRGroupDecomp make[3]: Leaving directory '/build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu' /usr/bin/cmake -E cmake_progress_start /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/CMakeFiles 0 make[2]: Leaving directory '/build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu' @@ -12861,7 +12892,7 @@ resolving references... /build/reproducible-path/rdkit-202409.4/Docs/Book/GettingStartedWithContributing.md:271: 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 @@ -15072,204 +15103,6 @@ 12: Test command: /usr/bin/python3 "/build/reproducible-path/rdkit-202409.4/Code/DataStructs/Wrap/testBV.py" 12: Working Directory: /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/DataStructs/Wrap 12: Test timeout computed to be: 1500 -3: [12:42:35] Testing Github940: property dictionaries leaking memory -3: [12:42:35] 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:0.003251 s -3: static RDAny:0.000366 s -3: dynamic RDAny:0.003143 s -3: static RDValue:1e-06 s -3: dynamic RDValue:0.000452 s -3: deleted! -3: [12:42:35] ------------------------------------- -3: [12:42:35] Testing String Pickle Roundtrips. -3: [12:42:35] done -3: [12:42:35] ------------------------------------- -3: [12:42:35] Testing conversion of vect to string. -3: [12:42:35] done -3: [12:42:35] ------------------------------------- -3: [12:42:35] Testing returning const references. -3: [12:42:35] any cast -3: [12:42:35] done: 0.002371 300000 -3: [12:42:35] copy -3: [12:42:35] done: 0.002529 300000 -3: [12:42:35] ref -3: [12:42:35] done: 0.0025 300000 -3: [12:42:35] dict -3: [12:42:35] done: 0.005702 300000 -3: [12:42:35] ref with hasVal -4: -- running tests -- -4: min: -2147483648 -2147483648 -4: min: 0 0 -4: min: 2.22507e-308 2.22507e-308 -4: min: 1.17549e-38 1.17549e-38 -4: min: 0 0 -4: == int -4: == double -4: == float -4: == unsigned int -4: == bool -4: == std::string -5: [12:42:35] -5: ----------------------------------------- -5: [12:42:35] Finished: testPushAndPop() -5: [12:42:35] -5: ----------------------------------------- -5: [12:42:35] -5: ----------------------------------------- -6: Randomness seeded to: 1885220664 -6: =============================================================================== -6: All tests passed (32 assertions in 2 test cases) -6: -7: [12:42:35] should not be silent -7: [12:42:35] should not be silent -7: Randomness seeded to: 2932247618 -7: [12:42:35] should not be silent -7: [12:42:35] should not be silent -7: [12:42:35] should not be silent -7: [12:42:35] should not be silent -7: [12:42:35] should not be silent -7: [12:42:35] should not be silent -7: [12:42:35] should not be silent -7: [12:42:35] should not be silent -7: =============================================================================== -7: All tests passed (26 assertions in 3 test cases) -7: -8: [12:42:35] pass -8: [12:42:35] v3 4 -8: [12:42:35] v4 5 -8: [12:42:35] SPARSE ----------------------------------- -8: [12:42:35] Set 10: 0 -8: [12:42:35] Set 11: 0 -8: [12:42:35] Set 14: 0 -8: [12:42:35] Set 10: 1 -8: [12:42:35] Get 14: 1 -8: [12:42:35] Num: 20 -8: [12:42:35] NumOn: 3 -8: [12:42:35] NumOff: 17 -8: 10, 11, 14, -8: [12:42:35] t2[19]: 0 -8: [12:42:35] t2[14]: 1 -8: [12:42:35] t2[19]: 0 -8: [12:42:35] t2[14]: 0 -8: t1: 10, 11, 14, -8: t2: 10, 11, 15, 17, -8: t1|t2: 10, 11, 14, 15, 17, -8: t1&t2: 10, 11, -8: t1^t2: 14, 15, 17, -8: ~t1: 0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 12, 13, 15, 16, 17, 18, 19, -8: except -8: [12:42:35] Explicit ---------------------------------- -8: [12:42:35] Set 10: 0 -8: [12:42:35] Set 11: 0 -8: [12:42:35] Set 14: 0 -8: [12:42:35] Set 10: 1 -8: [12:42:35] Get 14: 1 -8: [12:42:35] Num: 20 -8: [12:42:35] NumOn: 3 -8: [12:42:35] NumOff: 17 -8: 10, 11, 14, -8: [12:42:35] t2[19]: 0 -8: [12:42:35] t2[14]: 1 -8: [12:42:35] t2[19]: 0 -8: [12:42:35] t2[14]: 0 -8: t1: 10, 11, 14, -8: t2: 10, 11, 15, 17, -8: t1|t2: 10, 11, 14, 15, 17, -8: t1&t2: 10, 11, -8: t1^t2: 14, 15, 17, -8: ~t1: 0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 12, 13, 15, 16, 17, 18, 19, -8: except -8: [12:42:35] Done -8: [12:42:35] Test DiscreteValue Vectors 1 ---------------------------- -8: [12:42:35] Expected failure: Value out of range -8: [12:42:35] Expected failure: Value out of range -8: [12:42:35] Expected failure: Value out of range -8: [12:42:35] Expected failure: Value out of range -8: [12:42:35] Expected failure: Value out of range -8: [12:42:35] Test DiscreteValue Vectors 2 ------------------------------ -8: [12:42:35] Test DiscreteValue Vectors 3 --------------------------- -8: [12:42:35] Test DiscreteValue Operations ----------------------------- -8: [12:42:35] Test DiscreteValue Operations 2 -------------------------- -8: [12:42:35] Test SparseIntVect ------------------------------------ -8: [12:42:35] Test SparseIntVect Serialization -------------------------- -8: [12:42:35] Test BitVect Serialization ------------------------------- -8: [12:42:35] Test BitVect to FPS ------------------------------- -8: [12:42:35] Test BitVect to binary string ------------------------------- -8: [12:42:35] Test Similarity Measures BitVect ------------------------------- -8: [12:42:35] Test Similarity Measures SparseBitVect ------------------------------- -8: [12:42:35] Test BitVect with all ones ------------------------------- -8: [12:42:35] Test Explicit BitVects: Concatenation Operation ------------------------------- -8: [12:42:35] Test bitmap operations ------------------------------- -8: [12:42:35] Test bitmaps as properties ------------------------------- -8: [12:42:35] Test #3944: SparseIntVect copy constructor and assignment operators not clearing existing data------------------------------- -8: [12:42:35] Test RealValue Vectors 1: Constructors and Accessing Values ------------------------------- -8: [12:42:35] Test RealValue Vectors 2: L1Norm ------------------------------- -8: [12:42:35] Test RealValue Vectors 3: Pickles ------------------------------- -8: [12:42:35] Test RealValue Vectors 4: Vector Operations ------------------------------- - 1/236 Test #4: testRDValue ............................ Passed 0.03 sec - 2/236 Test #6: dictTestsCatch ......................... Passed 0.02 sec - 3/236 Test #7: logTestsCatch .......................... Passed 0.02 sec - 4/236 Test #8: testDataStructs ........................ Passed 0.02 sec -3: [12:42:35] done: 0.003683 300000 -3: [12:42:35] done -3: [12:42:35] ------------------------------------- -3: [12:42:35] Testing dict update. -3: [12:42:35] done -3: deleted! -3: deleted! -3: deleted! -3: deleted! -3: deleted! -3: deleted! - 5/236 Test #3: testDict ............................... Passed 0.03 sec - 6/236 Test #9: testFPB ................................ Passed 0.01 sec -test 13 - Start 13: pyDiscreteValueVect - -13: Test command: /usr/bin/python3 "/build/reproducible-path/rdkit-202409.4/Code/DataStructs/Wrap/testDiscreteValueVect.py" -13: Working Directory: /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/DataStructs/Wrap -13: Test timeout computed to be: 1500 -test 14 - Start 14: pyRealValueVect - -14: Test command: /usr/bin/python3 "/build/reproducible-path/rdkit-202409.4/Code/DataStructs/Wrap/testRealValueVect.py" -14: Working Directory: /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/DataStructs/Wrap -14: Test timeout computed to be: 1500 -test 15 - Start 15: pySparseIntVect - -15: Test command: /usr/bin/python3 "/build/reproducible-path/rdkit-202409.4/Code/DataStructs/Wrap/testSparseIntVect.py" -15: Working Directory: /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/DataStructs/Wrap -15: Test timeout computed to be: 1500 -test 16 - Start 16: pyFPB - -16: Test command: /usr/bin/python3 "/build/reproducible-path/rdkit-202409.4/Code/DataStructs/Wrap/testFPB.py" -16: Working Directory: /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/DataStructs/Wrap -16: Test timeout computed to be: 1500 -test 17 - Start 17: testTransforms - -17: Test command: /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/Geometry/testTransforms -17: Working Directory: /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/Geometry -17: Test timeout computed to be: 1500 -test 18 - Start 18: testGrid - -18: Test command: /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/Geometry/testGrid -18: Working Directory: /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/Geometry -18: Test timeout computed to be: 1500 -11: Randomness seeded to: 3234097402 -11: =============================================================================== -11: All tests passed (3 assertions in 1 test case) -11: - 7/236 Test #11: catchDataStructs ....................... Passed 0.03 sec - 8/236 Test #10: testMultiFPB ........................... Passed 0.03 sec 1: core 1: RDKit 2D 1: @@ -15512,18 +15345,6 @@ 1: 16 1 1 0 1: M END 1: -test 19 - Start 19: testRealValueGrid - -19: Test command: /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/Geometry/testRealValueGrid -19: Working Directory: /build/reproducible-path/rdkit-202409.4/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-202409.4/obj-aarch64-linux-gnu/Code/Geometry/geometryTestsCatch -20: Working Directory: /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/Geometry -20: Test timeout computed to be: 1500 1: core 1: RDKit 2D 1: @@ -15739,214 +15560,6 @@ 1: 2 5 1 0 1: M END 1: -17: **************************************** -17: testPointND -17: **************************************** -17: testPointOps3D -17: **************************************** -17: testPointOps2D -17: **************************************** -17: test12D -17: ref1: 2.27463 0.695251 ref2: 2.4813 4.91316 -17: pt1: 1.44586 3.36579 pt2: 2.79854 1.81242 -17: **************************************** -17: test23D -17: **************************************** -17: test3MatMultiply -17: Pt1: 1 0 0 Pt2: 2 0 0 -17: -Pt1: -1 -0 -0 -17: tp1: 0 0 0 tp2: 0 0 0 -17: tp1: 0 0 0 tp2: 0 0 0 -17: tp1: 0 0 3 tp2: 0 0 3 -17: npt1: 0 0 3 npt2: 0 0 4 -17: Pt1: 0 0 3 Pt2: 6.12323e-17 0 4 -17: **************************************** -17: testFromQuaternion -17: **************************************** - 9/236 Test #17: testTransforms ......................... Passed 0.02 sec -test 21 - Start 21: testPyGeometry - -21: Test command: /usr/bin/python3 "/build/reproducible-path/rdkit-202409.4/Code/Geometry/Wrap/testGeometry.py" -21: Working Directory: /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/Geometry/Wrap -21: Test timeout computed to be: 1500 -20: Randomness seeded to: 1221693481 -20: =============================================================================== -20: All tests passed (50 assertions in 5 test cases) -20: - 10/236 Test #20: geometryTestsCatch ..................... Passed 0.01 sec -test 22 - Start 22: testMatrices - -22: Test command: /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/Numerics/testMatrices -22: Working Directory: /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/Numerics -22: Test timeout computed to be: 1500 -22: [12:42:35] ----------------------------------------- -22: [12:42:35] Testing RDNumerics: vectors and matrices Code -22: [12:42:35] --------------------------------------- -22: [12:42:35] test1Vector -22: [12:42:35] --------------------------------------- -22: [12:42:35] test2Matrix -22: [12:42:35] --------------------------------------- -22: [12:42:35] test3SquareMatrix -22: [12:42:35] --------------------------------------- -22: [12:42:35] test4SymmMatrix - 11/236 Test #22: testMatrices ........................... Passed 0.01 sec -test 23 - Start 23: testConrec - -23: Test command: /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/Numerics/testConrec -23: Working Directory: /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/Numerics -23: Test timeout computed to be: 1500 -18: *********************************************************** -18: Testing Grid -18: --------------------------------- -18: testUniformGrid1 -18: -18: --------------------------------- -18: testUniformGrid2 -18: -18: --------------------------------- -18: testUniformGridPickling -18: -18: --------------------------------- -18: testGridOps -18: -18: --------------------------------- -18: testUniformGridIndexing -18: - 12/236 Test #18: testGrid ............................... Passed 0.03 sec -test 24 - Start 24: testAlignment - -24: Test command: /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/Numerics/Alignment/testAlignment -24: Working Directory: /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/Numerics/Alignment -24: Test timeout computed to be: 1500 -19: *********************************************************** -19: Testing RealValueGrid3D -19: --------------------------------- -19: test1UniformRealValueGrid3D -19: -19: --------------------------------- -19: test2UniformRealValueGrid3DPickling -19: -19: --------------------------------- -19: test3UniformRealValueGrid3DIndexing -19: -19: --------------------------------- -19: test4UniformRealValueGrid3DOps -19: - 13/236 Test #19: testRealValueGrid ...................... Passed 0.04 sec -test 25 - Start 25: pyAlignment - -25: Test command: /usr/bin/python3 "/build/reproducible-path/rdkit-202409.4/Code/Numerics/Alignment/Wrap/testAlignment.py" -25: Working Directory: /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/Numerics/Alignment/Wrap -25: Test timeout computed to be: 1500 -24: ----------------------------------------- -24: Testing Alignment Code -24: --------------------------------------- -24: testBasic -24: --------------------------------------- -24: testTriangle -24: --------------------------------------- -24: testFourPts -24: --------------------------------------- -24: testReflection -24: --------------------------------------- - 14/236 Test #24: testAlignment .......................... Passed 0.01 sec -test 26 - Start 26: testOptimizer - -26: Test command: /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/Numerics/Optimizer/testOptimizer -26: Working Directory: /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/Numerics/Optimizer -26: Test timeout computed to be: 1500 -26: ------------------------------------- -26: Testing linear search. -26: done -26: ------------------------------------- -26: Testing BFGS optimization. -26: done - 15/236 Test #26: testOptimizer .......................... Passed 0.01 sec -test 27 - Start 27: ForceFieldsCatch - -27: Test command: /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/ForceField/ForceFieldsCatch -27: Working Directory: /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/ForceField -27: Test timeout computed to be: 1500 -23: Randomness seeded to: 3510716960 -23: =============================================================================== -23: All tests passed (76 assertions in 3 test cases) -23: - 16/236 Test #23: testConrec ............................. Passed 0.03 sec -test 28 - Start 28: testUFFForceField - -28: Test command: /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/ForceField/UFF/testUFFForceField -28: Working Directory: /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/ForceField/UFF -28: Test timeout computed to be: 1500 -27: Randomness seeded to: 143001012 -27: =============================================================================== -27: All tests passed (20 assertions in 2 test cases) -27: -28: ------------------------------------- -28: Unit tests for force field basics. -28: done -28: ------------------------------------- -28: Unit tests for basics of UFF bond-stretch terms. -28: done -28: ------------------------------------- -28: Unit tests for UFF bond-stretch terms. -28: done -28: ------------------------------------- -28: Unit tests for basics of UFF angle terms. -28: done -28: ------------------------------------- -28: Unit tests for UFF angle-bend terms. -28: theta = 3.14159; theta0 = 3.14159 -28: theta = 2.094395, param1.theta0 = 2.094395 -28: done -28: ------------------------------------- -28: Test Simple UFF molecule optimizations. -28: done -28: ------------------------------------- -28: Unit tests for UFF nonbonded terms. -28: done -28: ------------------------------------- -28: Test UFF torsional terms. -28: done -28: ------------------------------------- -28: Test UFF Parameter objects -28: ------------------------------------- -28: Test Simple UFF molecule optimization, part 2. -28: done -28: ------------------------------------- -28: Test UFF Torsion Conflicts. -28: C 0.4783 -0.7477 -0.0753 -28: C -0.5465 -0.0176 0.3519 -28: C -0.5114 1.4472 0.0870 -28: H -1.5201 -0.4838 0.2485 -28: H 0.4696 1.8363 0.3367 -28: O -1.2618 1.9423 0.6934 -28: F -0.7163 1.6298 -0.9622 -28: done -28: ------------------------------------- -28: Unit tests for UFF distance constraint terms. -28: done -28: ------------------------------------- -28: Unit tests for all UFF constraint terms. - 17/236 Test #27: ForceFieldsCatch ....................... Passed 0.03 sec -test 29 - Start 29: testMMFFForceField - -29: Test command: /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/ForceField/MMFF/testMMFFForceField -29: Working Directory: /build/reproducible-path/rdkit-202409.4/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. 1: cyclosporine a 1: RDKit 2D 1: @@ -16307,18 +15920,374 @@ 1: 30 11 1 0 1: M END 1: -28: done -28: ------------------------------------- -28: Unit test for UFF butane scan. - 18/236 Test #1: testCoordGen ........................... Passed 0.20 sec -test 30 - Start 30: pyForceFieldConstraints +3: [21:37:26] Testing Github940: property dictionaries leaking memory +3: [21:37:26] done +3: Testing RDValue +3: Testing RDAny +3: dict set int vect +3: dict get int vect +3: static boost any:0.000218 s +3: dynamic boost any:0.001081 s +3: static RDAny:0.000144 s +3: dynamic RDAny:0.001092 s +3: static RDValue:1e-06 s +3: dynamic RDValue:0.000177 s +3: deleted! +3: [21:37:26] ------------------------------------- +3: [21:37:26] Testing String Pickle Roundtrips. +3: [21:37:26] done +3: [21:37:26] ------------------------------------- +3: [21:37:26] Testing conversion of vect to string. +3: [21:37:26] done +3: [21:37:26] ------------------------------------- +3: [21:37:26] Testing returning const references. +3: [21:37:26] any cast +3: [21:37:26] done: 0.000787 300000 +3: [21:37:26] copy +3: [21:37:26] done: 0.000801 300000 +3: [21:37:26] ref +3: [21:37:26] done: 0.000767 300000 +3: [21:37:26] dict +3: [21:37:26] done: 0.001885 300000 +3: [21:37:26] ref with hasVal +3: [21:37:26] done: 0.001234 300000 +3: [21:37:26] done +3: [21:37:26] ------------------------------------- +3: [21:37:26] Testing dict update. +3: [21:37:26] done +3: deleted! +3: deleted! +3: deleted! +3: deleted! +3: deleted! +3: deleted! +4: -- running tests -- +4: min: -2147483648 -2147483648 +4: min: 0 0 +4: min: 2.22507e-308 2.22507e-308 +4: min: 1.17549e-38 1.17549e-38 +4: min: 0 0 +4: == int +4: == double +4: == float +4: == unsigned int +4: == bool +4: == std::string +5: [21:37:26] +5: ----------------------------------------- +5: [21:37:26] Finished: testPushAndPop() +5: [21:37:26] +5: ----------------------------------------- +5: [21:37:26] +5: ----------------------------------------- +6: Randomness seeded to: 4284678684 +6: =============================================================================== +6: All tests passed (32 assertions in 2 test cases) +6: +7: [21:37:26] should not be silent +7: [21:37:26] should not be silent +7: Randomness seeded to: 1734721434 +7: [21:37:26] should not be silent +7: [21:37:26] should not be silent +7: [21:37:26] should not be silent +7: [21:37:26] should not be silent +7: [21:37:26] should not be silent +7: [21:37:26] should not be silent +7: [21:37:26] should not be silent +7: [21:37:26] should not be silent +7: =============================================================================== +7: All tests passed (26 assertions in 3 test cases) +7: +8: [21:37:26] pass +8: [21:37:26] v3 4 +8: [21:37:26] v4 5 +8: [21:37:26] SPARSE ----------------------------------- +8: [21:37:26] Set 10: 0 +8: [21:37:26] Set 11: 0 +8: [21:37:26] Set 14: 0 +8: [21:37:26] Set 10: 1 +8: [21:37:26] Get 14: 1 +8: [21:37:26] Num: 20 +8: [21:37:26] NumOn: 3 +8: [21:37:26] NumOff: 17 +8: 10, 11, 14, +8: [21:37:26] t2[19]: 0 +8: [21:37:26] t2[14]: 1 +8: [21:37:26] t2[19]: 0 +8: [21:37:26] t2[14]: 0 +8: t1: 10, 11, 14, +8: t2: 10, 11, 15, 17, +8: t1|t2: 10, 11, 14, 15, 17, +8: t1&t2: 10, 11, +8: t1^t2: 14, 15, 17, +8: ~t1: 0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 12, 13, 15, 16, 17, 18, 19, +8: except +8: [21:37:26] Explicit ---------------------------------- +8: [21:37:26] Set 10: 0 +8: [21:37:26] Set 11: 0 +8: [21:37:26] Set 14: 0 +8: [21:37:26] Set 10: 1 +8: [21:37:26] Get 14: 1 +8: [21:37:26] Num: 20 +8: [21:37:26] NumOn: 3 +8: [21:37:26] NumOff: 17 +8: 10, 11, 14, +8: [21:37:26] t2[19]: 0 +8: [21:37:26] t2[14]: 1 +8: [21:37:26] t2[19]: 0 +8: [21:37:26] t2[14]: 0 +8: t1: 10, 11, 14, +8: t2: 10, 11, 15, 17, +8: t1|t2: 10, 11, 14, 15, 17, +8: t1&t2: 10, 11, +8: t1^t2: 14, 15, 17, +8: ~t1: 0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 12, 13, 15, 16, 17, 18, 19, +8: except +8: [21:37:26] Done +8: [21:37:26] Test DiscreteValue Vectors 1 ---------------------------- +8: [21:37:26] Expected failure: Value out of range +8: [21:37:26] Expected failure: Value out of range +8: [21:37:26] Expected failure: Value out of range +8: [21:37:26] Expected failure: Value out of range +8: [21:37:26] Expected failure: Value out of range +8: [21:37:26] Test DiscreteValue Vectors 2 ------------------------------ +8: [21:37:26] Test DiscreteValue Vectors 3 --------------------------- +8: [21:37:26] Test DiscreteValue Operations ----------------------------- +8: [21:37:26] Test DiscreteValue Operations 2 -------------------------- +8: [21:37:26] Test SparseIntVect ------------------------------------ +8: [21:37:26] Test SparseIntVect Serialization -------------------------- +8: [21:37:26] Test BitVect Serialization ------------------------------- +8: [21:37:26] Test BitVect to FPS ------------------------------- +8: [21:37:26] Test BitVect to binary string ------------------------------- +8: [21:37:26] Test Similarity Measures BitVect ------------------------------- +8: [21:37:26] Test Similarity Measures SparseBitVect ------------------------------- +8: [21:37:26] Test BitVect with all ones ------------------------------- +8: [21:37:26] Test Explicit BitVects: Concatenation Operation ------------------------------- +8: [21:37:26] Test bitmap operations ------------------------------- +8: [21:37:26] Test bitmaps as properties ------------------------------- +8: [21:37:26] Test #3944: SparseIntVect copy constructor and assignment operators not clearing existing data------------------------------- +8: [21:37:26] Test RealValue Vectors 1: Constructors and Accessing Values ------------------------------- +8: [21:37:26] Test RealValue Vectors 2: L1Norm ------------------------------- +8: [21:37:26] Test RealValue Vectors 3: Pickles ------------------------------- +8: [21:37:26] Test RealValue Vectors 4: Vector Operations ------------------------------- +11: Randomness seeded to: 2192882402 +11: =============================================================================== +11: All tests passed (3 assertions in 1 test case) +11: + 1/236 Test #3: testDict ............................... Passed 0.19 sec + 2/236 Test #4: testRDValue ............................ Passed 0.17 sec + 3/236 Test #6: dictTestsCatch ......................... Passed 0.15 sec + 4/236 Test #7: logTestsCatch .......................... Passed 0.13 sec + 5/236 Test #8: testDataStructs ........................ Passed 0.11 sec + 6/236 Test #9: testFPB ................................ Passed 0.10 sec + 7/236 Test #11: catchDataStructs ....................... Passed 0.06 sec + 8/236 Test #1: testCoordGen ........................... Passed 0.22 sec +test 13 + Start 13: pyDiscreteValueVect -30: Test command: /usr/bin/python3 "/build/reproducible-path/rdkit-202409.4/Code/ForceField/Wrap/testConstraints.py" -30: Working Directory: /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/ForceField/Wrap -30: Test timeout computed to be: 1500 -29: -29: Computing MMFF94 energies for /build/reproducible-path/rdkit-202409.4/Code/ForceField/MMFF/test_data/MMFF94_dative.sdf... +13: Test command: /usr/bin/python3 "/build/reproducible-path/rdkit-202409.4/Code/DataStructs/Wrap/testDiscreteValueVect.py" +13: Working Directory: /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/DataStructs/Wrap +13: Test timeout computed to be: 1500 +test 14 + Start 14: pyRealValueVect + +14: Test command: /usr/bin/python3 "/build/reproducible-path/rdkit-202409.4/Code/DataStructs/Wrap/testRealValueVect.py" +14: Working Directory: /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/DataStructs/Wrap +14: Test timeout computed to be: 1500 +test 15 + Start 15: pySparseIntVect + +15: Test command: /usr/bin/python3 "/build/reproducible-path/rdkit-202409.4/Code/DataStructs/Wrap/testSparseIntVect.py" +15: Working Directory: /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/DataStructs/Wrap +15: Test timeout computed to be: 1500 +test 16 + Start 16: pyFPB + +16: Test command: /usr/bin/python3 "/build/reproducible-path/rdkit-202409.4/Code/DataStructs/Wrap/testFPB.py" +16: Working Directory: /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/DataStructs/Wrap +16: Test timeout computed to be: 1500 +test 17 + Start 17: testTransforms + +17: Test command: /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/Geometry/testTransforms +17: Working Directory: /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/Geometry +17: Test timeout computed to be: 1500 +test 18 + Start 18: testGrid + +18: Test command: /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/Geometry/testGrid +18: Working Directory: /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/Geometry +18: Test timeout computed to be: 1500 +test 19 + Start 19: testRealValueGrid + +19: Test command: /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/Geometry/testRealValueGrid +19: Working Directory: /build/reproducible-path/rdkit-202409.4/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-202409.4/obj-aarch64-linux-gnu/Code/Geometry/geometryTestsCatch +20: Working Directory: /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/Geometry +20: Test timeout computed to be: 1500 +17: **************************************** +17: testPointND +17: **************************************** +17: testPointOps3D +17: **************************************** +17: testPointOps2D +17: **************************************** +17: test12D +17: ref1: 0.291405 4.4636 ref2: 1.62979 4.16774 +17: pt1: 3.88876 3.57953 pt2: 0.513501 1.96862 +17: **************************************** +17: test23D +17: **************************************** +17: test3MatMultiply +17: Pt1: 1 0 0 Pt2: 2 0 0 +17: -Pt1: -1 -0 -0 +17: tp1: 0 0 0 tp2: 0 0 0 +17: tp1: 0 0 0 tp2: 0 0 0 +17: tp1: 0 0 3 tp2: 0 0 3 +17: npt1: 0 0 3 npt2: 0 0 4 +17: Pt1: 0 0 3 Pt2: 6.12323e-17 0 4 +17: **************************************** +17: testFromQuaternion +17: **************************************** +18: *********************************************************** +18: Testing Grid +18: --------------------------------- +18: testUniformGrid1 +18: +18: --------------------------------- +18: testUniformGrid2 +18: +18: --------------------------------- +18: testUniformGridPickling +18: +18: --------------------------------- +18: testGridOps +18: +18: --------------------------------- +18: testUniformGridIndexing +18: + 9/236 Test #10: testMultiFPB ........................... Passed 0.20 sec + 10/236 Test #17: testTransforms ......................... Passed 0.05 sec + 11/236 Test #18: testGrid ............................... Passed 0.05 sec +test 21 + Start 21: testPyGeometry + +21: Test command: /usr/bin/python3 "/build/reproducible-path/rdkit-202409.4/Code/Geometry/Wrap/testGeometry.py" +21: Working Directory: /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/Geometry/Wrap +21: Test timeout computed to be: 1500 +test 22 + Start 22: testMatrices + +22: Test command: /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/Numerics/testMatrices +22: Working Directory: /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/Numerics +22: Test timeout computed to be: 1500 +test 23 + Start 23: testConrec + +23: Test command: /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/Numerics/testConrec +23: Working Directory: /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/Numerics +23: Test timeout computed to be: 1500 +2: .... +2: ---------------------------------------------------------------------- +2: Ran 4 tests in 0.024s +2: +2: OK +20: Randomness seeded to: 3489945012 +20: =============================================================================== +20: All tests passed (50 assertions in 5 test cases) +20: +19: *********************************************************** +19: Testing RealValueGrid3D +19: --------------------------------- +19: test1UniformRealValueGrid3D +19: +19: --------------------------------- +19: test2UniformRealValueGrid3DPickling +19: +19: --------------------------------- +19: test3UniformRealValueGrid3DIndexing +19: +19: --------------------------------- +19: test4UniformRealValueGrid3DOps +19: +22: [21:37:27] ----------------------------------------- +22: [21:37:27] Testing RDNumerics: vectors and matrices Code +22: [21:37:27] --------------------------------------- +22: [21:37:27] test1Vector +22: [21:37:27] --------------------------------------- +22: [21:37:27] test2Matrix +22: [21:37:27] --------------------------------------- +22: [21:37:27] test3SquareMatrix +22: [21:37:27] --------------------------------------- +22: [21:37:27] test4SymmMatrix + 12/236 Test #19: testRealValueGrid ...................... Passed 0.09 sec + 13/236 Test #20: geometryTestsCatch ..................... Passed 0.07 sec + 14/236 Test #22: testMatrices ........................... Passed 0.03 sec +test 24 + Start 24: testAlignment + +24: Test command: /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/Numerics/Alignment/testAlignment +24: Working Directory: /build/reproducible-path/rdkit-202409.4/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-202409.4/Code/Numerics/Alignment/Wrap/testAlignment.py" +25: Working Directory: /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/Numerics/Alignment/Wrap +25: Test timeout computed to be: 1500 +test 26 + Start 26: testOptimizer + +26: Test command: /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/Numerics/Optimizer/testOptimizer +26: Working Directory: /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/Numerics/Optimizer +26: Test timeout computed to be: 1500 +23: Randomness seeded to: 278540209 +23: =============================================================================== +23: All tests passed (76 assertions in 3 test cases) +23: +24: ----------------------------------------- +24: Testing Alignment Code +24: --------------------------------------- +24: testBasic +24: --------------------------------------- +24: testTriangle +24: --------------------------------------- +24: testFourPts +24: --------------------------------------- +24: testReflection +24: --------------------------------------- +26: ------------------------------------- +26: Testing linear search. +26: done +26: ------------------------------------- +26: Testing BFGS optimization. +26: done + 15/236 Test #23: testConrec ............................. Passed 0.08 sec + 16/236 Test #24: testAlignment .......................... Passed 0.06 sec + 17/236 Test #26: testOptimizer .......................... Passed 0.01 sec +test 27 + Start 27: ForceFieldsCatch + +27: Test command: /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/ForceField/ForceFieldsCatch +27: Working Directory: /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/ForceField +27: Test timeout computed to be: 1500 +test 28 + Start 28: testUFFForceField + +28: Test command: /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/ForceField/UFF/testUFFForceField +28: Working Directory: /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/ForceField/UFF +28: Test timeout computed to be: 1500 +test 29 + Start 29: testMMFFForceField + +29: Test command: /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/ForceField/MMFF/testMMFFForceField +29: Working Directory: /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/ForceField/MMFF +29: Test timeout computed to be: 1500 13: ...... 13: ---------------------------------------------------------------------- 13: Ran 6 tests in 0.002s @@ -16329,28 +16298,85 @@ 14: Ran 6 tests in 0.001s 14: 14: OK -16: ......... -16: ---------------------------------------------------------------------- -16: Ran 9 tests in 0.004s -16: -16: OK -15: ......... -15: ---------------------------------------------------------------------- -15: Ran 9 tests in 0.004s -15: -15: OK -2: .... -2: ---------------------------------------------------------------------- -2: Ran 4 tests in 0.016s -2: -2: OK - 19/236 Test #13: pyDiscreteValueVect .................... Passed 0.23 sec +27: Randomness seeded to: 4237235113 +27: =============================================================================== +27: All tests passed (20 assertions in 2 test cases) +27: +28: ------------------------------------- +28: Unit tests for force field basics. +28: done +28: ------------------------------------- +28: Unit tests for basics of UFF bond-stretch terms. +28: done +28: ------------------------------------- +28: Unit tests for UFF bond-stretch terms. +28: done +28: ------------------------------------- +28: Unit tests for basics of UFF angle terms. +28: done +28: ------------------------------------- +28: Unit tests for UFF angle-bend terms. +28: theta = 3.14159; theta0 = 3.14159 +28: theta = 2.094395, param1.theta0 = 2.094395 +28: done +28: ------------------------------------- +28: Test Simple UFF molecule optimizations. +28: done +28: ------------------------------------- +28: Unit tests for UFF nonbonded terms. +28: done +28: ------------------------------------- +28: Test UFF torsional terms. +28: done +28: ------------------------------------- +28: Test UFF Parameter objects + 18/236 Test #2: pyCoordGen ............................. Passed 0.49 sec + 19/236 Test #27: ForceFieldsCatch ....................... Passed 0.05 sec +28: ------------------------------------- +28: Test Simple UFF molecule optimization, part 2. +28: done +28: ------------------------------------- +28: Test UFF Torsion Conflicts. +28: C 0.4783 -0.7477 -0.0753 +28: C -0.5465 -0.0176 0.3519 +28: C -0.5114 1.4472 0.0870 +28: H -1.5201 -0.4838 0.2485 +28: H 0.4696 1.8363 0.3367 +28: O -1.2618 1.9423 0.6934 +28: F -0.7163 1.6298 -0.9622 +28: done +28: ------------------------------------- +28: Unit tests for UFF distance constraint terms. +28: done +28: ------------------------------------- +28: Unit tests for all UFF constraint terms. +test 30 + Start 30: pyForceFieldConstraints + +30: Test command: /usr/bin/python3 "/build/reproducible-path/rdkit-202409.4/Code/ForceField/Wrap/testConstraints.py" +30: Working Directory: /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/ForceField/Wrap +30: Test timeout computed to be: 1500 test 31 Start 31: testDistGeom 31: Test command: /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/DistGeom/testDistGeom 31: Working Directory: /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/DistGeom 31: Test timeout computed to be: 1500 +29: ------------------------------------- +29: Official MMFF validation suite. + 20/236 Test #13: pyDiscreteValueVect .................... Passed 0.33 sec +test 32 + Start 32: pyDistGeom + +32: Test command: /usr/bin/python3 "/build/reproducible-path/rdkit-202409.4/Code/DistGeom/Wrap/rough_test.py" +32: Working Directory: /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/DistGeom/Wrap +32: Test timeout computed to be: 1500 +28: done +28: ------------------------------------- +28: Unit tests for copying UFF ForceFields. +28: done +28: ------------------------------------- +28: Unit test for UFF butane scan. 31: *********************************************************** 31: test1 31: *********************************************************** @@ -16362,52 +16388,20 @@ 31: 1 1 1 0 31: *********************************************************** 31: - 20/236 Test #14: pyRealValueVect ........................ Passed 0.24 sec -test 32 - Start 32: pyDistGeom - -32: Test command: /usr/bin/python3 "/build/reproducible-path/rdkit-202409.4/Code/DistGeom/Wrap/rough_test.py" -32: Working Directory: /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/DistGeom/Wrap -32: Test timeout computed to be: 1500 -25: ..... -25: ---------------------------------------------------------------------- -25: Ran 5 tests in 0.001s -25: -25: OK -25: Testing Alignment Wrapper code: - 21/236 Test #31: testDistGeom ........................... Passed 0.01 sec + 21/236 Test #31: testDistGeom ........................... Passed 0.05 sec test 33 Start 33: graphmolTest1 33: Test command: /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTest1 33: Working Directory: /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/GraphMol 33: Test timeout computed to be: 1500 -28: done - 22/236 Test #28: testUFFForceField ...................... Passed 0.18 sec + 22/236 Test #14: pyRealValueVect ........................ Passed 0.34 sec test 34 Start 34: graphmolcpTest 34: Test command: /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/GraphMol/graphmolcpTest 34: Working Directory: /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/GraphMol 34: Test timeout computed to be: 1500 - 23/236 Test #16: pyFPB .................................. Passed 0.25 sec -test 35 - Start 35: graphmolqueryTest - -35: Test command: /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/GraphMol/graphmolqueryTest -35: Working Directory: /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/GraphMol -35: Test timeout computed to be: 1500 -34: -34: -34: -34: COPY - 24/236 Test #15: pySparseIntVect ........................ Passed 0.25 sec -test 36 - Start 36: graphmolMolOpsTest - -36: Test command: /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/GraphMol/graphmolMolOpsTest -36: Working Directory: /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/GraphMol -36: Test timeout computed to be: 1500 33: Atoms: 33: 0 8 O chg: 0 deg: 2 exp: 2 imp: 0 hyb: 33: 1 6 C chg: 0 deg: 2 exp: 3 imp: 1 hyb: @@ -16426,7 +16420,7 @@ 33: 4 5->6 order: 3 33: 5 6->7 order: 1 33: 6 7->8 order: 2 -33: [12:42:35] +33: [21:37:27] 33: 33: **** 33: Pre-condition Violation @@ -16438,15 +16432,15 @@ 33: 0# Invar::Invariant::toString[abi:cxx11]() const in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu//lib/libRDKitRDGeneral.so.1 33: 1# Invar::operator<<(std::ostream&, Invar::Invariant const&) in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu//lib/libRDKitRDGeneral.so.1 33: 2# RDKit::RWMol::addBond(unsigned int, unsigned int, RDKit::Bond::BondType) in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu//lib/libRDKitGraphMol.so.1 -33: 3# 0x0000AAAABDBCB100 in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTest1 -33: 4# 0x0000AAAABDBC373C in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTest1 -33: 5# 0x0000FFFF9B9E229C in /lib/aarch64-linux-gnu/libc.so.6 +33: 3# 0x0000AAAACE82B100 in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTest1 +33: 4# 0x0000AAAACE82373C in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTest1 +33: 5# 0x0000FFFF9BD7229C in /lib/aarch64-linux-gnu/libc.so.6 33: 6# __libc_start_main in /lib/aarch64-linux-gnu/libc.so.6 -33: 7# 0x0000AAAABDBC3830 in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTest1 +33: 7# 0x0000AAAACE823830 in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTest1 33: ---------- 33: **** 33: -33: [12:42:35] +33: [21:37:27] 33: 33: **** 33: Pre-condition Violation @@ -16458,15 +16452,15 @@ 33: 0# Invar::Invariant::toString[abi:cxx11]() const in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu//lib/libRDKitRDGeneral.so.1 33: 1# Invar::operator<<(std::ostream&, Invar::Invariant const&) in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu//lib/libRDKitRDGeneral.so.1 33: 2# RDKit::RWMol::addBond(unsigned int, unsigned int, RDKit::Bond::BondType) in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu//lib/libRDKitGraphMol.so.1 -33: 3# 0x0000AAAABDBCB320 in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTest1 -33: 4# 0x0000AAAABDBC373C in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTest1 -33: 5# 0x0000FFFF9B9E229C in /lib/aarch64-linux-gnu/libc.so.6 +33: 3# 0x0000AAAACE82B320 in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTest1 +33: 4# 0x0000AAAACE82373C in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTest1 +33: 5# 0x0000FFFF9BD7229C in /lib/aarch64-linux-gnu/libc.so.6 33: 6# __libc_start_main in /lib/aarch64-linux-gnu/libc.so.6 -33: 7# 0x0000AAAABDBC3830 in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTest1 +33: 7# 0x0000AAAACE823830 in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTest1 33: ---------- 33: **** 33: -33: [12:42:35] +33: [21:37:27] 33: 33: **** 33: Pre-condition Violation @@ -16478,15 +16472,15 @@ 33: 0# Invar::Invariant::toString[abi:cxx11]() const in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu//lib/libRDKitRDGeneral.so.1 33: 1# Invar::operator<<(std::ostream&, Invar::Invariant const&) in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu//lib/libRDKitRDGeneral.so.1 33: 2# RDKit::RWMol::addBond(unsigned int, unsigned int, RDKit::Bond::BondType) in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu//lib/libRDKitGraphMol.so.1 -33: 3# 0x0000AAAABDBCB414 in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTest1 -33: 4# 0x0000AAAABDBC373C in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTest1 -33: 5# 0x0000FFFF9B9E229C in /lib/aarch64-linux-gnu/libc.so.6 +33: 3# 0x0000AAAACE82B414 in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTest1 +33: 4# 0x0000AAAACE82373C in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTest1 +33: 5# 0x0000FFFF9BD7229C in /lib/aarch64-linux-gnu/libc.so.6 33: 6# __libc_start_main in /lib/aarch64-linux-gnu/libc.so.6 -33: 7# 0x0000AAAABDBC3830 in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTest1 +33: 7# 0x0000AAAACE823830 in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTest1 33: ---------- 33: **** 33: -33: [12:42:35] +33: [21:37:27] 33: 33: **** 33: Pre-condition Violation @@ -16498,15 +16492,15 @@ 33: 0# Invar::Invariant::toString[abi:cxx11]() const in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu//lib/libRDKitRDGeneral.so.1 33: 1# Invar::operator<<(std::ostream&, Invar::Invariant const&) in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu//lib/libRDKitRDGeneral.so.1 33: 2# RDKit::ROMol::addBond(RDKit::Bond*, bool) in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu//lib/libRDKitGraphMol.so.1 -33: 3# 0x0000AAAABDBCB454 in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTest1 -33: 4# 0x0000AAAABDBC373C in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTest1 -33: 5# 0x0000FFFF9B9E229C in /lib/aarch64-linux-gnu/libc.so.6 +33: 3# 0x0000AAAACE82B454 in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTest1 +33: 4# 0x0000AAAACE82373C in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTest1 +33: 5# 0x0000FFFF9BD7229C in /lib/aarch64-linux-gnu/libc.so.6 33: 6# __libc_start_main in /lib/aarch64-linux-gnu/libc.so.6 -33: 7# 0x0000AAAABDBC3830 in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTest1 +33: 7# 0x0000AAAACE823830 in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTest1 33: ---------- 33: **** 33: -33: [12:42:35] +33: [21:37:27] 33: 33: **** 33: Pre-condition Violation @@ -16518,62 +16512,22 @@ 33: 0# Invar::Invariant::toString[abi:cxx11]() const in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu//lib/libRDKitRDGeneral.so.1 33: 1# Invar::operator<<(std::ostream&, Invar::Invariant const&) in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu//lib/libRDKitRDGeneral.so.1 33: 2# RDKit::ROMol::addBond(RDKit::Bond*, bool) in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu//lib/libRDKitGraphMol.so.1 -33: 3# 0x0000AAAABDBCB59C in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTest1 -33: 4# 0x0000AAAABDBC373C in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTest1 -33: 5# 0x0000FFFF9B9E229C in /lib/aarch64-linux-gnu/libc.so.6 +33: 3# 0x0000AAAACE82B59C in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTest1 +33: 4# 0x0000AAAACE82373C in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTest1 +33: 5# 0x0000FFFF9BD7229C in /lib/aarch64-linux-gnu/libc.so.6 33: 6# __libc_start_main in /lib/aarch64-linux-gnu/libc.so.6 -33: 7# 0x0000AAAABDBC3830 in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTest1 +33: 7# 0x0000AAAACE823830 in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTest1 33: ---------- 33: **** 33: -33: [12:42:35] Explicit valence for atom # 0 B, 4, is greater than permitted -33: [12:42:35] Explicit valence for atom # 0 B, 4, is greater than permitted -35: [12:42:35] ---------------------- Test1 - 25/236 Test #34: graphmolcpTest ......................... Passed 0.01 sec -test 37 - Start 37: graphmoltestChirality - -37: Test command: /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/GraphMol/graphmoltestChirality -37: Working Directory: /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/GraphMol -37: Test timeout computed to be: 1500 -35: [12:42:35] Done! -35: [12:42:35] ---------------------- Test2 -35: [12:42:35] Done! -35: [12:42:35] ---------------------- Test3 -35: [12:42:35] Done! -35: [12:42:35] ---------------------- Test4 -35: [12:42:35] Done! -35: [12:42:35] ---------------------- Test5 -35: [12:42:35] Done! -35: [12:42:35] Done! -35: [12:42:35] ---------------------- Test issue 2892580 -35: [12:42:35] Done! -35: [12:42:35] ---------------------- Test github issue 53: query molecules not matching [R] -35: [12:42:35] Done! -35: [12:42:35] ---------------------- Test queries using qualifiers instead of == -35: [12:42:35] Done! -35: [12:42:35] ---------------------- Test Github issue 165: radicals not used in atom-atom matching -35: [12:42:35] Done! -35: [12:42:35] ---------------------- Test extra atom queries -35: [12:42:35] Done! -35: [12:42:35] ---------------------- Test extra bond queries -35: [12:42:35] Done! -35: [12:42:35] ---------------------- Test num heteroatom neighbor queries -35: [12:42:35] Done! -35: [12:42:35] ---------------------- Test atom type queries -35: [12:42:35] Done! -35: [12:42:35] ---------------------- Test Github #2471: dummy atom queries are flagged as complex -35: [12:42:35] Done! -35: [12:42:35] ---------------------- Testing hasBondTypeQuery() and hasComplexBondTypeQuery() -35: [12:42:35] Done! - 26/236 Test #35: graphmolqueryTest ...................... Passed 0.01 sec -test 38 - Start 38: graphmoltestPickler - -38: Test command: /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/GraphMol/graphmoltestPickler -38: Working Directory: /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/GraphMol -38: Test timeout computed to be: 1500 -33: [12:42:35] +33: [21:37:27] Explicit valence for atom # 0 B, 4, is greater than permitted +33: [21:37:27] Explicit valence for atom # 0 B, 4, is greater than permitted +15: ......... +15: ---------------------------------------------------------------------- +15: Ran 9 tests in 0.011s +15: +15: OK +33: [21:37:27] 33: 33: **** 33: Post-condition Violation @@ -16585,44 +16539,70 @@ 33: 0# Invar::Invariant::toString[abi:cxx11]() const in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu//lib/libRDKitRDGeneral.so.1 33: 1# Invar::operator<<(std::ostream&, Invar::Invariant const&) in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu//lib/libRDKitRDGeneral.so.1 33: 2# RDKit::PeriodicTable::getAtomicNumber(std::__cxx11::basic_string, std::allocator > const&) const in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTest1 -33: 3# 0x0000AAAABDBF6168 in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTest1 -33: 4# 0x0000AAAABDBD9CB8 in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTest1 -33: 5# 0x0000AAAABDBC3748 in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTest1 -33: 6# 0x0000FFFF9B9E229C in /lib/aarch64-linux-gnu/libc.so.6 +33: 3# 0x0000AAAACE856168 in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTest1 +33: 4# 0x0000AAAACE839CB8 in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTest1 +33: 5# 0x0000AAAACE823748 in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTest1 +33: 6# 0x0000FFFF9BD7229C in /lib/aarch64-linux-gnu/libc.so.6 33: 7# __libc_start_main in /lib/aarch64-linux-gnu/libc.so.6 -33: 8# 0x0000AAAABDBC3830 in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTest1 +33: 8# 0x0000AAAACE823830 in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTest1 33: ---------- 33: **** 33: -33: [12:42:35] ------------------------------------- -33: [12:42:35] Test github381: thread-safe initialization of the periodic table -36: 1 1 2 -36: 1 1 1 -36: 2 1 0.75 -36: path: 2 -36: [12:42:35] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 10 ignored -36: [12:42:35] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 10 ignored -38: [12:42:35] ------------------------------------- -38: [12:42:35] Testing String Pickle Roundtrips. -37: -------------------------- -37: -------------------------- -37: C/C=C/C(C)Cl - 27/236 Test #2: pyCoordGen ............................. Passed 0.32 sec -test 39 - Start 39: graphmoltestPicklerGlobalSetting +33: [21:37:27] ------------------------------------- +33: [21:37:27] Test github381: thread-safe initialization of the periodic table +34: +34: +34: +34: COPY +29: +29: Computing MMFF94 energies for /build/reproducible-path/rdkit-202409.4/Code/ForceField/MMFF/test_data/MMFF94_dative.sdf... + 23/236 Test #34: graphmolcpTest ......................... Passed 0.04 sec +test 35 + Start 35: graphmolqueryTest -39: Test command: /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/GraphMol/graphmoltestPicklerGlobalSetting -39: Working Directory: /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/GraphMol -39: Test timeout computed to be: 1500 -36: [12:42:35] Explicit valence for atom # 0 B, 5, is greater than permitted -36: [12:42:35] Explicit valence for atom # 1 C, 5, is greater than permitted -36: [12:42:35] Explicit valence for atom # 1 C, 5, is greater than permitted -36: [12:42:35] Explicit valence for atom # 1 C, 5, is greater than permitted -36: [12:42:35] Explicit valence for atom # 1 Si, 7, is greater than permitted -33: [12:42:35] done -33: [12:42:35] ------------------------------------- -33: [12:42:35] Test github1041: Segfault for atom with no owner (expect some warnings) -33: [12:42:35] +35: Test command: /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/GraphMol/graphmolqueryTest +35: Working Directory: /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/GraphMol +35: Test timeout computed to be: 1500 +35: [21:37:27] ---------------------- Test1 +35: [21:37:27] Done! +35: [21:37:27] ---------------------- Test2 +35: [21:37:27] Done! +35: [21:37:27] ---------------------- Test3 +35: [21:37:27] Done! +35: [21:37:27] ---------------------- Test4 +35: [21:37:27] Done! +35: [21:37:27] ---------------------- Test5 +35: [21:37:27] Done! +35: [21:37:27] Done! +35: [21:37:27] ---------------------- Test issue 2892580 +35: [21:37:27] Done! +35: [21:37:27] ---------------------- Test github issue 53: query molecules not matching [R] +35: [21:37:27] Done! +35: [21:37:27] ---------------------- Test queries using qualifiers instead of == +35: [21:37:27] Done! +35: [21:37:27] ---------------------- Test Github issue 165: radicals not used in atom-atom matching +35: [21:37:27] Done! +35: [21:37:27] ---------------------- Test extra atom queries +35: [21:37:27] Done! +35: [21:37:27] ---------------------- Test extra bond queries +35: [21:37:27] Done! +35: [21:37:27] ---------------------- Test num heteroatom neighbor queries +35: [21:37:27] Done! +35: [21:37:27] ---------------------- Test atom type queries +35: [21:37:27] Done! +35: [21:37:27] ---------------------- Test Github #2471: dummy atom queries are flagged as complex +35: [21:37:27] Done! +35: [21:37:27] ---------------------- Testing hasBondTypeQuery() and hasComplexBondTypeQuery() +35: [21:37:27] Done! +16: ......... +16: ---------------------------------------------------------------------- +16: Ran 9 tests in 0.068s +16: +16: OK +33: [21:37:27] done +33: [21:37:27] ------------------------------------- +33: [21:37:27] Test github1041: Segfault for atom with no owner (expect some warnings) +33: [21:37:27] 33: 33: **** 33: Pre-condition Violation @@ -16633,15 +16613,15 @@ 33: Stacktrace: 33: 0# Invar::Invariant::toString[abi:cxx11]() const in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu//lib/libRDKitRDGeneral.so.1 33: 1# Invar::operator<<(std::ostream&, Invar::Invariant const&) in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu//lib/libRDKitRDGeneral.so.1 -33: 2# 0x0000AAAABDBEA398 in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTest1 -33: 3# 0x0000AAAABDBC376C in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTest1 -33: 4# 0x0000FFFF9B9E229C in /lib/aarch64-linux-gnu/libc.so.6 +33: 2# 0x0000AAAACE84A398 in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTest1 +33: 3# 0x0000AAAACE82376C in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTest1 +33: 4# 0x0000FFFF9BD7229C in /lib/aarch64-linux-gnu/libc.so.6 33: 5# __libc_start_main in /lib/aarch64-linux-gnu/libc.so.6 -33: 6# 0x0000AAAABDBC3830 in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTest1 +33: 6# 0x0000AAAACE823830 in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTest1 33: ---------- 33: **** 33: -33: [12:42:35] +33: [21:37:27] 33: 33: **** 33: Pre-condition Violation @@ -16652,18 +16632,18 @@ 33: Stacktrace: 33: 0# Invar::Invariant::toString[abi:cxx11]() const in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu//lib/libRDKitRDGeneral.so.1 33: 1# Invar::operator<<(std::ostream&, Invar::Invariant const&) in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu//lib/libRDKitRDGeneral.so.1 -33: 2# 0x0000AAAABDBEA774 in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTest1 -33: 3# 0x0000AAAABDBC376C in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTest1 -33: 4# 0x0000FFFF9B9E229C in /lib/aarch64-linux-gnu/libc.so.6 +33: 2# 0x0000AAAACE84A774 in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTest1 +33: 3# 0x0000AAAACE82376C in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTest1 +33: 4# 0x0000FFFF9BD7229C in /lib/aarch64-linux-gnu/libc.so.6 33: 5# __libc_start_main in /lib/aarch64-linux-gnu/libc.so.6 -33: 6# 0x0000AAAABDBC3830 in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTest1 +33: 6# 0x0000AAAACE823830 in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTest1 33: ---------- 33: **** 33: -33: [12:42:35] done -33: [12:42:35] ------------------------------------- -33: [12:42:35] Test github1041: Segfault for atom with no owner (expect some warnings) -33: [12:42:35] +33: [21:37:27] done +33: [21:37:27] ------------------------------------- +33: [21:37:27] Test github1041: Segfault for atom with no owner (expect some warnings) +33: [21:37:27] 33: 33: **** 33: Pre-condition Violation @@ -16674,15 +16654,15 @@ 33: Stacktrace: 33: 0# Invar::Invariant::toString[abi:cxx11]() const in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu//lib/libRDKitRDGeneral.so.1 33: 1# Invar::operator<<(std::ostream&, Invar::Invariant const&) in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu//lib/libRDKitRDGeneral.so.1 -33: 2# 0x0000AAAABDBEA398 in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTest1 -33: 3# 0x0000AAAABDBC3770 in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTest1 -33: 4# 0x0000FFFF9B9E229C in /lib/aarch64-linux-gnu/libc.so.6 +33: 2# 0x0000AAAACE84A398 in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTest1 +33: 3# 0x0000AAAACE823770 in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTest1 +33: 4# 0x0000FFFF9BD7229C in /lib/aarch64-linux-gnu/libc.so.6 33: 5# __libc_start_main in /lib/aarch64-linux-gnu/libc.so.6 -33: 6# 0x0000AAAABDBC3830 in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTest1 +33: 6# 0x0000AAAACE823830 in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTest1 33: ---------- 33: **** 33: -33: [12:42:35] +33: [21:37:27] 33: 33: **** 33: Pre-condition Violation @@ -16693,87 +16673,181 @@ 33: Stacktrace: 33: 0# Invar::Invariant::toString[abi:cxx11]() const in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu//lib/libRDKitRDGeneral.so.1 33: 1# Invar::operator<<(std::ostream&, Invar::Invariant const&) in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu//lib/libRDKitRDGeneral.so.1 -33: 2# 0x0000AAAABDBEA774 in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTest1 -33: 3# 0x0000AAAABDBC3770 in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTest1 -33: 4# 0x0000FFFF9B9E229C in /lib/aarch64-linux-gnu/libc.so.6 +33: 2# 0x0000AAAACE84A774 in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTest1 +33: 3# 0x0000AAAACE823770 in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTest1 +33: 4# 0x0000FFFF9BD7229C in /lib/aarch64-linux-gnu/libc.so.6 33: 5# __libc_start_main in /lib/aarch64-linux-gnu/libc.so.6 -33: 6# 0x0000AAAABDBC3830 in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTest1 +33: 6# 0x0000AAAACE823830 in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTest1 33: ---------- 33: **** 33: -33: [12:42:35] done -33: [12:42:35] ------------------------------------- -33: [12:42:35] Test github1453: RWMol.clear() should reset the numBonds count. -33: [12:42:35] done -33: [12:42:35] ------------------------------------- -33: [12:42:35] Test range-based for loops. -33: [12:42:35] done -33: [12:42:35] ------------------------------------- -33: [12:42:35] Test github1642: Atom index type is too low for big molecules. - 28/236 Test #25: pyAlignment ............................ Passed 0.23 sec +33: [21:37:27] done +33: [21:37:27] ------------------------------------- +33: [21:37:27] Test github1453: RWMol.clear() should reset the numBonds count. +33: [21:37:27] done +33: [21:37:27] ------------------------------------- +33: [21:37:27] Test range-based for loops. +33: [21:37:27] done +33: [21:37:27] ------------------------------------- +33: [21:37:27] Test github1642: Atom index type is too low for big molecules. + 24/236 Test #35: graphmolqueryTest ...................... Passed 0.03 sec +test 36 + Start 36: graphmolMolOpsTest + +36: Test command: /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/GraphMol/graphmolMolOpsTest +36: Working Directory: /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/GraphMol +36: Test timeout computed to be: 1500 +36: 1 1 2 +36: 1 1 1 +36: 2 1 0.75 +36: path: 2 +36: [21:37:27] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 10 ignored +36: [21:37:27] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 10 ignored +36: [21:37:27] Explicit valence for atom # 0 B, 5, is greater than permitted +36: [21:37:27] Explicit valence for atom # 1 C, 5, is greater than permitted +36: [21:37:27] Explicit valence for atom # 1 C, 5, is greater than permitted +36: [21:37:27] Explicit valence for atom # 1 C, 5, is greater than permitted +36: [21:37:27] Explicit valence for atom # 1 Si, 7, is greater than permitted +36: smi: Cc1ccc(S(=O)(=O)/N=C2\CC(=N\C(C)(C)C)/C2=N\C(C)(C)C)cc1 +25: ..... +25: ---------------------------------------------------------------------- +25: Ran 5 tests in 0.001s +25: +25: OK +25: Testing Alignment Wrapper code: + 25/236 Test #15: pySparseIntVect ........................ Passed 0.49 sec +test 37 + Start 37: graphmoltestChirality + +37: Test command: /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/GraphMol/graphmoltestChirality +37: Working Directory: /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/GraphMol +37: Test timeout computed to be: 1500 +32: ...... +32: ---------------------------------------------------------------------- +32: Ran 6 tests in 0.001s +32: +32: OK +28: done + 26/236 Test #28: testUFFForceField ...................... Passed 0.29 sec +test 38 + Start 38: graphmoltestPickler + +38: Test command: /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/GraphMol/graphmoltestPickler +38: Working Directory: /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/GraphMol +38: Test timeout computed to be: 1500 +36: [21:37:27] non-ring atom 0 marked aromatic +36: [21:37:27] non-ring atom 0 marked aromatic +36: [21:37:27] Conflicting single bond directions around double bond at index 17. +36: [21:37:27] BondStereo set to STEREONONE and single bond directions set to NONE. + 27/236 Test #16: pyFPB .................................. Passed 0.52 sec +37: -------------------------- +37: -------------------------- +37: C/C=C/C(C)Cl +test 39 + Start 39: graphmoltestPicklerGlobalSetting + +39: Test command: /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/GraphMol/graphmoltestPicklerGlobalSetting +39: Working Directory: /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/GraphMol +39: Test timeout computed to be: 1500 +37: [21:37:27] Conflicting single bond directions around double bond at index 2. +37: [21:37:27] BondStereo set to STEREONONE and single bond directions set to NONE. +37: [21:37:27] Conflicting single bond directions around double bond at index 4. +37: [21:37:27] BondStereo set to STEREONONE and single bond directions set to NONE. +37: [21:37:27] Conflicting single bond directions around double bond at index 15. +37: [21:37:27] BondStereo set to STEREONONE and single bond directions set to NONE. +37: [21:37:27] Conflicting single bond directions around double bond at index 2. +37: [21:37:27] BondStereo set to STEREONONE and single bond directions set to NONE. +37: [21:37:27] Conflicting single bond directions around double bond at index 1. +37: [21:37:27] BondStereo set to STEREONONE and single bond directions set to NONE. +38: [21:37:27] ------------------------------------- +38: [21:37:27] Testing String Pickle Roundtrips. +36: starting ring finding +36: done +36: starting ring finding +36: done +36: starting ring finding +36: done +36: 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 +36: starting sanitization +36: done +36: starting sanitization + 28/236 Test #32: pyDistGeom ............................. Passed 0.26 sec test 40 Start 40: graphmolIterTest 40: Test command: /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/GraphMol/graphmolIterTest 40: Working Directory: /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/GraphMol 40: Test timeout computed to be: 1500 -21: .................... -21: ---------------------------------------------------------------------- -21: Ran 20 tests in 0.025s -21: -21: OK -21: Testing Geometry wrapper -37: [12:42:35] Conflicting single bond directions around double bond at index 2. -37: [12:42:35] BondStereo set to STEREONONE and single bond directions set to NONE. -37: [12:42:35] Conflicting single bond directions around double bond at index 4. -37: [12:42:35] BondStereo set to STEREONONE and single bond directions set to NONE. -37: [12:42:35] Conflicting single bond directions around double bond at index 15. -37: [12:42:35] BondStereo set to STEREONONE and single bond directions set to NONE. -37: [12:42:35] Conflicting single bond directions around double bond at index 2. -37: [12:42:35] BondStereo set to STEREONONE and single bond directions set to NONE. -37: [12:42:35] Conflicting single bond directions around double bond at index 1. -37: [12:42:35] BondStereo set to STEREONONE and single bond directions set to NONE. +36: done +36: starting ring finding +36: done +36: starting ring finding +36: done +36: smiles: CC[C@]1(C(=O)c([nH])n)CC[C@](C)(O)CC1 +36: [21:37:27] WARNING: not removing hydrogen atom with dummy atom neighbors +36: ------------------------------- +36: [21:37:27] Explicit valence for atom # 0 N, 4, is greater than permitted 37: -------------------------------------------------- - 29/236 Test #37: graphmoltestChirality .................. Passed 0.04 sec +39: [21:37:27] done + 29/236 Test #37: graphmoltestChirality .................. Passed 0.09 sec + 30/236 Test #39: graphmoltestPicklerGlobalSetting ....... Passed 0.05 sec test 41 Start 41: hanoiTest 41: Test command: /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/GraphMol/hanoiTest 41: Working Directory: /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/GraphMol 41: Test timeout computed to be: 1500 - 30/236 Test #40: graphmolIterTest ....................... Passed 0.02 sec test 42 Start 42: graphmolMemTest1 42: Test command: /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/GraphMol/graphmolMemTest1 42: Working Directory: /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/GraphMol 42: Test timeout computed to be: 1500 -38: [12:42:35] done -38: [12:42:35] ------------------------------------- -38: [12:42:35] Testing reading existing pickle file (v2). -39: [12:42:35] done -41: [12:42:35] Testing the hanoi sort -41: [12:42:35] populating vectors - 31/236 Test #39: graphmoltestPicklerGlobalSetting ....... Passed 0.03 sec +36: [21:37:27] Can't kekulize mol. Unkekulized atoms: 0 1 2 3 4 +36: [21:37:27] Can't kekulize mol. Unkekulized atoms: 6 7 8 9 10 +36: [21:37:27] Can't kekulize mol. Unkekulized atoms: 0 1 2 3 4 +36: [21:37:27] WARNING: merging explicit H queries involved in ORs is not supported. This query will not be merged +36: [21:37:27] WARNING: merging explicit H queries involved in ORs is not supported. This query will not be merged +36: [21:37:27] WARNING: merging explicit H queries involved in ORs is not supported. This query will not be merged +36: [21:37:27] WARNING: merging explicit H queries involved in ORs is not supported. This query will not be merged +36: [21:37:27] WARNING: merging explicit H queries involved in ORs is not supported. This query will not be merged +36: +36: [21:37:27] WARNING: not removing hydrogen atom with dummy atom neighbors +38: [21:37:27] done +38: [21:37:27] ------------------------------------- +38: [21:37:27] Testing reading existing pickle file (v2). +41: [21:37:27] Testing the hanoi sort +41: [21:37:27] populating vectors + 31/236 Test #25: pyAlignment ............................ Passed 0.43 sec + 32/236 Test #40: graphmolIterTest ....................... Passed 0.05 sec test 43 Start 43: resMolSupplierTest 43: Test command: /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/GraphMol/resMolSupplierTest 43: Working Directory: /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/GraphMol 43: Test timeout computed to be: 1500 - 32/236 Test #42: graphmolMemTest1 ....................... Passed 0.01 sec test 44 Start 44: molBundleTest 44: Test command: /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/GraphMol/molBundleTest 44: Working Directory: /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/GraphMol 44: Test timeout computed to be: 1500 -36: smi: Cc1ccc(S(=O)(=O)/N=C2\CC(=N\C(C)(C)C)/C2=N\C(C)(C)C)cc1 -36: [12:42:35] non-ring atom 0 marked aromatic -36: [12:42:35] non-ring atom 0 marked aromatic -38: [12:42:35] done -38: [12:42:35] ------------------------------------- -38: [12:42:35] Testing combining molecules using pickles. + 33/236 Test #42: graphmolMemTest1 ....................... Passed 0.04 sec +test 45 + Start 45: testSGroup + +45: Test command: /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/GraphMol/testSGroup +45: Working Directory: /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/GraphMol +45: Test timeout computed to be: 1500 +21: .................... +21: ---------------------------------------------------------------------- +21: Ran 20 tests in 0.091s +21: +21: OK +21: Testing Geometry wrapper +38: [21:37:27] done +38: [21:37:27] ------------------------------------- +38: [21:37:27] Testing combining molecules using pickles. 38: Atoms: 38: 0 6 C chg: 0 deg: 2 exp: 2 imp: 2 hyb: SP3 38: 1 6 C chg: 0 deg: 2 exp: 2 imp: 2 hyb: SP3 @@ -16790,65 +16864,41 @@ 38: 4 4->5 order: 1 38: 5 5->6 order: 1 38: 6 6->3 order: 1 -38: [12:42:35] done -38: [12:42:35] ------------------------------------- -38: [12:42:35] Testing Issue164: Roundtrip Pickle Failure. - 33/236 Test #44: molBundleTest .......................... Passed 0.02 sec -36: [12:42:35] Conflicting single bond directions around double bond at index 17. -36: [12:42:35] BondStereo set to STEREONONE and single bond directions set to NONE. -test 45 - Start 45: testSGroup - -45: Test command: /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/GraphMol/testSGroup -45: Working Directory: /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/GraphMol -45: Test timeout computed to be: 1500 -36: starting ring finding -36: done -36: starting ring finding -38: [12:42:35] done -38: [12:42:35] ------------------------------------- -38: [12:42:35] Testing Issue219: Pickle Failure with Conformations. -38: [12:42:35] done -38: [12:42:35] ------------------------------------- -38: [12:42:35] Testing Issue220: Pickle problems with bond stereochemistry. -38: [12:42:35] done -38: [12:42:35] ------------------------------------- -38: [12:42:35] Testing query serialization. -36: done -36: starting ring finding -38: [12:42:35] C=[$(C=O)] -38: [12:42:35] S(=O)(=O)-[C&H2][F,Br,I,Cl] S(=O)(=O)-[C&H2][F,Br,I,Cl] -38: [12:42:35] done -38: [12:42:35] ------------------------------------- -38: [12:42:35] Testing radical handling in pickles. -38: [12:42:35] done -38: [12:42:35] done -38: [12:42:35] ------------------------------------- -38: [12:42:35] Testing sf.net issue 2788233. -38: [12:42:35] done -38: [12:42:35] ------------------------------------- -38: [12:42:35] Testing sf.net issue 3202580. +38: [21:37:27] done +38: [21:37:27] ------------------------------------- +38: [21:37:27] Testing Issue164: Roundtrip Pickle Failure. +38: [21:37:27] done +38: [21:37:27] ------------------------------------- +38: [21:37:27] Testing Issue219: Pickle Failure with Conformations. +38: [21:37:27] done +38: [21:37:27] ------------------------------------- +38: [21:37:27] Testing Issue220: Pickle problems with bond stereochemistry. +38: [21:37:27] done +38: [21:37:27] ------------------------------------- +38: [21:37:27] Testing query serialization. +38: [21:37:27] C=[$(C=O)] +38: [21:37:27] S(=O)(=O)-[C&H2][F,Br,I,Cl] S(=O)(=O)-[C&H2][F,Br,I,Cl] +38: [21:37:27] done +38: [21:37:27] ------------------------------------- +38: [21:37:27] Testing radical handling in pickles. +38: [21:37:27] done +38: [21:37:27] done +38: [21:37:27] ------------------------------------- +38: [21:37:27] Testing sf.net issue 2788233. +38: [21:37:27] done +38: [21:37:27] ------------------------------------- +38: [21:37:27] Testing sf.net issue 3202580. 38: mass! 13.0034 -38: [12:42:35] done -38: [12:42:35] ------------------------------------- -38: [12:42:35] Testing sf.net issue 3316407. -36: done -36: 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 -36: starting sanitization -38: [12:42:35] done -38: [12:42:35] ------------------------------------- -38: [12:42:35] Testing sf.net issue 3496759. +38: [21:37:27] done +38: [21:37:27] ------------------------------------- +38: [21:37:27] Testing sf.net issue 3316407. +38: [21:37:27] done +38: [21:37:27] ------------------------------------- +38: [21:37:27] Testing sf.net issue 3496759. 38: smi match: *C *C - 34/236 Test #21: testPyGeometry ......................... Passed 0.31 sec 38: smi match: **=* **=* 38: smi match: [N-]=[N+]=NC=O [N-]=[N+]=NC=O 38: smi match: *OS(=O)OC *OS(=O)OC -test 46 - Start 46: test-valgrind - -46: Test command: /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/GraphMol/test-valgrind -46: Working Directory: /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/GraphMol -46: Test timeout computed to be: 1500 38: smi match: *S(=O)(=O)OC *S(=O)(=O)OC 38: smi match: O=COC=O O=COC=O 38: smi match: OO OO @@ -16881,6 +16931,13 @@ 38: smi match: SS SS 38: smi match: [SH] [SH] 38: smi match: *1CC1 *1CC1 + 34/236 Test #44: molBundleTest .......................... Passed 0.04 sec +test 46 + Start 46: test-valgrind + +46: Test command: /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/GraphMol/test-valgrind +46: Working Directory: /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/GraphMol +46: Test timeout computed to be: 1500 38: smi match: [OH]ccc([OH])c[OH] [OH]ccc([OH])c[OH] 38: smi match: [OH]cc([OH])c[OH] [OH]cc([OH])c[OH] 38: smi match: NC(=S)N=N NC(=S)N=N @@ -16905,8 +16962,6 @@ 38: smi match: *=N~C *=N~C 38: smi match: CO*(=O)=O CO*(=O)=O 38: smi match: * * -36: done -36: starting sanitization 38: smi match: * * 38: smi match: *C=C *C=C 38: smi match: N#CS N#CS @@ -16934,25 +16989,26 @@ 38: smi match: S=CS S=CS 38: smi match: C=O C=O 38: smi match: *C=N *C=N -36: done 38: smi match: CCCCCCC CCCCCCC 38: smi match: CN=O CN=O 38: smi match: CS(=O)(=O)O CS(=O)(=O)O -36: starting ring finding -36: done 38: smi match: O=C1CCO1 O=C1CCO1 38: smi match: C=C(S)[SH]=O C=C(S)[SH]=O 38: smi match: C=CCO C=CCO 38: smi match: C=CC=N C=CC=N -36: starting ring finding -36: done 38: smi match: C=CC=O C=CC=O 38: smi match: C=CC(=O)C=C C=CC(=O)C=C 38: smi match: C=CC=S C=CC=S 38: smi match: C=CC(=S)S C=CC(=S)S -36: smiles: CC[C@]1(C(=O)c([nH])n)CC[C@](C)(O)CC1 38: smi match: *C=C(*)C=C *C=C(*)C=C 38: smi match: C=CC=N C=CC=N + 35/236 Test #45: testSGroup ............................. Passed 0.05 sec +test 47 + Start 47: graphmolTestsCatch + +47: Test command: /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch +47: Working Directory: /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/GraphMol +47: Test timeout computed to be: 1500 38: smi match: *N(*)C=C *N(*)C=C 38: smi match: C=CN(=O)=O C=CN(=O)=O 38: smi match: C=CN(O)=O C=CN(O)=O @@ -16961,7 +17017,6 @@ 38: smi match: C=CS C=CS 38: smi match: C=C[SH](=O)=O C=C[SH](=O)=O 38: smi match: C=NCO C=NCO - 35/236 Test #46: test-valgrind .......................... Passed 0.01 sec 38: smi match: C=NC=O C=NC=O 38: smi match: C=NN C=NN 38: smi match: C=NN=C C=NN=C @@ -16972,12 +17027,6 @@ 38: smi match: *CN=O *CN=O 38: smi match: NCN NCN 38: smi match: ON=CCN=O ON=CCN=O -test 47 - Start 47: graphmolTestsCatch - -47: Test command: /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch -47: Working Directory: /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/GraphMol -47: Test timeout computed to be: 1500 38: smi match: NC(S)=N[SH](=O)=O NC(S)=N[SH](=O)=O 38: smi match: N=C(N)S N=C(N)S 38: smi match: NC(=O)Oc1ccccc1 NC(=O)Oc1ccccc1 @@ -17012,19 +17061,12 @@ 38: smi match: [SiH4] [SiH4] 38: smi match: NS NS 38: smi match: NCN NCN - 36/236 Test #45: testSGroup ............................. Passed 0.02 sec 38: smi match: cC(c)(O)O cC(c)(O)O 38: smi match: *C(c)O *C(c)O 38: smi match: C=CS(c)(=O)=O C=CS(c)(=O)=O 38: smi match: cS(=O)(=O)O cS(=O)(=O)O 38: smi match: *c1ccccn1=O *c1ccccn1=O 38: smi match: *c1ccccn1 *c1ccccn1 -test 48 - Start 48: graphmolOrganometallicsCatch - -48: Test command: /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/GraphMol/graphmolOrganometallicsCatch -48: Working Directory: /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/GraphMol -48: Test timeout computed to be: 1500 38: smi match: *c1nccccn1 *c1nccccn1 38: smi match: C1COCOC1 C1COCOC1 38: smi match: C=S C=S @@ -17048,18 +17090,24 @@ 38: smi match: O=NO O=NO 38: smi match: ONO ONO 38: smi match: C1SCS1 C1SCS1 -36: [12:42:35] WARNING: not removing hydrogen atom with dummy atom neighbors 38: smi match: N=C=S N=C=S 38: smi match: N=C=N N=C=N 38: smi match: C1N=N1 C1N=N1 38: smi match: *CS *CS 38: smi match: SC(S)=C(S)S SC(S)=C(S)S 38: smi match: N=CC=NO N=CC=NO -36: ------------------------------- 38: smi match: N#CCC#N N#CCC#N 38: smi match: CON=O CON=O 38: smi match: C=CN C=CN 38: smi match: C=N[SH](=O)=O C=N[SH](=O)=O + 36/236 Test #46: test-valgrind .......................... Passed 0.04 sec +test 48 + Start 48: graphmolOrganometallicsCatch + +48: Test command: /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/GraphMol/graphmolOrganometallicsCatch +48: Working Directory: /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/GraphMol +48: Test timeout computed to be: 1500 +30: ...[21:37:27] Molecule does not have explicit Hs. Consider calling AddHs() 38: smi match: NN=O NN=O 38: smi match: NC(=O)S NC(=O)S 38: smi match: N#CS N#CS @@ -17069,7 +17117,6 @@ 38: smi match: C=NN[SH](=O)=O C=NN[SH](=O)=O 38: smi match: O=CC=O O=CC=O 38: smi match: O=CNOC=O O=CNOC=O -36: [12:42:35] Explicit valence for atom # 0 N, 4, is greater than permitted 38: smi match: O=C1C=CC(=O)C=C1 O=C1C=CC(=O)C=C1 38: smi match: ONO ONO 38: smi match: ON(~O)~O ON(~O)~O @@ -17098,17 +17145,8 @@ 38: smi match: *N *N 38: smi match: *P *P 38: smi match: *S *S -36: [12:42:35] Can't kekulize mol. Unkekulized atoms: 0 1 2 3 4 38: smi match: *C(*)(*)C=C *C(*)(*)C=C -36: [12:42:35] Can't kekulize mol. Unkekulized atoms: 6 7 8 9 10 -36: [12:42:35] Can't kekulize mol. Unkekulized atoms: 0 1 2 3 4 38: smi match: *C(*)(*)C=C *C(*)(*)C=C -36: [12:42:35] WARNING: merging explicit H queries involved in ORs is not supported. This query will not be merged -36: [12:42:35] WARNING: merging explicit H queries involved in ORs is not supported. This query will not be merged -36: [12:42:35] WARNING: merging explicit H queries involved in ORs is not supported. This query will not be merged -36: [12:42:35] WARNING: merging explicit H queries involved in ORs is not supported. This query will not be merged -36: [12:42:35] WARNING: merging explicit H queries involved in ORs is not supported. This query will not be merged -36: 38: smi match: *C(*)C=C *C(*)C=C 38: smi match: *CC=C *CC=C 38: smi match: CN=C=O CN=C=O @@ -17143,7 +17181,6 @@ 38: smi match: *C(*)(*)[SH](=O)=O *C(*)(*)[SH](=O)=O 38: smi match: *C(*)[SH](=O)=O *C(*)[SH](=O)=O 38: smi match: *C[SH](=O)=O *C[SH](=O)=O -36: [12:42:35] WARNING: not removing hydrogen atom with dummy atom neighbors 38: smi match: * * 38: smi match: *1CC1 *1CC1 38: smi match: O=COC=O O=COC=O @@ -17166,62 +17203,32 @@ 38: smi match: *C(*)NCN(*)* *C(*)NCN(*)* 38: smi match: *OCC#N *OCC#N 38: smi match: **C=C **C=C -47: Randomness seeded to: 2053787516 -47: [12:42:35] WARNING: not removing hydrogen atom without neighbors 38: smi match: C=C[O-] C=C[O-] 38: smi match: C=CO C=CO -47: [12:42:35] WARNING: could not find number of expected rings. Switching to an approximate ring finding algorithm. -47: [12:42:35] WARNING: could not find number of expected rings. Switching to an approximate ring finding algorithm. 38: smi match: * * -47: [12:42:35] WARNING: could not find number of expected rings. Switching to an approximate ring finding algorithm. 38: smi match: O=CON1C(=O)CCC1=O O=CON1C(=O)CCC1=O 38: smi match: O=COn1ccnc1 O=COn1ccnc1 -47: [12:42:35] WARNING: could not find number of expected rings. Switching to an approximate ring finding algorithm. 38: smi match: O=COc1c(F)c(F)c(F)c(F)c1F O=COc1c(F)c(F)c(F)c(F)c1F 38: smi match: CC(C)(C)S CC(C)(C)S -47: [12:42:35] WARNING: could not find number of expected rings. Switching to an approximate ring finding algorithm. 38: 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 38: smi match: [CH]=O [CH]=O 38: smi match: C~[CH2]~[CH2]~[CH2]~[CH2]~[CH2]~C C~[CH2]~[CH2]~[CH2]~[CH2]~[CH2]~C 38: smi match: SS SS 38: smi match: [SH] [SH] -47: [12:42:35] Explicit valence for atom # 1 N, 5, is greater than permitted 38: smi match: *C* *C* -47: [12:42:35] Explicit valence for atom # 1 N, 6, is greater than permitted 38: smi match: * * 38: smi match: C[nH3+] C[nH3+] -47: [12:42:35] Explicit valence for atom # 1 N, 5, is greater than permitted 38: smi match: cC(=N)[NH2] cC(=N)[NH2] -47: [12:42:35] Explicit valence for atom # 1 N, 5, is greater than permitted -47: [12:42:35] Explicit valence for atom # 2 O, 3, is greater than permitted -47: [12:42:35] Explicit valence for atom # 2 O, 3, is greater than permitted 38: smi match: O=CN[OH] O=CN[OH] 38: smi match: NN NN -47: [12:42:35] non-ring atom 2 marked aromatic -47: [12:42:35] non-ring atom 2 marked aromatic -47: [12:42:35] Can't kekulize mol. Unkekulized atoms: 0 1 2 3 4 -47: [12:42:35] Can't kekulize mol. Unkekulized atoms: 0 1 2 3 4 -47: [12:42:35] Can't kekulize mol. Unkekulized atoms: 1 2 3 -47: [12:42:35] Can't kekulize mol. Unkekulized atoms: 1 2 3 -47: [12:42:35] Can't kekulize mol. Unkekulized atoms: 0 1 2 -47: [12:42:35] Can't kekulize mol. Unkekulized atoms: 0 1 2 -47: [12:42:35] Explicit valence for atom # 1 O, 3, is greater than permitted -47: [12:42:35] Explicit valence for atom # 4 F, 2, is greater than permitted 38: smi match: * * 38: smi match: *OP(=O)O* *OP(=O)O* -47: [12:42:35] Can't kekulize mol. Unkekulized atoms: 6 7 8 38: smi match: * * 38: smi match: * * -47: [12:42:35] Explicit valence for atom # 1 C, 5, is greater than permitted 38: smi match: * * -47: [12:42:35] WARNING: not removing hydrogen atom with dummy atom neighbors -47: [12:42:35] WARNING: not removing hydrogen atom with dummy atom neighbors 38: smi match: *N=C(*)* *N=C(*)* 38: smi match: *C(*)(*)C=O *C(*)(*)C=O 38: smi match: CSC=O CSC=O -47: [12:42:35] WARNING: not removing hydrogen atom with wedged bond -47: [12:42:35] WARNING: not removing hydrogen atom without neighbors -47: [12:42:35] WARNING: not removing hydrogen atom without neighbors 38: smi match: * * 38: smi match: O=CCl O=CCl 38: smi match: *** *** @@ -17236,12 +17243,9 @@ 38: smi match: C#C C#C 38: smi match: *[CH]C=C *[CH]C=C 38: smi match: cCC(=O)[OH] cCC(=O)[OH] -47: [12:42:35] WARNING: not removing hydrogen atom without neighbors 38: smi match: *C(*)(*)C(=O)[OH] *C(*)(*)C(=O)[OH] -47: [12:42:35] WARNING: not removing hydrogen atom without neighbors 38: smi match: CC(=O)C(=O)[OH] CC(=O)C(=O)[OH] 38: smi match: C=CC(=O)[OH] C=CC(=O)[OH] -47: [12:42:35] Unreasonable formal charge on atom # 0. 38: smi match: N#CC(=O)[OH] N#CC(=O)[OH] 38: smi match: O=C([OH])CN(~O)~O O=C([OH])CN(~O)~O 38: smi match: *N(*)C*=O *N(*)C*=O @@ -17252,7 +17256,173 @@ 38: smi match: ** ** 38: smi match: *C[OH] *C[OH] 38: smi match: *C(*)=O *C(*)=O -47: [12:42:35] +38: smi match: * * +38: smi match: *CC(=O)[OH] *CC(=O)[OH] +38: smi match: CC(=O)OC(C)=O CC(=O)OC(C)=O +38: smi match: *c *c +38: smi match: CN(C)c CN(C)c +38: smi match: c c +38: smi match: *c *c +38: smi match: *c *c +38: smi match: **:*cF **:*cF +38: smi match: cB([OH])[OH] cB([OH])[OH] +38: smi match: N~N~N N~N~N +38: smi match: *N=N* *N=N* +38: smi match: *CC[OH] *CC[OH] +38: smi match: *CC[OH] *CC[OH] +38: smi match: *=CCC(=O)[OH] *=CCC(=O)[OH] +38: smi match: O=C([OH])CC[OH] O=C([OH])CC[OH] +38: smi match: *CCC(=O)[OH] *CCC(=O)[OH] +38: smi match: CC(=O)CC(=O)[OH] CC(=O)CC(=O)[OH] +47: Randomness seeded to: 3739483615 +47: [21:37:27] WARNING: not removing hydrogen atom without neighbors +47: [21:37:27] WARNING: could not find number of expected rings. Switching to an approximate ring finding algorithm. +47: [21:37:27] WARNING: could not find number of expected rings. Switching to an approximate ring finding algorithm. +47: [21:37:27] WARNING: could not find number of expected rings. Switching to an approximate ring finding algorithm. +47: [21:37:27] WARNING: could not find number of expected rings. Switching to an approximate ring finding algorithm. +47: [21:37:27] WARNING: could not find number of expected rings. Switching to an approximate ring finding algorithm. +38: smi match: *OC(=O)CC(C)=O *OC(=O)CC(C)=O +38: smi match: *OC(*)=O *OC(*)=O +38: smi match: *C(=O)[OH] *C(=O)[OH] +38: smi match: O=C[OH] O=C[OH] +38: smi match: *OC(=O)O* *OC(=O)O* +38: smi match: * * +38: smi match: *OC(=O)Cl *OC(=O)Cl +38: smi match: *C#N *C#N +38: smi match: NCC(=O)NCC=O NCC(=O)NCC=O +38: smi match: SS SS +38: smi match: * * +38: smi match: *=* *=* +38: smi match: *=* *=* +38: smi match: *=* *=* +38: smi match: *=* *=* +38: smi match: C1CO1 C1CO1 +38: smi match: *OC(*)=O *OC(*)=O +38: smi match: * * +38: smi match: *O*[OH] *O*[OH] +38: smi match: COC(C)(C)O COC(C)(C)O +38: smi match: *[OH] *[OH] +38: smi match: ** ** +38: smi match: C=N[NH2] C=N[NH2] +38: smi match: C=NC=O C=NC=O +38: smi match: * * +38: smi match: C#NC C#NC +38: smi match: CN=C=O CN=C=O +38: smi match: CN=C=S CN=C=S +38: smi match: *OC(*)(*)O* *OC(*)(*)O* +38: smi match: *C(*)=O *C(*)=O +38: smi match: C~C~C~C~C~C~C C~C~C~C~C~C~C +38: smi match: *~*=O *~*=O +38: smi match: *~*=O *~*=O +38: smi match: OC(=O)CC(=O)[OH] OC(=O)CC(=O)[OH] +38: smi match: * * +38: smi match: *C#N *C#N +38: smi match: *N(=O)~O *N(=O)~O +38: smi match: N N +38: smi match: OC(=O)C(O)=O OC(=O)C(O)=O +38: smi match: C=NO C=NO +38: smi match: O~O O~O +38: smi match: c[OH] c[OH] +38: smi match: O=P(~[OH])~O O=P(~[OH])~O +38: smi match: CO~P(=O)~O CO~P(=O)~O +38: smi match: O=P(~[OH])(~O)~O O=P(~[OH])(~O)~O +38: smi match: CO~P(=O)(~O)~O CO~P(=O)(~O)~O +38: smi match: O=P(~O)~O O=P(~O)~O +38: smi match: O=P(~O)(~O)~O O=P(~O)(~O)~O +38: smi match: C[NH2] C[NH2] +38: smi match: O~*1~**~*(~O)~**~1 O~*1~**~*(~O)~**~1 +38: smi match: * * +38: smi match: *1~*~*~C2~C(~*~1)~*~*~C1~C3~*~*~*~C~3~*~*~C~2~1 *1~*~*~C2~C(~*~1)~*~*~C1~C3~*~*~*~C~3~*~*~C~2~1 +38: smi match: CS(C)~O CS(C)~O +47: [21:37:27] Explicit valence for atom # 1 N, 5, is greater than permitted +47: [21:37:27] Explicit valence for atom # 1 N, 6, is greater than permitted +47: [21:37:27] Explicit valence for atom # 1 N, 5, is greater than permitted +47: [21:37:27] Explicit valence for atom # 1 N, 5, is greater than permitted +47: [21:37:27] Explicit valence for atom # 2 O, 3, is greater than permitted +47: [21:37:27] Explicit valence for atom # 2 O, 3, is greater than permitted +47: [21:37:27] non-ring atom 2 marked aromatic +47: [21:37:27] non-ring atom 2 marked aromatic +47: [21:37:27] Can't kekulize mol. Unkekulized atoms: 0 1 2 3 4 +47: [21:37:27] Can't kekulize mol. Unkekulized atoms: 0 1 2 3 4 +47: [21:37:27] Can't kekulize mol. Unkekulized atoms: 1 2 3 +47: [21:37:27] Can't kekulize mol. Unkekulized atoms: 1 2 3 +47: [21:37:27] Can't kekulize mol. Unkekulized atoms: 0 1 2 +47: [21:37:27] Can't kekulize mol. Unkekulized atoms: 0 1 2 +47: [21:37:27] Explicit valence for atom # 1 O, 3, is greater than permitted +47: [21:37:27] Explicit valence for atom # 4 F, 2, is greater than permitted +47: [21:37:27] Can't kekulize mol. Unkekulized atoms: 6 7 8 +47: [21:37:27] Explicit valence for atom # 1 C, 5, is greater than permitted +38: smi match: CS(C)(~O)~O CS(C)(~O)~O +38: smi match: CS(N)(~O)~O CS(N)(~O)~O +38: smi match: CS([OH])(~O)~O CS([OH])(~O)~O +38: smi match: COS(C)(~O)~O COS(C)(~O)~O +38: smi match: *S(C)(~O)~O *S(C)(~O)~O +38: smi match: CN(C)C CN(C)C +38: smi match: *c1nnc(=N)s1 *c1nnc(=N)s1 +38: smi match: *C(*)=S *C(*)=S +38: smi match: *OC(*)=S *OC(*)=S +38: smi match: * * +38: smi match: C[SH] C[SH] +38: smi match: c[SH] c[SH] +38: smi match: NC(N)=S NC(N)=S +38: smi match: * * +38: smi match: ***** ***** +38: smi match: NC(N)=O NC(N)=O +38: [21:37:27] done +38: [21:37:27] ------------------------------------- +38: [21:37:27] Testing sf.net issue 280. +38: [21:37:27] done +38: [21:37:27] ------------------------------------- +38: [21:37:27] Testing sf.net issue 285. +38: [21:37:27] done +38: [21:37:27] done +38: [21:37:27] done +38: [21:37:27] done +38: [21:37:27] done +38: [21:37:27] done +38: [21:37:27] done +38: [21:37:27] ------------------------------------- +38: [21:37:27] Testing Github2441: Add RDProps interface to Conformers. +38: [21:37:27] done +38: [21:37:27] ------------------------------------- +38: [21:37:27] Testing Issue2510: Pickle Confs as double. +38: [21:37:27] done +38: [21:37:27] ------------------------------------- +38: [21:37:27] Testing Github #2465: Negative atom-map numbers cause depickling to fail. +38: [21:37:27] done +38: [21:37:27] ------------------------------------- +38: [21:37:27] Testing loading pickled mols with conformers +38: [21:37:27] done +38: [21:37:27] ------------------------------------- +38: [21:37:27] Testing conformer reading/writing options +38: [21:37:27] done +38: [21:37:27] ------------------------------------- +38: [21:37:27] Testing property reading options +38: [21:37:27] done +38: [21:37:27] ------------------------------------- +38: [21:37:27] Testing property reading options +38: [21:37:27] done +38: [21:37:27] ------------------------------------- +38: [21:37:27] Testing boost::serialization integration +38: [21:37:27] done +38: [21:37:27] ------------------------------------- +38: [21:37:27] Testing github issue 6036 + 37/236 Test #38: graphmoltestPickler .................... Passed 0.24 sec +test 49 + Start 49: graphmolSGroupCatch + +49: Test command: /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/GraphMol/graphmolSGroupCatch +49: Working Directory: /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/GraphMol +49: Test timeout computed to be: 1500 +47: [21:37:27] WARNING: not removing hydrogen atom with dummy atom neighbors +47: [21:37:27] WARNING: not removing hydrogen atom with dummy atom neighbors +47: [21:37:27] WARNING: not removing hydrogen atom with wedged bond +47: [21:37:27] WARNING: not removing hydrogen atom without neighbors +47: [21:37:27] WARNING: not removing hydrogen atom without neighbors +47: [21:37:27] WARNING: not removing hydrogen atom without neighbors +47: [21:37:27] WARNING: not removing hydrogen atom without neighbors +47: [21:37:27] Unreasonable formal charge on atom # 0. +47: [21:37:27] 47: 47: **** 47: Pre-condition Violation @@ -17264,20 +17434,20 @@ 47: 0# Invar::Invariant::toString[abi:cxx11]() const in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu//lib/libRDKitRDGeneral.so.1 47: 1# Invar::operator<<(std::ostream&, Invar::Invariant const&) in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu//lib/libRDKitRDGeneral.so.1 47: 2# RDKit::ROMol::getAtomDegree(RDKit::Atom const*) const in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu//lib/libRDKitGraphMol.so.1 -47: 3# 0x0000AAAAB2CFA2C4 in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch -47: 4# 0x0000AAAAB2D4732C in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch -47: 5# 0x0000AAAAB2D47CE0 in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch -47: 6# 0x0000AAAAB2D48114 in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch -47: 7# 0x0000AAAAB2D1C638 in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch -47: 8# 0x0000AAAAB2D1CB84 in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch -47: 9# 0x0000AAAAB2C9D4F0 in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch -47: 10# 0x0000FFFF8930229C in /lib/aarch64-linux-gnu/libc.so.6 +47: 3# 0x0000AAAADC15A2C4 in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch +47: 4# 0x0000AAAADC1A732C in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch +47: 5# 0x0000AAAADC1A7CE0 in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch +47: 6# 0x0000AAAADC1A8114 in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch +47: 7# 0x0000AAAADC17C638 in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch +47: 8# 0x0000AAAADC17CB84 in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch +47: 9# 0x0000AAAADC0FD4F0 in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch +47: 10# 0x0000FFFFB649229C in /lib/aarch64-linux-gnu/libc.so.6 47: 11# __libc_start_main in /lib/aarch64-linux-gnu/libc.so.6 -47: 12# 0x0000AAAAB2C9D5B0 in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch +47: 12# 0x0000AAAADC0FD5B0 in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch 47: ---------- 47: **** 47: -47: [12:42:35] +47: [21:37:27] 47: 47: **** 47: Pre-condition Violation @@ -17289,20 +17459,20 @@ 47: 0# Invar::Invariant::toString[abi:cxx11]() const in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu//lib/libRDKitRDGeneral.so.1 47: 1# Invar::operator<<(std::ostream&, Invar::Invariant const&) in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu//lib/libRDKitRDGeneral.so.1 47: 2# RDKit::ROMol::getAtomDegree(RDKit::Atom const*) const in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu//lib/libRDKitGraphMol.so.1 -47: 3# 0x0000AAAAB2CFA338 in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch -47: 4# 0x0000AAAAB2D4732C in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch -47: 5# 0x0000AAAAB2D47CE0 in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch -47: 6# 0x0000AAAAB2D48114 in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch -47: 7# 0x0000AAAAB2D1C638 in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch -47: 8# 0x0000AAAAB2D1CB84 in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch -47: 9# 0x0000AAAAB2C9D4F0 in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch -47: 10# 0x0000FFFF8930229C in /lib/aarch64-linux-gnu/libc.so.6 +47: 3# 0x0000AAAADC15A338 in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch +47: 4# 0x0000AAAADC1A732C in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch +47: 5# 0x0000AAAADC1A7CE0 in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch +47: 6# 0x0000AAAADC1A8114 in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch +47: 7# 0x0000AAAADC17C638 in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch +47: 8# 0x0000AAAADC17CB84 in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch +47: 9# 0x0000AAAADC0FD4F0 in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch +47: 10# 0x0000FFFFB649229C in /lib/aarch64-linux-gnu/libc.so.6 47: 11# __libc_start_main in /lib/aarch64-linux-gnu/libc.so.6 -47: 12# 0x0000AAAAB2C9D5B0 in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch +47: 12# 0x0000AAAADC0FD5B0 in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch 47: ---------- 47: **** 47: -47: [12:42:35] +47: [21:37:27] 47: 47: **** 47: Pre-condition Violation @@ -17314,20 +17484,20 @@ 47: 0# Invar::Invariant::toString[abi:cxx11]() const in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu//lib/libRDKitRDGeneral.so.1 47: 1# Invar::operator<<(std::ostream&, Invar::Invariant const&) in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu//lib/libRDKitRDGeneral.so.1 47: 2# RDKit::ROMol::getAtomDegree(RDKit::Atom const*) const in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu//lib/libRDKitGraphMol.so.1 -47: 3# 0x0000AAAAB2CFA3B8 in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch -47: 4# 0x0000AAAAB2D4732C in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch -47: 5# 0x0000AAAAB2D47CE0 in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch -47: 6# 0x0000AAAAB2D48114 in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch -47: 7# 0x0000AAAAB2D1C638 in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch -47: 8# 0x0000AAAAB2D1CB84 in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch -47: 9# 0x0000AAAAB2C9D4F0 in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch -47: 10# 0x0000FFFF8930229C in /lib/aarch64-linux-gnu/libc.so.6 +47: 3# 0x0000AAAADC15A3B8 in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch +47: 4# 0x0000AAAADC1A732C in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch +47: 5# 0x0000AAAADC1A7CE0 in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch +47: 6# 0x0000AAAADC1A8114 in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch +47: 7# 0x0000AAAADC17C638 in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch +47: 8# 0x0000AAAADC17CB84 in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch +47: 9# 0x0000AAAADC0FD4F0 in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch +47: 10# 0x0000FFFFB649229C in /lib/aarch64-linux-gnu/libc.so.6 47: 11# __libc_start_main in /lib/aarch64-linux-gnu/libc.so.6 -47: 12# 0x0000AAAAB2C9D5B0 in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch +47: 12# 0x0000AAAADC0FD5B0 in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch 47: ---------- 47: **** 47: -47: [12:42:35] +47: [21:37:27] 47: 47: **** 47: Pre-condition Violation @@ -17339,20 +17509,20 @@ 47: 0# Invar::Invariant::toString[abi:cxx11]() const in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu//lib/libRDKitRDGeneral.so.1 47: 1# Invar::operator<<(std::ostream&, Invar::Invariant const&) in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu//lib/libRDKitRDGeneral.so.1 47: 2# RDKit::ROMol::getAtomNeighbors(RDKit::Atom const*) const in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu//lib/libRDKitGraphMol.so.1 -47: 3# 0x0000AAAAB2CFA480 in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch -47: 4# 0x0000AAAAB2D4732C in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch -47: 5# 0x0000AAAAB2D47CE0 in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch -47: 6# 0x0000AAAAB2D48114 in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch -47: 7# 0x0000AAAAB2D1C638 in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch -47: 8# 0x0000AAAAB2D1CB84 in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch -47: 9# 0x0000AAAAB2C9D4F0 in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch -47: 10# 0x0000FFFF8930229C in /lib/aarch64-linux-gnu/libc.so.6 +47: 3# 0x0000AAAADC15A480 in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch +47: 4# 0x0000AAAADC1A732C in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch +47: 5# 0x0000AAAADC1A7CE0 in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch +47: 6# 0x0000AAAADC1A8114 in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch +47: 7# 0x0000AAAADC17C638 in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch +47: 8# 0x0000AAAADC17CB84 in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch +47: 9# 0x0000AAAADC0FD4F0 in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch +47: 10# 0x0000FFFFB649229C in /lib/aarch64-linux-gnu/libc.so.6 47: 11# __libc_start_main in /lib/aarch64-linux-gnu/libc.so.6 -47: 12# 0x0000AAAAB2C9D5B0 in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch +47: 12# 0x0000AAAADC0FD5B0 in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch 47: ---------- 47: **** 47: -47: [12:42:35] +47: [21:37:27] 47: 47: **** 47: Pre-condition Violation @@ -17364,20 +17534,20 @@ 47: 0# Invar::Invariant::toString[abi:cxx11]() const in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu//lib/libRDKitRDGeneral.so.1 47: 1# Invar::operator<<(std::ostream&, Invar::Invariant const&) in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu//lib/libRDKitRDGeneral.so.1 47: 2# RDKit::ROMol::getAtomNeighbors(RDKit::Atom const*) const in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu//lib/libRDKitGraphMol.so.1 -47: 3# 0x0000AAAAB2CFA4F8 in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch -47: 4# 0x0000AAAAB2D4732C in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch -47: 5# 0x0000AAAAB2D47CE0 in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch -47: 6# 0x0000AAAAB2D48114 in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch -47: 7# 0x0000AAAAB2D1C638 in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch -47: 8# 0x0000AAAAB2D1CB84 in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch -47: 9# 0x0000AAAAB2C9D4F0 in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch -47: 10# 0x0000FFFF8930229C in /lib/aarch64-linux-gnu/libc.so.6 +47: 3# 0x0000AAAADC15A4F8 in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch +47: 4# 0x0000AAAADC1A732C in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch +47: 5# 0x0000AAAADC1A7CE0 in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch +47: 6# 0x0000AAAADC1A8114 in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch +47: 7# 0x0000AAAADC17C638 in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch +47: 8# 0x0000AAAADC17CB84 in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch +47: 9# 0x0000AAAADC0FD4F0 in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch +47: 10# 0x0000FFFFB649229C in /lib/aarch64-linux-gnu/libc.so.6 47: 11# __libc_start_main in /lib/aarch64-linux-gnu/libc.so.6 -47: 12# 0x0000AAAAB2C9D5B0 in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch +47: 12# 0x0000AAAADC0FD5B0 in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch 47: ---------- 47: **** 47: -47: [12:42:35] +47: [21:37:27] 47: 47: **** 47: Pre-condition Violation @@ -17389,63 +17559,22 @@ 47: 0# Invar::Invariant::toString[abi:cxx11]() const in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu//lib/libRDKitRDGeneral.so.1 47: 1# Invar::operator<<(std::ostream&, Invar::Invariant const&) in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu//lib/libRDKitRDGeneral.so.1 47: 2# RDKit::ROMol::getAtomNeighbors(RDKit::Atom const*) const in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu//lib/libRDKitGraphMol.so.1 -47: 3# 0x0000AAAAB2CFA57C in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch -47: 4# 0x0000AAAAB2D4732C in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch -47: 5# 0x0000AAAAB2D47CE0 in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch -47: 6# 0x0000AAAAB2D48114 in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch -47: 7# 0x0000AAAAB2D1C638 in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch -47: 8# 0x0000AAAAB2D1CB84 in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch -47: 9# 0x0000AAAAB2C9D4F0 in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch -47: 10# 0x0000FFFF8930229C in /lib/aarch64-linux-gnu/libc.so.6 +47: 3# 0x0000AAAADC15A57C in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch +47: 4# 0x0000AAAADC1A732C in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch +47: 5# 0x0000AAAADC1A7CE0 in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch +47: 6# 0x0000AAAADC1A8114 in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch +47: 7# 0x0000AAAADC17C638 in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch +47: 8# 0x0000AAAADC17CB84 in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch +47: 9# 0x0000AAAADC0FD4F0 in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch +47: 10# 0x0000FFFFB649229C in /lib/aarch64-linux-gnu/libc.so.6 47: 11# __libc_start_main in /lib/aarch64-linux-gnu/libc.so.6 -47: 12# 0x0000AAAAB2C9D5B0 in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch +47: 12# 0x0000AAAADC0FD5B0 in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch 47: ---------- 47: **** 47: -47: [12:42:35] +47: [21:37:27] 47: 47: **** -38: smi match: * * -38: smi match: *CC(=O)[OH] *CC(=O)[OH] -38: smi match: CC(=O)OC(C)=O CC(=O)OC(C)=O -38: smi match: *c *c -38: smi match: CN(C)c CN(C)c -38: smi match: c c -38: smi match: *c *c -38: smi match: *c *c -38: smi match: **:*cF **:*cF -38: smi match: cB([OH])[OH] cB([OH])[OH] -38: smi match: N~N~N N~N~N -38: smi match: *N=N* *N=N* -38: smi match: *CC[OH] *CC[OH] -38: smi match: *CC[OH] *CC[OH] -38: smi match: *=CCC(=O)[OH] *=CCC(=O)[OH] -38: smi match: O=C([OH])CC[OH] O=C([OH])CC[OH] -38: smi match: *CCC(=O)[OH] *CCC(=O)[OH] -38: smi match: CC(=O)CC(=O)[OH] CC(=O)CC(=O)[OH] -38: smi match: *OC(=O)CC(C)=O *OC(=O)CC(C)=O -38: smi match: *OC(*)=O *OC(*)=O -38: smi match: *C(=O)[OH] *C(=O)[OH] -38: smi match: O=C[OH] O=C[OH] -38: smi match: *OC(=O)O* *OC(=O)O* -38: smi match: * * -38: smi match: *OC(=O)Cl *OC(=O)Cl -38: smi match: *C#N *C#N -38: smi match: NCC(=O)NCC=O NCC(=O)NCC=O -38: smi match: SS SS -38: smi match: * * -38: smi match: *=* *=* -38: smi match: *=* *=* -38: smi match: *=* *=* -38: smi match: *=* *=* -38: smi match: C1CO1 C1CO1 -38: smi match: *OC(*)=O *OC(*)=O -38: smi match: * * -38: smi match: *O*[OH] *O*[OH] -38: smi match: COC(C)(C)O COC(C)(C)O -38: smi match: *[OH] *[OH] -38: smi match: ** ** -38: smi match: C=N[NH2] C=N[NH2] 47: Pre-condition Violation 47: no atom 47: Violation occurred on line 371 in file ./Code/GraphMol/ROMol.cpp @@ -17455,20 +17584,20 @@ 47: 0# Invar::Invariant::toString[abi:cxx11]() const in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu//lib/libRDKitRDGeneral.so.1 47: 1# Invar::operator<<(std::ostream&, Invar::Invariant const&) in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu//lib/libRDKitRDGeneral.so.1 47: 2# RDKit::ROMol::getAtomBonds(RDKit::Atom const*) const in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu//lib/libRDKitGraphMol.so.1 -47: 3# 0x0000AAAAB2CFAC90 in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch -47: 4# 0x0000AAAAB2D4732C in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch -47: 5# 0x0000AAAAB2D47CE0 in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch -47: 6# 0x0000AAAAB2D48114 in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch -47: 7# 0x0000AAAAB2D1C638 in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch -47: 8# 0x0000AAAAB2D1CB84 in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch -47: 9# 0x0000AAAAB2C9D4F0 in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch -47: 10# 0x0000FFFF8930229C in /lib/aarch64-linux-gnu/libc.so.6 +47: 3# 0x0000AAAADC15AC90 in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch +47: 4# 0x0000AAAADC1A732C in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch +47: 5# 0x0000AAAADC1A7CE0 in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch +47: 6# 0x0000AAAADC1A8114 in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch +47: 7# 0x0000AAAADC17C638 in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch +47: 8# 0x0000AAAADC17CB84 in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch +47: 9# 0x0000AAAADC0FD4F0 in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch +47: 10# 0x0000FFFFB649229C in /lib/aarch64-linux-gnu/libc.so.6 47: 11# __libc_start_main in /lib/aarch64-linux-gnu/libc.so.6 -47: 12# 0x0000AAAAB2C9D5B0 in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch +47: 12# 0x0000AAAADC0FD5B0 in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch 47: ---------- 47: **** 47: -47: [12:42:35] +47: [21:37:27] 47: 47: **** 47: Pre-condition Violation @@ -17480,20 +17609,20 @@ 47: 0# Invar::Invariant::toString[abi:cxx11]() const in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu//lib/libRDKitRDGeneral.so.1 47: 1# Invar::operator<<(std::ostream&, Invar::Invariant const&) in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu//lib/libRDKitRDGeneral.so.1 47: 2# RDKit::ROMol::getAtomBonds(RDKit::Atom const*) const in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu//lib/libRDKitGraphMol.so.1 -47: 3# 0x0000AAAAB2CFA6AC in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch -47: 4# 0x0000AAAAB2D4732C in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch -47: 5# 0x0000AAAAB2D47CE0 in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch -47: 6# 0x0000AAAAB2D48114 in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch -47: 7# 0x0000AAAAB2D1C638 in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch -47: 8# 0x0000AAAAB2D1CB84 in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch -47: 9# 0x0000AAAAB2C9D4F0 in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch -47: 10# 0x0000FFFF8930229C in /lib/aarch64-linux-gnu/libc.so.6 +47: 3# 0x0000AAAADC15A6AC in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch +47: 4# 0x0000AAAADC1A732C in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch +47: 5# 0x0000AAAADC1A7CE0 in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch +47: 6# 0x0000AAAADC1A8114 in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch +47: 7# 0x0000AAAADC17C638 in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch +47: 8# 0x0000AAAADC17CB84 in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch +47: 9# 0x0000AAAADC0FD4F0 in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch +47: 10# 0x0000FFFFB649229C in /lib/aarch64-linux-gnu/libc.so.6 47: 11# __libc_start_main in /lib/aarch64-linux-gnu/libc.so.6 -47: 12# 0x0000AAAAB2C9D5B0 in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch +47: 12# 0x0000AAAADC0FD5B0 in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch 47: ---------- 47: **** 47: -47: [12:42:35] +47: [21:37:27] 47: 47: **** 47: Pre-condition Violation @@ -17505,20 +17634,20 @@ 47: 0# Invar::Invariant::toString[abi:cxx11]() const in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu//lib/libRDKitRDGeneral.so.1 47: 1# Invar::operator<<(std::ostream&, Invar::Invariant const&) in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu//lib/libRDKitRDGeneral.so.1 47: 2# RDKit::ROMol::getAtomBonds(RDKit::Atom const*) const in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu//lib/libRDKitGraphMol.so.1 -47: 3# 0x0000AAAAB2CFA730 in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch -47: 4# 0x0000AAAAB2D4732C in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch -47: 5# 0x0000AAAAB2D47CE0 in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch -47: 6# 0x0000AAAAB2D48114 in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch -47: 7# 0x0000AAAAB2D1C638 in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch -47: 8# 0x0000AAAAB2D1CB84 in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch -47: 9# 0x0000AAAAB2C9D4F0 in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch -47: 10# 0x0000FFFF8930229C in /lib/aarch64-linux-gnu/libc.so.6 +47: 3# 0x0000AAAADC15A730 in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch +47: 4# 0x0000AAAADC1A732C in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch +47: 5# 0x0000AAAADC1A7CE0 in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch +47: 6# 0x0000AAAADC1A8114 in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch +47: 7# 0x0000AAAADC17C638 in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch +47: 8# 0x0000AAAADC17CB84 in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch +47: 9# 0x0000AAAADC0FD4F0 in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch +47: 10# 0x0000FFFFB649229C in /lib/aarch64-linux-gnu/libc.so.6 47: 11# __libc_start_main in /lib/aarch64-linux-gnu/libc.so.6 -47: 12# 0x0000AAAAB2C9D5B0 in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch +47: 12# 0x0000AAAADC0FD5B0 in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch 47: ---------- 47: **** 47: -47: [12:42:35] +47: [21:37:27] 47: 47: **** 47: Pre-condition Violation @@ -17530,20 +17659,20 @@ 47: 0# Invar::Invariant::toString[abi:cxx11]() const in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu//lib/libRDKitRDGeneral.so.1 47: 1# Invar::operator<<(std::ostream&, Invar::Invariant const&) in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu//lib/libRDKitRDGeneral.so.1 47: 2# RDKit::ROMol::addAtom(RDKit::Atom*, bool, bool) in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu//lib/libRDKitGraphMol.so.1 -47: 3# 0x0000AAAAB2CFAC74 in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch -47: 4# 0x0000AAAAB2D4732C in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch -47: 5# 0x0000AAAAB2D47CE0 in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch -47: 6# 0x0000AAAAB2D48114 in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch -47: 7# 0x0000AAAAB2D1C638 in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch -47: 8# 0x0000AAAAB2D1CB84 in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch -47: 9# 0x0000AAAAB2C9D4F0 in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch -47: 10# 0x0000FFFF8930229C in /lib/aarch64-linux-gnu/libc.so.6 +47: 3# 0x0000AAAADC15AC74 in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch +47: 4# 0x0000AAAADC1A732C in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch +47: 5# 0x0000AAAADC1A7CE0 in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch +47: 6# 0x0000AAAADC1A8114 in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch +47: 7# 0x0000AAAADC17C638 in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch +47: 8# 0x0000AAAADC17CB84 in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch +47: 9# 0x0000AAAADC0FD4F0 in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch +47: 10# 0x0000FFFFB649229C in /lib/aarch64-linux-gnu/libc.so.6 47: 11# __libc_start_main in /lib/aarch64-linux-gnu/libc.so.6 -47: 12# 0x0000AAAAB2C9D5B0 in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch +47: 12# 0x0000AAAADC0FD5B0 in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch 47: ---------- 47: **** 47: -47: [12:42:35] +47: [21:37:27] 47: 47: **** 47: Pre-condition Violation @@ -17555,20 +17684,20 @@ 47: 0# Invar::Invariant::toString[abi:cxx11]() const in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu//lib/libRDKitRDGeneral.so.1 47: 1# Invar::operator<<(std::ostream&, Invar::Invariant const&) in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu//lib/libRDKitRDGeneral.so.1 47: 2# RDKit::ROMol::addAtom(RDKit::Atom*, bool, bool) in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu//lib/libRDKitGraphMol.so.1 -47: 3# 0x0000AAAAB2CFA920 in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch -47: 4# 0x0000AAAAB2D4732C in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch -47: 5# 0x0000AAAAB2D47CE0 in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch -47: 6# 0x0000AAAAB2D48114 in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch -47: 7# 0x0000AAAAB2D1C638 in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch -47: 8# 0x0000AAAAB2D1CB84 in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch -47: 9# 0x0000AAAAB2C9D4F0 in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch -47: 10# 0x0000FFFF8930229C in /lib/aarch64-linux-gnu/libc.so.6 +47: 3# 0x0000AAAADC15A920 in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch +47: 4# 0x0000AAAADC1A732C in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch +47: 5# 0x0000AAAADC1A7CE0 in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch +47: 6# 0x0000AAAADC1A8114 in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch +47: 7# 0x0000AAAADC17C638 in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch +47: 8# 0x0000AAAADC17CB84 in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch +47: 9# 0x0000AAAADC0FD4F0 in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch +47: 10# 0x0000FFFFB649229C in /lib/aarch64-linux-gnu/libc.so.6 47: 11# __libc_start_main in /lib/aarch64-linux-gnu/libc.so.6 -47: 12# 0x0000AAAAB2C9D5B0 in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch +47: 12# 0x0000AAAADC0FD5B0 in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch 47: ---------- 47: **** 47: -47: [12:42:35] +47: [21:37:27] 47: 47: **** 47: Pre-condition Violation @@ -17580,24 +17709,24 @@ 47: 0# Invar::Invariant::toString[abi:cxx11]() const in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu//lib/libRDKitRDGeneral.so.1 47: 1# Invar::operator<<(std::ostream&, Invar::Invariant const&) in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu//lib/libRDKitRDGeneral.so.1 47: 2# RDKit::ROMol::addBond(RDKit::Bond*, bool) in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu//lib/libRDKitGraphMol.so.1 -47: 3# 0x0000AAAAB2CFAC54 in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch -47: 4# 0x0000AAAAB2D4732C in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch -47: 5# 0x0000AAAAB2D47CE0 in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch -47: 6# 0x0000AAAAB2D48114 in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch -47: 7# 0x0000AAAAB2D1C638 in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch -47: 8# 0x0000AAAAB2D1CB84 in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch -47: 9# 0x0000AAAAB2C9D4F0 in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch -47: 10# 0x0000FFFF8930229C in /lib/aarch64-linux-gnu/libc.so.6 +47: 3# 0x0000AAAADC15AC54 in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch +47: 4# 0x0000AAAADC1A732C in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch +47: 5# 0x0000AAAADC1A7CE0 in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch +47: 6# 0x0000AAAADC1A8114 in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch +47: 7# 0x0000AAAADC17C638 in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch +47: 8# 0x0000AAAADC17CB84 in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch +47: 9# 0x0000AAAADC0FD4F0 in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch +47: 10# 0x0000FFFFB649229C in /lib/aarch64-linux-gnu/libc.so.6 47: 11# __libc_start_main in /lib/aarch64-linux-gnu/libc.so.6 -47: 12# 0x0000AAAAB2C9D5B0 in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch +47: 12# 0x0000AAAADC0FD5B0 in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch 47: ---------- 47: **** 47: -47: [12:42:35] WARNING: could not find number of expected rings. Switching to an approximate ring finding algorithm. -47: [12:42:35] WARNING: could not find number of expected rings. Switching to an approximate ring finding algorithm. -47: [12:42:35] WARNING: not removing hydrogen atom without neighbors -47: [12:42:35] Explicit valence for atom # 1 F greater than permitted -47: [12:42:35] +47: [21:37:27] WARNING: could not find number of expected rings. Switching to an approximate ring finding algorithm. +47: [21:37:27] WARNING: could not find number of expected rings. Switching to an approximate ring finding algorithm. +47: [21:37:27] WARNING: not removing hydrogen atom without neighbors +47: [21:37:27] Explicit valence for atom # 1 F greater than permitted +47: [21:37:27] 47: 47: **** 47: Pre-condition Violation @@ -17609,20 +17738,20 @@ 47: 0# Invar::Invariant::toString[abi:cxx11]() const in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu//lib/libRDKitRDGeneral.so.1 47: 1# Invar::operator<<(std::ostream&, Invar::Invariant const&) in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu//lib/libRDKitRDGeneral.so.1 47: 2# RDKit::Atom::setQuery(Queries::Query*) in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu//lib/libRDKitGraphMol.so.1 -47: 3# 0x0000AAAAB2CAA66C in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch -47: 4# 0x0000AAAAB2D4732C in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch -47: 5# 0x0000AAAAB2D47CE0 in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch -47: 6# 0x0000AAAAB2D48114 in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch -47: 7# 0x0000AAAAB2D1C638 in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch -47: 8# 0x0000AAAAB2D1CB84 in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch -47: 9# 0x0000AAAAB2C9D4F0 in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch -47: 10# 0x0000FFFF8930229C in /lib/aarch64-linux-gnu/libc.so.6 +47: 3# 0x0000AAAADC10A66C in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch +47: 4# 0x0000AAAADC1A732C in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch +47: 5# 0x0000AAAADC1A7CE0 in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch +47: 6# 0x0000AAAADC1A8114 in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch +47: 7# 0x0000AAAADC17C638 in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch +47: 8# 0x0000AAAADC17CB84 in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch +47: 9# 0x0000AAAADC0FD4F0 in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch +47: 10# 0x0000FFFFB649229C in /lib/aarch64-linux-gnu/libc.so.6 47: 11# __libc_start_main in /lib/aarch64-linux-gnu/libc.so.6 -47: 12# 0x0000AAAAB2C9D5B0 in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch +47: 12# 0x0000AAAADC0FD5B0 in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch 47: ---------- 47: **** 47: -47: [12:42:35] +47: [21:37:27] 47: 47: **** 47: Pre-condition Violation @@ -17634,20 +17763,20 @@ 47: 0# Invar::Invariant::toString[abi:cxx11]() const in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu//lib/libRDKitRDGeneral.so.1 47: 1# Invar::operator<<(std::ostream&, Invar::Invariant const&) in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu//lib/libRDKitRDGeneral.so.1 47: 2# RDKit::Atom::expandQuery(Queries::Query*, Queries::CompositeQueryType, bool) in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu//lib/libRDKitGraphMol.so.1 -47: 3# 0x0000AAAAB2CAA6F8 in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch -47: 4# 0x0000AAAAB2D4732C in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch -47: 5# 0x0000AAAAB2D47CE0 in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch -47: 6# 0x0000AAAAB2D48114 in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch -47: 7# 0x0000AAAAB2D1C638 in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch -47: 8# 0x0000AAAAB2D1CB84 in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch -47: 9# 0x0000AAAAB2C9D4F0 in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch -47: 10# 0x0000FFFF8930229C in /lib/aarch64-linux-gnu/libc.so.6 +47: 3# 0x0000AAAADC10A6F8 in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch +47: 4# 0x0000AAAADC1A732C in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch +47: 5# 0x0000AAAADC1A7CE0 in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch +47: 6# 0x0000AAAADC1A8114 in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch +47: 7# 0x0000AAAADC17C638 in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch +47: 8# 0x0000AAAADC17CB84 in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch +47: 9# 0x0000AAAADC0FD4F0 in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch +47: 10# 0x0000FFFFB649229C in /lib/aarch64-linux-gnu/libc.so.6 47: 11# __libc_start_main in /lib/aarch64-linux-gnu/libc.so.6 -47: 12# 0x0000AAAAB2C9D5B0 in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch +47: 12# 0x0000AAAADC0FD5B0 in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch 47: ---------- 47: **** 47: -47: [12:42:35] +47: [21:37:27] 47: 47: **** 47: Pre-condition Violation @@ -17659,20 +17788,20 @@ 47: 0# Invar::Invariant::toString[abi:cxx11]() const in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu//lib/libRDKitRDGeneral.so.1 47: 1# Invar::operator<<(std::ostream&, Invar::Invariant const&) in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu//lib/libRDKitRDGeneral.so.1 47: 2# RDKit::Bond::setQuery(Queries::Query*) in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu//lib/libRDKitGraphMol.so.1 -47: 3# 0x0000AAAAB2CAA2BC in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch -47: 4# 0x0000AAAAB2D4732C in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch -47: 5# 0x0000AAAAB2D47CE0 in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch -47: 6# 0x0000AAAAB2D48114 in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch -47: 7# 0x0000AAAAB2D1C638 in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch -47: 8# 0x0000AAAAB2D1CB84 in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch -47: 9# 0x0000AAAAB2C9D4F0 in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch -47: 10# 0x0000FFFF8930229C in /lib/aarch64-linux-gnu/libc.so.6 +47: 3# 0x0000AAAADC10A2BC in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch +47: 4# 0x0000AAAADC1A732C in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch +47: 5# 0x0000AAAADC1A7CE0 in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch +47: 6# 0x0000AAAADC1A8114 in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch +47: 7# 0x0000AAAADC17C638 in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch +47: 8# 0x0000AAAADC17CB84 in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch +47: 9# 0x0000AAAADC0FD4F0 in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch +47: 10# 0x0000FFFFB649229C in /lib/aarch64-linux-gnu/libc.so.6 47: 11# __libc_start_main in /lib/aarch64-linux-gnu/libc.so.6 -47: 12# 0x0000AAAAB2C9D5B0 in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch +47: 12# 0x0000AAAADC0FD5B0 in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch 47: ---------- 47: **** 47: -47: [12:42:35] +47: [21:37:27] 47: 47: **** 47: Pre-condition Violation @@ -17684,372 +17813,282 @@ 47: 0# Invar::Invariant::toString[abi:cxx11]() const in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu//lib/libRDKitRDGeneral.so.1 47: 1# Invar::operator<<(std::ostream&, Invar::Invariant const&) in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu//lib/libRDKitRDGeneral.so.1 47: 2# RDKit::Bond::expandQuery(Queries::Query*, Queries::CompositeQueryType, bool) in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu//lib/libRDKitGraphMol.so.1 -47: 3# 0x0000AAAAB2CAA348 in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch -47: 4# 0x0000AAAAB2D4732C in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch -47: 5# 0x0000AAAAB2D47CE0 in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch -47: 6# 0x0000AAAAB2D48114 in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch -47: 7# 0x0000AAAAB2D1C638 in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch -47: 8# 0x0000AAAAB2D1CB84 in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch -47: 9# 0x0000AAAAB2C9D4F0 in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch -47: 10# 0x0000FFFF8930229C in /lib/aarch64-linux-gnu/libc.so.6 +47: 3# 0x0000AAAADC10A348 in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch +47: 4# 0x0000AAAADC1A732C in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch +47: 5# 0x0000AAAADC1A7CE0 in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch +47: 6# 0x0000AAAADC1A8114 in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch +47: 7# 0x0000AAAADC17C638 in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch +47: 8# 0x0000AAAADC17CB84 in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch +47: 9# 0x0000AAAADC0FD4F0 in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch +47: 10# 0x0000FFFFB649229C in /lib/aarch64-linux-gnu/libc.so.6 47: 11# __libc_start_main in /lib/aarch64-linux-gnu/libc.so.6 -47: 12# 0x0000AAAAB2C9D5B0 in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch +47: 12# 0x0000AAAADC0FD5B0 in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch 47: ---------- 47: **** 47: -47: [12:42:35] Can't kekulize mol. Unkekulized atoms: 0 1 2 3 4 -47: [12:42:35] Can't kekulize mol. Unkekulized atoms: 0 1 2 3 4 -47: [12:42:35] Can't kekulize mol. Unkekulized atoms: 6 7 8 9 10 -47: [12:42:35] Can't kekulize mol. Unkekulized atoms: 6 7 8 9 10 -47: [12:42:35] Can't kekulize mol. Unkekulized atoms: 0 1 2 3 4 -47: [12:42:35] Unusual charge on atom 0 number of radical electrons set to zero -47: [12:42:35] Unusual charge on atom 0 number of radical electrons set to zero -47: [12:42:35] Unusual charge on atom 0 number of radical electrons set to zero -47: [12:42:35] non-ring atom 0 marked aromatic -47: [12:42:35] non-ring atom 0 marked aromatic -47: [12:42:35] Explicit valence for atom # 1 C, 5, is greater than permitted -47: [12:42:35] Explicit valence for atom # 9 C, 5, is greater than permitted -47: [12:42:35] Explicit valence for atom # 3 N, 4, is greater than permitted -47: [12:42:35] Explicit valence for atom # 15 C, 5, is greater than permitted -47: [12:42:35] Explicit valence for atom # 11 C, 5, is greater than permitted -47: [12:42:35] Explicit valence for atom # 9 C, 5, is greater than permitted -47: [12:42:35] Explicit valence for atom # 9 C, 5, is greater than permitted -47: [12:42:35] Explicit valence for atom # 9 C, 6, is greater than permitted -47: [12:42:35] Can't kekulize mol. Unkekulized atoms: 0 1 2 3 4 -47: [12:42:35] Can't kekulize mol. Unkekulized atoms: 7 -47: [12:42:35] Can't kekulize mol. Unkekulized atoms: 3 -47: [12:42:35] Can't kekulize mol. Unkekulized atoms: 3 7 -47: [12:42:35] Can't kekulize mol. Unkekulized atoms: 3 7 -38: smi match: C=NC=O C=NC=O -38: smi match: * * -38: smi match: C#NC C#NC -38: smi match: CN=C=O CN=C=O -38: smi match: CN=C=S CN=C=S -38: smi match: *OC(*)(*)O* *OC(*)(*)O* -38: smi match: *C(*)=O *C(*)=O -38: smi match: C~C~C~C~C~C~C C~C~C~C~C~C~C -38: smi match: *~*=O *~*=O -38: smi match: *~*=O *~*=O -38: smi match: OC(=O)CC(=O)[OH] OC(=O)CC(=O)[OH] -38: smi match: * * -38: smi match: *C#N *C#N -38: smi match: *N(=O)~O *N(=O)~O -38: smi match: N N -38: smi match: OC(=O)C(O)=O OC(=O)C(O)=O -38: smi match: C=NO C=NO -38: smi match: O~O O~O -38: smi match: c[OH] c[OH] -38: smi match: O=P(~[OH])~O O=P(~[OH])~O -38: smi match: CO~P(=O)~O CO~P(=O)~O -38: smi match: O=P(~[OH])(~O)~O O=P(~[OH])(~O)~O -38: smi match: CO~P(=O)(~O)~O CO~P(=O)(~O)~O -38: smi match: O=P(~O)~O O=P(~O)~O -38: smi match: O=P(~O)(~O)~O O=P(~O)(~O)~O -38: smi match: C[NH2] C[NH2] -38: smi match: O~*1~**~*(~O)~**~1 O~*1~**~*(~O)~**~1 -38: smi match: * * -38: smi match: *1~*~*~C2~C(~*~1)~*~*~C1~C3~*~*~*~C~3~*~*~C~2~1 *1~*~*~C2~C(~*~1)~*~*~C1~C3~*~*~*~C~3~*~*~C~2~1 -38: smi match: CS(C)~O CS(C)~O -38: smi match: CS(C)(~O)~O CS(C)(~O)~O -38: smi match: CS(N)(~O)~O CS(N)(~O)~O -38: smi match: CS([OH])(~O)~O CS([OH])(~O)~O -38: smi match: COS(C)(~O)~O COS(C)(~O)~O -38: smi match: *S(C)(~O)~O *S(C)(~O)~O -38: smi match: CN(C)C CN(C)C -38: smi match: *c1nnc(=N)s1 *c1nnc(=N)s1 -38: smi match: *C(*)=S *C(*)=S -38: smi match: *OC(*)=S *OC(*)=S -38: smi match: * * -38: smi match: C[SH] C[SH] -38: smi match: c[SH] c[SH] -38: smi match: NC(N)=S NC(N)=S -38: smi match: * * -38: smi match: ***** ***** -38: smi match: NC(N)=O NC(N)=O -38: [12:42:35] done -38: [12:42:35] ------------------------------------- -38: [12:42:35] Testing sf.net issue 280. -38: [12:42:35] done -38: [12:42:35] ------------------------------------- -38: [12:42:35] Testing sf.net issue 285. -38: [12:42:35] done -38: [12:42:35] done -38: [12:42:35] done -38: [12:42:35] done -38: [12:42:35] done -38: [12:42:35] done -38: [12:42:35] done -38: [12:42:35] ------------------------------------- -38: [12:42:35] Testing Github2441: Add RDProps interface to Conformers. -38: [12:42:35] done -38: [12:42:35] ------------------------------------- -38: [12:42:35] Testing Issue2510: Pickle Confs as double. -38: [12:42:35] done -38: [12:42:35] ------------------------------------- -38: [12:42:35] Testing Github #2465: Negative atom-map numbers cause depickling to fail. -38: [12:42:35] done -38: [12:42:35] ------------------------------------- -38: [12:42:35] Testing loading pickled mols with conformers -38: [12:42:35] done -38: [12:42:35] ------------------------------------- -38: [12:42:35] Testing conformer reading/writing options -38: [12:42:35] done -38: [12:42:35] ------------------------------------- -38: [12:42:35] Testing property reading options -38: [12:42:35] done -38: [12:42:35] ------------------------------------- -38: [12:42:35] Testing property reading options -38: [12:42:35] done -38: [12:42:35] ------------------------------------- -38: [12:42:35] Testing boost::serialization integration -38: [12:42:35] done -38: [12:42:35] ------------------------------------- -38: [12:42:35] Testing github issue 6036 -30: ...[12:42:35] Molecule does not have explicit Hs. Consider calling AddHs() -48: Randomness seeded to: 3795588026 +47: [21:37:27] Can't kekulize mol. Unkekulized atoms: 0 1 2 3 4 +47: [21:37:27] Can't kekulize mol. Unkekulized atoms: 0 1 2 3 4 +47: [21:37:27] Can't kekulize mol. Unkekulized atoms: 6 7 8 9 10 +47: [21:37:27] Can't kekulize mol. Unkekulized atoms: 6 7 8 9 10 +47: [21:37:27] Can't kekulize mol. Unkekulized atoms: 0 1 2 3 4 +48: Randomness seeded to: 1409197622 48: =============================================================================== 48: All tests passed (62 assertions in 6 test cases) 48: - 37/236 Test #48: graphmolOrganometallicsCatch ........... Passed 0.04 sec -47: [12:42:35] WARNING: could not find number of expected rings. Switching to an approximate ring finding algorithm. -47: [12:42:35] WARNING: could not find number of expected rings. Switching to an approximate ring finding algorithm. - 38/236 Test #38: graphmoltestPickler .................... Passed 0.13 sec -32: ...... -32: ---------------------------------------------------------------------- -32: Ran 6 tests in 0.001s -32: -32: OK -test 49 - Start 49: graphmolSGroupCatch - -49: Test command: /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/GraphMol/graphmolSGroupCatch -49: Working Directory: /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/GraphMol -49: Test timeout computed to be: 1500 +47: [21:37:27] Unusual charge on atom 0 number of radical electrons set to zero +47: [21:37:27] Unusual charge on atom 0 number of radical electrons set to zero +47: [21:37:27] Unusual charge on atom 0 number of radical electrons set to zero +47: [21:37:27] non-ring atom 0 marked aromatic +47: [21:37:27] non-ring atom 0 marked aromatic +47: [21:37:27] Explicit valence for atom # 1 C, 5, is greater than permitted +47: [21:37:27] Explicit valence for atom # 9 C, 5, is greater than permitted +47: [21:37:27] Explicit valence for atom # 3 N, 4, is greater than permitted +47: [21:37:27] Explicit valence for atom # 15 C, 5, is greater than permitted +47: [21:37:27] Explicit valence for atom # 11 C, 5, is greater than permitted +47: [21:37:27] Explicit valence for atom # 9 C, 5, is greater than permitted +47: [21:37:27] Explicit valence for atom # 9 C, 5, is greater than permitted +47: [21:37:27] Explicit valence for atom # 9 C, 6, is greater than permitted +47: [21:37:27] Can't kekulize mol. Unkekulized atoms: 0 1 2 3 4 +47: [21:37:27] Can't kekulize mol. Unkekulized atoms: 7 +47: [21:37:27] Can't kekulize mol. Unkekulized atoms: 3 +47: [21:37:27] Can't kekulize mol. Unkekulized atoms: 3 7 +47: [21:37:27] Can't kekulize mol. Unkekulized atoms: 3 7 + 38/236 Test #48: graphmolOrganometallicsCatch ........... Passed 0.09 sec test 50 Start 50: graphmolAdjustQueryCatch 50: Test command: /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/GraphMol/graphmolAdjustQueryCatch 50: Working Directory: /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/GraphMol 50: Test timeout computed to be: 1500 -47: [12:42:35] Explicit valence for atom # 1 O, 3, is greater than permitted -47: [12:42:35] WARNING: merging explicit H queries involved in ORs is not supported. This query will not be merged -47: [12:42:35] WARNING: merging explicit H queries involved in ORs is not supported. This query will not be merged -47: [12:42:35] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -47: [12:42:35] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -47: [12:42:35] Invalid value for molAttachPoint: 4 on atom 1. Not expanding this atttachment point. -47: [12:42:35] Invalid value for _fromAttachPoint: -1 on atom 0. Not collapsing this atom -47: [12:42:35] Invalid value for _fromAttachPoint: 4 on atom 0. Not collapsing this atom -49: Randomness seeded to: 2617083398 +47: [21:37:27] WARNING: could not find number of expected rings. Switching to an approximate ring finding algorithm. +47: [21:37:27] WARNING: could not find number of expected rings. Switching to an approximate ring finding algorithm. +49: Randomness seeded to: 3381690423 49: =============================================================================== 49: All tests passed (136 assertions in 8 test cases) 49: -47: [12:42:35] non-ring atom 0 marked aromatic - 39/236 Test #49: graphmolSGroupCatch .................... Passed 0.02 sec + 39/236 Test #49: graphmolSGroupCatch .................... Passed 0.06 sec test 51 Start 51: chiralityTestsCatch 51: Test command: /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/GraphMol/chiralityTestsCatch 51: Working Directory: /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/GraphMol 51: Test timeout computed to be: 1500 -47: [12:42:35] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored -47: [12:42:35] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored -47: [12:42:35] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -41: [12:42:35] sorting (hanoi sort) vectors -47: [12:42:35] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -50: Randomness seeded to: 548612662 -50: =============================================================================== -50: All tests passed (281 assertions in 10 test cases) -50: -47: [12:42:35] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. - 40/236 Test #50: graphmolAdjustQueryCatch ............... Passed 0.03 sec + 40/236 Test #21: testPyGeometry ......................... Passed 0.74 sec test 52 Start 52: canonTestsCatch 52: Test command: /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/GraphMol/canonTestsCatch 52: Working Directory: /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/GraphMol 52: Test timeout computed to be: 1500 -47: [12:42:35] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 2 ignored -47: [12:42:35] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 2 ignored - 41/236 Test #32: pyDistGeom ............................. Passed 0.20 sec +47: [21:37:27] Explicit valence for atom # 1 O, 3, is greater than permitted +47: [21:37:27] WARNING: merging explicit H queries involved in ORs is not supported. This query will not be merged +47: [21:37:27] WARNING: merging explicit H queries involved in ORs is not supported. This query will not be merged +51: Randomness seeded to: 3586879154 +51: [21:37:27] unable to set wavy bonds for double bonds: 3 +41: [21:37:27] sorting (hanoi sort) vectors +47: [21:37:27] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +47: [21:37:27] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +47: [21:37:27] Invalid value for molAttachPoint: 4 on atom 1. Not expanding this atttachment point. +47: [21:37:27] Invalid value for _fromAttachPoint: -1 on atom 0. Not collapsing this atom +47: [21:37:27] Invalid value for _fromAttachPoint: 4 on atom 0. Not collapsing this atom +47: [21:37:27] non-ring atom 0 marked aromatic +50: Randomness seeded to: 1259802158 +50: =============================================================================== +50: All tests passed (281 assertions in 10 test cases) +50: + 41/236 Test #50: graphmolAdjustQueryCatch ............... Passed 0.07 sec test 53 Start 53: moliteratorTestsCatch 53: Test command: /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/GraphMol/moliteratorTestsCatch 53: Working Directory: /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/GraphMol 53: Test timeout computed to be: 1500 -47: [12:42:35] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -47: [12:42:35] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored -47: [12:42:35] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored -47: [12:42:35] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored -47: [12:42:35] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored -51: Randomness seeded to: 2168352985 -51: [12:42:35] unable to set wavy bonds for double bonds: 3 -47: [12:42:35] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -53: Randomness seeded to: 3684749306 +51: [21:37:27] WARNING: not removing hydrogen atom with neighbor that has non-tetrahedral stereochemistry +51: [21:37:27] WARNING: not removing hydrogen atom with neighbor that has non-tetrahedral stereochemistry +47: [21:37:27] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored +47: [21:37:27] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored +51: [21:37:27] Warning: ambiguous stereochemistry - zero-length (or near zero-length) bond - at atom 1 ignored. +51: [21:37:27] Warning: ambiguous stereochemistry - zero-length (or near zero-length) bond - at atom 1 ignored. +51: [21:37:27] Warning: ambiguous stereochemistry - overlapping neighbors - at atom 2 ignored +47: [21:37:27] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +53: Randomness seeded to: 1899483559 53: =============================================================================== 53: All tests passed (14 assertions in 4 test cases) 53: - 42/236 Test #53: moliteratorTestsCatch .................. Passed 0.01 sec + 42/236 Test #53: moliteratorTestsCatch .................. Passed 0.03 sec test 54 Start 54: queryTestsCatch 54: Test command: /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/GraphMol/queryTestsCatch 54: Working Directory: /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/GraphMol 54: Test timeout computed to be: 1500 -51: [12:42:35] WARNING: not removing hydrogen atom with neighbor that has non-tetrahedral stereochemistry -51: [12:42:35] WARNING: not removing hydrogen atom with neighbor that has non-tetrahedral stereochemistry -51: [12:42:35] Warning: ambiguous stereochemistry - zero-length (or near zero-length) bond - at atom 1 ignored. -51: [12:42:35] Warning: ambiguous stereochemistry - zero-length (or near zero-length) bond - at atom 1 ignored. -54: Randomness seeded to: 557965523 -54: =============================================================================== -54: All tests passed (10 assertions in 1 test case) -54: - 43/236 Test #54: queryTestsCatch ........................ Passed 0.01 sec +47: [21:37:27] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +47: [21:37:27] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +47: [21:37:27] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 2 ignored +47: [21:37:27] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 2 ignored +51: =============================================================================== +51: All tests passed (2267 assertions in 79 test cases) +51: + 43/236 Test #51: chiralityTestsCatch .................... Passed 0.10 sec test 55 Start 55: molbundleTestsCatch 55: Test command: /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/GraphMol/molbundleTestsCatch 55: Working Directory: /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/GraphMol 55: Test timeout computed to be: 1500 -51: [12:42:35] Warning: ambiguous stereochemistry - overlapping neighbors - at atom 2 ignored -51: =============================================================================== -51: All tests passed (2267 assertions in 79 test cases) -51: -47: [12:42:35] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -47: [12:42:35] Explicit valence for atom # 0 Al, 6, is greater than permitted -47: [12:42:35] Explicit valence for atom # 0 Al, 6, is greater than permitted -47: [12:42:35] Explicit valence for atom # 1 Si, 6, is greater than permitted -47: [12:42:35] Explicit valence for atom # 1 Si, 6, is greater than permitted -47: [12:42:35] Explicit valence for atom # 0 P, 6, is greater than permitted -47: [12:42:35] Explicit valence for atom # 0 P, 6, is greater than permitted -47: [12:42:35] Explicit valence for atom # 0 P, 7, is greater than permitted -47: [12:42:35] Explicit valence for atom # 0 P, 7, is greater than permitted -47: [12:42:35] Explicit valence for atom # 1 As, 6, is greater than permitted -47: [12:42:35] Explicit valence for atom # 1 As, 6, is greater than permitted -47: [12:42:35] Explicit valence for atom # 1 As, 7, is greater than permitted -47: [12:42:35] Explicit valence for atom # 1 As, 7, is greater than permitted -47: [12:42:35] Explicit valence for atom # 0 Sb, 6, is greater than permitted -47: [12:42:35] Explicit valence for atom # 0 Sb, 6, is greater than permitted -47: [12:42:35] Explicit valence for atom # 0 Sb, 7, is greater than permitted -47: [12:42:35] Explicit valence for atom # 0 Sb, 7, is greater than permitted -47: [12:42:35] Explicit valence for atom # 1 Bi, 6, is greater than permitted -47: [12:42:35] Explicit valence for atom # 1 Bi, 6, is greater than permitted -47: [12:42:35] Explicit valence for atom # 1 Bi, 8, is greater than permitted -47: [12:42:35] Explicit valence for atom # 1 Bi, 8, is greater than permitted -47: =============================================================================== -47: All tests passed (4464 assertions in 106 test cases) -47: - 44/236 Test #47: graphmolTestsCatch ..................... Passed 0.12 sec - 45/236 Test #51: chiralityTestsCatch .................... Passed 0.06 sec +36: [21:37:27] Maximum BFS search size exceeded. +36: This is likely due to a highly symmetric fused ring system. +54: Randomness seeded to: 36569288 +54: =============================================================================== +54: All tests passed (10 assertions in 1 test case) +54: +47: [21:37:27] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +47: [21:37:27] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored +47: [21:37:27] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored + 44/236 Test #54: queryTestsCatch ........................ Passed 0.03 sec test 56 Start 56: pickleTestsCatch 56: Test command: /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/GraphMol/pickleTestsCatch 56: Working Directory: /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/GraphMol 56: Test timeout computed to be: 1500 +47: [21:37:27] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored +47: [21:37:27] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored +47: [21:37:27] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +55: Randomness seeded to: 3625085791 +55: =============================================================================== +55: All tests passed (6 assertions in 1 test case) +55: + 45/236 Test #55: molbundleTestsCatch .................... Passed 0.04 sec test 57 Start 57: tableTestsCatch 57: Test command: /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/GraphMol/tableTestsCatch 57: Working Directory: /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/GraphMol 57: Test timeout computed to be: 1500 -55: Randomness seeded to: 1499068929 -55: =============================================================================== -55: All tests passed (6 assertions in 1 test case) -55: - 46/236 Test #55: molbundleTestsCatch .................... Passed 0.02 sec +47: [21:37:27] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +47: [21:37:27] Explicit valence for atom # 0 Al, 6, is greater than permitted +47: [21:37:27] Explicit valence for atom # 0 Al, 6, is greater than permitted +47: [21:37:27] Explicit valence for atom # 1 Si, 6, is greater than permitted +47: [21:37:27] Explicit valence for atom # 1 Si, 6, is greater than permitted +47: [21:37:27] Explicit valence for atom # 0 P, 6, is greater than permitted +47: [21:37:27] Explicit valence for atom # 0 P, 6, is greater than permitted +47: [21:37:27] Explicit valence for atom # 0 P, 7, is greater than permitted +47: [21:37:27] Explicit valence for atom # 0 P, 7, is greater than permitted +47: [21:37:27] Explicit valence for atom # 1 As, 6, is greater than permitted +47: [21:37:27] Explicit valence for atom # 1 As, 6, is greater than permitted +47: [21:37:27] Explicit valence for atom # 1 As, 7, is greater than permitted +47: [21:37:27] Explicit valence for atom # 1 As, 7, is greater than permitted +47: [21:37:27] Explicit valence for atom # 0 Sb, 6, is greater than permitted +47: [21:37:27] Explicit valence for atom # 0 Sb, 6, is greater than permitted +47: [21:37:27] Explicit valence for atom # 0 Sb, 7, is greater than permitted +47: [21:37:27] Explicit valence for atom # 0 Sb, 7, is greater than permitted +47: [21:37:27] Explicit valence for atom # 1 Bi, 6, is greater than permitted +47: [21:37:27] Explicit valence for atom # 1 Bi, 6, is greater than permitted +47: [21:37:27] Explicit valence for atom # 1 Bi, 8, is greater than permitted +47: [21:37:27] Explicit valence for atom # 1 Bi, 8, is greater than permitted +47: =============================================================================== +47: All tests passed (4464 assertions in 106 test cases) +47: + 46/236 Test #47: graphmolTestsCatch ..................... Passed 0.29 sec test 58 Start 58: molopsTestsCatch 58: Test command: /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/GraphMol/molopsTestsCatch 58: Working Directory: /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/GraphMol 58: Test timeout computed to be: 1500 -57: Randomness seeded to: 2512871427 +56: Randomness seeded to: 1424874629 +56: =============================================================================== +56: All tests passed (45 assertions in 4 test cases) +56: +57: Randomness seeded to: 3233599428 57: =============================================================================== 57: All tests passed (7 assertions in 2 test cases) 57: - 47/236 Test #57: tableTestsCatch ........................ Passed 0.01 sec + 47/236 Test #56: pickleTestsCatch ....................... Passed 0.06 sec + 48/236 Test #57: tableTestsCatch ........................ Passed 0.03 sec test 59 Start 59: smiTest1 59: Test command: /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/GraphMol/SmilesParse/smiTest1 59: Working Directory: /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/GraphMol/SmilesParse 59: Test timeout computed to be: 1500 -56: Randomness seeded to: 3214435896 -56: =============================================================================== -56: All tests passed (45 assertions in 4 test cases) -56: - 48/236 Test #56: pickleTestsCatch ....................... Passed 0.02 sec test 60 Start 60: smiTest2 60: Test command: /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/GraphMol/SmilesParse/smiTest2 60: Working Directory: /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/GraphMol/SmilesParse 60: Test timeout computed to be: 1500 -60: [12:42:35] SMILES Parse Error: Failed parsing SMILES 'CO' for input: 'CO' -60: [12:42:35] SMILES Parse Error: Failed parsing SMILES 'C-O' for input: 'C-O' -60: [12:42:35] SMILES Parse Error: syntax error while parsing: - -60: [12:42:35] SMILES Parse Error: check for mistakes around position 1: -60: [12:42:35] - -60: [12:42:35] ^ -60: [12:42:35] SMILES Parse Error: Failed parsing SMILES '-' for input: '-' -60: [12:42:35] SMILES Parse Error: Failed parsing SMILES '[Bg]' for input: '[Bg]' -60: [12:42:35] SMILES Parse Error: Failed parsing SMILES 'C' for input: 'C' -60: [12:42:35] SMILES Parse Error: Failed parsing SMILES 'C-O' for input: 'C-O' -60: [12:42:35] SMILES Parse Error: Failed parsing SMILES '*' for input: '*' -60: [12:42:35] SMARTS Parse Error: Failed parsing SMARTS 'CO' for input: 'CO' -60: [12:42:35] SMARTS Parse Error: Failed parsing SMARTS 'C-O' for input: 'C-O' -60: [12:42:35] SMARTS Parse Error: Failed parsing SMARTS '-' for input: '-' -60: [12:42:35] SMARTS Parse Error: Failed parsing SMARTS '[Bg]' for input: '[Bg]' -60: [12:42:35] SMARTS Parse Error: Failed parsing SMARTS 'C' for input: 'C' -60: [12:42:35] SMARTS Parse Error: Failed parsing SMARTS '-O' for input: '-O' -60: [12:42:35] SMARTS Parse Error: Failed parsing SMARTS '*' for input: '*' - 49/236 Test #60: smiTest2 ............................... Passed 0.01 sec -58: Randomness seeded to: 455600991 +30: ......[21:37:27] Molecule does not have explicit Hs. Consider calling AddHs() +58: Randomness seeded to: 3527739472 58: =============================================================================== 58: All tests passed (77 assertions in 5 test cases) 58: + 49/236 Test #58: molopsTestsCatch ....................... Passed 0.05 sec test 61 Start 61: cxsmilesTest 61: Test command: /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/GraphMol/SmilesParse/cxsmilesTest 61: Working Directory: /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/GraphMol/SmilesParse 61: Test timeout computed to be: 1500 -59: [12:42:35] WARNING: not removing hydrogen atom without neighbors -59: [12:42:35] WARNING: not removing hydrogen atom without neighbors - 50/236 Test #58: molopsTestsCatch ....................... Passed 0.03 sec -59: [12:42:35] WARNING: not removing hydrogen atom without neighbors -59: [12:42:35] WARNING: not removing hydrogen atom without neighbors -59: [12:42:35] WARNING: not removing hydrogen atom without neighbors -59: [12:42:35] WARNING: not removing hydrogen atom without neighbors -59: [12:42:35] WARNING: not removing hydrogen atom without neighbors -59: [12:42:35] WARNING: not removing hydrogen atom without neighbors -59: [12:42:35] WARNING: not removing hydrogen atom without neighbors -59: [12:42:35] WARNING: not removing hydrogen atom without neighbors +60: [21:37:28] SMILES Parse Error: Failed parsing SMILES 'CO' for input: 'CO' +60: [21:37:28] SMILES Parse Error: Failed parsing SMILES 'C-O' for input: 'C-O' +60: [21:37:28] SMILES Parse Error: syntax error while parsing: - +60: [21:37:28] SMILES Parse Error: check for mistakes around position 1: +60: [21:37:28] - +60: [21:37:28] ^ +60: [21:37:28] SMILES Parse Error: Failed parsing SMILES '-' for input: '-' +60: [21:37:28] SMILES Parse Error: Failed parsing SMILES '[Bg]' for input: '[Bg]' +60: [21:37:28] SMILES Parse Error: Failed parsing SMILES 'C' for input: 'C' +60: [21:37:28] SMILES Parse Error: Failed parsing SMILES 'C-O' for input: 'C-O' +60: [21:37:28] SMILES Parse Error: Failed parsing SMILES '*' for input: '*' +60: [21:37:28] SMARTS Parse Error: Failed parsing SMARTS 'CO' for input: 'CO' +60: [21:37:28] SMARTS Parse Error: Failed parsing SMARTS 'C-O' for input: 'C-O' +60: [21:37:28] SMARTS Parse Error: Failed parsing SMARTS '-' for input: '-' +60: [21:37:28] SMARTS Parse Error: Failed parsing SMARTS '[Bg]' for input: '[Bg]' +60: [21:37:28] SMARTS Parse Error: Failed parsing SMARTS 'C' for input: 'C' +60: [21:37:28] SMARTS Parse Error: Failed parsing SMARTS '-O' for input: '-O' +60: [21:37:28] SMARTS Parse Error: Failed parsing SMARTS '*' for input: '*' +59: [21:37:28] WARNING: not removing hydrogen atom without neighbors +59: [21:37:28] WARNING: not removing hydrogen atom without neighbors +59: [21:37:28] WARNING: not removing hydrogen atom without neighbors +59: [21:37:28] WARNING: not removing hydrogen atom without neighbors +59: [21:37:28] WARNING: not removing hydrogen atom without neighbors +59: [21:37:28] WARNING: not removing hydrogen atom without neighbors +59: [21:37:28] WARNING: not removing hydrogen atom without neighbors +59: [21:37:28] WARNING: not removing hydrogen atom without neighbors +59: [21:37:28] WARNING: not removing hydrogen atom without neighbors +59: [21:37:28] WARNING: not removing hydrogen atom without neighbors + 50/236 Test #60: smiTest2 ............................... Passed 0.04 sec test 62 Start 62: smaTest1 62: Test command: /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/GraphMol/SmilesParse/smaTest1 62: Working Directory: /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/GraphMol/SmilesParse 62: Test timeout computed to be: 1500 -59: [12:42:35] WARNING: not removing hydrogen atom without neighbors -59: [12:42:35] Invalid chiral specification on atom 0 -59: [12:42:35] Invalid chiral specification on atom 0 -59: [12:42:35] Invalid chiral specification on atom 0 -59: [12:42:35] Invalid chiral specification on atom 0 -59: [12:42:35] Invalid chiral specification on atom 0 -59: [12:42:35] SMILES Parse Error: unclosed ring for input: 'C1.C11.C' -59: [12:42:35] SMILES Parse Error: unclosed ring for input: 'C1C.CC11CCC' -36: [12:42:35] Maximum BFS search size exceeded. -36: This is likely due to a highly symmetric fused ring system. +59: [21:37:28] WARNING: not removing hydrogen atom without neighbors +59: [21:37:28] Invalid chiral specification on atom 0 +59: [21:37:28] Invalid chiral specification on atom 0 +59: [21:37:28] Invalid chiral specification on atom 0 +59: [21:37:28] Invalid chiral specification on atom 0 +59: [21:37:28] Invalid chiral specification on atom 0 +59: [21:37:28] SMILES Parse Error: unclosed ring for input: 'C1.C11.C' +59: [21:37:28] SMILES Parse Error: unclosed ring for input: 'C1C.CC11CCC' 59: --C1CCC2(CC1)CCCCC2CCC1CCCC1 -62: [12:42:35] SMARTS Parse Error: syntax error while parsing: [C:10H3]CC -62: [12:42:35] SMARTS Parse Error: Failed parsing SMARTS '[C:10H3]CC' for input: '[C:10H3]CC' -62: [12:42:35] SMARTS Parse Error: syntax error while parsing: [C:10:3]ON -62: [12:42:35] SMARTS Parse Error: Failed parsing SMARTS '[C:10:3]ON' for input: '[C:10:3]ON' -62: [12:42:35] WARNING: merging explicit H queries involved in ORs is not supported. This query will not be merged -62: [12:42:35] WARNING: merging explicit H queries involved in ORs is not supported. This query will not be merged -61: Randomness seeded to: 3785286280 +62: [21:37:28] SMARTS Parse Error: syntax error while parsing: [C:10H3]CC +62: [21:37:28] SMARTS Parse Error: Failed parsing SMARTS '[C:10H3]CC' for input: '[C:10H3]CC' +62: [21:37:28] SMARTS Parse Error: syntax error while parsing: [C:10:3]ON +62: [21:37:28] SMARTS Parse Error: Failed parsing SMARTS '[C:10:3]ON' for input: '[C:10:3]ON' +62: [21:37:28] WARNING: merging explicit H queries involved in ORs is not supported. This query will not be merged +62: [21:37:28] WARNING: merging explicit H queries involved in ORs is not supported. This query will not be merged + 51/236 Test #62: smaTest1 ............................... Passed 0.16 sec +test 63 + Start 63: smiTestCatch + +63: Test command: /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/GraphMol/SmilesParse/smiTestCatch +63: Working Directory: /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/GraphMol/SmilesParse +63: Test timeout computed to be: 1500 +61: Randomness seeded to: 2700697078 61: Test 61: 61: ShortAtropisomerNoCoords.cxsmi @@ -18110,16 +18149,21 @@ 61: 61: BMS-986142_atrop5.cxsmi 61: -61: [12:42:35] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored -61: [12:42:35] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored -61: [12:42:35] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored -61: [12:42:35] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored -61: [12:42:35] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored -61: [12:42:35] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored -61: [12:42:35] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored -61: [12:42:35] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored -61: [12:42:35] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored -61: [12:42:35] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored +61: [21:37:28] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored +61: [21:37:28] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored +61: [21:37:28] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored +61: [21:37:28] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored +61: [21:37:28] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored +61: [21:37:28] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored +61: [21:37:28] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored +61: [21:37:28] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored +61: [21:37:28] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored +61: [21:37:28] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored +30: ... +30: ---------------------------------------------------------------------- +30: Ran 12 tests in 0.557s +30: +30: OK 59: smi: ClC1CCCCC1 59: smi: ClC1CCCCC1 59: smi: ClC1CCCCC1Br @@ -18128,18 +18172,23 @@ 59: smi: c1cc[nH]c1 59: smi: c1cc[nH]c1 59: smi: c1cc[pH]c1 - 51/236 Test #62: smaTest1 ............................... Passed 0.07 sec -test 63 - Start 63: smiTestCatch - -63: Test command: /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/GraphMol/SmilesParse/smiTestCatch -63: Working Directory: /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/GraphMol/SmilesParse -63: Test timeout computed to be: 1500 59: CbC(aC)aC 59: CaC(bC)aC 59: CbC(bC)aC 59: O.C 59: 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 +59: [21:37:28] SMILES Parse Error: syntax error while parsing: c%()ccccc%() +59: [21:37:28] SMILES Parse Error: check for mistakes around position 4: +59: [21:37:28] c%()ccccc%() +59: [21:37:28] ~~~^ +59: [21:37:28] SMILES Parse Error: Failed parsing SMILES 'c%()ccccc%()' for input: 'c%()ccccc%()' +59: [21:37:28] SMILES Parse Error: syntax error while parsing: c%(100000)ccccc%(100000) +59: [21:37:28] SMILES Parse Error: check for mistakes around position 9: +59: [21:37:28] c%(100000)ccccc%(100000) +59: [21:37:28] ~~~~~~~~^ +59: [21:37:28] SMILES Parse Error: Failed parsing SMILES 'c%(100000)ccccc%(100000)' for input: 'c%(100000)ccccc%(100000)' +59: [21:37:28] SMILES Parse Error: duplicated ring closure 1 bonds atom 2 to itself for input: 'C1CC111' +59: [21:37:28] SMILES Parse Error: ring closure 1 duplicates bond between atom 0 and atom 1 for input: 'C1C1' 61: Test 61: 61: BMS-986142_atrop6.cxsmi @@ -18148,83 +18197,68 @@ 61: 61: BMS-986142_atropBad1.cxsmi 61: -61: [12:42:35] The 2 defining bonds for an atropisomer are co-planar - atoms are: 6 7 -59: [12:42:35] SMILES Parse Error: syntax error while parsing: c%()ccccc%() -59: [12:42:35] SMILES Parse Error: check for mistakes around position 4: -59: [12:42:35] c%()ccccc%() -59: [12:42:35] ~~~^ -59: [12:42:35] SMILES Parse Error: Failed parsing SMILES 'c%()ccccc%()' for input: 'c%()ccccc%()' -59: [12:42:35] SMILES Parse Error: syntax error while parsing: c%(100000)ccccc%(100000) -59: [12:42:35] SMILES Parse Error: check for mistakes around position 9: -59: [12:42:35] c%(100000)ccccc%(100000) -59: [12:42:35] ~~~~~~~~^ -59: [12:42:35] SMILES Parse Error: Failed parsing SMILES 'c%(100000)ccccc%(100000)' for input: 'c%(100000)ccccc%(100000)' -59: [12:42:35] SMILES Parse Error: duplicated ring closure 1 bonds atom 2 to itself for input: 'C1CC111' -61: [12:42:35] The 2 defining bonds for an atropisomer are co-planar - atoms are: 6 7 -61: [12:42:35] The 2 defining bonds for an atropisomer are co-planar - atoms are: 6 7 -59: [12:42:35] SMILES Parse Error: ring closure 1 duplicates bond between atom 0 and atom 1 for input: 'C1C1' -61: [12:42:35] The 2 defining bonds for an atropisomer are co-planar - atoms are: 6 7 -61: [12:42:35] The 2 defining bonds for an atropisomer are co-planar - atoms are: 6 7 +61: [21:37:28] The 2 defining bonds for an atropisomer are co-planar - atoms are: 6 7 +61: [21:37:28] The 2 defining bonds for an atropisomer are co-planar - atoms are: 6 7 +59: [21:37:28] SMILES Parse Error: syntax error while parsing: COc(c1)cccc1C# +59: [21:37:28] SMILES Parse Error: check for mistakes around position 14: +59: [21:37:28] COc(c1)cccc1C# +59: [21:37:28] ~~~~~~~~~~~~~^ +61: [21:37:28] The 2 defining bonds for an atropisomer are co-planar - atoms are: 6 7 +61: [21:37:28] The 2 defining bonds for an atropisomer are co-planar - atoms are: 6 7 +61: [21:37:28] The 2 defining bonds for an atropisomer are co-planar - atoms are: 6 7 61: Test 61: 61: BMS-986142_atropBad2.cxsmi 61: -61: [12:42:35] The bonds on one end of an atropisomer are both UP or both DOWN - atoms are: 6 7 -61: [12:42:35] The bonds on one end of an atropisomer are both UP or both DOWN - atoms are: 6 7 -61: [12:42:35] The bonds on one end of an atropisomer are both UP or both DOWN - atoms are: 6 7 -61: [12:42:35] The bonds on one end of an atropisomer are both UP or both DOWN - atoms are: 6 7 -61: [12:42:35] The bonds on one end of an atropisomer are both UP or both DOWN - atoms are: 6 7 -59: [12:42:35] SMILES Parse Error: syntax error while parsing: COc(c1)cccc1C# -59: [12:42:35] SMILES Parse Error: check for mistakes around position 14: -59: [12:42:35] COc(c1)cccc1C# -59: [12:42:35] ~~~~~~~~~~~~~^ -59: [12:42:35] SMILES Parse Error: Failed parsing SMILES 'COc(c1)cccc1C#' for input: 'COc(c1)cccc1C#' -59: [12:42:35] SMARTS Parse Error: syntax error while parsing: COc(c1)cccc1C# -59: [12:42:35] SMARTS Parse Error: Failed parsing SMARTS 'COc(c1)cccc1C#' for input: 'COc(c1)cccc1C#' -59: [12:42:35] SMILES Parse Error: syntax error while parsing: COc(c1)cccc1C# -59: [12:42:35] SMILES Parse Error: check for mistakes around position 14: -59: [12:42:35] COc(c1)cccc1C# -59: [12:42:35] ~~~~~~~~~~~~~^ -59: [12:42:35] SMILES Parse Error: Failed parsing SMILES 'COc(c1)cccc1C#' for input: 'COc(c1)cccc1C#' -59: [12:42:35] SMARTS Parse Error: syntax error while parsing: COc(c1)cccc1C# -59: [12:42:35] SMARTS Parse Error: Failed parsing SMARTS 'COc(c1)cccc1C#' for input: 'COc(c1)cccc1C#' -59: [12:42:35] SMILES Parse Error: syntax error while parsing: COc(c1)cccc1C# -59: [12:42:35] SMILES Parse Error: check for mistakes around position 14: -59: [12:42:35] COc(c1)cccc1C# -59: [12:42:35] ~~~~~~~~~~~~~^ -59: [12:42:35] SMILES Parse Error: Failed parsing SMILES 'COc(c1)cccc1C#' for input: 'COc(c1)cccc1C#' -59: [12:42:35] SMARTS Parse Error: syntax error while parsing: COc(c1)cccc1C# -59: [12:42:35] SMARTS Parse Error: Failed parsing SMARTS 'COc(c1)cccc1C#' for input: 'COc(c1)cccc1C#' +61: [21:37:28] The bonds on one end of an atropisomer are both UP or both DOWN - atoms are: 6 7 +63: Randomness seeded to: 2035354135 +63: [21:37:28] SMILES Parse Error: unclosed ring for input: 'c1ccccc' +63: [21:37:28] Can't kekulize mol. Unkekulized atoms: 0 1 2 3 4 +63: [21:37:28] SMARTS Parse Error: unclosed ring for input: 'c1ccccc' +59: [21:37:28] SMILES Parse Error: Failed parsing SMILES 'COc(c1)cccc1C#' for input: 'COc(c1)cccc1C#' +59: [21:37:28] SMARTS Parse Error: syntax error while parsing: COc(c1)cccc1C# +59: [21:37:28] SMARTS Parse Error: Failed parsing SMARTS 'COc(c1)cccc1C#' for input: 'COc(c1)cccc1C#' +59: [21:37:28] SMILES Parse Error: syntax error while parsing: COc(c1)cccc1C# +59: [21:37:28] SMILES Parse Error: check for mistakes around position 14: +59: [21:37:28] COc(c1)cccc1C# +59: [21:37:28] ~~~~~~~~~~~~~^ +59: [21:37:28] SMILES Parse Error: Failed parsing SMILES 'COc(c1)cccc1C#' for input: 'COc(c1)cccc1C#' +59: [21:37:28] SMARTS Parse Error: syntax error while parsing: COc(c1)cccc1C# +59: [21:37:28] SMARTS Parse Error: Failed parsing SMARTS 'COc(c1)cccc1C#' for input: 'COc(c1)cccc1C#' +59: [21:37:28] SMILES Parse Error: syntax error while parsing: COc(c1)cccc1C# +59: [21:37:28] SMILES Parse Error: check for mistakes around position 14: +59: [21:37:28] COc(c1)cccc1C# +59: [21:37:28] ~~~~~~~~~~~~~^ +59: [21:37:28] SMILES Parse Error: Failed parsing SMILES 'COc(c1)cccc1C#' for input: 'COc(c1)cccc1C#' +59: [21:37:28] SMARTS Parse Error: syntax error while parsing: COc(c1)cccc1C# +59: [21:37:28] SMARTS Parse Error: Failed parsing SMARTS 'COc(c1)cccc1C#' for input: 'COc(c1)cccc1C#' 59: C=c1s/c2n(c1=O)CCCCCCC\N=2 59: C1=C\C/C=C2C3=C\C/C=C\C=C/C/3C\2\C=C/1 -59: [12:42:35] SMILES Parse Error: extra close parentheses while parsing: C) -59: [12:42:35] SMILES Parse Error: check for mistakes around position 2: -59: [12:42:35] C) -59: [12:42:35] ~^ -59: [12:42:35] SMILES Parse Error: Failed parsing SMILES 'C)' for input: 'C)' - 52/236 Test #59: smiTest1 ............................... Passed 0.10 sec +59: [21:37:28] SMILES Parse Error: extra close parentheses while parsing: C) +59: [21:37:28] SMILES Parse Error: check for mistakes around position 2: +59: [21:37:28] C) +59: [21:37:28] ~^ +59: [21:37:28] SMILES Parse Error: Failed parsing SMILES 'C)' for input: 'C)' + 52/236 Test #59: smiTest1 ............................... Passed 0.26 sec test 64 Start 64: nontetrahedralCatch 64: Test command: /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/GraphMol/SmilesParse/nontetrahedralCatch 64: Working Directory: /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/GraphMol/SmilesParse 64: Test timeout computed to be: 1500 -63: Randomness seeded to: 1471499768 -63: [12:42:35] SMILES Parse Error: unclosed ring for input: 'c1ccccc' -63: [12:42:35] Can't kekulize mol. Unkekulized atoms: 0 1 2 3 4 -63: [12:42:35] SMARTS Parse Error: unclosed ring for input: 'c1ccccc' -63: [12:42:35] SMARTS Parse Error: unclosed ring for input: 'C1C' -63: [12:42:35] Can't kekulize mol. Unkekulized atoms: 0 1 2 3 4 -63: [12:42:35] SMARTS Parse Error: syntax error while parsing: C)foo -63: [12:42:35] SMARTS Parse Error: Failed parsing SMARTS 'C)foo' for input: 'C)foo' -63: [12:42:35] SMARTS Parse Error: syntax error while parsing: CCC |$foo;;bar$| -63: [12:42:35] SMARTS Parse Error: Failed parsing SMARTS 'CCC |$foo;;bar$|' for input: 'CCC |$foo;;bar$|' -64: Randomness seeded to: 810402964 -64: [12:42:35] WARNING: not removing hydrogen atom with neighbor that has non-tetrahedral stereochemistry -63: [12:42:35] unrecognized CXSMILES CONNECT value: 'EU'. Assuming 'eu' -64: [12:42:35] WARNING: not removing hydrogen atom with neighbor that has non-tetrahedral stereochemistry -64: [12:42:35] WARNING: not removing hydrogen atom with neighbor that has non-tetrahedral stereochemistry -64: [12:42:35] WARNING: not removing hydrogen atom with neighbor that has non-tetrahedral stereochemistry +63: [21:37:28] SMARTS Parse Error: unclosed ring for input: 'C1C' +63: [21:37:28] Can't kekulize mol. Unkekulized atoms: 0 1 2 3 4 +63: [21:37:28] SMARTS Parse Error: syntax error while parsing: C)foo +63: [21:37:28] SMARTS Parse Error: Failed parsing SMARTS 'C)foo' for input: 'C)foo' +63: [21:37:28] SMARTS Parse Error: syntax error while parsing: CCC |$foo;;bar$| +63: [21:37:28] SMARTS Parse Error: Failed parsing SMARTS 'CCC |$foo;;bar$|' for input: 'CCC |$foo;;bar$|' +63: [21:37:28] unrecognized CXSMILES CONNECT value: 'EU'. Assuming 'eu' +61: [21:37:28] The bonds on one end of an atropisomer are both UP or both DOWN - atoms are: 6 7 +61: [21:37:28] The bonds on one end of an atropisomer are both UP or both DOWN - atoms are: 6 7 +61: [21:37:28] The bonds on one end of an atropisomer are both UP or both DOWN - atoms are: 6 7 +61: [21:37:28] The bonds on one end of an atropisomer are both UP or both DOWN - atoms are: 6 7 +64: Randomness seeded to: 4285529942 +64: [21:37:28] WARNING: not removing hydrogen atom with neighbor that has non-tetrahedral stereochemistry 61: Test 61: 61: JDQ443_3d.cxsmi @@ -18249,19 +18283,19 @@ 61: 61: JDQ443_atropBad1.cxsmi 61: -61: [12:42:35] The 2 defining bonds for an atropisomer are co-planar - atoms are: 2 3 -61: [12:42:35] The 2 defining bonds for an atropisomer are co-planar - atoms are: 2 3 -61: [12:42:35] The 2 defining bonds for an atropisomer are co-planar - atoms are: 2 3 -61: [12:42:35] The 2 defining bonds for an atropisomer are co-planar - atoms are: 2 3 -61: [12:42:35] The 2 defining bonds for an atropisomer are co-planar - atoms are: 2 3 -64: [12:42:35] WARNING: not removing hydrogen atom with neighbor that has non-tetrahedral stereochemistry -64: [12:42:35] WARNING: not removing hydrogen atom with neighbor that has non-tetrahedral stereochemistry -64: [12:42:35] WARNING: not removing hydrogen atom with neighbor that has non-tetrahedral stereochemistry -64: [12:42:35] WARNING: not removing hydrogen atom with neighbor that has non-tetrahedral stereochemistry -64: [12:42:35] ignoring non-tetrahedral stereo specification since setAllowNontetrahedralChirality() is false. -64: =============================================================================== -64: All tests passed (308 assertions in 9 test cases) -64: +61: [21:37:28] The 2 defining bonds for an atropisomer are co-planar - atoms are: 2 3 +61: [21:37:28] The 2 defining bonds for an atropisomer are co-planar - atoms are: 2 3 +61: [21:37:28] The 2 defining bonds for an atropisomer are co-planar - atoms are: 2 3 +61: [21:37:28] The 2 defining bonds for an atropisomer are co-planar - atoms are: 2 3 +64: [21:37:28] WARNING: not removing hydrogen atom with neighbor that has non-tetrahedral stereochemistry +61: [21:37:28] The 2 defining bonds for an atropisomer are co-planar - atoms are: 2 3 +64: [21:37:28] WARNING: not removing hydrogen atom with neighbor that has non-tetrahedral stereochemistry +64: [21:37:28] WARNING: not removing hydrogen atom with neighbor that has non-tetrahedral stereochemistry +64: [21:37:28] WARNING: not removing hydrogen atom with neighbor that has non-tetrahedral stereochemistry +64: [21:37:28] WARNING: not removing hydrogen atom with neighbor that has non-tetrahedral stereochemistry +63: [21:37:28] w block attempts to set wedging on bond 0 more than once. +63: [21:37:28] improperly formatted w block +63: [21:37:28] atom 3 is not associated with bond 1(1-2) in w block 61: Test 61: 61: RP-6306_atrop1.cxsmi @@ -18282,24 +18316,18 @@ 61: 61: RP-6306_atrop5.cxsmi 61: -61: [12:42:35] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored -61: [12:42:35] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored -61: [12:42:35] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored -61: [12:42:35] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored - 53/236 Test #64: nontetrahedralCatch .................... Passed 0.03 sec -61: [12:42:35] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored -61: [12:42:35] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored -test 65 - Start 65: v2smiTestCatch - -65: Test command: /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/GraphMol/SmilesParse/v2smiTestCatch -65: Working Directory: /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/GraphMol/SmilesParse -65: Test timeout computed to be: 1500 -61: [12:42:35] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored -61: [12:42:35] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored -61: [12:42:35] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored -61: [12:42:35] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored -30: ......[12:42:35] Molecule does not have explicit Hs. Consider calling AddHs() +61: [21:37:28] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored +61: [21:37:28] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored +61: [21:37:28] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored +61: [21:37:28] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored +64: [21:37:28] WARNING: not removing hydrogen atom with neighbor that has non-tetrahedral stereochemistry +64: [21:37:28] WARNING: not removing hydrogen atom with neighbor that has non-tetrahedral stereochemistry +61: [21:37:28] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored +61: [21:37:28] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored +61: [21:37:28] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored +61: [21:37:28] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored +61: [21:37:28] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored +61: [21:37:28] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored 61: Test 61: 61: RP-6306_atrop6.cxsmi @@ -18308,69 +18336,27 @@ 61: 61: RP-6306_atropBad1.cxsmi 61: -61: [12:42:35] The 2 defining bonds for an atropisomer are co-planar - atoms are: 4 5 -61: [12:42:35] The 2 defining bonds for an atropisomer are co-planar - atoms are: 4 5 -61: [12:42:35] The 2 defining bonds for an atropisomer are co-planar - atoms are: 4 5 -61: [12:42:35] The 2 defining bonds for an atropisomer are co-planar - atoms are: 4 5 -61: [12:42:35] The 2 defining bonds for an atropisomer are co-planar - atoms are: 4 5 +61: [21:37:28] The 2 defining bonds for an atropisomer are co-planar - atoms are: 4 5 +36: [21:37:28] Maximum BFS search size exceeded. +36: This is likely due to a highly symmetric fused ring system. +64: [21:37:28] ignoring non-tetrahedral stereo specification since setAllowNontetrahedralChirality() is false. +64: =============================================================================== +64: All tests passed (308 assertions in 9 test cases) +64: +61: [21:37:28] The 2 defining bonds for an atropisomer are co-planar - atoms are: 4 5 +61: [21:37:28] The 2 defining bonds for an atropisomer are co-planar - atoms are: 4 5 +61: [21:37:28] The 2 defining bonds for an atropisomer are co-planar - atoms are: 4 5 +61: [21:37:28] The 2 defining bonds for an atropisomer are co-planar - atoms are: 4 5 61: Test 61: 61: RP-6306_atropBad2.cxsmi 61: -61: [12:42:35] The bonds on one end of an atropisomer are both UP or both DOWN - atoms are: 4 5 -61: [12:42:35] The bonds on one end of an atropisomer are both UP or both DOWN - atoms are: 4 5 -61: [12:42:35] The bonds on one end of an atropisomer are both UP or both DOWN - atoms are: 4 5 -61: [12:42:35] The bonds on one end of an atropisomer are both UP or both DOWN - atoms are: 4 5 -61: [12:42:35] The bonds on one end of an atropisomer are both UP or both DOWN - atoms are: 4 5 -65: Randomness seeded to: 3340397243 -65: =============================================================================== -65: All tests passed (14 assertions in 2 test cases) -65: - 54/236 Test #65: v2smiTestCatch ......................... Passed 0.01 sec -test 66 - Start 66: testDepictor - -66: Test command: /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/GraphMol/Depictor/testDepictor -66: Working Directory: /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/GraphMol/Depictor -66: Test timeout computed to be: 1500 -63: [12:42:35] w block attempts to set wedging on bond 0 more than once. -63: [12:42:35] improperly formatted w block -63: [12:42:35] atom 3 is not associated with bond 1(1-2) in w block -61: Test -61: -61: RP-6306_3d.cxsmi -61: -61: Test -61: -61: Sotorasib_atrop1.cxsmi -61: -61: Test -61: -61: Sotorasib_atrop2.cxsmi -61: -61: Test -61: -61: Sotorasib_atrop3.cxsmi -61: -61: Test -61: -61: Sotorasib_atrop4.cxsmi -61: -61: Test -61: -61: Sotorasib_atrop5.cxsmi -61: -61: [12:42:35] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 13 ignored -61: [12:42:35] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 13 ignored -61: [12:42:35] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 13 ignored -61: [12:42:35] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 13 ignored -61: [12:42:35] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 13 ignored -61: [12:42:35] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 13 ignored -61: [12:42:35] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 13 ignored -61: [12:42:35] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 13 ignored -61: [12:42:35] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 13 ignored -61: [12:42:35] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 13 ignored -63: [12:42:35] +61: [21:37:28] The bonds on one end of an atropisomer are both UP or both DOWN - atoms are: 4 5 +61: [21:37:28] The bonds on one end of an atropisomer are both UP or both DOWN - atoms are: 4 5 +61: [21:37:28] The bonds on one end of an atropisomer are both UP or both DOWN - atoms are: 4 5 +61: [21:37:28] The bonds on one end of an atropisomer are both UP or both DOWN - atoms are: 4 5 +61: [21:37:28] The bonds on one end of an atropisomer are both UP or both DOWN - atoms are: 4 5 +63: [21:37:28] 63: 63: **** 63: Range Error @@ -18386,38 +18372,34 @@ 63: 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-202409.4/obj-aarch64-linux-gnu//lib/libRDKitSmilesParse.so.1 63: 5# RDKit::SmilesWrite::detail::MolToSmiles[abi:cxx11](RDKit::ROMol const&, RDKit::SmilesWriteParams const&, bool) in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu//lib/libRDKitSmilesParse.so.1 63: 6# RDKit::MolToSmiles[abi:cxx11](RDKit::ROMol const&, RDKit::SmilesWriteParams const&) in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu//lib/libRDKitSmilesParse.so.1 -63: 7# 0x0000AAAABA258F78 in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/GraphMol/SmilesParse/smiTestCatch -63: 8# 0x0000AAAABA2AB86C in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/GraphMol/SmilesParse/smiTestCatch -63: 9# 0x0000AAAABA2AC220 in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/GraphMol/SmilesParse/smiTestCatch -63: 10# 0x0000AAAABA2AC654 in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/GraphMol/SmilesParse/smiTestCatch -63: 11# 0x0000AAAABA27FB58 in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/GraphMol/SmilesParse/smiTestCatch -63: 12# 0x0000AAAABA2800A4 in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/GraphMol/SmilesParse/smiTestCatch -63: 13# 0x0000AAAABA215070 in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/GraphMol/SmilesParse/smiTestCatch -63: 14# 0x0000FFFFAE14229C in /lib/aarch64-linux-gnu/libc.so.6 +63: 7# 0x0000AAAAD24E8F78 in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/GraphMol/SmilesParse/smiTestCatch +63: 8# 0x0000AAAAD253B86C in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/GraphMol/SmilesParse/smiTestCatch +63: 9# 0x0000AAAAD253C220 in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/GraphMol/SmilesParse/smiTestCatch +63: 10# 0x0000AAAAD253C654 in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/GraphMol/SmilesParse/smiTestCatch +63: 11# 0x0000AAAAD250FB58 in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/GraphMol/SmilesParse/smiTestCatch +63: 12# 0x0000AAAAD25100A4 in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/GraphMol/SmilesParse/smiTestCatch +63: 13# 0x0000AAAAD24A5070 in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/GraphMol/SmilesParse/smiTestCatch +63: 14# 0x0000FFFF8298229C in /lib/aarch64-linux-gnu/libc.so.6 63: 15# __libc_start_main in /lib/aarch64-linux-gnu/libc.so.6 -63: 16# 0x0000AAAABA215130 in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/GraphMol/SmilesParse/smiTestCatch +63: 16# 0x0000AAAAD24A5130 in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/GraphMol/SmilesParse/smiTestCatch 63: ---------- 63: **** 63: -61: Test -61: -61: Sotorasib_atropBad1.cxsmi -61: -61: [12:42:35] The 2 defining bonds for an atropisomer are co-planar - atoms are: 13 14 -61: [12:42:35] The 2 defining bonds for an atropisomer are co-planar - atoms are: 13 14 -61: [12:42:35] The 2 defining bonds for an atropisomer are co-planar - atoms are: 13 14 -61: [12:42:35] The 2 defining bonds for an atropisomer are co-planar - atoms are: 13 14 -61: [12:42:35] The 2 defining bonds for an atropisomer are co-planar - atoms are: 13 14 -61: Test -61: -61: Sotorasib_atropBad2.cxsmi -61: -61: [12:42:35] The bonds on one end of an atropisomer are both UP or both DOWN - atoms are: 13 14 -61: [12:42:35] The bonds on one end of an atropisomer are both UP or both DOWN - atoms are: 13 14 -61: [12:42:35] The bonds on one end of an atropisomer are both UP or both DOWN - atoms are: 13 14 -61: [12:42:35] The bonds on one end of an atropisomer are both UP or both DOWN - atoms are: 13 14 -61: [12:42:35] The bonds on one end of an atropisomer are both UP or both DOWN - atoms are: 13 14 -63: [12:42:35] + 53/236 Test #30: pyForceFieldConstraints ................ Passed 1.12 sec +test 65 + Start 65: v2smiTestCatch + +65: Test command: /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/GraphMol/SmilesParse/v2smiTestCatch +65: Working Directory: /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/GraphMol/SmilesParse +65: Test timeout computed to be: 1500 + 54/236 Test #64: nontetrahedralCatch .................... Passed 0.14 sec +test 66 + Start 66: testDepictor + +66: Test command: /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/GraphMol/Depictor/testDepictor +66: Working Directory: /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/GraphMol/Depictor +66: Test timeout computed to be: 1500 +63: [21:37:28] 63: 63: **** 63: Range Error @@ -18433,32 +18415,39 @@ 63: 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-202409.4/obj-aarch64-linux-gnu//lib/libRDKitSmilesParse.so.1 63: 5# RDKit::SmilesWrite::detail::MolToSmiles[abi:cxx11](RDKit::ROMol const&, RDKit::SmilesWriteParams const&, bool) in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu//lib/libRDKitSmilesParse.so.1 63: 6# RDKit::MolToSmiles[abi:cxx11](RDKit::ROMol const&, RDKit::SmilesWriteParams const&) in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu//lib/libRDKitSmilesParse.so.1 -63: 7# 0x0000AAAABA258F78 in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/GraphMol/SmilesParse/smiTestCatch -63: 8# 0x0000AAAABA2AB86C in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/GraphMol/SmilesParse/smiTestCatch -63: 9# 0x0000AAAABA2AC220 in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/GraphMol/SmilesParse/smiTestCatch -63: 10# 0x0000AAAABA2AC654 in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/GraphMol/SmilesParse/smiTestCatch -63: 11# 0x0000AAAABA27FB58 in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/GraphMol/SmilesParse/smiTestCatch -63: 12# 0x0000AAAABA2800A4 in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/GraphMol/SmilesParse/smiTestCatch -63: 13# 0x0000AAAABA215070 in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/GraphMol/SmilesParse/smiTestCatch -63: 14# 0x0000FFFFAE14229C in /lib/aarch64-linux-gnu/libc.so.6 +63: 7# 0x0000AAAAD24E8F78 in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/GraphMol/SmilesParse/smiTestCatch +63: 8# 0x0000AAAAD253B86C in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/GraphMol/SmilesParse/smiTestCatch +63: 9# 0x0000AAAAD253C220 in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/GraphMol/SmilesParse/smiTestCatch +63: 10# 0x0000AAAAD253C654 in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/GraphMol/SmilesParse/smiTestCatch +63: 11# 0x0000AAAAD250FB58 in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/GraphMol/SmilesParse/smiTestCatch +63: 12# 0x0000AAAAD25100A4 in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/GraphMol/SmilesParse/smiTestCatch +63: 13# 0x0000AAAAD24A5070 in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/GraphMol/SmilesParse/smiTestCatch +63: 14# 0x0000FFFF8298229C in /lib/aarch64-linux-gnu/libc.so.6 63: 15# __libc_start_main in /lib/aarch64-linux-gnu/libc.so.6 -63: 16# 0x0000AAAABA215130 in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/GraphMol/SmilesParse/smiTestCatch +63: 16# 0x0000AAAAD24A5130 in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/GraphMol/SmilesParse/smiTestCatch 63: ---------- 63: **** 63: -63: [12:42:35] SMARTS Parse Error: unclosed ring for input: 'C1.C2.C3.C4.C5' -63: [12:42:35] SMILES Parse Error: unclosed ring for input: 'C1.C2.C3.C4.C5' -63: [12:42:35] SMARTS Parse Error: syntax error while parsing: C1C)foo -63: [12:42:35] SMARTS Parse Error: Failed parsing SMARTS 'C1C)foo' for input: 'C1C)foo' -63: [12:42:35] SMILES Parse Error: extra close parentheses while parsing: C1C)foo -63: [12:42:35] SMILES Parse Error: check for mistakes around position 4: -63: [12:42:35] C1C)foo -63: [12:42:35] ~~~^ -63: [12:42:35] SMILES Parse Error: Failed parsing SMILES 'C1C)foo' for input: 'C1C)foo' +63: [21:37:28] SMARTS Parse Error: unclosed ring for input: 'C1.C2.C3.C4.C5' +63: [21:37:28] SMILES Parse Error: unclosed ring for input: 'C1.C2.C3.C4.C5' +63: [21:37:28] SMARTS Parse Error: syntax error while parsing: C1C)foo +63: [21:37:28] SMARTS Parse Error: Failed parsing SMARTS 'C1C)foo' for input: 'C1C)foo' +63: [21:37:28] SMILES Parse Error: extra close parentheses while parsing: C1C)foo +63: [21:37:28] SMILES Parse Error: check for mistakes around position 4: +63: [21:37:28] C1C)foo +63: [21:37:28] ~~~^ +63: [21:37:28] SMILES Parse Error: Failed parsing SMILES 'C1C)foo' for input: 'C1C)foo' 63: =============================================================================== 63: All tests passed (1582 assertions in 67 test cases) 63: - 55/236 Test #63: smiTestCatch ........................... Passed 0.08 sec + 55/236 Test #63: smiTestCatch ........................... Passed 0.22 sec +36: F/C=C/Cl +36: [H]/C(F)=C(/[H])Cl +36: F/C=C/Cl +36: F/C=C/Cl +36: C/C(F)=C(/C)Cl +36: [21:37:28] ----------------------- +36: Testing isRingFused test 67 Start 67: depictorCatch @@ -18467,6 +18456,76 @@ 67: Test timeout computed to be: 1500 61: Test 61: +61: RP-6306_3d.cxsmi +61: +61: Test +61: +61: Sotorasib_atrop1.cxsmi +61: +61: Test +61: +61: Sotorasib_atrop2.cxsmi +61: +61: Test +61: +61: Sotorasib_atrop3.cxsmi +61: +61: Test +61: +61: Sotorasib_atrop4.cxsmi +61: +61: Test +61: +61: Sotorasib_atrop5.cxsmi +61: +61: [21:37:28] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 13 ignored +61: [21:37:28] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 13 ignored +61: [21:37:28] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 13 ignored +61: [21:37:28] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 13 ignored +61: [21:37:28] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 13 ignored +61: [21:37:28] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 13 ignored +61: [21:37:28] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 13 ignored +61: [21:37:28] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 13 ignored +61: [21:37:28] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 13 ignored +61: [21:37:28] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 13 ignored +61: Test +61: +61: Sotorasib_atropBad1.cxsmi +61: +61: [21:37:28] The 2 defining bonds for an atropisomer are co-planar - atoms are: 13 14 +61: [21:37:28] The 2 defining bonds for an atropisomer are co-planar - atoms are: 13 14 +61: [21:37:28] The 2 defining bonds for an atropisomer are co-planar - atoms are: 13 14 +61: [21:37:28] The 2 defining bonds for an atropisomer are co-planar - atoms are: 13 14 +61: [21:37:28] The 2 defining bonds for an atropisomer are co-planar - atoms are: 13 14 +61: Test +61: +61: Sotorasib_atropBad2.cxsmi +61: +61: [21:37:28] The bonds on one end of an atropisomer are both UP or both DOWN - atoms are: 13 14 +61: [21:37:28] The bonds on one end of an atropisomer are both UP or both DOWN - atoms are: 13 14 +61: [21:37:28] The bonds on one end of an atropisomer are both UP or both DOWN - atoms are: 13 14 +61: [21:37:28] The bonds on one end of an atropisomer are both UP or both DOWN - atoms are: 13 14 +61: [21:37:28] The bonds on one end of an atropisomer are both UP or both DOWN - atoms are: 13 14 +65: Randomness seeded to: 128558313 +65: =============================================================================== +65: All tests passed (14 assertions in 2 test cases) +65: + 56/236 Test #65: v2smiTestCatch ......................... Passed 0.07 sec +test 68 + Start 68: pyDepictor + +68: Test command: /usr/bin/python3 "/build/reproducible-path/rdkit-202409.4/Code/GraphMol/Depictor/Wrap/testDepictor.py" +68: Working Directory: /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/GraphMol/Depictor/Wrap +68: Test timeout computed to be: 1500 + 57/236 Test #36: graphmolMolOpsTest ..................... Passed 1.05 sec +test 69 + Start 69: testMrvToMol + +69: Test command: /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/GraphMol/MarvinParse/testMrvToMol +69: Working Directory: /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/GraphMol/MarvinParse +69: Test timeout computed to be: 1500 +61: Test +61: 61: Sotorasib_3d.cxsmi 61: 61: Test @@ -18489,11 +18548,15 @@ 61: 61: ZM374979_atropBad1.cxsmi 61: -61: [12:42:35] The 2 defining bonds for an atropisomer are co-planar - atoms are: 0 31 -61: [12:42:35] The 2 defining bonds for an atropisomer are co-planar - atoms are: 0 31 -61: [12:42:35] The 2 defining bonds for an atropisomer are co-planar - atoms are: 0 31 -61: [12:42:35] The 2 defining bonds for an atropisomer are co-planar - atoms are: 0 31 -61: [12:42:35] The 2 defining bonds for an atropisomer are co-planar - atoms are: 0 31 +61: [21:37:28] The 2 defining bonds for an atropisomer are co-planar - atoms are: 0 31 +61: [21:37:28] The 2 defining bonds for an atropisomer are co-planar - atoms are: 0 31 +61: [21:37:28] The 2 defining bonds for an atropisomer are co-planar - atoms are: 0 31 +61: [21:37:28] The 2 defining bonds for an atropisomer are co-planar - atoms are: 0 31 +61: [21:37:28] The 2 defining bonds for an atropisomer are co-planar - atoms are: 0 31 +67: Randomness seeded to: 732500889 +67: =============================================================================== +67: All tests passed (580 assertions in 18 test cases) +67: 61: Test 61: 61: Mrtx1719_3d.cxsmi @@ -18518,51 +18581,18 @@ 61: 61: Mrtx1719_atropBad1.cxsmi 61: -61: [12:42:35] The 2 defining bonds for an atropisomer are co-planar - atoms are: 11 12 -61: [12:42:35] The 2 defining bonds for an atropisomer are co-planar - atoms are: 11 12 -61: [12:42:35] The 2 defining bonds for an atropisomer are co-planar - atoms are: 11 12 -61: [12:42:35] The 2 defining bonds for an atropisomer are co-planar - atoms are: 11 12 -61: [12:42:35] The 2 defining bonds for an atropisomer are co-planar - atoms are: 11 12 -67: Randomness seeded to: 262685997 -67: =============================================================================== -67: All tests passed (580 assertions in 18 test cases) -67: - 56/236 Test #67: depictorCatch .......................... Passed 0.08 sec -test 68 - Start 68: pyDepictor - -68: Test command: /usr/bin/python3 "/build/reproducible-path/rdkit-202409.4/Code/GraphMol/Depictor/Wrap/testDepictor.py" -68: Working Directory: /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/GraphMol/Depictor/Wrap -68: Test timeout computed to be: 1500 -36: [12:42:35] Maximum BFS search size exceeded. -36: This is likely due to a highly symmetric fused ring system. -36: F/C=C/Cl -36: [H]/C(F)=C(/[H])Cl -36: F/C=C/Cl -36: F/C=C/Cl -36: C/C(F)=C(/C)Cl -36: [12:42:35] ----------------------- -36: Testing isRingFused - 57/236 Test #36: graphmolMolOpsTest ..................... Passed 0.54 sec -test 69 - Start 69: testMrvToMol - -69: Test command: /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/GraphMol/MarvinParse/testMrvToMol -69: Working Directory: /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/GraphMol/MarvinParse -69: Test timeout computed to be: 1500 -66: [12:42:35] Warning: stereochemistry around double bond may be incorrect in depiction. -30: ... -30: ---------------------------------------------------------------------- -30: Ran 12 tests in 0.483s -30: -30: OK - 58/236 Test #66: testDepictor ........................... Passed 0.20 sec +61: [21:37:28] The 2 defining bonds for an atropisomer are co-planar - atoms are: 11 12 +61: [21:37:28] The 2 defining bonds for an atropisomer are co-planar - atoms are: 11 12 +61: [21:37:28] The 2 defining bonds for an atropisomer are co-planar - atoms are: 11 12 +61: [21:37:28] The 2 defining bonds for an atropisomer are co-planar - atoms are: 11 12 + 58/236 Test #67: depictorCatch .......................... Passed 0.12 sec test 70 Start 70: fileParsersTest1 70: Test command: /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersTest1 70: Working Directory: /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers 70: Test timeout computed to be: 1500 +61: [21:37:28] The 2 defining bonds for an atropisomer are co-planar - atoms are: 11 12 69: Using new chirality perception 69: Test 69: @@ -18600,97 +18630,111 @@ 69: 69: ProblemShort.mol 69: -69: [12:42:36] For a MultipleSgroup expansion, the matching orphaned bond was not found +69: [21:37:28] For a MultipleSgroup expansion, the matching orphaned bond was not found 69: The multiple sgroup will be ignored 70: *************************************** 70: *************************************** -70: [12:42:36] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -70: [12:42:36] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -70: [12:42:36] bond with order 0 found on line 7. This is not part of the MDL specification. -70: [12:42:36] Skipping unrecognized collection type at line 26: MDLV30/HILITE BONDS=(1 7) -70: [12:42:36] Skipping unrecognized collection type at line 27: MDLV30/HILITE ATOMS=(1 7) -70: [12:42:36] 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: [21:37:28] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +70: [21:37:28] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +70: [21:37:28] bond with order 0 found on line 7. This is not part of the MDL specification. +70: [21:37:28] Skipping unrecognized collection type at line 26: MDLV30/HILITE BONDS=(1 7) +70: [21:37:28] Skipping unrecognized collection type at line 27: MDLV30/HILITE ATOMS=(1 7) +70: [21:37:28] 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: generating smiles 70: 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 70: converting back 70: check isomorphism - 59/236 Test #30: pyForceFieldConstraints ................ Passed 0.74 sec +66: [21:37:28] Warning: stereochemistry around double bond may be incorrect in depiction. + 59/236 Test #66: testDepictor ........................... Passed 0.40 sec test 71 Start 71: testAtropisomers 71: Test command: /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/testAtropisomers 71: Working Directory: /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers 71: Test timeout computed to be: 1500 -71: [12:42:36] ---- Running with POSIX locale ----- -71: [12:42:36] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -71: [12:42:36] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -71: [12:42:36] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -71: [12:42:36] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -71: [12:42:36] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -71: [12:42:36] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -71: [12:42:36] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored -71: [12:42:36] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored -71: [12:42:36] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored -71: [12:42:36] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored -71: [12:42:36] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored -71: [12:42:36] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored -71: [12:42:36] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored -71: [12:42:36] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored -71: [12:42:36] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored -71: [12:42:36] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored -71: [12:42:36] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored -71: [12:42:36] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored -71: [12:42:36] The bonds on one end of an atropisomer are both UP or both DOWN - atoms are: 7 29 -71: [12:42:36] The bonds on one end of an atropisomer are both UP or both DOWN - atoms are: 7 29 -71: [12:42:36] The bonds on one end of an atropisomer are both UP or both DOWN - atoms are: 7 29 -71: [12:42:36] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -71: [12:42:36] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -71: [12:42:36] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -71: [12:42:36] The 2 defining bonds for an atropisomer are co-planar - atoms are: 17 21 -71: [12:42:36] The 2 defining bonds for an atropisomer are co-planar - atoms are: 17 21 -71: [12:42:36] The 2 defining bonds for an atropisomer are co-planar - atoms are: 17 21 -71: [12:42:36] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 2 ignored -71: [12:42:36] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 2 ignored -71: [12:42:36] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 2 ignored -71: [12:42:36] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 2 ignored -71: [12:42:36] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 2 ignored -71: [12:42:36] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 2 ignored -71: [12:42:36] The bonds on one end of an atropisomer are both UP or both DOWN - atoms are: 2 8 -71: [12:42:36] The bonds on one end of an atropisomer are both UP or both DOWN - atoms are: 2 8 -71: [12:42:36] The bonds on one end of an atropisomer are both UP or both DOWN - atoms are: 2 8 -71: [12:42:36] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 2 ignored -71: [12:42:36] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 2 ignored -71: [12:42:36] The 2 defining bonds for an atropisomer are co-planar - atoms are: 2 8 -71: [12:42:36] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 2 ignored -71: [12:42:36] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 2 ignored -71: [12:42:36] The 2 defining bonds for an atropisomer are co-planar - atoms are: 2 8 -71: [12:42:36] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 2 ignored -71: [12:42:36] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 2 ignored -71: [12:42:36] The 2 defining bonds for an atropisomer are co-planar - atoms are: 2 8 -71: [12:42:36] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -71: [12:42:36] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -71: [12:42:36] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -71: [12:42:36] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored -71: [12:42:36] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored -71: [12:42:36] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored -71: [12:42:36] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored -71: [12:42:36] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored -71: [12:42:36] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored -71: [12:42:36] The 2 defining bonds for an atropisomer are co-planar - atoms are: 7 20 -71: [12:42:36] The 2 defining bonds for an atropisomer are co-planar - atoms are: 7 20 -71: [12:42:36] The 2 defining bonds for an atropisomer are co-planar - atoms are: 7 20 -71: [12:42:36] The bonds on one end of an atropisomer are both UP or both DOWN - atoms are: 7 20 -71: [12:42:36] The bonds on one end of an atropisomer are both UP or both DOWN - atoms are: 7 20 -71: [12:42:36] The bonds on one end of an atropisomer are both UP or both DOWN - atoms are: 7 20 -71: [12:42:36] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -71: [12:42:36] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -71: [12:42:36] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -71: [12:42:36] The 2 defining bonds for an atropisomer are co-planar - atoms are: 0 31 -71: [12:42:36] The 2 defining bonds for an atropisomer are co-planar - atoms are: 0 31 -71: [12:42:36] The 2 defining bonds for an atropisomer are co-planar - atoms are: 0 31 -71: [12:42:36] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -71: [12:42:36] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -71: [12:42:36] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +71: [21:37:28] ---- Running with POSIX locale ----- +71: [21:37:28] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +71: [21:37:28] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +71: [21:37:28] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +71: [21:37:28] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +71: [21:37:28] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +71: [21:37:28] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +71: [21:37:28] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored +71: [21:37:28] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored +71: [21:37:28] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored +71: [21:37:28] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored +71: [21:37:28] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored +71: [21:37:28] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored +71: [21:37:28] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored +71: [21:37:28] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored +71: [21:37:28] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored +71: [21:37:28] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored +71: [21:37:28] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored +71: [21:37:28] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored +71: [21:37:28] The bonds on one end of an atropisomer are both UP or both DOWN - atoms are: 7 29 +71: [21:37:28] The bonds on one end of an atropisomer are both UP or both DOWN - atoms are: 7 29 +71: [21:37:28] The bonds on one end of an atropisomer are both UP or both DOWN - atoms are: 7 29 +71: [21:37:28] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +71: [21:37:28] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +71: [21:37:28] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +71: [21:37:28] The 2 defining bonds for an atropisomer are co-planar - atoms are: 17 21 +71: [21:37:28] The 2 defining bonds for an atropisomer are co-planar - atoms are: 17 21 +71: [21:37:28] The 2 defining bonds for an atropisomer are co-planar - atoms are: 17 21 +71: [21:37:28] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 2 ignored +71: [21:37:28] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 2 ignored +71: [21:37:28] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 2 ignored +71: [21:37:28] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 2 ignored +71: [21:37:28] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 2 ignored +71: [21:37:28] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 2 ignored +71: [21:37:28] The bonds on one end of an atropisomer are both UP or both DOWN - atoms are: 2 8 +71: [21:37:28] The bonds on one end of an atropisomer are both UP or both DOWN - atoms are: 2 8 +71: [21:37:28] The bonds on one end of an atropisomer are both UP or both DOWN - atoms are: 2 8 +71: [21:37:28] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 2 ignored +71: [21:37:28] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 2 ignored +71: [21:37:28] The 2 defining bonds for an atropisomer are co-planar - atoms are: 2 8 +71: [21:37:28] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 2 ignored +71: [21:37:28] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 2 ignored +71: [21:37:28] The 2 defining bonds for an atropisomer are co-planar - atoms are: 2 8 +71: [21:37:28] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 2 ignored +71: [21:37:28] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 2 ignored +71: [21:37:28] The 2 defining bonds for an atropisomer are co-planar - atoms are: 2 8 +71: [21:37:28] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +71: [21:37:28] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +71: [21:37:28] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +71: [21:37:28] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored +71: [21:37:28] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored +71: [21:37:28] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored +71: [21:37:28] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored +71: [21:37:28] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored +71: [21:37:28] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored +71: [21:37:28] The 2 defining bonds for an atropisomer are co-planar - atoms are: 7 20 +71: [21:37:28] The 2 defining bonds for an atropisomer are co-planar - atoms are: 7 20 +71: [21:37:28] The 2 defining bonds for an atropisomer are co-planar - atoms are: 7 20 +71: [21:37:28] The bonds on one end of an atropisomer are both UP or both DOWN - atoms are: 7 20 +71: [21:37:28] The bonds on one end of an atropisomer are both UP or both DOWN - atoms are: 7 20 +71: [21:37:28] The bonds on one end of an atropisomer are both UP or both DOWN - atoms are: 7 20 +71: [21:37:28] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +71: [21:37:28] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +71: [21:37:28] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +71: [21:37:28] The 2 defining bonds for an atropisomer are co-planar - atoms are: 0 31 +71: [21:37:28] The 2 defining bonds for an atropisomer are co-planar - atoms are: 0 31 +71: [21:37:28] The 2 defining bonds for an atropisomer are co-planar - atoms are: 0 31 +71: [21:37:28] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +71: [21:37:28] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +71: [21:37:28] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +71: [21:37:28] The 2 defining bonds for an atropisomer are co-planar - atoms are: 15 16 +71: [21:37:28] The 2 defining bonds for an atropisomer are co-planar - atoms are: 15 16 +71: [21:37:28] The 2 defining bonds for an atropisomer are co-planar - atoms are: 15 16 +71: Atropisomers- 1 hits 3 misses +71: Final results: +71: Found atropisomers in TestMultInSDF.sdf - 1 hits 4 misses + 60/236 Test #71: testAtropisomers ....................... Passed 0.20 sec +test 72 + Start 72: testSquiggleDoubleBonds + +72: Test command: /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/testSquiggleDoubleBonds +72: Working Directory: /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers +72: Test timeout computed to be: 1500 69: Test 69: 69: badWedgeError.sdf @@ -19003,8 +19047,19 @@ 69: 69: MulticenterSgroup.mrv 69: -69: [12:42:36] Can't kekulize mol. Unkekulized atoms: 6 7 8 9 10 -69: [12:42:36] Can't kekulize mol. Unkekulized atoms: 6 7 8 9 10 +69: [21:37:28] Can't kekulize mol. Unkekulized atoms: 6 7 8 9 10 +69: [21:37:28] Can't kekulize mol. Unkekulized atoms: 6 7 8 9 10 +72: Randomness seeded to: 1327251158 +72: =============================================================================== +72: All tests passed (15 assertions in 3 test cases) +72: + 61/236 Test #72: testSquiggleDoubleBonds ................ Passed 0.02 sec +test 73 + Start 73: testMolSupplier + +73: Test command: /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/testMolSupplier +73: Working Directory: /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers +73: Test timeout computed to be: 1500 69: Test 69: 69: GenericSgroup.mrv @@ -19037,7 +19092,7 @@ 69: 69: MarvinBadMissingMolID.mrv 69: -69: [12:42:36] +69: [21:37:29] 69: 69: **** 69: Test Assert @@ -19048,12 +19103,12 @@ 69: Stacktrace: 69: 0# Invar::Invariant::toString[abi:cxx11]() const in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu//lib/libRDKitRDGeneral.so.1 69: 1# Invar::operator<<(std::ostream&, Invar::Invariant const&) in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu//lib/libRDKitRDGeneral.so.1 -69: 2# 0x0000AAAACB8FA99C in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/GraphMol/MarvinParse/testMrvToMol -69: 3# 0x0000AAAACB905A20 in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/GraphMol/MarvinParse/testMrvToMol -69: 4# 0x0000AAAACB8F4658 in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/GraphMol/MarvinParse/testMrvToMol -69: 5# 0x0000FFFF8919229C in /lib/aarch64-linux-gnu/libc.so.6 +69: 2# 0x0000AAAADDA2A99C in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/GraphMol/MarvinParse/testMrvToMol +69: 3# 0x0000AAAADDA35A20 in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/GraphMol/MarvinParse/testMrvToMol +69: 4# 0x0000AAAADDA24658 in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/GraphMol/MarvinParse/testMrvToMol +69: 5# 0x0000FFFF8B73229C in /lib/aarch64-linux-gnu/libc.so.6 69: 6# __libc_start_main in /lib/aarch64-linux-gnu/libc.so.6 -69: 7# 0x0000AAAACB8F48B0 in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/GraphMol/MarvinParse/testMrvToMol +69: 7# 0x0000AAAADDA248B0 in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/GraphMol/MarvinParse/testMrvToMol 69: ---------- 69: **** 69: @@ -19178,24 +19233,36 @@ 69: MarvinBadSupMissingAttachBond.mrv 69: 69: No attachment point found for bond to the condensed atom in a superatomSgroup +29: Checking against /build/reproducible-path/rdkit-202409.4/Code/ForceField/MMFF/test_data/MMFF94_reference.log... +73: [21:37:29] +73: ----------------------------------------- 69: Test 69: 69: MarvinBadSupMissingAttachOrder.mrv 69: 69: Expected atom, order and bond, for an AttachmentPoint definition in MRV file -71: [12:42:36] The 2 defining bonds for an atropisomer are co-planar - atoms are: 15 16 -71: [12:42:36] The 2 defining bonds for an atropisomer are co-planar - atoms are: 15 16 -71: [12:42:36] The 2 defining bonds for an atropisomer are co-planar - atoms are: 15 16 -71: Atropisomers- 1 hits 3 misses -71: Final results: -71: Found atropisomers in TestMultInSDF.sdf - 1 hits 4 misses - 60/236 Test #71: testAtropisomers ....................... Passed 0.14 sec -test 72 - Start 72: testSquiggleDoubleBonds - -72: Test command: /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/testSquiggleDoubleBonds -72: Working Directory: /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers -72: Test timeout computed to be: 1500 +73: [21:37:29] +73: +73: **** +73: Invariant Violation +73: bad prop value +73: Violation occurred on line 155 in file ./Code/GraphMol/FileParsers/MaeMolSupplier.cpp +73: Failed Expression: nSwaps < 2 +73: ---------- +73: Stacktrace: +73: 0# Invar::Invariant::toString[abi:cxx11]() const in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu//lib/libRDKitRDGeneral.so.1 +73: 1# Invar::operator<<(std::ostream&, Invar::Invariant const&) in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu//lib/libRDKitRDGeneral.so.1 +73: 2# 0x0000FFFFBEE56AB8 in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu//lib/libRDKitFileParsers.so.1 +73: 3# RDKit::v2::FileParsers::MaeMolSupplier::next() in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu//lib/libRDKitFileParsers.so.1 +73: 4# 0x0000AAAAC5FDE17C in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/testMolSupplier +73: 5# 0x0000AAAAC5FD2528 in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/testMolSupplier +73: 6# 0x0000AAAAC5FA0874 in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/testMolSupplier +73: 7# 0x0000FFFFBE45229C in /lib/aarch64-linux-gnu/libc.so.6 +73: 8# __libc_start_main in /lib/aarch64-linux-gnu/libc.so.6 +73: 9# 0x0000AAAAC5FA21B0 in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/testMolSupplier +73: ---------- +73: **** +73: 69: Test 69: 69: marvin03.mrv @@ -19260,8 +19327,8 @@ 69: 69: BMS-986142_atrop5.mrv 69: -69: [12:42:36] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored -69: [12:42:36] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored +69: [21:37:29] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored +69: [21:37:29] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored 69: Test 69: 69: BMS-986142_atrop6.mrv @@ -19274,24 +19341,14 @@ 69: 69: BMS-986142_atrop8.mrv 69: -69: [12:42:36] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored -69: [12:42:36] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored +69: [21:37:29] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored +69: [21:37:29] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored +29: All 191 tests passed 69: Test 69: 69: BMS-986142_atropBad2.mrv 69: -69: [12:42:36] The bonds on one end of an atropisomer are both UP or both DOWN - atoms are: 7 29 -72: Randomness seeded to: 3932628798 -72: =============================================================================== -72: All tests passed (15 assertions in 3 test cases) -72: - 61/236 Test #72: testSquiggleDoubleBonds ................ Passed 0.02 sec -test 73 - Start 73: testMolSupplier - -73: Test command: /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/testMolSupplier -73: Working Directory: /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers -73: Test timeout computed to be: 1500 +69: [21:37:29] The bonds on one end of an atropisomer are both UP or both DOWN - atoms are: 7 29 69: Test 69: 69: JDQ443_3d.mrv @@ -19312,7 +19369,15 @@ 69: 69: JDQ443_atropBad1.mrv 69: -69: [12:42:36] The 2 defining bonds for an atropisomer are co-planar - atoms are: 17 21 +69: [21:37:29] The 2 defining bonds for an atropisomer are co-planar - atoms are: 17 21 +73: [21:37:29] Finished: testMolSup() +73: [21:37:29] ----------------------------------------- +73: +73: [21:37:29] ----------------------------------------- +73: [21:37:29] Finished: testRandMolSup() +73: [21:37:29] ----------------------------------------- +73: +73: [21:37:29] ----------------------------------------- 69: Test 69: 69: RP-6306_atrop1.mrv @@ -19333,52 +19398,46 @@ 69: 69: RP-6306_atrop5.mrv 69: -69: [12:42:36] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 2 ignored -69: [12:42:36] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 2 ignored -73: [12:42:36] -73: ----------------------------------------- +69: [21:37:29] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 2 ignored +69: [21:37:29] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 2 ignored +29: +29: Computing MMFF94 energies for /build/reproducible-path/rdkit-202409.4/Code/ForceField/MMFF/test_data/MMFF94_hypervalent.sdf... 69: Test 69: 69: RP-6306_atropBad1.mrv 69: -69: [12:42:36] The bonds on one end of an atropisomer are both UP or both DOWN - atoms are: 2 8 +69: [21:37:29] The bonds on one end of an atropisomer are both UP or both DOWN - atoms are: 2 8 69: Test 69: 69: RP-6306_atropBad2.mrv 69: -69: [12:42:36] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 2 ignored -69: [12:42:36] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 2 ignored -69: [12:42:36] The 2 defining bonds for an atropisomer are co-planar - atoms are: 2 8 -61: Test -61: -61: AtropCanon1.cxsmi -61: -61: Test -61: -61: AtropCanon2.cxsmi -61: -61: Test -61: -61: AtropCanon3.cxsmi -61: -61: Test -61: -61: BMS-986142_3d_chiral.cxsmi -61: -61: Test -61: -61: BMS-986142_3d.cxsmi -61: -61: =============================================================================== -61: All tests passed (2445 assertions in 29 test cases) -61: - 62/236 Test #61: cxsmilesTest ........................... Passed 0.58 sec -test 74 - Start 74: testGeneralFileReader - -74: Test command: /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/testGeneralFileReader -74: Working Directory: /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers -74: Test timeout computed to be: 1500 +69: [21:37:29] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 2 ignored +69: [21:37:29] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 2 ignored +69: [21:37:29] The 2 defining bonds for an atropisomer are co-planar - atoms are: 2 8 +73: [21:37:29] Finished: testSmilesSup() +73: [21:37:29] ----------------------------------------- +73: +73: [21:37:29] ----------------------------------------- +73: [21:37:29] ------------------------------------------------------ +73: [21:37:29] SMILES Parse Error: syntax error while parsing: fail +73: [21:37:29] SMILES Parse Error: check for mistakes around position 1: +73: [21:37:29] fail +73: [21:37:29] ^ +73: [21:37:29] SMILES Parse Error: Failed parsing SMILES 'fail' for input: 'fail' +73: [21:37:29] ERROR: Smiles parse error on line 3 +73: [21:37:29] ERROR: Cannot create molecule from : 'fail' +73: [21:37:29] ------------------------------------------------------ +73: [21:37:29] ------------------------------------------------------ +73: [21:37:29] >>> This may result in an infinite loop. It should finish almost immediately: +73: [21:37:29] <<< done. +73: [21:37:29] Finished: testSmilesSupFromText() +73: [21:37:29] ----------------------------------------- +73: +73: [21:37:29] ----------------------------------------- +73: [21:37:29] Finished: testSmilesWriter() +73: [21:37:29] ----------------------------------------- +73: +73: [21:37:29] ----------------------------------------- 69: Test 69: 69: RP-6306_3d.mrv @@ -19403,57 +19462,136 @@ 69: 69: Sotorasib_atrop5.mrv 69: -69: [12:42:36] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored -69: [12:42:36] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored +69: [21:37:29] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored +69: [21:37:29] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored 69: Test 69: 69: Sotorasib_atropBad1.mrv 69: -69: [12:42:36] The 2 defining bonds for an atropisomer are co-planar - atoms are: 7 20 -74: [12:42:36] -74: ----------------------------------------- -74: [12:42:36] Finished: testDetermineFormat() -74: [12:42:36] ----------------------------------------- -74: -74: [12:42:36] -74: ----------------------------------------- -73: [12:42:36] +69: [21:37:29] The 2 defining bonds for an atropisomer are co-planar - atoms are: 7 20 +73: [21:37:29] Finished: testSDWriter() +73: [21:37:29] ----------------------------------------- 73: -73: **** -73: Invariant Violation -73: bad prop value -73: Violation occurred on line 155 in file ./Code/GraphMol/FileParsers/MaeMolSupplier.cpp -73: Failed Expression: nSwaps < 2 -73: ---------- -73: Stacktrace: -73: 0# Invar::Invariant::toString[abi:cxx11]() const in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu//lib/libRDKitRDGeneral.so.1 -73: 1# Invar::operator<<(std::ostream&, Invar::Invariant const&) in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu//lib/libRDKitRDGeneral.so.1 -73: 2# 0x0000FFFF9F1C6AB8 in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu//lib/libRDKitFileParsers.so.1 -73: 3# RDKit::v2::FileParsers::MaeMolSupplier::next() in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu//lib/libRDKitFileParsers.so.1 -73: 4# 0x0000AAAAC37EE17C in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/testMolSupplier -73: 5# 0x0000AAAAC37E2528 in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/testMolSupplier -73: 6# 0x0000AAAAC37B0874 in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/testMolSupplier -73: 7# 0x0000FFFF9E7C229C in /lib/aarch64-linux-gnu/libc.so.6 -73: 8# __libc_start_main in /lib/aarch64-linux-gnu/libc.so.6 -73: 9# 0x0000AAAAC37B21B0 in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/testMolSupplier -73: ---------- -73: **** +73: [21:37:29] ----------------------------------------- +73: [21:37:29] Finished: testSDSupplierEnding() +73: [21:37:29] ----------------------------------------- 73: +73: [21:37:29] ----------------------------------------- +73: [21:37:29] Finished: testSuppliersEmptyFile() +73: [21:37:29] ----------------------------------------- +73: +73: [21:37:29] ----------------------------------------- +73: [21:37:29] Finished: testCisTrans() +73: [21:37:29] ----------------------------------------- +73: +73: [21:37:29] ----------------------------------------- 69: Test 69: 69: Sotorasib_atropBad2.mrv 69: -69: [12:42:36] The bonds on one end of an atropisomer are both UP or both DOWN - atoms are: 7 20 -74: [12:42:36] Finished: testSdf() -74: [12:42:36] ----------------------------------------- -74: -74: [12:42:36] -74: ----------------------------------------- -74: [12:42:36] Finished: testSmi() -74: [12:42:36] ----------------------------------------- -74: -74: [12:42:36] -74: ----------------------------------------- +69: [21:37:29] The bonds on one end of an atropisomer are both UP or both DOWN - atoms are: 7 20 +73: [21:37:29] Finished: testStereoRound() +73: [21:37:29] ----------------------------------------- +73: +73: [21:37:29] ----------------------------------------- +73: [21:37:29] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +73: [21:37:29] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +73: [21:37:29] Finished: testIssue226() +73: [21:37:29] ----------------------------------------- +73: +73: [21:37:29] ----------------------------------------- +73: [21:37:29] Finished: testTDTSupplier1() +73: [21:37:29] ----------------------------------------- +73: +73: [21:37:29] ----------------------------------------- +73: [21:37:29] Finished: testTDTSupplier2() +73: [21:37:29] ----------------------------------------- +73: +73: [21:37:29] ----------------------------------------- +73: [21:37:29] Finished: testTDTSupplier3() +73: [21:37:29] ----------------------------------------- +73: +73: [21:37:29] ----------------------------------------- +73: [21:37:29] Finished: testSDSupplierFromText() +73: [21:37:29] ----------------------------------------- +73: +73: [21:37:29] ----------------------------------------- +73: [21:37:29] ERROR: Problems encountered parsing data fields +73: [21:37:29] ERROR: moving to the beginning of the next molecule +73: [21:37:29] ERROR: Problems encountered parsing data fields +73: [21:37:29] ERROR: moving to the beginning of the next molecule +73: [21:37:29] Spurious data before the first property will be ignored +73: [21:37:29] Property will be truncated after the first blank line +73: [21:37:29] Property will be truncated after the first blank line +73: [21:37:29] Property will be truncated after the first blank line +73: [21:37:29] Finished: testSDSupplierStrLax1() +73: [21:37:29] ----------------------------------------- +73: +73: [21:37:29] ----------------------------------------- +73: [21:37:29] ERROR: Problems encountered parsing data fields +73: [21:37:29] ERROR: moving to the beginning of the next molecule +73: [21:37:29] Property will be truncated after the first blank line +73: [21:37:29] Finished: testSDSupplierStrLax2() +73: [21:37:29] ----------------------------------------- +73: +73: [21:37:29] ----------------------------------------- +73: [21:37:29] ERROR: Problems encountered parsing data fields +73: [21:37:29] ERROR: moving to the beginning of the next molecule +73: [21:37:29] ERROR: Problems encountered parsing data fields +73: [21:37:29] ERROR: moving to the beginning of the next molecule +73: [21:37:29] Spurious data before the first property will be ignored +73: [21:37:29] Property will be truncated after the first blank line +73: [21:37:29] Property will be truncated after the first blank line +73: [21:37:29] Property will be truncated after the first blank line +73: [21:37:29] Finished: testSDSupplierFromTextStrLax1() +73: [21:37:29] ----------------------------------------- +73: +73: [21:37:29] ----------------------------------------- +73: [21:37:29] ERROR: Problems encountered parsing data fields +73: [21:37:29] ERROR: moving to the beginning of the next molecule +73: [21:37:29] Property will be truncated after the first blank line +73: [21:37:29] Finished: testSDSupplierFromTextStrLax2() +73: [21:37:29] ----------------------------------------- +73: +73: [21:37:29] ----------------------------------------- +73: [21:37:29] Finished: testIssue265() +73: [21:37:29] ----------------------------------------- +73: +73: [21:37:29] ----------------------------------------- +73: [21:37:29] ERROR: End of data field name not found +73: [21:37:29] ERROR: moving to the beginning of the next molecule +73: [21:37:29] Explicit valence for atom # 0 F, 2, is greater than permitted +73: [21:37:29] ERROR: Could not sanitize molecule ending on line 16 +73: [21:37:29] ERROR: Explicit valence for atom # 0 F, 2, is greater than permitted +73: [21:37:29] ERROR: Atom line too short: ' 1 2 1 0 0 0 0' on line 12 +73: [21:37:29] ERROR: moving to the beginning of the next molecule +73: [21:37:29] ERROR: Bond line too short: 'M END' on line 18 +73: [21:37:29] ERROR: moving to the beginning of the next molecule +73: [21:37:29] Finished: testSDErrorHandling() +73: [21:37:29] ----------------------------------------- +73: +73: [21:37:29] ----------------------------------------- +73: [21:37:29] Finished: testIssue381() +73: [21:37:29] ----------------------------------------- +73: +73: [21:37:29] ----------------------------------------- +73: [21:37:29] Finished: testSetStreamIndices() +73: [21:37:29] ----------------------------------------- +73: +73: [21:37:29] ----------------------------------------- +73: [21:37:29] Finished: testMixIterAndRandom() +73: [21:37:29] ----------------------------------------- +73: +73: [21:37:29] ----------------------------------------- +73: build: +73: [21:37:29] Finished: testRemoveHs() +73: [21:37:29] ----------------------------------------- +73: +73: [21:37:29] ----------------------------------------- +73: [21:37:29] Finished: testGetItemText() +73: [21:37:29] ----------------------------------------- +73: +73: [21:37:29] ----------------------------------------- 69: Test 69: 69: Sotorasib_3d.mrv @@ -19474,12 +19612,113 @@ 69: 69: ZM374979_atropBad1.mrv 69: -69: [12:42:36] The 2 defining bonds for an atropisomer are co-planar - atoms are: 0 31 -68: ..............[12:42:36] SMILES Parse Error: syntax error while parsing: invalidsmiles -68: [12:42:36] SMILES Parse Error: check for mistakes around position 1: -68: [12:42:36] invalidsmiles -68: [12:42:36] ^ -68: [12:42:36] SMILES Parse Error: Failed parsing SMILES 'invalidsmiles' for input: 'invalidsmiles' +69: [21:37:29] The 2 defining bonds for an atropisomer are co-planar - atoms are: 0 31 +73: [21:37:29] Finished: testForwardSDSupplier() +73: [21:37:29] ----------------------------------------- +73: +73: [21:37:29] ----------------------------------------- +73: [21:37:29] Finished: testMissingCRSDSupplier() +73: [21:37:29] ----------------------------------------- +73: +73: [21:37:29] ----------------------------------------- +73: [21:37:29] Finished: testIssue3482695() +73: [21:37:29] ----------------------------------------- +73: +73: [21:37:29] ----------------------------------------- +73: [21:37:29] ERROR: Cannot convert 'foo' to unsigned int on line 557 +73: [21:37:29] ERROR: moving to the beginning of the next molecule +73: [21:37:29] Finished: testIssue3525673() +73: [21:37:29] ----------------------------------------- +73: +73: [21:37:29] ----------------------------------------- +73: [21:37:29] Finished: testBlankLinesInProps() +73: [21:37:29] ----------------------------------------- +73: +73: [21:37:29] ----------------------------------------- +73: [21:37:29] Finished: testSkipLines() +73: [21:37:29] ----------------------------------------- +73: +73: [21:37:29] ----------------------------------------- +73: [21:37:29] Finished: testGitHub23() +73: [21:37:29] ----------------------------------------- +73: +73: [21:37:29] ----------------------------------------- +73: [21:37:29] Finished: testGitHub88() +73: [21:37:29] ----------------------------------------- +73: +73: [21:37:29] ----------------------------------------- +73: [21:37:29] Finished: testGitHub2285() +73: [21:37:29] ----------------------------------------- +73: +73: [21:37:29] ----------------------------------------- +73: [21:37:29] SMILES Parse Error: unclosed ring for input: 'c1ccccc' +73: [21:37:29] ERROR: Smiles parse error on line 1 +73: [21:37:29] ERROR: Cannot create molecule from : 'c1ccccc' +73: [21:37:29] SMILES Parse Error: extra open parentheses while parsing: C(C +73: [21:37:29] SMILES Parse Error: check for mistakes around position 2: +73: [21:37:29] C(C +73: [21:37:29] ~^ +73: [21:37:29] SMILES Parse Error: Failed parsing SMILES 'C(C' for input: 'C(C' +73: [21:37:29] ERROR: Smiles parse error on line 3 +73: [21:37:29] ERROR: Cannot create molecule from : 'C(C' +73: [21:37:29] Explicit valence for atom # 1 C, 5, is greater than permitted +73: [21:37:29] ERROR: Could not sanitize molecule on line 5 +73: [21:37:29] ERROR: Explicit valence for atom # 1 C, 5, is greater than permitted +73: [21:37:29] Explicit valence for atom # 1 F, 2, is greater than permitted +73: [21:37:29] ERROR: Could not sanitize molecule ending on line 21 +73: [21:37:29] ERROR: Explicit valence for atom # 1 F, 2, is greater than permitted +73: [21:37:29] Explicit valence for atom # 1 F, 2, is greater than permitted +73: [21:37:29] ERROR: Could not sanitize molecule ending on line 21 +73: [21:37:29] ERROR: Explicit valence for atom # 1 F, 2, is greater than permitted +73: [21:37:29] Explicit valence for atom # 1 F, 2, is greater than permitted +73: [21:37:29] ERROR: Could not sanitize molecule ending on line 21 +73: [21:37:29] ERROR: Explicit valence for atom # 1 F, 2, is greater than permitted +73: [21:37:29] ERROR: Atom line too short: ' -9.6' on line 28 +73: [21:37:29] ERROR: moving to the beginning of the next molecule +73: [21:37:29] Explicit valence for atom # 1 F, 2, is greater than permitted +73: [21:37:29] ERROR: Could not sanitize molecule ending on line 21 +73: [21:37:29] ERROR: Explicit valence for atom # 1 F, 2, is greater than permitted +73: [21:37:29] ERROR: Atom line too short: ' -9.6' on line 28 +73: [21:37:29] ERROR: moving to the beginning of the next molecule +73: [21:37:29] Finished: testGitHub2479() +73: [21:37:29] ----------------------------------------- +73: +73: [21:37:29] ----------------------------------------- +73: [21:37:29] +73: +73: **** +73: Invariant Violation +73: bad chiral bond +73: Violation occurred on line 161 in file ./Code/GraphMol/FileParsers/MaeMolSupplier.cpp +73: Failed Expression: bnd +73: ---------- +73: Stacktrace: +73: 0# Invar::Invariant::toString[abi:cxx11]() const in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu//lib/libRDKitRDGeneral.so.1 +73: 1# Invar::operator<<(std::ostream&, Invar::Invariant const&) in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu//lib/libRDKitRDGeneral.so.1 +73: 2# 0x0000FFFFBEE56FE4 in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu//lib/libRDKitFileParsers.so.1 +73: 3# RDKit::v2::FileParsers::MaeMolSupplier::next() in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu//lib/libRDKitFileParsers.so.1 +73: 4# 0x0000AAAAC5FA3120 in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/testMolSupplier +73: 5# 0x0000AAAAC5FA1EF4 in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/testMolSupplier +73: 6# 0x0000FFFFBE45229C in /lib/aarch64-linux-gnu/libc.so.6 +73: 7# __libc_start_main in /lib/aarch64-linux-gnu/libc.so.6 +73: 8# 0x0000AAAAC5FA21B0 in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/testMolSupplier +73: ---------- +73: **** +73: +73: [21:37:29] Finished: testGitHub2881() +73: [21:37:29] ----------------------------------------- +73: +73: [21:37:29] ----------------------------------------- +73: [21:37:29] Finished: testGitHub3517() +73: [21:37:29] ----------------------------------------- +73: + 62/236 Test #73: testMolSupplier ........................ Passed 0.28 sec +test 74 + Start 74: testGeneralFileReader + +74: Test command: /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/testGeneralFileReader +74: Working Directory: /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers +74: Test timeout computed to be: 1500 69: Test 69: 69: mrtx1719_3d.mrv @@ -19500,30 +19739,29 @@ 69: 69: mrtx1719_atropBad1.mrv 69: -69: [12:42:36] The 2 defining bonds for an atropisomer are co-planar - atoms are: 15 16 -73: [12:42:36] Finished: testMolSup() -73: [12:42:36] ----------------------------------------- -73: -73: [12:42:36] ----------------------------------------- -73: [12:42:36] Finished: testRandMolSup() -73: [12:42:36] ----------------------------------------- -73: -73: [12:42:36] ----------------------------------------- -74: [12:42:36] Finished: testMae() -74: [12:42:36] ----------------------------------------- +69: [21:37:29] The 2 defining bonds for an atropisomer are co-planar - atoms are: 15 16 +74: [21:37:29] +74: ----------------------------------------- +74: [21:37:29] Finished: testDetermineFormat() +74: [21:37:29] ----------------------------------------- 74: -74: [12:42:36] +74: [21:37:29] 74: ----------------------------------------- -74: [12:42:36] Finished: testTdt() -74: [12:42:36] ----------------------------------------- +68: ..............[21:37:29] SMILES Parse Error: syntax error while parsing: invalidsmiles +68: [21:37:29] SMILES Parse Error: check for mistakes around position 1: +68: [21:37:29] invalidsmiles +68: [21:37:29] ^ +68: [21:37:29] SMILES Parse Error: Failed parsing SMILES 'invalidsmiles' for input: 'invalidsmiles' +74: [21:37:29] Finished: testSdf() +74: [21:37:29] ----------------------------------------- 74: - 63/236 Test #74: testGeneralFileReader .................. Passed 0.06 sec -test 75 - Start 75: testMultithreadedMolSupplier - -75: Test command: /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/testMultithreadedMolSupplier -75: Working Directory: /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers -75: Test timeout computed to be: 1500 +74: [21:37:29] +74: ----------------------------------------- +74: [21:37:29] Finished: testSmi() +74: [21:37:29] ----------------------------------------- +74: +74: [21:37:29] +74: ----------------------------------------- 69: Test 69: 69: FalseAtropisomer.mrv @@ -19580,32 +19818,8 @@ 69: 69: BMS-986142_atrop5.mrv 69: -69: [12:42:36] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored -69: [12:42:36] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored -73: [12:42:36] Finished: testSmilesSup() -73: [12:42:36] ----------------------------------------- -73: -73: [12:42:36] ----------------------------------------- -73: [12:42:36] ------------------------------------------------------ -73: [12:42:36] SMILES Parse Error: syntax error while parsing: fail -73: [12:42:36] SMILES Parse Error: check for mistakes around position 1: -73: [12:42:36] fail -73: [12:42:36] ^ -73: [12:42:36] SMILES Parse Error: Failed parsing SMILES 'fail' for input: 'fail' -73: [12:42:36] ERROR: Smiles parse error on line 3 -73: [12:42:36] ERROR: Cannot create molecule from : 'fail' -73: [12:42:36] ------------------------------------------------------ -73: [12:42:36] ------------------------------------------------------ -73: [12:42:36] >>> This may result in an infinite loop. It should finish almost immediately: -73: [12:42:36] <<< done. -73: [12:42:36] Finished: testSmilesSupFromText() -73: [12:42:36] ----------------------------------------- -73: -73: [12:42:36] ----------------------------------------- -73: [12:42:36] Finished: testSmilesWriter() -73: [12:42:36] ----------------------------------------- -73: -73: [12:42:36] ----------------------------------------- +69: [21:37:29] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored +69: [21:37:29] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored 69: Test 69: 69: BMS-986142_atrop6.mrv @@ -19618,129 +19832,84 @@ 69: 69: BMS-986142_atrop8.mrv 69: -69: [12:42:36] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored -69: [12:42:36] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored +69: [21:37:29] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored +69: [21:37:29] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored 69: Test 69: 69: BMS-986142_atropBad2.mrv 69: -69: [12:42:36] The bonds on one end of an atropisomer are both UP or both DOWN - atoms are: 7 29 -73: [12:42:36] Finished: testSDWriter() -73: [12:42:36] ----------------------------------------- -73: -73: [12:42:36] ----------------------------------------- -73: [12:42:36] Finished: testSDSupplierEnding() -73: [12:42:36] ----------------------------------------- -73: -73: [12:42:36] ----------------------------------------- -73: [12:42:36] Finished: testSuppliersEmptyFile() -73: [12:42:36] ----------------------------------------- -73: -73: [12:42:36] ----------------------------------------- -73: [12:42:36] Finished: testCisTrans() -73: [12:42:36] ----------------------------------------- -73: -73: [12:42:36] ----------------------------------------- -75: [12:42:36] -75: ----------------------------------------- -73: [12:42:36] Finished: testStereoRound() -73: [12:42:36] ----------------------------------------- -73: -73: [12:42:36] ----------------------------------------- -73: [12:42:36] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -73: [12:42:36] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -73: [12:42:36] Finished: testIssue226() -73: [12:42:36] ----------------------------------------- -73: -73: [12:42:36] ----------------------------------------- -73: [12:42:36] Finished: testTDTSupplier1() -73: [12:42:36] ----------------------------------------- -73: -73: [12:42:36] ----------------------------------------- -73: [12:42:36] Finished: testTDTSupplier2() -73: [12:42:36] ----------------------------------------- -73: -73: [12:42:36] ----------------------------------------- -73: [12:42:36] Finished: testTDTSupplier3() -73: [12:42:36] ----------------------------------------- -73: -73: [12:42:36] ----------------------------------------- -73: [12:42:36] Finished: testSDSupplierFromText() -73: [12:42:36] ----------------------------------------- -73: -73: [12:42:36] ----------------------------------------- -73: [12:42:36] ERROR: Problems encountered parsing data fields -73: [12:42:36] ERROR: moving to the beginning of the next molecule -73: [12:42:36] ERROR: Problems encountered parsing data fields -73: [12:42:36] ERROR: moving to the beginning of the next molecule -73: [12:42:36] Spurious data before the first property will be ignored -73: [12:42:36] Property will be truncated after the first blank line -73: [12:42:36] Property will be truncated after the first blank line -73: [12:42:36] Property will be truncated after the first blank line -73: [12:42:36] Finished: testSDSupplierStrLax1() -73: [12:42:36] ----------------------------------------- -73: -73: [12:42:36] ----------------------------------------- -73: [12:42:36] ERROR: Problems encountered parsing data fields -73: [12:42:36] ERROR: moving to the beginning of the next molecule -73: [12:42:36] Property will be truncated after the first blank line -73: [12:42:36] Finished: testSDSupplierStrLax2() -73: [12:42:36] ----------------------------------------- -73: -73: [12:42:36] ----------------------------------------- -73: [12:42:36] ERROR: Problems encountered parsing data fields -73: [12:42:36] ERROR: moving to the beginning of the next molecule -73: [12:42:36] ERROR: Problems encountered parsing data fields -73: [12:42:36] ERROR: moving to the beginning of the next molecule -73: [12:42:36] Spurious data before the first property will be ignored -73: [12:42:36] Property will be truncated after the first blank line -73: [12:42:36] Property will be truncated after the first blank line -73: [12:42:36] Property will be truncated after the first blank line -73: [12:42:36] Finished: testSDSupplierFromTextStrLax1() -73: [12:42:36] ----------------------------------------- -73: -73: [12:42:36] ----------------------------------------- -73: [12:42:36] ERROR: Problems encountered parsing data fields -73: [12:42:36] ERROR: moving to the beginning of the next molecule -73: [12:42:36] Property will be truncated after the first blank line -73: [12:42:36] Finished: testSDSupplierFromTextStrLax2() -73: [12:42:36] ----------------------------------------- -73: -73: [12:42:36] ----------------------------------------- -73: [12:42:36] Finished: testIssue265() -73: [12:42:36] ----------------------------------------- -73: -73: [12:42:36] ----------------------------------------- -73: [12:42:36] ERROR: End of data field name not found -73: [12:42:36] ERROR: moving to the beginning of the next molecule -73: [12:42:36] Explicit valence for atom # 0 F, 2, is greater than permitted -73: [12:42:36] ERROR: Could not sanitize molecule ending on line 16 -73: [12:42:36] ERROR: Explicit valence for atom # 0 F, 2, is greater than permitted -73: [12:42:36] ERROR: Atom line too short: ' 1 2 1 0 0 0 0' on line 12 -73: [12:42:36] ERROR: moving to the beginning of the next molecule -73: [12:42:36] ERROR: Bond line too short: 'M END' on line 18 -73: [12:42:36] ERROR: moving to the beginning of the next molecule -73: [12:42:36] Finished: testSDErrorHandling() -73: [12:42:36] ----------------------------------------- -73: -73: [12:42:36] ----------------------------------------- -73: [12:42:36] Finished: testIssue381() -73: [12:42:36] ----------------------------------------- -73: -73: [12:42:36] ----------------------------------------- -73: [12:42:36] Finished: testSetStreamIndices() -73: [12:42:36] ----------------------------------------- -73: -73: [12:42:36] ----------------------------------------- -73: [12:42:36] Finished: testMixIterAndRandom() -73: [12:42:36] ----------------------------------------- -73: -73: [12:42:36] ----------------------------------------- -73: build: -73: [12:42:36] Finished: testRemoveHs() -73: [12:42:36] ----------------------------------------- -73: -73: [12:42:36] ----------------------------------------- +69: [21:37:29] The bonds on one end of an atropisomer are both UP or both DOWN - atoms are: 7 29 +74: [21:37:29] Finished: testMae() +74: [21:37:29] ----------------------------------------- +74: +74: [21:37:29] +74: ----------------------------------------- +74: [21:37:29] Finished: testTdt() +74: [21:37:29] ----------------------------------------- +74: + 63/236 Test #74: testGeneralFileReader .................. Passed 0.13 sec +test 75 + Start 75: testMultithreadedMolSupplier + +75: Test command: /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/testMultithreadedMolSupplier +75: Working Directory: /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers +75: Test timeout computed to be: 1500 +70: [21:37:29] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 1 ignored +70: [21:37:29] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 1 ignored +70: [21:37:29] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 1 ignored +70: [21:37:29] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 1 ignored +70: [21:37:29] deprecated group abbreviation ignored on line 24 +70: smiles: [1*]c1c([2*])c([3*])c([4*])c(-c2c([9*])oc3c([8*])c([7*])c([6*])c([5*])c3c2=O)c1[10*] +70: [21:37:29] +70: +70: **** +70: Post-condition Violation +70: Element 'Mv' not found +70: Violation occurred on line 93 in file ./Code/GraphMol/PeriodicTable.h +70: Failed Expression: anum > -1 +70: ---------- +70: Stacktrace: +70: 0# Invar::Invariant::toString[abi:cxx11]() const in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu//lib/libRDKitRDGeneral.so.1 +70: 1# Invar::operator<<(std::ostream&, Invar::Invariant const&) in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu//lib/libRDKitRDGeneral.so.1 +70: 2# RDKit::PeriodicTable::getAtomicNumber(std::__cxx11::basic_string, std::allocator > const&) const in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu//lib/libRDKitFileParsers.so.1 +70: 3# 0x0000FFFFA6B97D24 in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu//lib/libRDKitFileParsers.so.1 +70: 4# 0x0000FFFFA6BA5920 in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu//lib/libRDKitFileParsers.so.1 +70: 5# 0x0000FFFFA6BA684C in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu//lib/libRDKitFileParsers.so.1 +70: 6# RDKit::FileParserUtils::ParseV2000CTAB(std::istream*, unsigned int&, RDKit::RWMol*, RDKit::Conformer*&, bool&, unsigned int&, unsigned int&, bool) in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu//lib/libRDKitFileParsers.so.1 +70: 7# RDKit::v2::FileParsers::MolFromMolDataStream(std::istream&, unsigned int&, RDKit::v2::FileParsers::MolFileParserParams const&) in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu//lib/libRDKitFileParsers.so.1 +70: 8# RDKit::v2::FileParsers::MolFromMolFile(std::__cxx11::basic_string, std::allocator > const&, RDKit::v2::FileParsers::MolFileParserParams const&) in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu//lib/libRDKitFileParsers.so.1 +70: 9# 0x0000AAAAB18FF21C in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersTest1 +70: 10# 0x0000AAAAB1974524 in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersTest1 +70: 11# 0x0000AAAAB18E5638 in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersTest1 +70: 12# 0x0000FFFFA626229C in /lib/aarch64-linux-gnu/libc.so.6 +70: 13# __libc_start_main in /lib/aarch64-linux-gnu/libc.so.6 +70: 14# 0x0000AAAAB18E5870 in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersTest1 +70: ---------- +70: **** +70: +61: Test +61: +61: AtropCanon1.cxsmi +61: +61: Test +61: +61: AtropCanon2.cxsmi +61: +61: Test +61: +61: AtropCanon3.cxsmi +61: +61: Test +61: +61: BMS-986142_3d_chiral.cxsmi +61: +61: Test +61: +61: BMS-986142_3d.cxsmi +61: +61: =============================================================================== +61: All tests passed (2445 assertions in 29 test cases) +61: 69: Test 69: 69: JDQ443_3d.mrv @@ -19761,16 +19930,14 @@ 69: 69: JDQ443_atropBad1.mrv 69: -69: [12:42:36] The 2 defining bonds for an atropisomer are co-planar - atoms are: 17 21 -68: ..... -68: ---------------------------------------------------------------------- -68: Ran 19 tests in 0.232s -68: -68: OK -73: [12:42:36] Finished: testGetItemText() -73: [12:42:36] ----------------------------------------- -73: -73: [12:42:36] ----------------------------------------- +69: [21:37:29] The 2 defining bonds for an atropisomer are co-planar - atoms are: 17 21 + 64/236 Test #61: cxsmilesTest ........................... Passed 1.42 sec +test 76 + Start 76: testMolWriter + +76: Test command: /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/testMolWriter +76: Working Directory: /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers +76: Test timeout computed to be: 1500 69: Test 69: 69: RP-6306_atrop1.mrv @@ -19791,127 +19958,27 @@ 69: 69: RP-6306_atrop5.mrv 69: -69: [12:42:36] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 2 ignored -69: [12:42:36] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 2 ignored +69: [21:37:29] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 2 ignored +69: [21:37:29] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 2 ignored 69: Test 69: 69: RP-6306_atropBad1.mrv 69: -69: [12:42:36] The bonds on one end of an atropisomer are both UP or both DOWN - atoms are: 2 8 -73: [12:42:36] Finished: testForwardSDSupplier() -73: [12:42:36] ----------------------------------------- -73: -73: [12:42:36] ----------------------------------------- -73: [12:42:36] Finished: testMissingCRSDSupplier() -73: [12:42:36] ----------------------------------------- -73: -73: [12:42:36] ----------------------------------------- -73: [12:42:36] Finished: testIssue3482695() -73: [12:42:36] ----------------------------------------- -73: -73: [12:42:36] ----------------------------------------- +69: [21:37:29] The bonds on one end of an atropisomer are both UP or both DOWN - atoms are: 2 8 69: Test 69: 69: RP-6306_atropBad2.mrv 69: -69: [12:42:36] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 2 ignored -69: [12:42:36] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 2 ignored -69: [12:42:36] The 2 defining bonds for an atropisomer are co-planar - atoms are: 2 8 -29: Checking against /build/reproducible-path/rdkit-202409.4/Code/ForceField/MMFF/test_data/MMFF94_reference.log... -73: [12:42:36] ERROR: Cannot convert 'foo' to unsigned int on line 557 -73: [12:42:36] ERROR: moving to the beginning of the next molecule -73: [12:42:36] Finished: testIssue3525673() -73: [12:42:36] ----------------------------------------- -73: -73: [12:42:36] ----------------------------------------- -73: [12:42:36] Finished: testBlankLinesInProps() -73: [12:42:36] ----------------------------------------- -73: -73: [12:42:36] ----------------------------------------- -73: [12:42:36] Finished: testSkipLines() -73: [12:42:36] ----------------------------------------- -73: -73: [12:42:36] ----------------------------------------- -73: [12:42:36] Finished: testGitHub23() -73: [12:42:36] ----------------------------------------- -73: -73: [12:42:36] ----------------------------------------- -73: [12:42:36] Finished: testGitHub88() -73: [12:42:36] ----------------------------------------- -73: -73: [12:42:36] ----------------------------------------- -73: [12:42:36] Finished: testGitHub2285() -73: [12:42:36] ----------------------------------------- -73: -73: [12:42:36] ----------------------------------------- -73: [12:42:36] SMILES Parse Error: unclosed ring for input: 'c1ccccc' -73: [12:42:36] ERROR: Smiles parse error on line 1 -73: [12:42:36] ERROR: Cannot create molecule from : 'c1ccccc' -73: [12:42:36] SMILES Parse Error: extra open parentheses while parsing: C(C -73: [12:42:36] SMILES Parse Error: check for mistakes around position 2: -73: [12:42:36] C(C -73: [12:42:36] ~^ -73: [12:42:36] SMILES Parse Error: Failed parsing SMILES 'C(C' for input: 'C(C' -73: [12:42:36] ERROR: Smiles parse error on line 3 -73: [12:42:36] ERROR: Cannot create molecule from : 'C(C' -73: [12:42:36] Explicit valence for atom # 1 C, 5, is greater than permitted -73: [12:42:36] ERROR: Could not sanitize molecule on line 5 -73: [12:42:36] ERROR: Explicit valence for atom # 1 C, 5, is greater than permitted -73: [12:42:36] Explicit valence for atom # 1 F, 2, is greater than permitted -73: [12:42:36] ERROR: Could not sanitize molecule ending on line 21 -73: [12:42:36] ERROR: Explicit valence for atom # 1 F, 2, is greater than permitted -73: [12:42:36] Explicit valence for atom # 1 F, 2, is greater than permitted -73: [12:42:36] ERROR: Could not sanitize molecule ending on line 21 -73: [12:42:36] ERROR: Explicit valence for atom # 1 F, 2, is greater than permitted -73: [12:42:36] Explicit valence for atom # 1 F, 2, is greater than permitted -73: [12:42:36] ERROR: Could not sanitize molecule ending on line 21 -73: [12:42:36] ERROR: Explicit valence for atom # 1 F, 2, is greater than permitted -73: [12:42:36] ERROR: Atom line too short: ' -9.6' on line 28 -73: [12:42:36] ERROR: moving to the beginning of the next molecule -73: [12:42:36] Explicit valence for atom # 1 F, 2, is greater than permitted -73: [12:42:36] ERROR: Could not sanitize molecule ending on line 21 -73: [12:42:36] ERROR: Explicit valence for atom # 1 F, 2, is greater than permitted -73: [12:42:36] ERROR: Atom line too short: ' -9.6' on line 28 -73: [12:42:36] ERROR: moving to the beginning of the next molecule -73: [12:42:36] Finished: testGitHub2479() -73: [12:42:36] ----------------------------------------- -73: -73: [12:42:36] ----------------------------------------- -73: [12:42:36] -73: -73: **** -73: Invariant Violation -73: bad chiral bond -73: Violation occurred on line 161 in file ./Code/GraphMol/FileParsers/MaeMolSupplier.cpp -73: Failed Expression: bnd -73: ---------- -73: Stacktrace: -73: 0# Invar::Invariant::toString[abi:cxx11]() const in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu//lib/libRDKitRDGeneral.so.1 -73: 1# Invar::operator<<(std::ostream&, Invar::Invariant const&) in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu//lib/libRDKitRDGeneral.so.1 -73: 2# 0x0000FFFF9F1C6FE4 in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu//lib/libRDKitFileParsers.so.1 -73: 3# RDKit::v2::FileParsers::MaeMolSupplier::next() in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu//lib/libRDKitFileParsers.so.1 -73: 4# 0x0000AAAAC37B3120 in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/testMolSupplier -73: 5# 0x0000AAAAC37B1EF4 in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/testMolSupplier -73: 6# 0x0000FFFF9E7C229C in /lib/aarch64-linux-gnu/libc.so.6 -73: 7# __libc_start_main in /lib/aarch64-linux-gnu/libc.so.6 -73: 8# 0x0000AAAAC37B21B0 in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/testMolSupplier -73: ---------- -73: **** -73: -73: [12:42:36] Finished: testGitHub2881() -73: [12:42:36] ----------------------------------------- -73: -73: [12:42:36] ----------------------------------------- -73: [12:42:36] Finished: testGitHub3517() -73: [12:42:36] ----------------------------------------- -73: - 64/236 Test #73: testMolSupplier ........................ Passed 0.14 sec -test 76 - Start 76: testMolWriter - -76: Test command: /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/testMolWriter -76: Working Directory: /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers -76: Test timeout computed to be: 1500 +69: [21:37:29] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 2 ignored +69: [21:37:29] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 2 ignored +69: [21:37:29] The 2 defining bonds for an atropisomer are co-planar - atoms are: 2 8 +75: [21:37:29] +75: ----------------------------------------- +68: ..... +68: ---------------------------------------------------------------------- +68: Ran 19 tests in 0.571s +68: +68: OK 69: Test 69: 69: RP-6306_3d.mrv @@ -19936,18 +20003,18 @@ 69: 69: Sotorasib_atrop5.mrv 69: -69: [12:42:36] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored -69: [12:42:36] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored +69: [21:37:29] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored +69: [21:37:29] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored 69: Test 69: 69: Sotorasib_atropBad1.mrv 69: -69: [12:42:36] The 2 defining bonds for an atropisomer are co-planar - atoms are: 7 20 +69: [21:37:29] The 2 defining bonds for an atropisomer are co-planar - atoms are: 7 20 69: Test 69: 69: Sotorasib_atropBad2.mrv 69: -69: [12:42:36] The bonds on one end of an atropisomer are both UP or both DOWN - atoms are: 7 20 +69: [21:37:29] The bonds on one end of an atropisomer are both UP or both DOWN - atoms are: 7 20 69: Test 69: 69: Sotorasib_3d.mrv @@ -19968,7 +20035,7 @@ 69: 69: ZM374979_atropBad1.mrv 69: -69: [12:42:36] The 2 defining bonds for an atropisomer are co-planar - atoms are: 0 31 +69: [21:37:29] The 2 defining bonds for an atropisomer are co-planar - atoms are: 0 31 69: Test 69: 69: mrtx1719_3d.mrv @@ -19989,16 +20056,41 @@ 69: 69: mrtx1719_atropBad1.mrv 69: -69: [12:42:36] The 2 defining bonds for an atropisomer are co-planar - atoms are: 15 16 - 65/236 Test #68: pyDepictor ............................. Passed 0.50 sec +69: [21:37:29] The 2 defining bonds for an atropisomer are co-planar - atoms are: 15 16 +70: [21:37:29] 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: [21:37:29] Warning: molecule is tagged as 3D, but all Z coords are zero and 2D stereo markers have been found, marking the mol as 2D. +76: [21:37:29] Warning: molecule is tagged as 3D, but all Z coords are zero and 2D stereo markers have been found, marking the mol as 2D. +76: 0.40201265 0.40201265 +76: -0.13299436 -0.13299436 +76: 1.00000017 1.00000017 +76: 0.8762226 0.8762226 +76: 0.9973909 0.9973909 +76: 1.00000003 1.00000003 +76: 0.36613799 0.36613799 +76: 2.1107185 2.1107185 +76: 0.99999982 0.99999982 +76: 2.48696157 2.48696157 +76: 1.00479935 1.00479935 +76: 0.99999999 0.99999999 +76: 3.03311841 3.03311841 +76: 2.23739955 2.23739955 +76: 1.0000001 1.0000001 +76: 3.00772337 3.00772337 +76: 0.37399294 0.37399294 +76: 2.07713325 2.07713325 +76: 3.0077234 3.0077234 +76: 0.37399312 0.37399312 +76: -0.07713336 -0.07713336 +76: [21:37:29] bond with order 0 found on line 11. This is not part of the MDL specification. +76: [21:37:29] bond with order 0 found on line 16. This is not part of the MDL specification. + 65/236 Test #76: testMolWriter .......................... Passed 0.17 sec test 77 Start 77: testTplParser 77: Test command: /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/testTplParser 77: Working Directory: /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers 77: Test timeout computed to be: 1500 -29: All 191 tests passed - 66/236 Test #77: testTplParser .......................... Passed 0.02 sec + 66/236 Test #68: pyDepictor ............................. Passed 1.19 sec test 78 Start 78: testMol2ToMol @@ -20045,7 +20137,21 @@ 69: 69: EmptyRxn.mrv 69: -69: [12:42:36] initialization failed +69: [21:37:29] initialization failed + 67/236 Test #77: testTplParser .......................... Passed 0.03 sec +test 79 + Start 79: testSequence + +79: Test command: /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/testSequence +79: Working Directory: /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers +79: Test timeout computed to be: 1500 + 68/236 Test #78: testMol2ToMol .......................... Passed 0.04 sec +test 80 + Start 80: testExtendedStereoParsing + +80: Test command: /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/testExtendedStereoParsing +80: Working Directory: /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers +80: Test timeout computed to be: 1500 69: Test 69: 69: RxnNoCoords.mrv @@ -20134,55 +20240,37 @@ 69: 69: Smiles1 69: - 67/236 Test #78: testMol2ToMol .......................... Passed 0.02 sec -test 79 - Start 79: testSequence - -79: Test command: /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/testSequence -79: Working Directory: /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers -79: Test timeout computed to be: 1500 - 68/236 Test #69: testMrvToMol ........................... Passed 0.50 sec -test 80 - Start 80: testExtendedStereoParsing + 69/236 Test #69: testMrvToMol ........................... Passed 1.23 sec +test 81 + Start 81: fileParsersCatchTest -80: Test command: /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/testExtendedStereoParsing -80: Working Directory: /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers -80: Test timeout computed to be: 1500 -70: [12:42:36] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 1 ignored -70: [12:42:36] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 1 ignored -70: [12:42:36] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 1 ignored -70: [12:42:36] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 1 ignored -70: [12:42:36] deprecated group abbreviation ignored on line 24 -70: smiles: [1*]c1c([2*])c([3*])c([4*])c(-c2c([9*])oc3c([8*])c([7*])c([6*])c([5*])c3c2=O)c1[10*] -70: [12:42:36] +81: Test command: /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +81: Working Directory: /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers +81: Test timeout computed to be: 1500 +70: ---------------------------------- +70: ---------------------------------- +70: [21:37:29] 70: 70: **** -70: Post-condition Violation -70: Element 'Mv' not found -70: Violation occurred on line 93 in file ./Code/GraphMol/PeriodicTable.h -70: Failed Expression: anum > -1 +70: Pre-condition Violation +70: rlabel out of range for MDL files +70: Violation occurred on line 857 in file ./Code/GraphMol/Atom.cpp +70: Failed Expression: rlabel >= 0 && rlabel < 100 70: ---------- 70: Stacktrace: 70: 0# Invar::Invariant::toString[abi:cxx11]() const in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu//lib/libRDKitRDGeneral.so.1 70: 1# Invar::operator<<(std::ostream&, Invar::Invariant const&) in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu//lib/libRDKitRDGeneral.so.1 -70: 2# RDKit::PeriodicTable::getAtomicNumber(std::__cxx11::basic_string, std::allocator > const&) const in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu//lib/libRDKitFileParsers.so.1 -70: 3# 0x0000FFFF8EDC7D24 in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu//lib/libRDKitFileParsers.so.1 -70: 4# 0x0000FFFF8EDD5920 in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu//lib/libRDKitFileParsers.so.1 -70: 5# 0x0000FFFF8EDD684C in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu//lib/libRDKitFileParsers.so.1 -70: 6# RDKit::FileParserUtils::ParseV2000CTAB(std::istream*, unsigned int&, RDKit::RWMol*, RDKit::Conformer*&, bool&, unsigned int&, unsigned int&, bool) in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu//lib/libRDKitFileParsers.so.1 -70: 7# RDKit::v2::FileParsers::MolFromMolDataStream(std::istream&, unsigned int&, RDKit::v2::FileParsers::MolFileParserParams const&) in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu//lib/libRDKitFileParsers.so.1 -70: 8# RDKit::v2::FileParsers::MolFromMolFile(std::__cxx11::basic_string, std::allocator > const&, RDKit::v2::FileParsers::MolFileParserParams const&) in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu//lib/libRDKitFileParsers.so.1 -70: 9# 0x0000AAAAD6B7F21C in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersTest1 -70: 10# 0x0000AAAAD6BF4524 in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersTest1 -70: 11# 0x0000AAAAD6B65638 in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersTest1 -70: 12# 0x0000FFFF8E49229C in /lib/aarch64-linux-gnu/libc.so.6 -70: 13# __libc_start_main in /lib/aarch64-linux-gnu/libc.so.6 -70: 14# 0x0000AAAAD6B65870 in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersTest1 +70: 2# RDKit::setAtomRLabel(RDKit::Atom*, int) in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu//lib/libRDKitGraphMol.so.1 +70: 3# 0x0000AAAAB190ECE0 in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersTest1 +70: 4# 0x0000AAAAB1974584 in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersTest1 +70: 5# 0x0000AAAAB18E5638 in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersTest1 +70: 6# 0x0000FFFFA626229C in /lib/aarch64-linux-gnu/libc.so.6 +70: 7# __libc_start_main in /lib/aarch64-linux-gnu/libc.so.6 +70: 8# 0x0000AAAAB18E5870 in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersTest1 70: ---------- 70: **** 70: -29: -29: Computing MMFF94 energies for /build/reproducible-path/rdkit-202409.4/Code/ForceField/MMFF/test_data/MMFF94_hypervalent.sdf... +70: [21:37:29] WARNING: could not find number of expected rings. Switching to an approximate ring finding algorithm. 79: Sequence: GREG 79: HELM: PEPTIDE1{G.R.E.G}$$$$ 79: Smiles: N=C(N)NCCC[C@H](NC(=O)CN)C(=O)N[C@@H](CCC(=O)O)C(=O)NCC(=O)O @@ -21167,39 +21255,8 @@ 79: CONECT 27 28 28 29 79: END 79: -76: [12:42:36] Warning: molecule is tagged as 3D, but all Z coords are zero and 2D stereo markers have been found, marking the mol as 2D. -76: 0.40201265 0.40201265 -76: -0.13299436 -0.13299436 -76: 1.00000017 1.00000017 -76: 0.8762226 0.8762226 -76: 0.9973909 0.9973909 -76: 1.00000003 1.00000003 -76: 0.36613799 0.36613799 -76: 2.1107185 2.1107185 -76: 0.99999982 0.99999982 -76: 2.48696157 2.48696157 -76: 1.00479935 1.00479935 -76: 0.99999999 0.99999999 -76: 3.03311841 3.03311841 -76: 2.23739955 2.23739955 -76: 1.0000001 1.0000001 -76: 3.00772337 3.00772337 -76: 0.37399294 0.37399294 -76: 2.07713325 2.07713325 -76: 3.0077234 3.0077234 -76: 0.37399312 0.37399312 -76: -0.07713336 -0.07713336 -76: [12:42:36] bond with order 0 found on line 11. This is not part of the MDL specification. -76: [12:42:36] bond with order 0 found on line 16. This is not part of the MDL specification. - 69/236 Test #76: testMolWriter .......................... Passed 0.15 sec - 70/236 Test #79: testSequence ........................... Passed 0.06 sec - 71/236 Test #80: testExtendedStereoParsing .............. Passed 0.06 sec -test 81 - Start 81: fileParsersCatchTest - -81: Test command: /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -81: Working Directory: /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers -81: Test timeout computed to be: 1500 + 70/236 Test #79: testSequence ........................... Passed 0.09 sec + 71/236 Test #80: testExtendedStereoParsing .............. Passed 0.07 sec test 82 Start 82: testPropertyLists @@ -21212,39 +21269,26 @@ 83: Test command: /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/XYZFileParserCatchTest 83: Working Directory: /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers 83: Test timeout computed to be: 1500 -70: [12:42:36] 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: [12:42:36] Warning: molecule is tagged as 3D, but all Z coords are zero and 2D stereo markers have been found, marking the mol as 2D. -82: Randomness seeded to: 1742570430 -82: =============================================================================== -82: All tests passed (95 assertions in 4 test cases) -82: - 72/236 Test #82: testPropertyLists ...................... Passed 0.02 sec -test 84 - Start 84: cdxmlParserCatchTest - -84: Test command: /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/cdxmlParserCatchTest -84: Working Directory: /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers -84: Test timeout computed to be: 1500 -81: Randomness seeded to: 2514678478 -81: [12:42:36] SGroup SAP line too short: 'M SAP 1 1 8' on line 29 -81: [12:42:36] SGroup SAP line too short: 'M SAP 1 1 8' on line 28 -81: [12:42:36] Could not infer missing lvIdx on malformed SAP line for SGroup 1 -81: [12:42:36] SGroup 1 is invalid and will be ignored -81: [12:42:36] SGroup SAP line too short: 'M SAP 1 1 8' on line 28 -81: [12:42:36] Could not infer missing lvIdx on malformed SAP line for SGroup 1 -81: [12:42:36] SGroup 1 is invalid and will be ignored -81: [12:42:36] SGroup SAP line too short: 'M SAP 1 1 8' on line 35 -81: [12:42:36] SGroup SAP line too short: 'M SAP 2 1 12' on line 39 -81: [12:42:36] SGroup SAP line too short: 'M SAP 1 1 8' on line 34 -81: [12:42:36] SGroup SAP line too short: 'M SAP 2 1 12' on line 38 -81: [12:42:36] Could not infer missing lvIdx on malformed SAP line for SGroup 1 -81: [12:42:36] SGroup 1 is invalid and will be ignored -81: [12:42:36] SGroup SAP line too short: 'M SAP 1 1 8' on line 34 -81: [12:42:36] SGroup SAP line too short: 'M SAP 2 1 12' on line 39 -81: [12:42:36] Could not infer missing lvIdx on malformed SAP line for SGroup 1 -81: [12:42:36] SGroup 1 is invalid and will be ignored -81: [12:42:36] SGroup 3 referenced on line 40 not found. -81: [12:42:36] +81: Randomness seeded to: 572362979 +81: [21:37:29] SGroup SAP line too short: 'M SAP 1 1 8' on line 29 +81: [21:37:29] SGroup SAP line too short: 'M SAP 1 1 8' on line 28 +81: [21:37:29] Could not infer missing lvIdx on malformed SAP line for SGroup 1 +81: [21:37:29] SGroup 1 is invalid and will be ignored +81: [21:37:29] SGroup SAP line too short: 'M SAP 1 1 8' on line 28 +81: [21:37:29] Could not infer missing lvIdx on malformed SAP line for SGroup 1 +81: [21:37:29] SGroup 1 is invalid and will be ignored +81: [21:37:29] SGroup SAP line too short: 'M SAP 1 1 8' on line 35 +81: [21:37:29] SGroup SAP line too short: 'M SAP 2 1 12' on line 39 +81: [21:37:29] SGroup SAP line too short: 'M SAP 1 1 8' on line 34 +81: [21:37:29] SGroup SAP line too short: 'M SAP 2 1 12' on line 38 +81: [21:37:29] Could not infer missing lvIdx on malformed SAP line for SGroup 1 +81: [21:37:29] SGroup 1 is invalid and will be ignored +81: [21:37:29] SGroup SAP line too short: 'M SAP 1 1 8' on line 34 +81: [21:37:29] SGroup SAP line too short: 'M SAP 2 1 12' on line 39 +81: [21:37:29] Could not infer missing lvIdx on malformed SAP line for SGroup 1 +81: [21:37:29] SGroup 1 is invalid and will be ignored +81: [21:37:29] SGroup 3 referenced on line 40 not found. +81: [21:37:29] 81: 81: **** 81: Pre-condition Violation @@ -21257,24 +21301,24 @@ 81: 1# Invar::operator<<(std::ostream&, Invar::Invariant const&) in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu//lib/libRDKitRDGeneral.so.1 81: 2# RDKit::SubstanceGroup::addCState(unsigned int, RDGeom::Point3D const&) in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu//lib/libRDKitGraphMol.so.1 81: 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-202409.4/obj-aarch64-linux-gnu//lib/libRDKitFileParsers.so.1 -81: 4# 0x0000FFFFB198EBE8 in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu//lib/libRDKitFileParsers.so.1 +81: 4# 0x0000FFFF9A8FEBE8 in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu//lib/libRDKitFileParsers.so.1 81: 5# RDKit::v2::FileParsers::MolFromMolDataStream(std::istream&, unsigned int&, RDKit::v2::FileParsers::MolFileParserParams const&) in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu//lib/libRDKitFileParsers.so.1 81: 6# RDKit::v2::FileParsers::MolFromMolBlock(std::__cxx11::basic_string, std::allocator > const&, RDKit::v2::FileParsers::MolFileParserParams const&) in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu//lib/libRDKitFileParsers.so.1 -81: 7# 0x0000AAAAC19F94BC in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -81: 8# 0x0000AAAAC1A6E02C in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -81: 9# 0x0000AAAAC1A6E9E0 in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -81: 10# 0x0000AAAAC1A6EE14 in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -81: 11# 0x0000AAAAC1A433F8 in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -81: 12# 0x0000AAAAC1A43944 in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -81: 13# 0x0000AAAAC19BB8D0 in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -81: 14# 0x0000FFFFB105229C in /lib/aarch64-linux-gnu/libc.so.6 +81: 7# 0x0000AAAAE21494BC in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +81: 8# 0x0000AAAAE21BE02C in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +81: 9# 0x0000AAAAE21BE9E0 in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +81: 10# 0x0000AAAAE21BEE14 in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +81: 11# 0x0000AAAAE21933F8 in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +81: 12# 0x0000AAAAE2193944 in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +81: 13# 0x0000AAAAE210B8D0 in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +81: 14# 0x0000FFFF99FC229C in /lib/aarch64-linux-gnu/libc.so.6 81: 15# __libc_start_main in /lib/aarch64-linux-gnu/libc.so.6 -81: 16# 0x0000AAAAC19BB9B0 in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +81: 16# 0x0000AAAAE210B9B0 in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest 81: ---------- 81: **** 81: -81: [12:42:36] SGroup 3 referenced on line 40 not found. -81: [12:42:36] +81: [21:37:29] SGroup 3 referenced on line 40 not found. +81: [21:37:29] 81: 81: **** 81: Pre-condition Violation @@ -21287,29 +21331,29 @@ 81: 1# Invar::operator<<(std::ostream&, Invar::Invariant const&) in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu//lib/libRDKitRDGeneral.so.1 81: 2# RDKit::SubstanceGroup::addCState(unsigned int, RDGeom::Point3D const&) in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu//lib/libRDKitGraphMol.so.1 81: 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-202409.4/obj-aarch64-linux-gnu//lib/libRDKitFileParsers.so.1 -81: 4# 0x0000FFFFB198EBE8 in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu//lib/libRDKitFileParsers.so.1 +81: 4# 0x0000FFFF9A8FEBE8 in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu//lib/libRDKitFileParsers.so.1 81: 5# RDKit::v2::FileParsers::MolFromMolDataStream(std::istream&, unsigned int&, RDKit::v2::FileParsers::MolFileParserParams const&) in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu//lib/libRDKitFileParsers.so.1 81: 6# RDKit::v2::FileParsers::MolFromMolBlock(std::__cxx11::basic_string, std::allocator > const&, RDKit::v2::FileParsers::MolFileParserParams const&) in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu//lib/libRDKitFileParsers.so.1 -81: 7# 0x0000AAAAC19F953C in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -81: 8# 0x0000AAAAC1A6E02C in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -81: 9# 0x0000AAAAC1A6E9E0 in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -81: 10# 0x0000AAAAC1A6EE14 in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -81: 11# 0x0000AAAAC1A433F8 in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -81: 12# 0x0000AAAAC1A43944 in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -81: 13# 0x0000AAAAC19BB8D0 in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -81: 14# 0x0000FFFFB105229C in /lib/aarch64-linux-gnu/libc.so.6 +81: 7# 0x0000AAAAE214953C in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +81: 8# 0x0000AAAAE21BE02C in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +81: 9# 0x0000AAAAE21BE9E0 in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +81: 10# 0x0000AAAAE21BEE14 in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +81: 11# 0x0000AAAAE21933F8 in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +81: 12# 0x0000AAAAE2193944 in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +81: 13# 0x0000AAAAE210B8D0 in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +81: 14# 0x0000FFFF99FC229C in /lib/aarch64-linux-gnu/libc.so.6 81: 15# __libc_start_main in /lib/aarch64-linux-gnu/libc.so.6 -81: 16# 0x0000AAAAC19BB9B0 in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +81: 16# 0x0000AAAAE210B9B0 in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest 81: ---------- 81: **** 81: -81: [12:42:36] no bonds -81: [12:42:36] SGroup 1 is invalid and will be ignored -81: [12:42:36] SGroup line too short: 'M SBV 1 6' on line 42 -81: [12:42:36] SGroup 1 is invalid and will be ignored -81: [12:42:36] SGroup line too short: 'M SBL 2 3 9 10' on line 46 -81: [12:42:36] SGroup 2 is invalid and will be ignored -81: [12:42:36] +81: [21:37:29] no bonds +81: [21:37:29] SGroup 1 is invalid and will be ignored +81: [21:37:29] SGroup line too short: 'M SBV 1 6' on line 42 +81: [21:37:29] SGroup 1 is invalid and will be ignored +81: [21:37:29] SGroup line too short: 'M SBL 2 3 9 10' on line 46 +81: [21:37:29] SGroup 2 is invalid and will be ignored +81: [21:37:29] 81: 81: **** 81: Pre-condition Violation @@ -21323,23 +21367,23 @@ 81: 2# RDKit::ROMol::getUniqueBondWithBookmark(int) in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu//lib/libRDKitGraphMol.so.1 81: 3# RDKit::SubstanceGroup::addBondWithBookmark(int) in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu//lib/libRDKitGraphMol.so.1 81: 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-202409.4/obj-aarch64-linux-gnu//lib/libRDKitFileParsers.so.1 -81: 5# 0x0000FFFFB198EB50 in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu//lib/libRDKitFileParsers.so.1 +81: 5# 0x0000FFFF9A8FEB50 in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu//lib/libRDKitFileParsers.so.1 81: 6# RDKit::v2::FileParsers::MolFromMolDataStream(std::istream&, unsigned int&, RDKit::v2::FileParsers::MolFileParserParams const&) in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu//lib/libRDKitFileParsers.so.1 81: 7# RDKit::v2::FileParsers::MolFromMolBlock(std::__cxx11::basic_string, std::allocator > const&, RDKit::v2::FileParsers::MolFileParserParams const&) in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu//lib/libRDKitFileParsers.so.1 -81: 8# 0x0000AAAAC19F9EE4 in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -81: 9# 0x0000AAAAC1A6E02C in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -81: 10# 0x0000AAAAC1A6E9E0 in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -81: 11# 0x0000AAAAC1A6EE14 in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -81: 12# 0x0000AAAAC1A433F8 in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -81: 13# 0x0000AAAAC1A43944 in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -81: 14# 0x0000AAAAC19BB8D0 in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -81: 15# 0x0000FFFFB105229C in /lib/aarch64-linux-gnu/libc.so.6 +81: 8# 0x0000AAAAE2149EE4 in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +81: 9# 0x0000AAAAE21BE02C in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +81: 10# 0x0000AAAAE21BE9E0 in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +81: 11# 0x0000AAAAE21BEE14 in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +81: 12# 0x0000AAAAE21933F8 in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +81: 13# 0x0000AAAAE2193944 in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +81: 14# 0x0000AAAAE210B8D0 in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +81: 15# 0x0000FFFF99FC229C in /lib/aarch64-linux-gnu/libc.so.6 81: 16# __libc_start_main in /lib/aarch64-linux-gnu/libc.so.6 -81: 17# 0x0000AAAAC19BB9B0 in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +81: 17# 0x0000AAAAE210B9B0 in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest 81: ---------- 81: **** 81: -81: [12:42:36] +81: [21:37:29] 81: 81: **** 81: Pre-condition Violation @@ -21353,24 +21397,24 @@ 81: 2# RDKit::ROMol::getUniqueBondWithBookmark(int) in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu//lib/libRDKitGraphMol.so.1 81: 3# RDKit::SubstanceGroup::addBondWithBookmark(int) in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu//lib/libRDKitGraphMol.so.1 81: 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-202409.4/obj-aarch64-linux-gnu//lib/libRDKitFileParsers.so.1 -81: 5# 0x0000FFFFB198EB50 in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu//lib/libRDKitFileParsers.so.1 +81: 5# 0x0000FFFF9A8FEB50 in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu//lib/libRDKitFileParsers.so.1 81: 6# RDKit::v2::FileParsers::MolFromMolDataStream(std::istream&, unsigned int&, RDKit::v2::FileParsers::MolFileParserParams const&) in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu//lib/libRDKitFileParsers.so.1 81: 7# RDKit::v2::FileParsers::MolFromMolBlock(std::__cxx11::basic_string, std::allocator > const&, RDKit::v2::FileParsers::MolFileParserParams const&) in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu//lib/libRDKitFileParsers.so.1 -81: 8# 0x0000AAAAC19F9F64 in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -81: 9# 0x0000AAAAC1A6E02C in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -81: 10# 0x0000AAAAC1A6E9E0 in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -81: 11# 0x0000AAAAC1A6EE14 in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -81: 12# 0x0000AAAAC1A433F8 in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -81: 13# 0x0000AAAAC1A43944 in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -81: 14# 0x0000AAAAC19BB8D0 in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -81: 15# 0x0000FFFFB105229C in /lib/aarch64-linux-gnu/libc.so.6 +81: 8# 0x0000AAAAE2149F64 in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +81: 9# 0x0000AAAAE21BE02C in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +81: 10# 0x0000AAAAE21BE9E0 in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +81: 11# 0x0000AAAAE21BEE14 in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +81: 12# 0x0000AAAAE21933F8 in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +81: 13# 0x0000AAAAE2193944 in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +81: 14# 0x0000AAAAE210B8D0 in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +81: 15# 0x0000FFFF99FC229C in /lib/aarch64-linux-gnu/libc.so.6 81: 16# __libc_start_main in /lib/aarch64-linux-gnu/libc.so.6 -81: 17# 0x0000AAAAC19BB9B0 in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +81: 17# 0x0000AAAAE210B9B0 in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest 81: ---------- 81: **** 81: -81: [12:42:36] bookmark not found -81: [12:42:36] +81: [21:37:29] bookmark not found +81: [21:37:29] 81: 81: **** 81: Pre-condition Violation @@ -21384,25 +21428,25 @@ 81: 2# RDKit::SubstanceGroup::getBondType(unsigned int) const in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu//lib/libRDKitGraphMol.so.1 81: 3# RDKit::SubstanceGroup::addCState(unsigned int, RDGeom::Point3D const&) in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu//lib/libRDKitGraphMol.so.1 81: 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-202409.4/obj-aarch64-linux-gnu//lib/libRDKitFileParsers.so.1 -81: 5# 0x0000FFFFB198EBE8 in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu//lib/libRDKitFileParsers.so.1 +81: 5# 0x0000FFFF9A8FEBE8 in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu//lib/libRDKitFileParsers.so.1 81: 6# RDKit::v2::FileParsers::MolFromMolDataStream(std::istream&, unsigned int&, RDKit::v2::FileParsers::MolFileParserParams const&) in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu//lib/libRDKitFileParsers.so.1 81: 7# RDKit::v2::FileParsers::MolFromMolBlock(std::__cxx11::basic_string, std::allocator > const&, RDKit::v2::FileParsers::MolFileParserParams const&) in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu//lib/libRDKitFileParsers.so.1 -81: 8# 0x0000AAAAC19F9F64 in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -81: 9# 0x0000AAAAC1A6E02C in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -81: 10# 0x0000AAAAC1A6E9E0 in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -81: 11# 0x0000AAAAC1A6EE14 in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -81: 12# 0x0000AAAAC1A433F8 in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -81: 13# 0x0000AAAAC1A43944 in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -81: 14# 0x0000AAAAC19BB8D0 in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -81: 15# 0x0000FFFFB105229C in /lib/aarch64-linux-gnu/libc.so.6 +81: 8# 0x0000AAAAE2149F64 in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +81: 9# 0x0000AAAAE21BE02C in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +81: 10# 0x0000AAAAE21BE9E0 in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +81: 11# 0x0000AAAAE21BEE14 in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +81: 12# 0x0000AAAAE21933F8 in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +81: 13# 0x0000AAAAE2193944 in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +81: 14# 0x0000AAAAE210B8D0 in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +81: 15# 0x0000FFFF99FC229C in /lib/aarch64-linux-gnu/libc.so.6 81: 16# __libc_start_main in /lib/aarch64-linux-gnu/libc.so.6 -81: 17# 0x0000AAAAC19BB9B0 in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +81: 17# 0x0000AAAAE210B9B0 in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest 81: ---------- 81: **** 81: -81: [12:42:36] bond is not part of the SubstanceGroup -81: [12:42:36] SGroup 2 is invalid and will be ignored -81: [12:42:36] +81: [21:37:29] bond is not part of the SubstanceGroup +81: [21:37:29] SGroup 2 is invalid and will be ignored +81: [21:37:29] 81: 81: **** 81: Pre-condition Violation @@ -21416,23 +21460,23 @@ 81: 2# RDKit::ROMol::getUniqueAtomWithBookmark(int) in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu//lib/libRDKitGraphMol.so.1 81: 3# RDKit::SubstanceGroup::addAtomWithBookmark(int) in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu//lib/libRDKitGraphMol.so.1 81: 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-202409.4/obj-aarch64-linux-gnu//lib/libRDKitFileParsers.so.1 -81: 5# 0x0000FFFFB198EB50 in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu//lib/libRDKitFileParsers.so.1 +81: 5# 0x0000FFFF9A8FEB50 in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu//lib/libRDKitFileParsers.so.1 81: 6# RDKit::v2::FileParsers::MolFromMolDataStream(std::istream&, unsigned int&, RDKit::v2::FileParsers::MolFileParserParams const&) in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu//lib/libRDKitFileParsers.so.1 81: 7# RDKit::v2::FileParsers::MolFromMolBlock(std::__cxx11::basic_string, std::allocator > const&, RDKit::v2::FileParsers::MolFileParserParams const&) in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu//lib/libRDKitFileParsers.so.1 -81: 8# 0x0000AAAAC19FA254 in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -81: 9# 0x0000AAAAC1A6E02C in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -81: 10# 0x0000AAAAC1A6E9E0 in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -81: 11# 0x0000AAAAC1A6EE14 in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -81: 12# 0x0000AAAAC1A433F8 in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -81: 13# 0x0000AAAAC1A43944 in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -81: 14# 0x0000AAAAC19BB8D0 in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -81: 15# 0x0000FFFFB105229C in /lib/aarch64-linux-gnu/libc.so.6 +81: 8# 0x0000AAAAE214A254 in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +81: 9# 0x0000AAAAE21BE02C in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +81: 10# 0x0000AAAAE21BE9E0 in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +81: 11# 0x0000AAAAE21BEE14 in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +81: 12# 0x0000AAAAE21933F8 in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +81: 13# 0x0000AAAAE2193944 in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +81: 14# 0x0000AAAAE210B8D0 in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +81: 15# 0x0000FFFF99FC229C in /lib/aarch64-linux-gnu/libc.so.6 81: 16# __libc_start_main in /lib/aarch64-linux-gnu/libc.so.6 -81: 17# 0x0000AAAAC19BB9B0 in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +81: 17# 0x0000AAAAE210B9B0 in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest 81: ---------- 81: **** 81: -81: [12:42:36] +81: [21:37:29] 81: 81: **** 81: Pre-condition Violation @@ -21446,27 +21490,27 @@ 81: 2# RDKit::ROMol::getUniqueAtomWithBookmark(int) in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu//lib/libRDKitGraphMol.so.1 81: 3# RDKit::SubstanceGroup::addAtomWithBookmark(int) in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu//lib/libRDKitGraphMol.so.1 81: 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-202409.4/obj-aarch64-linux-gnu//lib/libRDKitFileParsers.so.1 -81: 5# 0x0000FFFFB198EB50 in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu//lib/libRDKitFileParsers.so.1 +81: 5# 0x0000FFFF9A8FEB50 in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu//lib/libRDKitFileParsers.so.1 81: 6# RDKit::v2::FileParsers::MolFromMolDataStream(std::istream&, unsigned int&, RDKit::v2::FileParsers::MolFileParserParams const&) in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu//lib/libRDKitFileParsers.so.1 81: 7# RDKit::v2::FileParsers::MolFromMolBlock(std::__cxx11::basic_string, std::allocator > const&, RDKit::v2::FileParsers::MolFileParserParams const&) in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu//lib/libRDKitFileParsers.so.1 -81: 8# 0x0000AAAAC19FA2D4 in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -81: 9# 0x0000AAAAC1A6E02C in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -81: 10# 0x0000AAAAC1A6E9E0 in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -81: 11# 0x0000AAAAC1A6EE14 in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -81: 12# 0x0000AAAAC1A433F8 in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -81: 13# 0x0000AAAAC1A43944 in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -81: 14# 0x0000AAAAC19BB8D0 in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -81: 15# 0x0000FFFFB105229C in /lib/aarch64-linux-gnu/libc.so.6 +81: 8# 0x0000AAAAE214A2D4 in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +81: 9# 0x0000AAAAE21BE02C in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +81: 10# 0x0000AAAAE21BE9E0 in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +81: 11# 0x0000AAAAE21BEE14 in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +81: 12# 0x0000AAAAE21933F8 in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +81: 13# 0x0000AAAAE2193944 in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +81: 14# 0x0000AAAAE210B8D0 in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +81: 15# 0x0000FFFF99FC229C in /lib/aarch64-linux-gnu/libc.so.6 81: 16# __libc_start_main in /lib/aarch64-linux-gnu/libc.so.6 -81: 17# 0x0000AAAAC19BB9B0 in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +81: 17# 0x0000AAAAE210B9B0 in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest 81: ---------- 81: **** 81: -81: [12:42:36] bookmark not found -81: [12:42:36] Neither beginning nor ending atoms of bond 9 is in this SubstanceGroup. -81: [12:42:36] SGroup 2 is invalid and will be ignored -81: [12:42:36] WARNING: final character of V3000 array is not ')' -81: [12:42:36] +81: [21:37:29] bookmark not found +81: [21:37:29] Neither beginning nor ending atoms of bond 9 is in this SubstanceGroup. +81: [21:37:29] SGroup 2 is invalid and will be ignored +81: [21:37:29] WARNING: final character of V3000 array is not ')' +81: [21:37:29] 81: 81: **** 81: Pre-condition Violation @@ -21484,21 +21528,21 @@ 81: 6# RDKit::FileParserUtils::ParseV3000CTAB(std::istream*, unsigned int&, RDKit::RWMol*, RDKit::Conformer*&, bool&, unsigned int&, unsigned int&, bool, bool) in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu//lib/libRDKitFileParsers.so.1 81: 7# RDKit::v2::FileParsers::MolFromMolDataStream(std::istream&, unsigned int&, RDKit::v2::FileParsers::MolFileParserParams const&) in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu//lib/libRDKitFileParsers.so.1 81: 8# RDKit::v2::FileParsers::MolFromMolBlock(std::__cxx11::basic_string, std::allocator > const&, RDKit::v2::FileParsers::MolFileParserParams const&) in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu//lib/libRDKitFileParsers.so.1 -81: 9# 0x0000AAAAC19F7ED8 in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -81: 10# 0x0000AAAAC1A6E02C in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -81: 11# 0x0000AAAAC1A6E9E0 in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -81: 12# 0x0000AAAAC1A6EE14 in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -81: 13# 0x0000AAAAC1A433F8 in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -81: 14# 0x0000AAAAC1A43944 in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -81: 15# 0x0000AAAAC19BB8D0 in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -81: 16# 0x0000FFFFB105229C in /lib/aarch64-linux-gnu/libc.so.6 +81: 9# 0x0000AAAAE2147ED8 in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +81: 10# 0x0000AAAAE21BE02C in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +81: 11# 0x0000AAAAE21BE9E0 in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +81: 12# 0x0000AAAAE21BEE14 in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +81: 13# 0x0000AAAAE21933F8 in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +81: 14# 0x0000AAAAE2193944 in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +81: 15# 0x0000AAAAE210B8D0 in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +81: 16# 0x0000FFFF99FC229C in /lib/aarch64-linux-gnu/libc.so.6 81: 17# __libc_start_main in /lib/aarch64-linux-gnu/libc.so.6 -81: 18# 0x0000AAAAC19BB9B0 in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +81: 18# 0x0000AAAAE210B9B0 in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest 81: ---------- 81: **** 81: -81: [12:42:36] WARNING: final character of V3000 array is not ')' -81: [12:42:36] +81: [21:37:29] WARNING: final character of V3000 array is not ')' +81: [21:37:29] 81: 81: **** 81: Pre-condition Violation @@ -21516,23 +21560,23 @@ 81: 6# RDKit::FileParserUtils::ParseV3000CTAB(std::istream*, unsigned int&, RDKit::RWMol*, RDKit::Conformer*&, bool&, unsigned int&, unsigned int&, bool, bool) in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu//lib/libRDKitFileParsers.so.1 81: 7# RDKit::v2::FileParsers::MolFromMolDataStream(std::istream&, unsigned int&, RDKit::v2::FileParsers::MolFileParserParams const&) in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu//lib/libRDKitFileParsers.so.1 81: 8# RDKit::v2::FileParsers::MolFromMolBlock(std::__cxx11::basic_string, std::allocator > const&, RDKit::v2::FileParsers::MolFileParserParams const&) in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu//lib/libRDKitFileParsers.so.1 -81: 9# 0x0000AAAAC19F7F54 in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -81: 10# 0x0000AAAAC1A6E02C in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -81: 11# 0x0000AAAAC1A6E9E0 in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -81: 12# 0x0000AAAAC1A6EE14 in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -81: 13# 0x0000AAAAC1A433F8 in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -81: 14# 0x0000AAAAC1A43944 in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -81: 15# 0x0000AAAAC19BB8D0 in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -81: 16# 0x0000FFFFB105229C in /lib/aarch64-linux-gnu/libc.so.6 +81: 9# 0x0000AAAAE2147F54 in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +81: 10# 0x0000AAAAE21BE02C in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +81: 11# 0x0000AAAAE21BE9E0 in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +81: 12# 0x0000AAAAE21BEE14 in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +81: 13# 0x0000AAAAE21933F8 in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +81: 14# 0x0000AAAAE2193944 in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +81: 15# 0x0000AAAAE210B8D0 in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +81: 16# 0x0000FFFF99FC229C in /lib/aarch64-linux-gnu/libc.so.6 81: 17# __libc_start_main in /lib/aarch64-linux-gnu/libc.so.6 -81: 18# 0x0000AAAAC19BB9B0 in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +81: 18# 0x0000AAAAE210B9B0 in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest 81: ---------- 81: **** 81: -81: [12:42:36] bookmark not found -81: [12:42:36] SGroup 1 is invalid and will be ignored -81: [12:42:36] WARNING: final character of V3000 array is not ')' -81: [12:42:36] +81: [21:37:29] bookmark not found +81: [21:37:29] SGroup 1 is invalid and will be ignored +81: [21:37:29] WARNING: final character of V3000 array is not ')' +81: [21:37:29] 81: 81: **** 81: Pre-condition Violation @@ -21550,21 +21594,21 @@ 81: 6# RDKit::FileParserUtils::ParseV3000CTAB(std::istream*, unsigned int&, RDKit::RWMol*, RDKit::Conformer*&, bool&, unsigned int&, unsigned int&, bool, bool) in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu//lib/libRDKitFileParsers.so.1 81: 7# RDKit::v2::FileParsers::MolFromMolDataStream(std::istream&, unsigned int&, RDKit::v2::FileParsers::MolFileParserParams const&) in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu//lib/libRDKitFileParsers.so.1 81: 8# RDKit::v2::FileParsers::MolFromMolBlock(std::__cxx11::basic_string, std::allocator > const&, RDKit::v2::FileParsers::MolFileParserParams const&) in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu//lib/libRDKitFileParsers.so.1 -81: 9# 0x0000AAAAC19F8228 in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -81: 10# 0x0000AAAAC1A6E02C in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -81: 11# 0x0000AAAAC1A6E9E0 in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -81: 12# 0x0000AAAAC1A6EE14 in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -81: 13# 0x0000AAAAC1A433F8 in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -81: 14# 0x0000AAAAC1A43944 in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -81: 15# 0x0000AAAAC19BB8D0 in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -81: 16# 0x0000FFFFB105229C in /lib/aarch64-linux-gnu/libc.so.6 +81: 9# 0x0000AAAAE2148228 in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +81: 10# 0x0000AAAAE21BE02C in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +81: 11# 0x0000AAAAE21BE9E0 in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +81: 12# 0x0000AAAAE21BEE14 in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +81: 13# 0x0000AAAAE21933F8 in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +81: 14# 0x0000AAAAE2193944 in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +81: 15# 0x0000AAAAE210B8D0 in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +81: 16# 0x0000FFFF99FC229C in /lib/aarch64-linux-gnu/libc.so.6 81: 17# __libc_start_main in /lib/aarch64-linux-gnu/libc.so.6 -81: 18# 0x0000AAAAC19BB9B0 in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +81: 18# 0x0000AAAAE210B9B0 in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest 81: ---------- 81: **** 81: -81: [12:42:36] WARNING: final character of V3000 array is not ')' -81: [12:42:36] +81: [21:37:29] WARNING: final character of V3000 array is not ')' +81: [21:37:29] 81: 81: **** 81: Pre-condition Violation @@ -21582,35 +21626,24 @@ 81: 6# RDKit::FileParserUtils::ParseV3000CTAB(std::istream*, unsigned int&, RDKit::RWMol*, RDKit::Conformer*&, bool&, unsigned int&, unsigned int&, bool, bool) in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu//lib/libRDKitFileParsers.so.1 81: 7# RDKit::v2::FileParsers::MolFromMolDataStream(std::istream&, unsigned int&, RDKit::v2::FileParsers::MolFileParserParams const&) in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu//lib/libRDKitFileParsers.so.1 81: 8# RDKit::v2::FileParsers::MolFromMolBlock(std::__cxx11::basic_string, std::allocator > const&, RDKit::v2::FileParsers::MolFileParserParams const&) in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu//lib/libRDKitFileParsers.so.1 -81: 9# 0x0000AAAAC19F82A4 in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -81: 10# 0x0000AAAAC1A6E02C in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -81: 11# 0x0000AAAAC1A6E9E0 in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -81: 12# 0x0000AAAAC1A6EE14 in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -81: 13# 0x0000AAAAC1A433F8 in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -81: 14# 0x0000AAAAC1A43944 in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -81: 15# 0x0000AAAAC19BB8D0 in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -81: 16# 0x0000FFFFB105229C in /lib/aarch64-linux-gnu/libc.so.6 +81: 9# 0x0000AAAAE21482A4 in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +81: 10# 0x0000AAAAE21BE02C in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +81: 11# 0x0000AAAAE21BE9E0 in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +81: 12# 0x0000AAAAE21BEE14 in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +81: 13# 0x0000AAAAE21933F8 in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +81: 14# 0x0000AAAAE2193944 in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +81: 15# 0x0000AAAAE210B8D0 in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +81: 16# 0x0000FFFF99FC229C in /lib/aarch64-linux-gnu/libc.so.6 81: 17# __libc_start_main in /lib/aarch64-linux-gnu/libc.so.6 -81: 18# 0x0000AAAAC19BB9B0 in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +81: 18# 0x0000AAAAE210B9B0 in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest 81: ---------- 81: **** 81: -81: [12:42:36] bookmark not found -83: Randomness seeded to: 2301956549 -83: =============================================================================== -83: All tests passed (100 assertions in 2 test cases) -83: - 73/236 Test #83: XYZFileParserCatchTest ................. Passed 0.02 sec -81: [12:42:36] SGroup 1 is invalid and will be ignored -81: [12:42:36] +81: [21:37:29] bookmark not found +81: [21:37:29] SGroup 1 is invalid and will be ignored +81: [21:37:29] 81: 81: **** -test 85 - Start 85: molfileStereoCatchTest - -85: Test command: /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/molfileStereoCatchTest -85: Working Directory: /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers -85: Test timeout computed to be: 1500 81: Pre-condition Violation 81: bookmark not found 81: Violation occurred on line 267 in file ./Code/GraphMol/ROMol.cpp @@ -21626,20 +21659,20 @@ 81: 6# RDKit::FileParserUtils::ParseV3000CTAB(std::istream*, unsigned int&, RDKit::RWMol*, RDKit::Conformer*&, bool&, unsigned int&, unsigned int&, bool, bool) in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu//lib/libRDKitFileParsers.so.1 81: 7# RDKit::v2::FileParsers::MolFromMolDataStream(std::istream&, unsigned int&, RDKit::v2::FileParsers::MolFileParserParams const&) in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu//lib/libRDKitFileParsers.so.1 81: 8# RDKit::v2::FileParsers::MolFromMolBlock(std::__cxx11::basic_string, std::allocator > const&, RDKit::v2::FileParsers::MolFileParserParams const&) in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu//lib/libRDKitFileParsers.so.1 -81: 9# 0x0000AAAAC19F8578 in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -81: 10# 0x0000AAAAC1A6E02C in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -81: 11# 0x0000AAAAC1A6E9E0 in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -81: 12# 0x0000AAAAC1A6EE14 in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -81: 13# 0x0000AAAAC1A433F8 in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -81: 14# 0x0000AAAAC1A43944 in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -81: 15# 0x0000AAAAC19BB8D0 in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -81: 16# 0x0000FFFFB105229C in /lib/aarch64-linux-gnu/libc.so.6 +81: 9# 0x0000AAAAE2148578 in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +81: 10# 0x0000AAAAE21BE02C in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +81: 11# 0x0000AAAAE21BE9E0 in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +81: 12# 0x0000AAAAE21BEE14 in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +81: 13# 0x0000AAAAE21933F8 in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +81: 14# 0x0000AAAAE2193944 in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +81: 15# 0x0000AAAAE210B8D0 in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +81: 16# 0x0000FFFF99FC229C in /lib/aarch64-linux-gnu/libc.so.6 81: 17# __libc_start_main in /lib/aarch64-linux-gnu/libc.so.6 -81: 18# 0x0000AAAAC19BB9B0 in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +81: 18# 0x0000AAAAE210B9B0 in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest 81: ---------- 81: **** 81: -81: [12:42:36] +81: [21:37:29] 81: 81: **** 81: Pre-condition Violation @@ -21657,22 +21690,22 @@ 81: 6# RDKit::FileParserUtils::ParseV3000CTAB(std::istream*, unsigned int&, RDKit::RWMol*, RDKit::Conformer*&, bool&, unsigned int&, unsigned int&, bool, bool) in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu//lib/libRDKitFileParsers.so.1 81: 7# RDKit::v2::FileParsers::MolFromMolDataStream(std::istream&, unsigned int&, RDKit::v2::FileParsers::MolFileParserParams const&) in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu//lib/libRDKitFileParsers.so.1 81: 8# RDKit::v2::FileParsers::MolFromMolBlock(std::__cxx11::basic_string, std::allocator > const&, RDKit::v2::FileParsers::MolFileParserParams const&) in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu//lib/libRDKitFileParsers.so.1 -81: 9# 0x0000AAAAC19F85F4 in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -81: 10# 0x0000AAAAC1A6E02C in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -81: 11# 0x0000AAAAC1A6E9E0 in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -81: 12# 0x0000AAAAC1A6EE14 in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -81: 13# 0x0000AAAAC1A433F8 in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -81: 14# 0x0000AAAAC1A43944 in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -81: 15# 0x0000AAAAC19BB8D0 in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -81: 16# 0x0000FFFFB105229C in /lib/aarch64-linux-gnu/libc.so.6 +81: 9# 0x0000AAAAE21485F4 in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +81: 10# 0x0000AAAAE21BE02C in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +81: 11# 0x0000AAAAE21BE9E0 in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +81: 12# 0x0000AAAAE21BEE14 in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +81: 13# 0x0000AAAAE21933F8 in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +81: 14# 0x0000AAAAE2193944 in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +81: 15# 0x0000AAAAE210B8D0 in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +81: 16# 0x0000FFFF99FC229C in /lib/aarch64-linux-gnu/libc.so.6 81: 17# __libc_start_main in /lib/aarch64-linux-gnu/libc.so.6 -81: 18# 0x0000AAAAC19BB9B0 in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +81: 18# 0x0000AAAAE210B9B0 in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest 81: ---------- 81: **** 81: -81: [12:42:36] bookmark not found -81: [12:42:36] SGroup 2 is invalid and will be ignored -81: [12:42:36] +81: [21:37:29] bookmark not found +81: [21:37:29] SGroup 2 is invalid and will be ignored +81: [21:37:29] 81: 81: **** 81: Pre-condition Violation @@ -21690,20 +21723,20 @@ 81: 6# RDKit::FileParserUtils::ParseV3000CTAB(std::istream*, unsigned int&, RDKit::RWMol*, RDKit::Conformer*&, bool&, unsigned int&, unsigned int&, bool, bool) in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu//lib/libRDKitFileParsers.so.1 81: 7# RDKit::v2::FileParsers::MolFromMolDataStream(std::istream&, unsigned int&, RDKit::v2::FileParsers::MolFileParserParams const&) in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu//lib/libRDKitFileParsers.so.1 81: 8# RDKit::v2::FileParsers::MolFromMolBlock(std::__cxx11::basic_string, std::allocator > const&, RDKit::v2::FileParsers::MolFileParserParams const&) in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu//lib/libRDKitFileParsers.so.1 -81: 9# 0x0000AAAAC19F88C8 in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -81: 10# 0x0000AAAAC1A6E02C in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -81: 11# 0x0000AAAAC1A6E9E0 in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -81: 12# 0x0000AAAAC1A6EE14 in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -81: 13# 0x0000AAAAC1A433F8 in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -81: 14# 0x0000AAAAC1A43944 in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -81: 15# 0x0000AAAAC19BB8D0 in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -81: 16# 0x0000FFFFB105229C in /lib/aarch64-linux-gnu/libc.so.6 +81: 9# 0x0000AAAAE21488C8 in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +81: 10# 0x0000AAAAE21BE02C in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +81: 11# 0x0000AAAAE21BE9E0 in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +81: 12# 0x0000AAAAE21BEE14 in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +81: 13# 0x0000AAAAE21933F8 in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +81: 14# 0x0000AAAAE2193944 in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +81: 15# 0x0000AAAAE210B8D0 in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +81: 16# 0x0000FFFF99FC229C in /lib/aarch64-linux-gnu/libc.so.6 81: 17# __libc_start_main in /lib/aarch64-linux-gnu/libc.so.6 -81: 18# 0x0000AAAAC19BB9B0 in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +81: 18# 0x0000AAAAE210B9B0 in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest 81: ---------- 81: **** 81: -81: [12:42:36] +81: [21:37:29] 81: 81: **** 81: Pre-condition Violation @@ -21721,30 +21754,30 @@ 81: 6# RDKit::FileParserUtils::ParseV3000CTAB(std::istream*, unsigned int&, RDKit::RWMol*, RDKit::Conformer*&, bool&, unsigned int&, unsigned int&, bool, bool) in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu//lib/libRDKitFileParsers.so.1 81: 7# RDKit::v2::FileParsers::MolFromMolDataStream(std::istream&, unsigned int&, RDKit::v2::FileParsers::MolFileParserParams const&) in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu//lib/libRDKitFileParsers.so.1 81: 8# RDKit::v2::FileParsers::MolFromMolBlock(std::__cxx11::basic_string, std::allocator > const&, RDKit::v2::FileParsers::MolFileParserParams const&) in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu//lib/libRDKitFileParsers.so.1 -81: 9# 0x0000AAAAC19F8944 in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -81: 10# 0x0000AAAAC1A6E02C in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -81: 11# 0x0000AAAAC1A6E9E0 in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -81: 12# 0x0000AAAAC1A6EE14 in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -81: 13# 0x0000AAAAC1A433F8 in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -81: 14# 0x0000AAAAC1A43944 in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -81: 15# 0x0000AAAAC19BB8D0 in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -81: 16# 0x0000FFFFB105229C in /lib/aarch64-linux-gnu/libc.so.6 +81: 9# 0x0000AAAAE2148944 in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +81: 10# 0x0000AAAAE21BE02C in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +81: 11# 0x0000AAAAE21BE9E0 in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +81: 12# 0x0000AAAAE21BEE14 in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +81: 13# 0x0000AAAAE21933F8 in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +81: 14# 0x0000AAAAE2193944 in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +81: 15# 0x0000AAAAE210B8D0 in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +81: 16# 0x0000FFFF99FC229C in /lib/aarch64-linux-gnu/libc.so.6 81: 17# __libc_start_main in /lib/aarch64-linux-gnu/libc.so.6 -81: 18# 0x0000AAAAC19BB9B0 in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +81: 18# 0x0000AAAAE210B9B0 in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest 81: ---------- 81: **** 81: -81: [12:42:36] bookmark not found -81: [12:42:36] SGroup 2 is invalid and will be ignored -81: [12:42:36] Explicit valence for atom # 2 O, 3, is greater than permitted -81: [12:42:36] Explicit valence for atom # 1 O, 3, is greater than permitted -81: [12:42:36] Explicit valence for atom # 1 C, 5, is greater than permitted -81: [12:42:36] sanitize [12:42:36] UNK: [12:42:36] Warning: molecule is tagged as 3D, but all Z coords are zero and 2D stereo markers have been found, marking the mol as 2D. -81: [12:42:36] skipping block at line 7: 'BEGIN ATOM' +81: [21:37:29] bookmark not found +81: [21:37:29] SGroup 2 is invalid and will be ignored +81: [21:37:29] Explicit valence for atom # 2 O, 3, is greater than permitted +81: [21:37:29] Explicit valence for atom # 1 O, 3, is greater than permitted +81: [21:37:29] Explicit valence for atom # 1 C, 5, is greater than permitted +81: [21:37:29] sanitize [21:37:29] UNK: [21:37:29] Warning: molecule is tagged as 3D, but all Z coords are zero and 2D stereo markers have been found, marking the mol as 2D. +81: [21:37:29] skipping block at line 7: 'BEGIN ATOM' 81: ATOM 1 CHLO CHL 0 0.000 0.000 0.000 1.00 0.00 CL 81: END 81: -81: [12:42:36] +81: [21:37:29] 81: 81: **** 81: Pre-condition Violation @@ -21756,21 +21789,21 @@ 81: 0# Invar::Invariant::toString[abi:cxx11]() const in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu//lib/libRDKitRDGeneral.so.1 81: 1# Invar::operator<<(std::ostream&, Invar::Invariant const&) in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu//lib/libRDKitRDGeneral.so.1 81: 2# RDKit::v2::FileParsers::SDMolSupplier::next() in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu//lib/libRDKitFileParsers.so.1 -81: 3# 0x0000AAAAC1A2E4E0 in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -81: 4# 0x0000AAAAC19EA8C4 in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -81: 5# 0x0000AAAAC1A6E02C in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -81: 6# 0x0000AAAAC1A6E9E0 in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -81: 7# 0x0000AAAAC1A6EE14 in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -81: 8# 0x0000AAAAC1A433F8 in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -81: 9# 0x0000AAAAC1A43944 in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -81: 10# 0x0000AAAAC19BB8D0 in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -81: 11# 0x0000FFFFB105229C in /lib/aarch64-linux-gnu/libc.so.6 +81: 3# 0x0000AAAAE217E4E0 in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +81: 4# 0x0000AAAAE213A8C4 in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +81: 5# 0x0000AAAAE21BE02C in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +81: 6# 0x0000AAAAE21BE9E0 in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +81: 7# 0x0000AAAAE21BEE14 in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +81: 8# 0x0000AAAAE21933F8 in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +81: 9# 0x0000AAAAE2193944 in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +81: 10# 0x0000AAAAE210B8D0 in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +81: 11# 0x0000FFFF99FC229C in /lib/aarch64-linux-gnu/libc.so.6 81: 12# __libc_start_main in /lib/aarch64-linux-gnu/libc.so.6 -81: 13# 0x0000AAAAC19BB9B0 in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +81: 13# 0x0000AAAAE210B9B0 in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest 81: ---------- 81: **** 81: -81: [12:42:36] +81: [21:37:29] 81: 81: **** 81: Pre-condition Violation @@ -21782,21 +21815,21 @@ 81: 0# Invar::Invariant::toString[abi:cxx11]() const in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu//lib/libRDKitRDGeneral.so.1 81: 1# Invar::operator<<(std::ostream&, Invar::Invariant const&) in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu//lib/libRDKitRDGeneral.so.1 81: 2# RDKit::v2::FileParsers::ForwardSDMolSupplier::next() in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu//lib/libRDKitFileParsers.so.1 -81: 3# 0x0000AAAAC1A2E4E0 in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -81: 4# 0x0000AAAAC19EAA34 in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -81: 5# 0x0000AAAAC1A6E02C in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -81: 6# 0x0000AAAAC1A6E9E0 in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -81: 7# 0x0000AAAAC1A6EE14 in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -81: 8# 0x0000AAAAC1A433F8 in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -81: 9# 0x0000AAAAC1A43944 in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -81: 10# 0x0000AAAAC19BB8D0 in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -81: 11# 0x0000FFFFB105229C in /lib/aarch64-linux-gnu/libc.so.6 +81: 3# 0x0000AAAAE217E4E0 in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +81: 4# 0x0000AAAAE213AA34 in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +81: 5# 0x0000AAAAE21BE02C in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +81: 6# 0x0000AAAAE21BE9E0 in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +81: 7# 0x0000AAAAE21BEE14 in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +81: 8# 0x0000AAAAE21933F8 in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +81: 9# 0x0000AAAAE2193944 in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +81: 10# 0x0000AAAAE210B8D0 in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +81: 11# 0x0000FFFF99FC229C in /lib/aarch64-linux-gnu/libc.so.6 81: 12# __libc_start_main in /lib/aarch64-linux-gnu/libc.so.6 -81: 13# 0x0000AAAAC19BB9B0 in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +81: 13# 0x0000AAAAE210B9B0 in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest 81: ---------- 81: **** 81: -81: [12:42:36] +81: [21:37:29] 81: 81: **** 81: Pre-condition Violation @@ -21808,21 +21841,21 @@ 81: 0# Invar::Invariant::toString[abi:cxx11]() const in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu//lib/libRDKitRDGeneral.so.1 81: 1# Invar::operator<<(std::ostream&, Invar::Invariant const&) in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu//lib/libRDKitRDGeneral.so.1 81: 2# RDKit::v2::FileParsers::SmilesMolSupplier::next() in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu//lib/libRDKitFileParsers.so.1 -81: 3# 0x0000AAAAC1A2E4E0 in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -81: 4# 0x0000AAAAC19EAD68 in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -81: 5# 0x0000AAAAC1A6E02C in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -81: 6# 0x0000AAAAC1A6E9E0 in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -81: 7# 0x0000AAAAC1A6EE14 in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -81: 8# 0x0000AAAAC1A433F8 in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -81: 9# 0x0000AAAAC1A43944 in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -81: 10# 0x0000AAAAC19BB8D0 in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -81: 11# 0x0000FFFFB105229C in /lib/aarch64-linux-gnu/libc.so.6 +81: 3# 0x0000AAAAE217E4E0 in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +81: 4# 0x0000AAAAE213AD68 in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +81: 5# 0x0000AAAAE21BE02C in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +81: 6# 0x0000AAAAE21BE9E0 in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +81: 7# 0x0000AAAAE21BEE14 in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +81: 8# 0x0000AAAAE21933F8 in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +81: 9# 0x0000AAAAE2193944 in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +81: 10# 0x0000AAAAE210B8D0 in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +81: 11# 0x0000FFFF99FC229C in /lib/aarch64-linux-gnu/libc.so.6 81: 12# __libc_start_main in /lib/aarch64-linux-gnu/libc.so.6 -81: 13# 0x0000AAAAC19BB9B0 in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +81: 13# 0x0000AAAAE210B9B0 in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest 81: ---------- 81: **** 81: -81: [12:42:36] +81: [21:37:29] 81: 81: **** 81: Pre-condition Violation @@ -21834,21 +21867,21 @@ 81: 0# Invar::Invariant::toString[abi:cxx11]() const in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu//lib/libRDKitRDGeneral.so.1 81: 1# Invar::operator<<(std::ostream&, Invar::Invariant const&) in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu//lib/libRDKitRDGeneral.so.1 81: 2# RDKit::v2::FileParsers::TDTMolSupplier::next() in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu//lib/libRDKitFileParsers.so.1 -81: 3# 0x0000AAAAC1A2E4E0 in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -81: 4# 0x0000AAAAC19EB004 in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -81: 5# 0x0000AAAAC1A6E02C in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -81: 6# 0x0000AAAAC1A6E9E0 in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -81: 7# 0x0000AAAAC1A6EE14 in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -81: 8# 0x0000AAAAC1A433F8 in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -81: 9# 0x0000AAAAC1A43944 in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -81: 10# 0x0000AAAAC19BB8D0 in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -81: 11# 0x0000FFFFB105229C in /lib/aarch64-linux-gnu/libc.so.6 +81: 3# 0x0000AAAAE217E4E0 in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +81: 4# 0x0000AAAAE213B004 in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +81: 5# 0x0000AAAAE21BE02C in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +81: 6# 0x0000AAAAE21BE9E0 in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +81: 7# 0x0000AAAAE21BEE14 in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +81: 8# 0x0000AAAAE21933F8 in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +81: 9# 0x0000AAAAE2193944 in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +81: 10# 0x0000AAAAE210B8D0 in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +81: 11# 0x0000FFFF99FC229C in /lib/aarch64-linux-gnu/libc.so.6 81: 12# __libc_start_main in /lib/aarch64-linux-gnu/libc.so.6 -81: 13# 0x0000AAAAC19BB9B0 in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +81: 13# 0x0000AAAAE210B9B0 in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest 81: ---------- 81: **** 81: -81: [12:42:36] +81: [21:37:29] 81: 81: **** 81: Pre-condition Violation @@ -21860,29 +21893,29 @@ 81: 0# Invar::Invariant::toString[abi:cxx11]() const in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu//lib/libRDKitRDGeneral.so.1 81: 1# Invar::operator<<(std::ostream&, Invar::Invariant const&) in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu//lib/libRDKitRDGeneral.so.1 81: 2# RDKit::v2::FileParsers::MaeMolSupplier::next() in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu//lib/libRDKitFileParsers.so.1 -81: 3# 0x0000AAAAC1A2E4E0 in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -81: 4# 0x0000AAAAC19EB1FC in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -81: 5# 0x0000AAAAC1A6E02C in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -81: 6# 0x0000AAAAC1A6E9E0 in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -81: 7# 0x0000AAAAC1A6EE14 in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -81: 8# 0x0000AAAAC1A433F8 in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -81: 9# 0x0000AAAAC1A43944 in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -81: 10# 0x0000AAAAC19BB8D0 in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -81: 11# 0x0000FFFFB105229C in /lib/aarch64-linux-gnu/libc.so.6 +81: 3# 0x0000AAAAE217E4E0 in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +81: 4# 0x0000AAAAE213B1FC in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +81: 5# 0x0000AAAAE21BE02C in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +81: 6# 0x0000AAAAE21BE9E0 in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +81: 7# 0x0000AAAAE21BEE14 in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +81: 8# 0x0000AAAAE21933F8 in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +81: 9# 0x0000AAAAE2193944 in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +81: 10# 0x0000AAAAE210B8D0 in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +81: 11# 0x0000FFFF99FC229C in /lib/aarch64-linux-gnu/libc.so.6 81: 12# __libc_start_main in /lib/aarch64-linux-gnu/libc.so.6 -81: 13# 0x0000AAAAC19BB9B0 in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +81: 13# 0x0000AAAAE210B9B0 in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest 81: ---------- 81: **** 81: -81: [12:42:36] Found a SCD/SED line with missing/empty SDT specification at line 21 -81: [12:42:36] Found a SCD/SED line with missing/empty SDT specification at line 20 -81: [12:42:36] BEGIN SGROUP line not found on line 14 -81: [12:42:36] Unhandled CTAB feature: 'Unsupported SGroup type '' on line 18'. Molecule skipped. -81: [12:42:36] END SGROUP line not found on line 14 -81: [12:42:36] END SGROUP line not found on line 14 -81: [12:42:36] MRV_COORDINATE_BOND_TYPE SGroup with value 0 does not reference a query bond, ignoring. -81: [12:42:36] MRV_COORDINATE_BOND_TYPE SGroup with value 1 does not reference a query bond, ignoring. -81: [12:42:36] +81: [21:37:29] Found a SCD/SED line with missing/empty SDT specification at line 21 +81: [21:37:29] Found a SCD/SED line with missing/empty SDT specification at line 20 +81: [21:37:29] BEGIN SGROUP line not found on line 14 +81: [21:37:29] Unhandled CTAB feature: 'Unsupported SGroup type '' on line 18'. Molecule skipped. +81: [21:37:29] END SGROUP line not found on line 14 +81: [21:37:29] END SGROUP line not found on line 14 +81: [21:37:29] MRV_COORDINATE_BOND_TYPE SGroup with value 0 does not reference a query bond, ignoring. +81: [21:37:29] MRV_COORDINATE_BOND_TYPE SGroup with value 1 does not reference a query bond, ignoring. +81: [21:37:29] 81: 81: **** 81: Range Error @@ -21897,53 +21930,42 @@ 81: 3# RDKit::FileParserUtils::finishMolProcessing(RDKit::RWMol*, bool, RDKit::v2::FileParsers::MolFileParserParams const&) in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu//lib/libRDKitFileParsers.so.1 81: 4# RDKit::v2::FileParsers::MolFromMolDataStream(std::istream&, unsigned int&, RDKit::v2::FileParsers::MolFileParserParams const&) in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu//lib/libRDKitFileParsers.so.1 81: 5# RDKit::v2::FileParsers::MolFromMolBlock(std::__cxx11::basic_string, std::allocator > const&, RDKit::v2::FileParsers::MolFileParserParams const&) in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu//lib/libRDKitFileParsers.so.1 -81: 6# 0x0000AAAAC1A2E154 in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -81: 7# 0x0000AAAAC19F0250 in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -81: 8# 0x0000AAAAC1A6E02C in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -81: 9# 0x0000AAAAC1A6E9E0 in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -81: 10# 0x0000AAAAC1A6EE14 in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -81: 11# 0x0000AAAAC1A433F8 in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -81: 12# 0x0000AAAAC1A43944 in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -81: 13# 0x0000AAAAC19BB8D0 in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -81: 14# 0x0000FFFFB105229C in /lib/aarch64-linux-gnu/libc.so.6 +81: 6# 0x0000AAAAE217E154 in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +81: 7# 0x0000AAAAE2140250 in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +81: 8# 0x0000AAAAE21BE02C in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +81: 9# 0x0000AAAAE21BE9E0 in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +81: 10# 0x0000AAAAE21BEE14 in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +81: 11# 0x0000AAAAE21933F8 in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +81: 12# 0x0000AAAAE2193944 in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +81: 13# 0x0000AAAAE210B8D0 in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +81: 14# 0x0000FFFF99FC229C in /lib/aarch64-linux-gnu/libc.so.6 81: 15# __libc_start_main in /lib/aarch64-linux-gnu/libc.so.6 -81: 16# 0x0000AAAAC19BB9B0 in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +81: 16# 0x0000AAAAE210B9B0 in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest 81: ---------- 81: **** 81: -81: [12:42:36] molecule does not contain a bond matching the MRV_COORDINATE_BOND_TYPE SGroup for bond 99, ignoring. -81: [12:42:36] Multiple ATTCHPT values for atom 2 on line 9 -81: [12:42:36] Found a SCD/SED line with missing/empty SDT specification at line 12 -81: [12:42:36] SMARTS Parse Error: syntax error while parsing: [#6;R -81: [12:42:36] SMARTS Parse Error: Failed parsing SMARTS '[#6;R' for input: '[#6;R' -81: [12:42:36] SMARTS for SMARTSQ '[#6;R' could not be parsed or has no atoms. Ignoring it. -81: [12:42:36] Skipping empty SMARTS value for SMARTSQ. -81: [12:42:36] unrecognized QUERYOP '>' for SMARTSQ. Query ignored. -81: [12:42:36] Found a SCD/SED line with missing/empty SDT specification at line 12 -81: [12:42:36] Can't kekulize mol. Unkekulized atoms: 0 1 2 3 4 -84: Randomness seeded to: 536831689 -84: [12:42:36] Invalid or missing fragment id from CDXML fragment, assigning new one... -84: [12:42:36] Explicit valence for atom # 3 N, 4, is greater than permitted -84: [12:42:36] CDXMLParser: failed sanitizing skipping fragment 32 -84: [12:42:36] Bad bond in CDXML skipping fragment 58... -84: [12:42:36] Invalid or missing fragment id from CDXML fragment, assigning new one... -84: [12:42:36] Bad bond in CDXML skipping fragment 58... -85: Randomness seeded to: 2875489699 -85: [12:42:36] Warning: ambiguous stereochemistry - opposing bonds have opposite wedging - at atom 2 ignored. -85: [12:42:36] Warning: ambiguous stereochemistry - opposing bonds have opposite wedging - at atom 2 ignored. -85: [12:42:36] Warning: ambiguous stereochemistry - opposing bonds have opposite wedging - at atom 2 ignored. -85: [12:42:36] Warning: ambiguous stereochemistry - opposing bonds have opposite wedging - at atom 2 ignored. -85: =============================================================================== -85: All tests passed (142 assertions in 6 test cases) -85: -81: [12:42:36] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -81: [12:42:36] WARNING: Skipping property bar because the value includes an illegal blank line -81: [12:42:36] WARNING: Skipping property baz because the value includes an illegal blank line -81: [12:42:36] WARNING: Skipping property bletch +81: [21:37:29] molecule does not contain a bond matching the MRV_COORDINATE_BOND_TYPE SGroup for bond 99, ignoring. +81: [21:37:29] Multiple ATTCHPT values for atom 2 on line 9 +81: [21:37:29] Found a SCD/SED line with missing/empty SDT specification at line 12 +81: [21:37:29] SMARTS Parse Error: syntax error while parsing: [#6;R +81: [21:37:29] SMARTS Parse Error: Failed parsing SMARTS '[#6;R' for input: '[#6;R' +81: [21:37:29] SMARTS for SMARTSQ '[#6;R' could not be parsed or has no atoms. Ignoring it. +81: [21:37:29] Skipping empty SMARTS value for SMARTSQ. +81: [21:37:29] unrecognized QUERYOP '>' for SMARTSQ. Query ignored. +81: [21:37:29] Found a SCD/SED line with missing/empty SDT specification at line 12 +81: [21:37:29] Can't kekulize mol. Unkekulized atoms: 0 1 2 3 4 +82: Randomness seeded to: 1806575980 +82: =============================================================================== +82: All tests passed (95 assertions in 4 test cases) +82: +81: [21:37:29] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +81: [21:37:29] WARNING: Skipping property bar because the value includes an illegal blank line +81: [21:37:29] WARNING: Skipping property baz because the value includes an illegal blank line +81: [21:37:29] WARNING: Skipping property bletch 81: nope because the name includes a newline -81: [12:42:36] WARNING: Skipping property bletch +81: [21:37:29] WARNING: Skipping property bletch 81: nope2 because the name includes a newline -81: [12:42:36] +81: [21:37:29] 81: 81: **** 81: Post-condition Violation @@ -21955,26 +21977,26 @@ 81: 0# Invar::Invariant::toString[abi:cxx11]() const in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu//lib/libRDKitRDGeneral.so.1 81: 1# Invar::operator<<(std::ostream&, Invar::Invariant const&) in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu//lib/libRDKitRDGeneral.so.1 81: 2# RDKit::PeriodicTable::getAtomicNumber(std::__cxx11::basic_string, std::allocator > const&) const in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu//lib/libRDKitFileParsers.so.1 -81: 3# 0x0000FFFFB1977D24 in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu//lib/libRDKitFileParsers.so.1 -81: 4# 0x0000FFFFB1987F90 in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu//lib/libRDKitFileParsers.so.1 -81: 5# 0x0000FFFFB1988BCC in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu//lib/libRDKitFileParsers.so.1 +81: 3# 0x0000FFFF9A8E7D24 in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu//lib/libRDKitFileParsers.so.1 +81: 4# 0x0000FFFF9A8F7F90 in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu//lib/libRDKitFileParsers.so.1 +81: 5# 0x0000FFFF9A8F8BCC in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu//lib/libRDKitFileParsers.so.1 81: 6# RDKit::FileParserUtils::ParseV3000CTAB(std::istream*, unsigned int&, RDKit::RWMol*, RDKit::Conformer*&, bool&, unsigned int&, unsigned int&, bool, bool) in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu//lib/libRDKitFileParsers.so.1 81: 7# RDKit::v2::FileParsers::MolFromMolDataStream(std::istream&, unsigned int&, RDKit::v2::FileParsers::MolFileParserParams const&) in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu//lib/libRDKitFileParsers.so.1 81: 8# RDKit::v2::FileParsers::MolFromMolBlock(std::__cxx11::basic_string, std::allocator > const&, RDKit::v2::FileParsers::MolFileParserParams const&) in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu//lib/libRDKitFileParsers.so.1 -81: 9# 0x0000AAAAC19C46D4 in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -81: 10# 0x0000AAAAC1A6E02C in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -81: 11# 0x0000AAAAC1A6E9E0 in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -81: 12# 0x0000AAAAC1A6EE14 in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -81: 13# 0x0000AAAAC1A433F8 in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -81: 14# 0x0000AAAAC1A43944 in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -81: 15# 0x0000AAAAC19BB8D0 in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -81: 16# 0x0000FFFFB105229C in /lib/aarch64-linux-gnu/libc.so.6 +81: 9# 0x0000AAAAE21146D4 in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +81: 10# 0x0000AAAAE21BE02C in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +81: 11# 0x0000AAAAE21BE9E0 in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +81: 12# 0x0000AAAAE21BEE14 in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +81: 13# 0x0000AAAAE21933F8 in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +81: 14# 0x0000AAAAE2193944 in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +81: 15# 0x0000AAAAE210B8D0 in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +81: 16# 0x0000FFFF99FC229C in /lib/aarch64-linux-gnu/libc.so.6 81: 17# __libc_start_main in /lib/aarch64-linux-gnu/libc.so.6 -81: 18# 0x0000AAAAC19BB9B0 in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +81: 18# 0x0000AAAAE210B9B0 in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest 81: ---------- 81: **** 81: -81: [12:42:36] +81: [21:37:29] 81: 81: **** 81: Post-condition Violation @@ -21986,26 +22008,26 @@ 81: 0# Invar::Invariant::toString[abi:cxx11]() const in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu//lib/libRDKitRDGeneral.so.1 81: 1# Invar::operator<<(std::ostream&, Invar::Invariant const&) in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu//lib/libRDKitRDGeneral.so.1 81: 2# RDKit::PeriodicTable::getAtomicNumber(std::__cxx11::basic_string, std::allocator > const&) const in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu//lib/libRDKitFileParsers.so.1 -81: 3# 0x0000FFFFB1977D24 in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu//lib/libRDKitFileParsers.so.1 -81: 4# 0x0000FFFFB1987F90 in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu//lib/libRDKitFileParsers.so.1 -81: 5# 0x0000FFFFB1988BCC in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu//lib/libRDKitFileParsers.so.1 +81: 3# 0x0000FFFF9A8E7D24 in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu//lib/libRDKitFileParsers.so.1 +81: 4# 0x0000FFFF9A8F7F90 in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu//lib/libRDKitFileParsers.so.1 +81: 5# 0x0000FFFF9A8F8BCC in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu//lib/libRDKitFileParsers.so.1 81: 6# RDKit::FileParserUtils::ParseV3000CTAB(std::istream*, unsigned int&, RDKit::RWMol*, RDKit::Conformer*&, bool&, unsigned int&, unsigned int&, bool, bool) in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu//lib/libRDKitFileParsers.so.1 81: 7# RDKit::v2::FileParsers::MolFromMolDataStream(std::istream&, unsigned int&, RDKit::v2::FileParsers::MolFileParserParams const&) in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu//lib/libRDKitFileParsers.so.1 81: 8# RDKit::v2::FileParsers::MolFromMolBlock(std::__cxx11::basic_string, std::allocator > const&, RDKit::v2::FileParsers::MolFileParserParams const&) in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu//lib/libRDKitFileParsers.so.1 -81: 9# 0x0000AAAAC19C3FF8 in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -81: 10# 0x0000AAAAC1A6E02C in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -81: 11# 0x0000AAAAC1A6E9E0 in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -81: 12# 0x0000AAAAC1A6EE14 in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -81: 13# 0x0000AAAAC1A433F8 in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -81: 14# 0x0000AAAAC1A43944 in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -81: 15# 0x0000AAAAC19BB8D0 in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -81: 16# 0x0000FFFFB105229C in /lib/aarch64-linux-gnu/libc.so.6 +81: 9# 0x0000AAAAE2113FF8 in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +81: 10# 0x0000AAAAE21BE02C in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +81: 11# 0x0000AAAAE21BE9E0 in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +81: 12# 0x0000AAAAE21BEE14 in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +81: 13# 0x0000AAAAE21933F8 in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +81: 14# 0x0000AAAAE2193944 in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +81: 15# 0x0000AAAAE210B8D0 in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +81: 16# 0x0000FFFF99FC229C in /lib/aarch64-linux-gnu/libc.so.6 81: 17# __libc_start_main in /lib/aarch64-linux-gnu/libc.so.6 -81: 18# 0x0000AAAAC19BB9B0 in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +81: 18# 0x0000AAAAE210B9B0 in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest 81: ---------- 81: **** 81: -81: [12:42:36] +81: [21:37:29] 81: 81: **** 81: Post-condition Violation @@ -22017,29 +22039,28 @@ 81: 0# Invar::Invariant::toString[abi:cxx11]() const in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu//lib/libRDKitRDGeneral.so.1 81: 1# Invar::operator<<(std::ostream&, Invar::Invariant const&) in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu//lib/libRDKitRDGeneral.so.1 81: 2# RDKit::PeriodicTable::getAtomicNumber(std::__cxx11::basic_string, std::allocator > const&) const in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu//lib/libRDKitFileParsers.so.1 -81: 3# 0x0000FFFFB1977D24 in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu//lib/libRDKitFileParsers.so.1 -81: 4# 0x0000FFFFB1985920 in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu//lib/libRDKitFileParsers.so.1 -81: 5# 0x0000FFFFB198684C in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu//lib/libRDKitFileParsers.so.1 +81: 3# 0x0000FFFF9A8E7D24 in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu//lib/libRDKitFileParsers.so.1 +81: 4# 0x0000FFFF9A8F5920 in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu//lib/libRDKitFileParsers.so.1 +81: 5# 0x0000FFFF9A8F684C in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu//lib/libRDKitFileParsers.so.1 81: 6# RDKit::FileParserUtils::ParseV2000CTAB(std::istream*, unsigned int&, RDKit::RWMol*, RDKit::Conformer*&, bool&, unsigned int&, unsigned int&, bool) in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu//lib/libRDKitFileParsers.so.1 81: 7# RDKit::v2::FileParsers::MolFromMolDataStream(std::istream&, unsigned int&, RDKit::v2::FileParsers::MolFileParserParams const&) in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu//lib/libRDKitFileParsers.so.1 81: 8# RDKit::v2::FileParsers::MolFromMolBlock(std::__cxx11::basic_string, std::allocator > const&, RDKit::v2::FileParsers::MolFileParserParams const&) in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu//lib/libRDKitFileParsers.so.1 -81: 9# 0x0000AAAAC19C4690 in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -81: 10# 0x0000AAAAC1A6E02C in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -81: 11# 0x0000AAAAC1A6E9E0 in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -81: 12# 0x0000AAAAC1A6EE14 in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -81: 13# 0x0000AAAAC1A433F8 in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -81: 14# 0x0000AAAAC1A43944 in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -81: 15# 0x0000AAAAC19BB8D0 in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -81: 16# 0x0000FFFFB105229C in /lib/aarch64-linux-gnu/libc.so.6 +81: 9# 0x0000AAAAE2114690 in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +81: 10# 0x0000AAAAE21BE02C in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +81: 11# 0x0000AAAAE21BE9E0 in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +81: 12# 0x0000AAAAE21BEE14 in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +81: 13# 0x0000AAAAE21933F8 in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +81: 14# 0x0000AAAAE2193944 in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +81: 15# 0x0000AAAAE210B8D0 in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +81: 16# 0x0000FFFF99FC229C in /lib/aarch64-linux-gnu/libc.so.6 81: 17# __libc_start_main in /lib/aarch64-linux-gnu/libc.so.6 -81: 18# 0x0000AAAAC19BB9B0 in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +81: 18# 0x0000AAAAE210B9B0 in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest 81: ---------- 81: **** 81: -81: [12:42:36] +81: [21:37:29] 81: 81: **** - 74/236 Test #85: molfileStereoCatchTest ................. Passed 0.03 sec 81: Post-condition Violation 81: Element 'QQQ' not found 81: Violation occurred on line 93 in file ./Code/GraphMol/PeriodicTable.h @@ -22049,33 +22070,45 @@ 81: 0# Invar::Invariant::toString[abi:cxx11]() const in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu//lib/libRDKitRDGeneral.so.1 81: 1# Invar::operator<<(std::ostream&, Invar::Invariant const&) in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu//lib/libRDKitRDGeneral.so.1 81: 2# RDKit::PeriodicTable::getAtomicNumber(std::__cxx11::basic_string, std::allocator > const&) const in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu//lib/libRDKitFileParsers.so.1 -81: 3# 0x0000FFFFB1977D24 in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu//lib/libRDKitFileParsers.so.1 -81: 4# 0x0000FFFFB1985920 in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu//lib/libRDKitFileParsers.so.1 -81: 5# 0x0000FFFFB198684C in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu//lib/libRDKitFileParsers.so.1 +81: 3# 0x0000FFFF9A8E7D24 in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu//lib/libRDKitFileParsers.so.1 +81: 4# 0x0000FFFF9A8F5920 in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu//lib/libRDKitFileParsers.so.1 +81: 5# 0x0000FFFF9A8F684C in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu//lib/libRDKitFileParsers.so.1 81: 6# RDKit::FileParserUtils::ParseV2000CTAB(std::istream*, unsigned int&, RDKit::RWMol*, RDKit::Conformer*&, bool&, unsigned int&, unsigned int&, bool) in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu//lib/libRDKitFileParsers.so.1 81: 7# RDKit::v2::FileParsers::MolFromMolDataStream(std::istream&, unsigned int&, RDKit::v2::FileParsers::MolFileParserParams const&) in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu//lib/libRDKitFileParsers.so.1 81: 8# RDKit::v2::FileParsers::MolFromMolBlock(std::__cxx11::basic_string, std::allocator > const&, RDKit::v2::FileParsers::MolFileParserParams const&) in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu//lib/libRDKitFileParsers.so.1 -81: 9# 0x0000AAAAC19C43C8 in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -81: 10# 0x0000AAAAC1A6E02C in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -81: 11# 0x0000AAAAC1A6E9E0 in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -81: 12# 0x0000AAAAC1A6EE14 in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -81: 13# 0x0000AAAAC1A433F8 in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -81: 14# 0x0000AAAAC1A43944 in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -81: 15# 0x0000AAAAC19BB8D0 in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -81: 16# 0x0000FFFFB105229C in /lib/aarch64-linux-gnu/libc.so.6 +81: 9# 0x0000AAAAE21143C8 in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +81: 10# 0x0000AAAAE21BE02C in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +81: 11# 0x0000AAAAE21BE9E0 in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +81: 12# 0x0000AAAAE21BEE14 in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +81: 13# 0x0000AAAAE21933F8 in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +81: 14# 0x0000AAAAE2193944 in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +81: 15# 0x0000AAAAE210B8D0 in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +81: 16# 0x0000FFFF99FC229C in /lib/aarch64-linux-gnu/libc.so.6 81: 17# __libc_start_main in /lib/aarch64-linux-gnu/libc.so.6 -81: 18# 0x0000AAAAC19BB9B0 in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +81: 18# 0x0000AAAAE210B9B0 in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest 81: ---------- 81: **** 81: -81: [12:42:36] atom 3 has a negative isotope value. line: 15 -test 86 - Start 86: connectTheDotsTest +81: [21:37:29] atom 3 has a negative isotope value. line: 15 +83: Randomness seeded to: 3771364531 +83: =============================================================================== +83: All tests passed (100 assertions in 2 test cases) +83: + 72/236 Test #82: testPropertyLists ...................... Passed 0.09 sec + 73/236 Test #83: XYZFileParserCatchTest ................. Passed 0.07 sec +test 84 + Start 84: cdxmlParserCatchTest -86: Test command: /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/connectTheDotsTest -86: Working Directory: /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers -86: Test timeout computed to be: 1500 -81: [12:42:36] +84: Test command: /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/cdxmlParserCatchTest +84: Working Directory: /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers +84: Test timeout computed to be: 1500 +test 85 + Start 85: molfileStereoCatchTest + +85: Test command: /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/molfileStereoCatchTest +85: Working Directory: /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers +85: Test timeout computed to be: 1500 +81: [21:37:29] 81: 81: **** 81: Invariant Violation @@ -22086,23 +22119,23 @@ 81: Stacktrace: 81: 0# Invar::Invariant::toString[abi:cxx11]() const in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu//lib/libRDKitRDGeneral.so.1 81: 1# Invar::operator<<(std::ostream&, Invar::Invariant const&) in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu//lib/libRDKitRDGeneral.so.1 -81: 2# 0x0000FFFFB1A46AB8 in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu//lib/libRDKitFileParsers.so.1 +81: 2# 0x0000FFFF9A9B6AB8 in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu//lib/libRDKitFileParsers.so.1 81: 3# RDKit::v2::FileParsers::MaeMolSupplier::next() in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu//lib/libRDKitFileParsers.so.1 -81: 4# 0x0000AAAAC1A2E4E0 in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -81: 5# 0x0000AAAAC1A015E0 in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -81: 6# 0x0000AAAAC1A6E02C in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -81: 7# 0x0000AAAAC1A6E9E0 in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -81: 8# 0x0000AAAAC1A6EE14 in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -81: 9# 0x0000AAAAC1A433F8 in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -81: 10# 0x0000AAAAC1A43944 in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -81: 11# 0x0000AAAAC19BB8D0 in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -81: 12# 0x0000FFFFB105229C in /lib/aarch64-linux-gnu/libc.so.6 +81: 4# 0x0000AAAAE217E4E0 in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +81: 5# 0x0000AAAAE21515E0 in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +81: 6# 0x0000AAAAE21BE02C in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +81: 7# 0x0000AAAAE21BE9E0 in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +81: 8# 0x0000AAAAE21BEE14 in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +81: 9# 0x0000AAAAE21933F8 in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +81: 10# 0x0000AAAAE2193944 in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +81: 11# 0x0000AAAAE210B8D0 in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +81: 12# 0x0000FFFF99FC229C in /lib/aarch64-linux-gnu/libc.so.6 81: 13# __libc_start_main in /lib/aarch64-linux-gnu/libc.so.6 -81: 14# 0x0000AAAAC19BB9B0 in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +81: 14# 0x0000AAAAE210B9B0 in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest 81: ---------- 81: **** 81: -81: [12:42:36] +81: [21:37:29] 81: 81: **** 81: Pre-condition Violation @@ -22115,113 +22148,133 @@ 81: 1# Invar::operator<<(std::ostream&, Invar::Invariant const&) in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu//lib/libRDKitRDGeneral.so.1 81: 2# RDKit::v2::FileParsers::MaeMolSupplier::init() in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu//lib/libRDKitFileParsers.so.1 81: 3# RDKit::v2::FileParsers::MaeMolSupplier::reset() in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu//lib/libRDKitFileParsers.so.1 -81: 4# 0x0000AAAAC1A01904 in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -81: 5# 0x0000AAAAC1A6E02C in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -81: 6# 0x0000AAAAC1A6E9E0 in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -81: 7# 0x0000AAAAC1A6EE14 in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -81: 8# 0x0000AAAAC1A433F8 in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -81: 9# 0x0000AAAAC1A43944 in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -81: 10# 0x0000AAAAC19BB8D0 in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -81: 11# 0x0000FFFFB105229C in /lib/aarch64-linux-gnu/libc.so.6 +81: 4# 0x0000AAAAE2151904 in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +81: 5# 0x0000AAAAE21BE02C in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +81: 6# 0x0000AAAAE21BE9E0 in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +81: 7# 0x0000AAAAE21BEE14 in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +81: 8# 0x0000AAAAE21933F8 in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +81: 9# 0x0000AAAAE2193944 in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +81: 10# 0x0000AAAAE210B8D0 in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +81: 11# 0x0000FFFF99FC229C in /lib/aarch64-linux-gnu/libc.so.6 81: 12# __libc_start_main in /lib/aarch64-linux-gnu/libc.so.6 -81: 13# 0x0000AAAAC19BB9B0 in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +81: 13# 0x0000AAAAE210B9B0 in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest 81: ---------- 81: **** 81: -70: ---------------------------------- -70: ---------------------------------- -70: [12:42:36] -70: -70: **** -70: Pre-condition Violation -70: rlabel out of range for MDL files -70: Violation occurred on line 857 in file ./Code/GraphMol/Atom.cpp -70: Failed Expression: rlabel >= 0 && rlabel < 100 -70: ---------- -70: Stacktrace: -70: 0# Invar::Invariant::toString[abi:cxx11]() const in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu//lib/libRDKitRDGeneral.so.1 -70: 1# Invar::operator<<(std::ostream&, Invar::Invariant const&) in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu//lib/libRDKitRDGeneral.so.1 -70: 2# RDKit::setAtomRLabel(RDKit::Atom*, int) in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu//lib/libRDKitGraphMol.so.1 -70: 3# 0x0000AAAAD6B8ECE0 in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersTest1 -70: 4# 0x0000AAAAD6BF4584 in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersTest1 -70: 5# 0x0000AAAAD6B65638 in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersTest1 -70: 6# 0x0000FFFF8E49229C in /lib/aarch64-linux-gnu/libc.so.6 -70: 7# __libc_start_main in /lib/aarch64-linux-gnu/libc.so.6 -70: 8# 0x0000AAAAD6B65870 in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersTest1 -70: ---------- -70: **** -70: -70: [12:42:36] WARNING: could not find number of expected rings. Switching to an approximate ring finding algorithm. -84: [12:42:36] WARNING: not removing hydrogen atom without neighbors -84: [12:42:36] WARNING: not removing hydrogen atom without neighbors -84: [12:42:36] WARNING: not removing hydrogen atom without neighbors -84: [12:42:36] WARNING: not removing hydrogen atom without neighbors -84: [12:42:36] WARNING: not removing hydrogen atom without neighbors -84: [12:42:36] WARNING: not removing hydrogen atom without neighbors -84: [12:42:36] WARNING: not removing hydrogen atom without neighbors -84: [12:42:36] WARNING: not removing hydrogen atom without neighbors -84: [12:42:36] WARNING: not removing hydrogen atom without neighbors -84: [12:42:36] WARNING: not removing hydrogen atom without neighbors -84: [12:42:36] CDXMLParser: Schema 80180 step 80181 ReactionStepAgents reaction fragment 64603 not found in document. -84: [12:42:36] Incomplete atom labelling, cannot make bond -84: [12:42:36] Incomplete atom labelling, cannot make bond -86: Randomness seeded to: 4179732068 +81: [21:37:29] ERROR: molecules without atoms cannot be exported to Maestro files. +81: [21:37:29] Can't kekulize mol. Unkekulized atoms: 0 1 2 3 4 +81: [21:37:29] ERROR: the mol cannot be kekulized, and will not be written to the output file. +81: [21:37:29] ERROR: Bond 0 has a type that is not supported by maeparser. The mol will not be written to the output file. +81: [21:37:29] 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.[21:37:29] Warning: molecule is tagged as 3D, but all Z coords are zero and 2D stereo markers have been found, marking the mol as 2D. +81: [21:37:29] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +81: [21:37:29] Warning: molecule is tagged as 3D, but all Z coords are zero and 2D stereo markers have been found, marking the mol as 2D. +81: [21:37:29] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +84: Randomness seeded to: 295738978 +84: [21:37:29] Invalid or missing fragment id from CDXML fragment, assigning new one... +84: [21:37:29] Explicit valence for atom # 3 N, 4, is greater than permitted +84: [21:37:29] CDXMLParser: failed sanitizing skipping fragment 32 +84: [21:37:29] Bad bond in CDXML skipping fragment 58... +84: [21:37:29] Invalid or missing fragment id from CDXML fragment, assigning new one... +84: [21:37:29] Bad bond in CDXML skipping fragment 58... +12: .................. +12: ---------------------------------------------------------------------- +12: Ran 18 tests in 2.742s +12: +12: OK +85: Randomness seeded to: 528037862 +85: [21:37:29] Warning: ambiguous stereochemistry - opposing bonds have opposite wedging - at atom 2 ignored. +85: [21:37:29] Warning: ambiguous stereochemistry - opposing bonds have opposite wedging - at atom 2 ignored. +85: [21:37:29] Warning: ambiguous stereochemistry - opposing bonds have opposite wedging - at atom 2 ignored. +85: [21:37:29] Warning: ambiguous stereochemistry - opposing bonds have opposite wedging - at atom 2 ignored. +85: =============================================================================== +85: All tests passed (142 assertions in 6 test cases) +85: + 74/236 Test #85: molfileStereoCatchTest ................. Passed 0.08 sec +test 86 + Start 86: connectTheDotsTest + +86: Test command: /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/connectTheDotsTest +86: Working Directory: /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers +86: Test timeout computed to be: 1500 +84: [21:37:29] WARNING: not removing hydrogen atom without neighbors +84: [21:37:29] WARNING: not removing hydrogen atom without neighbors +84: [21:37:29] WARNING: not removing hydrogen atom without neighbors +84: [21:37:29] WARNING: not removing hydrogen atom without neighbors +84: [21:37:29] WARNING: not removing hydrogen atom without neighbors +84: [21:37:29] WARNING: not removing hydrogen atom without neighbors +84: [21:37:29] WARNING: not removing hydrogen atom without neighbors +84: [21:37:29] WARNING: not removing hydrogen atom without neighbors +84: [21:37:29] WARNING: not removing hydrogen atom without neighbors +84: [21:37:29] WARNING: not removing hydrogen atom without neighbors +84: [21:37:29] CDXMLParser: Schema 80180 step 80181 ReactionStepAgents reaction fragment 64603 not found in document. +86: Randomness seeded to: 2901318562 86: =============================================================================== 86: All tests passed (8 assertions in 1 test case) 86: - 75/236 Test #86: connectTheDotsTest ..................... Passed 0.03 sec + 75/236 Test #86: connectTheDotsTest ..................... Passed 0.05 sec test 87 Start 87: v2MolSuppliers 87: Test command: /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/v2MolSuppliers 87: Working Directory: /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers 87: Test timeout computed to be: 1500 -84: [12:42:36] Incomplete atom labelling, cannot make bond -81: [12:42:36] ERROR: molecules without atoms cannot be exported to Maestro files. -81: [12:42:36] Can't kekulize mol. Unkekulized atoms: 0 1 2 3 4 -81: [12:42:36] ERROR: the mol cannot be kekulized, and will not be written to the output file. -81: [12:42:36] ERROR: Bond 0 has a type that is not supported by maeparser. The mol will not be written to the output file. -81: [12:42:36] WARNING: atom 1 in input Maestro file has atomic number '0', which is reserved for internal use, and not allowed in inputs. The atom will be ignored.[12:42:36] Warning: molecule is tagged as 3D, but all Z coords are zero and 2D stereo markers have been found, marking the mol as 2D. -81: [12:42:36] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -81: [12:42:36] Warning: molecule is tagged as 3D, but all Z coords are zero and 2D stereo markers have been found, marking the mol as 2D. -81: [12:42:36] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -84: [12:42:36] Failed to parse XML fragment 5 node: n attribute: id: mydoghasfleas -84: [12:42:36] Failed to parse XML fragment 5 node: n attribute: id: mydoghasfleas -84: [12:42:36] Failed to parse XML fragment 5 node: b attribute: Order: slartibartfast -84: [12:42:36] Failed to parse XML fragment 5 node: b attribute: Order: 5 -84: [12:42:36] Invalid or missing fragment id from CDXML fragment, assigning new one... -87: Randomness seeded to: 1779316308 +84: [21:37:29] Incomplete atom labelling, cannot make bond +70: [21:37:29] SMARTS Parse Error: syntax error while parsing: MyDogHasFleas +70: [21:37:29] SMARTS Parse Error: Failed parsing SMARTS 'MyDogHasFleas' for input: 'MyDogHasFleas' +84: [21:37:29] Incomplete atom labelling, cannot make bond +84: [21:37:29] Incomplete atom labelling, cannot make bond +87: Randomness seeded to: 442388562 87: =============================================================================== 87: All tests passed (12 assertions in 5 test cases) 87: -84: =============================================================================== -84: All tests passed (263 assertions in 7 test cases) -84: - 76/236 Test #87: v2MolSuppliers ......................... Passed 0.02 sec + 76/236 Test #87: v2MolSuppliers ......................... Passed 0.04 sec test 88 Start 88: v2FileParsersCatchTest 88: Test command: /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/v2FileParsersCatchTest 88: Working Directory: /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers 88: Test timeout computed to be: 1500 - 77/236 Test #84: cdxmlParserCatchTest ................... Passed 0.09 sec +84: [21:37:30] Failed to parse XML fragment 5 node: n attribute: id: mydoghasfleas +84: [21:37:30] Failed to parse XML fragment 5 node: n attribute: id: mydoghasfleas +84: [21:37:30] Failed to parse XML fragment 5 node: b attribute: Order: slartibartfast +84: [21:37:30] Failed to parse XML fragment 5 node: b attribute: Order: 5 +84: [21:37:30] Invalid or missing fragment id from CDXML fragment, assigning new one... +70: [21:37:30] Empty atom list: 'M ALS 1 0 F' on line 8. +70: de_DE.UTF-8 +70: [21:37:30] ------------------------------------- +70: [21:37:30] Test multithreading Locale Switching +84: =============================================================================== +84: All tests passed (263 assertions in 7 test cases) +84: + 77/236 Test #84: cdxmlParserCatchTest ................... Passed 0.21 sec test 89 Start 89: multithreadedSupplierCatchTest 89: Test command: /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/multithreadedSupplierCatchTest 89: Working Directory: /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers 89: Test timeout computed to be: 1500 -88: Randomness seeded to: 4158994317 -88: =============================================================================== -88: All tests passed (6 assertions in 1 test case) -88: - 78/236 Test #88: v2FileParsersCatchTest ................. Passed 0.02 sec + 78/236 Test #12: pyBV ................................... Passed 3.16 sec test 90 Start 90: testSubstructMatch 90: Test command: /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/GraphMol/Substruct/testSubstructMatch 90: Working Directory: /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/GraphMol/Substruct 90: Test timeout computed to be: 1500 +88: Randomness seeded to: 949255798 +88: =============================================================================== +88: All tests passed (6 assertions in 1 test case) +88: + 79/236 Test #88: v2FileParsersCatchTest ................. Passed 0.06 sec +test 91 + Start 91: substructTestCatch + +91: Test command: /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/GraphMol/Substruct/substructTestCatch +91: Working Directory: /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/GraphMol/Substruct +91: Test timeout computed to be: 1500 +70: [21:37:30] Test multithreading (Done) +70: [21:37:30] ------------------------------------- +70: *************************************** +70: *************************************** 90: ----------------- Test 1 90: Done 90: @@ -22246,21 +22299,27 @@ 90: ----------------- Testing serial numbers on recursive queries 90: Done 90: -90: [12:42:36] ------------------------------------- -90: [12:42:36] Test multithreading +90: [21:37:30] ------------------------------------- +90: [21:37:30] Test multithreading 90: reading molecules +70: [21:37:30] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +70: [21:37:30] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +70: [21:37:30] bond with order 0 found on line 7. This is not part of the MDL specification. +70: [21:37:30] Skipping unrecognized collection type at line 26: MDLV30/HILITE BONDS=(1 7) +70: [21:37:30] Skipping unrecognized collection type at line 27: MDLV30/HILITE ATOMS=(1 7) +70: [21:37:30] 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 -70: [12:42:36] SMARTS Parse Error: syntax error while parsing: MyDogHasFleas -70: [12:42:36] SMARTS Parse Error: Failed parsing SMARTS 'MyDogHasFleas' for input: 'MyDogHasFleas' -70: [12:42:36] Empty atom list: 'M ALS 1 0 F' on line 8. -70: de_DE.UTF-8 -70: [12:42:36] ------------------------------------- -70: [12:42:36] Test multithreading Locale Switching +70: generating smiles +70: 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 +70: converting back +70: check isomorphism +41: [21:37:30] done: 500000 +41: [21:37:30] Done 90: done 90: hits2: 1111110111111111111111011111100011011011111101010111011110111101111111111111111111111011111011111110 90: processing2 @@ -22268,6 +22327,29 @@ 90: launch2 :1 90: launch2 :2 90: launch2 :3 +91: Randomness seeded to: 3714999341 +91: m1 +91: m2 +91: m3 +91: =============================================================================== +91: All tests passed (226 assertions in 10 test cases) +91: +41: [21:37:30] Testing hanoi with a functor. + 80/236 Test #91: substructTestCatch ..................... Passed 0.22 sec +test 92 + Start 92: testGenericGroups + +92: Test command: /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/GraphMol/GenericGroups/testGenericGroups +92: Working Directory: /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/GraphMol/GenericGroups +92: Test timeout computed to be: 1500 +41: [21:37:30] Done +41: [21:37:30] Testing basic partition refinement. +41: [21:37:30] Done +41: [21:37:30] Testing partition refinement with neighbors. +41: [21:37:30] Done +41: [21:37:30] testing canonicalization via tie breaking. +41: [21:37:30] Done +41: [21:37:30] testing canonicalization using the wrapper. 90: done 90: preprocessing 3 90: hits3: 1110100011001000010011100110100011011000010101000100110010101111011100101000001111110000010100100110 @@ -22276,72 +22358,45 @@ 90: launch3 :1 90: launch3 :2 90: launch3 :3 +41: [21:37:30] Done +41: [21:37:30] testing some specific ordering problems +41: [21:37:30] Finished +41: [21:37:30] testing chiral invariants. +41: [21:37:30] Finished +41: [21:37:30] testing unique ranks in w.r.t. renumbering. +41: [21:37:30] Finished +41: [21:37:30] testing mol fragments. +41: [21:37:30] Finished +41: [21:37:30] testing protein round-tripping. 90: done -90: [12:42:36] done -90: [12:42:36] ------------------------------------- -90: [12:42:36] Test GitHub issue 15 -90: [12:42:36] done -90: [12:42:36] ------------------------------------- -90: [12:42:36] Test GitHub issue 409 -90: [12:42:36] done -90: [12:42:36] ------------------------------------- -90: [12:42:36] Test chiral matching -89: Randomness seeded to: 203834680 -89: [12:42:36] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -90: [12:42:36] done -90: [12:42:36] ------------------------------------- -90: [12:42:36] Test GitHub issue 688: partially specified chiral substructure queries don't work properly -89: [12:42:36] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [12:42:36] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [12:42:36] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [12:42:36] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [12:42:36] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [12:42:36] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -90: [12:42:36] done -90: [12:42:36] ------------------------------------- -90: [12:42:36] Test dative-bond matching -90: [12:42:36] done -90: [12:42:36] ------------------------------------- -90: [12:42:36] Test cis/trans matching -89: [12:42:36] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [12:42:36] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [12:42:36] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [12:42:36] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [12:42:36] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [12:42:36] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [12:42:36] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -90: [12:42:36] done -90: [12:42:36] ------------------------------------- -90: [12:42:36] Test cis/trans matching part 2 -90: [12:42:36] done -90: [12:42:36] ------------------------------------- -90: [12:42:36] Testing Github #1389: Substructure matching with chirality failure when query is built from SMARTS -90: [12:42:36] done -70: [12:42:36] Test multithreading (Done) -70: [12:42:36] ------------------------------------- -89: [12:42:36] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [12:42:36] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [12:42:36] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [12:42:36] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [12:42:36] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [12:42:36] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [12:42:36] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [12:42:36] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [12:42:36] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [12:42:36] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [12:42:36] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [12:42:36] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [12:42:36] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [12:42:36] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -90: [12:42:36] ------------------------------------- -90: [12:42:36] Testing matching E/Z against Cis/Trans stereo bonds -89: [12:42:36] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [12:42:36] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [12:42:36] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [12:42:36] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [12:42:36] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [12:42:36] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -90: [12:42:36] +90: [21:37:30] done +90: [21:37:30] ------------------------------------- +90: [21:37:30] Test GitHub issue 15 +90: [21:37:30] done +90: [21:37:30] ------------------------------------- +90: [21:37:30] Test GitHub issue 409 +90: [21:37:30] done +90: [21:37:30] ------------------------------------- +90: [21:37:30] Test chiral matching +90: [21:37:30] done +90: [21:37:30] ------------------------------------- +90: [21:37:30] Test GitHub issue 688: partially specified chiral substructure queries don't work properly +90: [21:37:30] done +90: [21:37:30] ------------------------------------- +90: [21:37:30] Test dative-bond matching +90: [21:37:30] done +90: [21:37:30] ------------------------------------- +90: [21:37:30] Test cis/trans matching +90: [21:37:30] done +90: [21:37:30] ------------------------------------- +90: [21:37:30] Test cis/trans matching part 2 +90: [21:37:30] done +90: [21:37:30] ------------------------------------- +90: [21:37:30] Testing Github #1389: Substructure matching with chirality failure when query is built from SMARTS +90: [21:37:30] done +90: [21:37:30] ------------------------------------- +90: [21:37:30] Testing matching E/Z against Cis/Trans stereo bonds +90: [21:37:30] 90: 90: **** 90: Pre-condition Violation @@ -22354,24 +22409,17 @@ 90: 1# Invar::operator<<(std::ostream&, Invar::Invariant const&) in /build/reproducible-path/rdkit-202409.4/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-202409.4/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-202409.4/obj-aarch64-linux-gnu//lib/libRDKitSubstructMatch.so.1 -90: 4# 0x0000AAAADB70AB30 in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/GraphMol/Substruct/testSubstructMatch -90: 5# 0x0000AAAADB6F9728 in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/GraphMol/Substruct/testSubstructMatch -90: 6# 0x0000FFFF9B95229C in /lib/aarch64-linux-gnu/libc.so.6 +90: 4# 0x0000AAAAE357AB30 in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/GraphMol/Substruct/testSubstructMatch +90: 5# 0x0000AAAAE3569728 in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/GraphMol/Substruct/testSubstructMatch +90: 6# 0x0000FFFF9C04229C in /lib/aarch64-linux-gnu/libc.so.6 90: 7# __libc_start_main in /lib/aarch64-linux-gnu/libc.so.6 -90: 8# 0x0000AAAADB6F9930 in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/GraphMol/Substruct/testSubstructMatch +90: 8# 0x0000AAAAE3569930 in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/GraphMol/Substruct/testSubstructMatch 90: ---------- 90: **** 90: -90: [12:42:36] +90: [21:37:30] 90: 90: **** -89: [12:42:36] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [12:42:36] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [12:42:36] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [12:42:36] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [12:42:36] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [12:42:36] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [12:42:36] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. 90: Pre-condition Violation 90: matches must not be empty 90: Violation occurred on line 44 in file ./Code/GraphMol/Substruct/SubstructUtils.cpp @@ -22382,445 +22430,496 @@ 90: 1# Invar::operator<<(std::ostream&, Invar::Invariant const&) in /build/reproducible-path/rdkit-202409.4/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-202409.4/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-202409.4/obj-aarch64-linux-gnu//lib/libRDKitSubstructMatch.so.1 -90: 4# 0x0000AAAADB70B180 in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/GraphMol/Substruct/testSubstructMatch -90: 5# 0x0000AAAADB6F9728 in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/GraphMol/Substruct/testSubstructMatch -90: 6# 0x0000FFFF9B95229C in /lib/aarch64-linux-gnu/libc.so.6 +90: 4# 0x0000AAAAE357B180 in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/GraphMol/Substruct/testSubstructMatch +90: 5# 0x0000AAAAE3569728 in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/GraphMol/Substruct/testSubstructMatch +90: 6# 0x0000FFFF9C04229C in /lib/aarch64-linux-gnu/libc.so.6 90: 7# __libc_start_main in /lib/aarch64-linux-gnu/libc.so.6 -90: 8# 0x0000AAAADB6F9930 in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/GraphMol/Substruct/testSubstructMatch +90: 8# 0x0000AAAAE3569930 in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/GraphMol/Substruct/testSubstructMatch 90: ---------- 90: **** 90: -90: [12:42:36] ------------------------------------- -90: [12:42:36] Test substructure matching with a pathological case for symmetric SSSR -90: [12:42:36] ------------------------------------- -90: [12:42:36] Test isAtomTerminalRGroupOrQueryHydrogen -70: *************************************** -70: *************************************** -70: [12:42:36] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -70: [12:42:36] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -89: [12:42:36] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [12:42:36] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [12:42:36] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [12:42:36] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [12:42:36] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. - 79/236 Test #90: testSubstructMatch ..................... Passed 0.17 sec -test 91 - Start 91: substructTestCatch - -91: Test command: /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/GraphMol/Substruct/substructTestCatch -91: Working Directory: /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/GraphMol/Substruct -91: Test timeout computed to be: 1500 -89: [12:42:36] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [12:42:36] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [12:42:36] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [12:42:36] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [12:42:36] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [12:42:36] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [12:42:36] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [12:42:36] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [12:42:36] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [12:42:36] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [12:42:36] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [12:42:36] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [12:42:36] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [12:42:36] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [12:42:36] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [12:42:36] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [12:42:36] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [12:42:36] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [12:42:36] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [12:42:36] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [12:42:36] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [12:42:36] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [12:42:36] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [12:42:36] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [12:42:36] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [12:42:36] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [12:42:36] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [12:42:36] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [12:42:36] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [12:42:36] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [12:42:36] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [12:42:36] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [12:42:36] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [12:42:36] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [12:42:36] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [12:42:36] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [12:42:36] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [12:42:36] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [12:42:36] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [12:42:36] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [12:42:36] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [12:42:36] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [12:42:36] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [12:42:36] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [12:42:36] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [12:42:36] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [12:42:36] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -70: [12:42:36] bond with order 0 found on line 7. This is not part of the MDL specification. -89: [12:42:36] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [12:42:36] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [12:42:36] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [12:42:36] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [12:42:36] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [12:42:36] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [12:42:36] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [12:42:36] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [12:42:36] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [12:42:36] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [12:42:36] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [12:42:36] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [12:42:36] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [12:42:36] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [12:42:36] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [12:42:36] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [12:42:36] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [12:42:36] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [12:42:36] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [12:42:36] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [12:42:36] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [12:42:36] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [12:42:36] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [12:42:36] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [12:42:36] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [12:42:36] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [12:42:36] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [12:42:36] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [12:42:36] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [12:42:36] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [12:42:36] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [12:42:36] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [12:42:36] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [12:42:36] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [12:42:36] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [12:42:36] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [12:42:36] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [12:42:36] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [12:42:36] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -70: [12:42:36] Skipping unrecognized collection type at line 26: MDLV30/HILITE BONDS=(1 7) -70: [12:42:36] Skipping unrecognized collection type at line 27: MDLV30/HILITE ATOMS=(1 7) -70: [12:42:36] 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: [12:42:36] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [12:42:36] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [12:42:36] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [12:42:36] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [12:42:36] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [12:42:36] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [12:42:36] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [12:42:36] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [12:42:36] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [12:42:36] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [12:42:36] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [12:42:36] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [12:42:36] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [12:42:36] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [12:42:36] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [12:42:36] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [12:42:36] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [12:42:36] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [12:42:36] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [12:42:36] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [12:42:36] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [12:42:36] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [12:42:36] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [12:42:36] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -70: generating smiles -70: 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 -70: converting back -89: [12:42:36] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [12:42:36] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [12:42:36] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [12:42:36] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [12:42:36] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [12:42:36] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [12:42:36] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [12:42:36] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [12:42:36] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [12:42:36] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [12:42:36] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [12:42:36] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [12:42:36] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [12:42:36] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [12:42:36] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [12:42:36] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [12:42:36] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [12:42:36] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [12:42:36] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [12:42:36] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [12:42:36] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [12:42:36] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [12:42:36] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [12:42:36] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [12:42:36] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [12:42:36] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [12:42:36] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [12:42:36] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [12:42:36] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [12:42:36] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [12:42:36] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [12:42:36] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [12:42:36] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [12:42:36] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [12:42:36] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -70: check isomorphism -89: [12:42:36] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [12:42:36] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [12:42:36] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [12:42:36] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [12:42:36] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [12:42:36] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [12:42:36] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [12:42:36] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [12:42:36] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [12:42:36] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -41: [12:42:36] done: 500000 -41: [12:42:36] Done -41: [12:42:36] Testing hanoi with a functor. -41: [12:42:36] Done -41: [12:42:36] Testing basic partition refinement. -41: [12:42:36] Done -41: [12:42:36] Testing partition refinement with neighbors. -41: [12:42:36] Done -41: [12:42:36] testing canonicalization via tie breaking. -41: [12:42:36] Done -41: [12:42:36] testing canonicalization using the wrapper. -41: [12:42:36] Done -41: [12:42:36] testing some specific ordering problems -41: [12:42:36] Finished -41: [12:42:36] testing chiral invariants. -41: [12:42:36] Finished -41: [12:42:36] testing unique ranks in w.r.t. renumbering. -41: [12:42:36] Finished -41: [12:42:36] testing mol fragments. -41: [12:42:36] Finished -41: [12:42:36] testing protein round-tripping. -91: Randomness seeded to: 2114460451 -91: m1 -91: m2 -91: m3 -91: =============================================================================== -91: All tests passed (226 assertions in 10 test cases) -91: - 80/236 Test #91: substructTestCatch ..................... Passed 0.16 sec -test 92 - Start 92: testGenericGroups - -92: Test command: /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/GraphMol/GenericGroups/testGenericGroups -92: Working Directory: /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/GraphMol/GenericGroups -92: Test timeout computed to be: 1500 -89: [12:42:37] Explicit valence for atom # 9 N, 6, is greater than permitted -12: .................. -12: ---------------------------------------------------------------------- -12: Ran 18 tests in 1.767s -12: -12: OK -89: [12:42:37] Explicit valence for atom # 3 Al, 6, is greater than permitted -41: [12:42:37] Finished -41: [12:42:37] testing stability w.r.t. renumbering. - 81/236 Test #12: pyBV ................................... Passed 2.03 sec +90: [21:37:30] ------------------------------------- +90: [21:37:30] Test substructure matching with a pathological case for symmetric SSSR +90: [21:37:30] ------------------------------------- +90: [21:37:30] Test isAtomTerminalRGroupOrQueryHydrogen + 81/236 Test #90: testSubstructMatch ..................... Passed 0.39 sec test 93 Start 93: testReaction 93: Test command: /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/GraphMol/ChemReactions/testReaction 93: Working Directory: /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/GraphMol/ChemReactions 93: Test timeout computed to be: 1500 -89: [12:42:37] Explicit valence for atom # 4 Al, 6, is greater than permitted -41: [12:42:37] Finished -41: [12:42:37] testing smiles round-tripping. 93: smi: O=C1CNC(=O)CN1 93: 1: O=C1CNC(=O)CN1 93: 2: COOC -93: [12:42:37] SMARTS Parse Error: syntax error while parsing: [Q:1][C:2][C:3](=[O:4])[O:5] -93: [12:42:37] 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: [21:37:30] SMARTS Parse Error: syntax error while parsing: [Q:1][C:2][C:3](=[O:4])[O:5] +93: [21:37:30] 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 -92: Randomness seeded to: 838647218 -92: =============================================================================== -92: All tests passed (11480 assertions in 38 test cases) -92: - 82/236 Test #92: testGenericGroups ...................... Passed 0.23 sec -93: [12:42:37] product atom-mapping number 1 found multiple times. -93: [12:42:37] mapped atoms in the reactants were not mapped in the products. +93: [21:37:30] product atom-mapping number 1 found multiple times. +93: [21:37:30] mapped atoms in the reactants were not mapped in the products. 93: unmapped numbers are: 4 -test 94 - Start 94: testReactionFingerprints - -94: Test command: /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/GraphMol/ChemReactions/testReactionFingerprints -94: Working Directory: /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/GraphMol/ChemReactions -94: Test timeout computed to be: 1500 -93: [12:42:37] atom 0 in product 0 has multiple charge specifications. +93: [21:37:30] atom 0 in product 0 has multiple charge specifications. 93: mass: 15.0001 -89: [12:42:37] Explicit valence for atom # 10 Si, 6, is greater than permitted 93: Oc1ccccn1 93: Oc1ccc[nH]1 -93: [12:42:37] SMARTS Parse Error: syntax error while parsing: ([C:1](=O)O.[C:2] -93: [12:42:37] SMARTS Parse Error: Failed parsing SMARTS '([C:1](=O)O.[C:2]' for input: '([C:1](=O)O.[C:2]' -93: [12:42:37] SMARTS Parse Error: syntax error while parsing: ([C:2] -93: [12:42:37] SMARTS Parse Error: Failed parsing SMARTS '([C:2]' for input: '([C:2]' -93: [12:42:37] SMARTS Parse Error: syntax error while parsing: [C:1](=O)O).[C:2] -93: [12:42:37] SMARTS Parse Error: Failed parsing SMARTS '[C:1](=O)O).[C:2]' for input: '[C:1](=O)O).[C:2]' -93: [12:42:37] SMARTS Parse Error: syntax error while parsing: [C:2]) -93: [12:42:37] SMARTS Parse Error: Failed parsing SMARTS '[C:2])' for input: '[C:2])' -93: [12:42:37] SMILES Parse Error: syntax error while parsing: [Q:1][C:2][C:3](=[O:4])[O:5] -93: [12:42:37] SMILES Parse Error: check for mistakes around position 2: -93: [12:42:37] [Q:1][C:2][C:3](=[O:4])[O:5] -93: [12:42:37] ~^ -93: [12:42:37] SMILES Parse Error: Failed parsing SMILES '[Q:1][C:2][C:3](=[O:4])[O:5]' for input: '[Q:1][C:2][C:3](=[O:4])[O:5]' -93: [12:42:37] reactant 2 has no mapped atoms. -93: [12:42:37] >> Atoms within one molecule have different RXN roles. -93: [12:42:37] >> Fragment 0 not included in the reaction, atoms do not have a correct RXN role. -94: [12:42:37] ------------------------------------- -94: [12:42:37] Test Reaction StructuralFingerprint -93: [12:42:37] SMARTS Parse Error: syntax error while parsing: ([C:1][C:2] -93: [12:42:37] SMARTS Parse Error: Failed parsing SMARTS '([C:1][C:2]' for input: '([C:1][C:2]' -93: [12:42:37] SMARTS Parse Error: syntax error while parsing: ([C:2] -93: [12:42:37] SMARTS Parse Error: Failed parsing SMARTS '([C:2]' for input: '([C:2]' -93: [12:42:37] SMARTS Parse Error: syntax error while parsing: [C:1][C:2]) -93: [12:42:37] SMARTS Parse Error: Failed parsing SMARTS '[C:1][C:2])' for input: '[C:1][C:2])' -93: [12:42:37] SMARTS Parse Error: syntax error while parsing: [C:1]).[C:2] -93: [12:42:37] SMARTS Parse Error: Failed parsing SMARTS '[C:1]).[C:2]' for input: '[C:1]).[C:2]' -93: [12:42:37] reactant 0 has no mapped atoms. -93: [12:42:37] reactant 1 has no mapped atoms. -93: [12:42:37] reactant 3 has no mapped atoms. -93: [12:42:37] product atom-mapping number 2 found multiple times. -93: [12:42:37] product atom-mapping number 3 found multiple times. -93: [12:42:37] product atom-mapping number 4 found multiple times. -93: [12:42:37] product atom-mapping number 5 found multiple times. -93: [12:42:37] product atom-mapping number 6 found multiple times. -93: [12:42:37] product atom-mapping number 7 found multiple times. -93: [12:42:37] product atom-mapping number 8 found multiple times. -93: [12:42:37] product atom-mapping number 12 found multiple times. -93: [12:42:37] product atom-mapping number 9 found multiple times. -93: [12:42:37] product atom-mapping number 10 found multiple times. -93: [12:42:37] product atom-mapping number 11 found multiple times. -93: [12:42:37] reactant 0 has no mapped atoms. -93: [12:42:37] reactant 1 has no mapped atoms. -93: [12:42:37] reactant 3 has no mapped atoms. -93: [12:42:37] reactant atom-mapping number 19 found multiple times. -93: [12:42:37] reactant atom-mapping number 25 found multiple times. -93: [12:42:37] reactant atom-mapping number 20 found multiple times. -93: [12:42:37] reactant atom-mapping number 21 found multiple times. -93: [12:42:37] reactant atom-mapping number 22 found multiple times. -93: [12:42:37] reactant atom-mapping number 23 found multiple times. -93: [12:42:37] reactant atom-mapping number 24 found multiple times. -93: [12:42:37] product atom-mapping number 1 found multiple times. -93: [12:42:37] product atom-mapping number 1 found multiple times. -93: [12:42:37] product atom-mapping number 1 found multiple times. -93: [12:42:37] product atom-mapping number 1 found multiple times. -93: [12:42:37] product atom-mapping number 2 found multiple times. -93: [12:42:37] product atom-mapping number 1 found multiple times. -93: [12:42:37] product atom-mapping number 2 found multiple times. -93: [12:42:37] product atom-mapping number 1 found multiple times. -93: [12:42:37] product atom-mapping number 2 found multiple times. -93: [12:42:37] product atom-mapping number 1 found multiple times. -93: [12:42:37] product atom-mapping number 2 found multiple times. -93: [12:42:37] product atom-mapping number 1 found multiple times. +93: [21:37:30] SMARTS Parse Error: syntax error while parsing: ([C:1](=O)O.[C:2] +93: [21:37:30] SMARTS Parse Error: Failed parsing SMARTS '([C:1](=O)O.[C:2]' for input: '([C:1](=O)O.[C:2]' +93: [21:37:30] SMARTS Parse Error: syntax error while parsing: ([C:2] +93: [21:37:30] SMARTS Parse Error: Failed parsing SMARTS '([C:2]' for input: '([C:2]' +93: [21:37:30] SMARTS Parse Error: syntax error while parsing: [C:1](=O)O).[C:2] +93: [21:37:30] SMARTS Parse Error: Failed parsing SMARTS '[C:1](=O)O).[C:2]' for input: '[C:1](=O)O).[C:2]' +93: [21:37:30] SMARTS Parse Error: syntax error while parsing: [C:2]) +93: [21:37:30] SMARTS Parse Error: Failed parsing SMARTS '[C:2])' for input: '[C:2])' +93: [21:37:30] SMILES Parse Error: syntax error while parsing: [Q:1][C:2][C:3](=[O:4])[O:5] +93: [21:37:30] SMILES Parse Error: check for mistakes around position 2: +93: [21:37:30] [Q:1][C:2][C:3](=[O:4])[O:5] +93: [21:37:30] ~^ +93: [21:37:30] 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: [21:37:30] reactant 2 has no mapped atoms. +93: [21:37:30] >> Atoms within one molecule have different RXN roles. +93: [21:37:30] >> Fragment 0 not included in the reaction, atoms do not have a correct RXN role. +93: [21:37:30] SMARTS Parse Error: syntax error while parsing: ([C:1][C:2] +93: [21:37:30] SMARTS Parse Error: Failed parsing SMARTS '([C:1][C:2]' for input: '([C:1][C:2]' +93: [21:37:30] SMARTS Parse Error: syntax error while parsing: ([C:2] +93: [21:37:30] SMARTS Parse Error: Failed parsing SMARTS '([C:2]' for input: '([C:2]' +93: [21:37:30] SMARTS Parse Error: syntax error while parsing: [C:1][C:2]) +93: [21:37:30] SMARTS Parse Error: Failed parsing SMARTS '[C:1][C:2])' for input: '[C:1][C:2])' +93: [21:37:30] SMARTS Parse Error: syntax error while parsing: [C:1]).[C:2] +93: [21:37:30] SMARTS Parse Error: Failed parsing SMARTS '[C:1]).[C:2]' for input: '[C:1]).[C:2]' +93: [21:37:30] reactant 0 has no mapped atoms. +93: [21:37:30] reactant 1 has no mapped atoms. +93: [21:37:30] reactant 3 has no mapped atoms. +93: [21:37:30] product atom-mapping number 2 found multiple times. +93: [21:37:30] product atom-mapping number 3 found multiple times. +93: [21:37:30] product atom-mapping number 4 found multiple times. +93: [21:37:30] product atom-mapping number 5 found multiple times. +93: [21:37:30] product atom-mapping number 6 found multiple times. +93: [21:37:30] product atom-mapping number 7 found multiple times. +93: [21:37:30] product atom-mapping number 8 found multiple times. +93: [21:37:30] product atom-mapping number 12 found multiple times. +93: [21:37:30] product atom-mapping number 9 found multiple times. +93: [21:37:30] product atom-mapping number 10 found multiple times. +93: [21:37:30] product atom-mapping number 11 found multiple times. +93: [21:37:30] reactant 0 has no mapped atoms. +93: [21:37:30] reactant 1 has no mapped atoms. +93: [21:37:30] reactant 3 has no mapped atoms. +93: [21:37:30] reactant atom-mapping number 19 found multiple times. +93: [21:37:30] reactant atom-mapping number 25 found multiple times. +93: [21:37:30] reactant atom-mapping number 20 found multiple times. +93: [21:37:30] reactant atom-mapping number 21 found multiple times. +93: [21:37:30] reactant atom-mapping number 22 found multiple times. +93: [21:37:30] reactant atom-mapping number 23 found multiple times. +93: [21:37:30] reactant atom-mapping number 24 found multiple times. +93: [21:37:30] product atom-mapping number 1 found multiple times. +93: [21:37:30] product atom-mapping number 1 found multiple times. +93: [21:37:30] product atom-mapping number 1 found multiple times. +93: [21:37:30] product atom-mapping number 1 found multiple times. +93: [21:37:30] product atom-mapping number 2 found multiple times. +93: [21:37:30] product atom-mapping number 1 found multiple times. +93: [21:37:30] product atom-mapping number 2 found multiple times. +93: [21:37:30] product atom-mapping number 1 found multiple times. +93: [21:37:30] product atom-mapping number 2 found multiple times. +93: [21:37:30] product atom-mapping number 1 found multiple times. +93: [21:37:30] product atom-mapping number 2 found multiple times. +93: [21:37:30] product atom-mapping number 1 found multiple times. 93: F[C@@](Cl)(Br)ONO[C@](F)(Cl)Br -93: [12:42:37] product atom-mapping number 2 found multiple times. -93: [12:42:37] product atom-mapping number 1 found multiple times. -93: [12:42:37] product atom-mapping number 2 found multiple times. -93: [12:42:37] product atom-mapping number 1 found multiple times. +93: [21:37:30] product atom-mapping number 2 found multiple times. +93: [21:37:30] product atom-mapping number 1 found multiple times. +93: [21:37:30] product atom-mapping number 2 found multiple times. +93: [21:37:30] product atom-mapping number 1 found multiple times. 93: F[C@](Cl)(Br)ONO[C@](F)(Cl)Br -93: [12:42:37] product atom-mapping number 5 found multiple times. -93: [12:42:37] product atom-mapping number 2 found multiple times. -93: [12:42:37] product atom-mapping number 3 found multiple times. -93: [12:42:37] product atom-mapping number 1 found multiple times. -93: [12:42:37] product atom-mapping number 4 found multiple times. -93: [12:42:37] product atom-mapping number 5 found multiple times. -93: [12:42:37] product atom-mapping number 2 found multiple times. -93: [12:42:37] product atom-mapping number 3 found multiple times. -93: [12:42:37] product atom-mapping number 1 found multiple times. -93: [12:42:37] product atom-mapping number 4 found multiple times. +93: [21:37:30] product atom-mapping number 5 found multiple times. +93: [21:37:30] product atom-mapping number 2 found multiple times. +93: [21:37:30] product atom-mapping number 3 found multiple times. +93: [21:37:30] product atom-mapping number 1 found multiple times. +93: [21:37:30] product atom-mapping number 4 found multiple times. +93: [21:37:30] product atom-mapping number 5 found multiple times. +93: [21:37:30] product atom-mapping number 2 found multiple times. +93: [21:37:30] product atom-mapping number 3 found multiple times. +93: [21:37:30] product atom-mapping number 1 found multiple times. +93: [21:37:30] product atom-mapping number 4 found multiple times. 93: F[C@@](Cl)(Br)ONO[C@](F)(Cl)Br -93: [12:42:37] product atom-mapping number 5 found multiple times. -93: [12:42:37] product atom-mapping number 2 found multiple times. -93: [12:42:37] product atom-mapping number 3 found multiple times. -93: [12:42:37] product atom-mapping number 1 found multiple times. -93: [12:42:37] product atom-mapping number 4 found multiple times. -93: [12:42:37] product atom-mapping number 5 found multiple times. -93: [12:42:37] product atom-mapping number 2 found multiple times. -93: [12:42:37] product atom-mapping number 3 found multiple times. -93: [12:42:37] product atom-mapping number 1 found multiple times. -93: [12:42:37] product atom-mapping number 4 found multiple times. +93: [21:37:30] product atom-mapping number 5 found multiple times. +93: [21:37:30] product atom-mapping number 2 found multiple times. +93: [21:37:30] product atom-mapping number 3 found multiple times. +93: [21:37:30] product atom-mapping number 1 found multiple times. +93: [21:37:30] product atom-mapping number 4 found multiple times. +93: [21:37:30] product atom-mapping number 5 found multiple times. +93: [21:37:30] product atom-mapping number 2 found multiple times. +93: [21:37:30] product atom-mapping number 3 found multiple times. +93: [21:37:30] product atom-mapping number 1 found multiple times. +93: [21:37:30] product atom-mapping number 4 found multiple times. 93: F[C@](Cl)(Br)ONO[C@](F)(Cl)Br -93: [12:42:37] product atom-mapping number 2 found multiple times. -93: [12:42:37] product atom-mapping number 3 found multiple times. -93: [12:42:37] product atom-mapping number 1 found multiple times. -93: [12:42:37] product atom-mapping number 4 found multiple times. -93: [12:42:37] product atom-mapping number 2 found multiple times. -93: [12:42:37] product atom-mapping number 3 found multiple times. -93: [12:42:37] product atom-mapping number 1 found multiple times. -93: [12:42:37] product atom-mapping number 4 found multiple times. +93: [21:37:30] product atom-mapping number 2 found multiple times. +93: [21:37:30] product atom-mapping number 3 found multiple times. +93: [21:37:30] product atom-mapping number 1 found multiple times. +93: [21:37:30] product atom-mapping number 4 found multiple times. +93: [21:37:30] product atom-mapping number 2 found multiple times. +93: [21:37:30] product atom-mapping number 3 found multiple times. +93: [21:37:30] product atom-mapping number 1 found multiple times. +93: [21:37:30] product atom-mapping number 4 found multiple times. 93: F[C@@](Cl)(Br)O[C@](F)(Cl)Br -93: [12:42:37] product atom-mapping number 2 found multiple times. -93: [12:42:37] product atom-mapping number 3 found multiple times. -93: [12:42:37] product atom-mapping number 1 found multiple times. -93: [12:42:37] product atom-mapping number 4 found multiple times. -93: [12:42:37] product atom-mapping number 2 found multiple times. -93: [12:42:37] product atom-mapping number 3 found multiple times. -93: [12:42:37] product atom-mapping number 1 found multiple times. -93: [12:42:37] product atom-mapping number 4 found multiple times. +93: [21:37:30] product atom-mapping number 2 found multiple times. +93: [21:37:30] product atom-mapping number 3 found multiple times. +93: [21:37:30] product atom-mapping number 1 found multiple times. +93: [21:37:30] product atom-mapping number 4 found multiple times. +93: [21:37:30] product atom-mapping number 2 found multiple times. +93: [21:37:30] product atom-mapping number 3 found multiple times. +93: [21:37:30] product atom-mapping number 1 found multiple times. +93: [21:37:30] product atom-mapping number 4 found multiple times. 93: F[C@](Cl)(Br)O[C@](F)(Cl)Br -93: [12:42:37] product atom-mapping number 4 found multiple times. -93: [12:42:37] product atom-mapping number 3 found multiple times. -93: [12:42:37] product atom-mapping number 2 found multiple times. -93: [12:42:37] product atom-mapping number 1 found multiple times. -93: [12:42:37] product atom-mapping number 4 found multiple times. -93: [12:42:37] product atom-mapping number 3 found multiple times. -93: [12:42:37] product atom-mapping number 2 found multiple times. -93: [12:42:37] product atom-mapping number 1 found multiple times. -93: [12:42:37] product atom-mapping number 4 found multiple times. -93: [12:42:37] product atom-mapping number 3 found multiple times. -93: [12:42:37] product atom-mapping number 2 found multiple times. -93: [12:42:37] product atom-mapping number 1 found multiple times. -93: [12:42:37] product atom-mapping number 4 found multiple times. -93: [12:42:37] product atom-mapping number 3 found multiple times. -93: [12:42:37] product atom-mapping number 2 found multiple times. -93: [12:42:37] product atom-mapping number 1 found multiple times. -93: [12:42:37] product atom-mapping number 3 found multiple times. -93: [12:42:37] product atom-mapping number 2 found multiple times. -93: [12:42:37] product atom-mapping number 1 found multiple times. -93: [12:42:37] mapped atoms in the reactants were not mapped in the products. +93: [21:37:30] product atom-mapping number 4 found multiple times. +93: [21:37:30] product atom-mapping number 3 found multiple times. +93: [21:37:30] product atom-mapping number 2 found multiple times. +93: [21:37:30] product atom-mapping number 1 found multiple times. +93: [21:37:30] product atom-mapping number 4 found multiple times. +93: [21:37:30] product atom-mapping number 3 found multiple times. +93: [21:37:30] product atom-mapping number 2 found multiple times. +93: [21:37:30] product atom-mapping number 1 found multiple times. +93: [21:37:30] product atom-mapping number 4 found multiple times. +93: [21:37:30] product atom-mapping number 3 found multiple times. +93: [21:37:30] product atom-mapping number 2 found multiple times. +93: [21:37:30] product atom-mapping number 1 found multiple times. +93: [21:37:30] product atom-mapping number 4 found multiple times. +93: [21:37:30] product atom-mapping number 3 found multiple times. +93: [21:37:30] product atom-mapping number 2 found multiple times. +93: [21:37:30] product atom-mapping number 1 found multiple times. +93: [21:37:30] product atom-mapping number 3 found multiple times. +93: [21:37:30] product atom-mapping number 2 found multiple times. +93: [21:37:30] product atom-mapping number 1 found multiple times. +93: [21:37:30] mapped atoms in the reactants were not mapped in the products. 93: unmapped numbers are: 4 -93: [12:42:37] product atom-mapping number 3 found multiple times. -93: [12:42:37] product atom-mapping number 2 found multiple times. -93: [12:42:37] product atom-mapping number 1 found multiple times. -93: [12:42:37] mapped atoms in the reactants were not mapped in the products. +93: [21:37:30] product atom-mapping number 3 found multiple times. +93: [21:37:30] product atom-mapping number 2 found multiple times. +93: [21:37:30] product atom-mapping number 1 found multiple times. +93: [21:37:30] mapped atoms in the reactants were not mapped in the products. 93: unmapped numbers are: 4 -93: [12:42:37] product atom-mapping number 6 not found in reactants. -93: [12:42:37] product atom-mapping number 7 not found in reactants. -93: [12:42:37] product atom-mapping number 8 not found in reactants. -93: [12:42:37] product atom-mapping number 7 not found in reactants. -93: [12:42:37] product atom-mapping number 8 not found in reactants. -93: [12:42:37] product atom-mapping number 9 not found in reactants. -93: [12:42:37] product atom-mapping number 10 not found in reactants. -93: [12:42:37] mapped atoms in the reactants were not mapped in the products. +93: [21:37:30] product atom-mapping number 6 not found in reactants. +93: [21:37:30] product atom-mapping number 7 not found in reactants. +93: [21:37:30] product atom-mapping number 8 not found in reactants. +93: [21:37:30] product atom-mapping number 7 not found in reactants. +93: [21:37:30] product atom-mapping number 8 not found in reactants. +93: [21:37:30] product atom-mapping number 9 not found in reactants. +93: [21:37:30] product atom-mapping number 10 not found in reactants. +93: [21:37:30] mapped atoms in the reactants were not mapped in the products. 93: unmapped numbers are: 6 -93: [12:42:37] product atom-mapping number 7 not found in reactants. -93: [12:42:37] product atom-mapping number 8 not found in reactants. -93: [12:42:37] product atom-mapping number 9 not found in reactants. -93: [12:42:37] product atom-mapping number 10 not found in reactants. -93: [12:42:37] mapped atoms in the reactants were not mapped in the products. +93: [21:37:30] product atom-mapping number 7 not found in reactants. +93: [21:37:30] product atom-mapping number 8 not found in reactants. +93: [21:37:30] product atom-mapping number 9 not found in reactants. +93: [21:37:30] product atom-mapping number 10 not found in reactants. +93: [21:37:30] mapped atoms in the reactants were not mapped in the products. 93: unmapped numbers are: 6 93: smi1 [C:1][C:2][C:3]([O:4])([N:5])[Cl:6]>>[C:1][C:3]([C:2])([O:4])[N:5].[ClH:6] 93: smi2 [C:1][C:2][C:3]([O:4])([N:5])[Cl:6]>>[C:1][C:3]([C:2])([O:4])[N:5].[ClH:6] -94: [12:42:37] ------------------------------------- -94: [12:42:37] Test Reaction DifferenceFingerprint - 83/236 Test #94: testReactionFingerprints ............... Passed 0.03 sec +93: [21:37:30] mapped atoms in the reactants were not mapped in the products. +93: unmapped numbers are: 7 8 9 10 11 12 13 14 15 16 +93: [21:37:30] product atom-mapping number 17 not found in reactants. +93: [21:37:30] product atom-mapping number 18 not found in reactants. +93: [21:37:30] mapped atoms in the reactants were not mapped in the products. +93: unmapped numbers are: 12 +93: [21:37:30] Reaction has explicit hydrogens, reactants will need explicit hydrogens (addHs) +93: [21:37:30] Reaction has explicit hydrogens, reactants will need explicit hydrogens (addHs) +93: +93: [21:37:30] Mismatched potential rlabels: 1 unmapped reactant dummy atom rlabels,0 unmappped product dummy atom rlabels +93: ------------- +93: CCOc1ccccc1 +41: [21:37:30] Finished +92: Randomness seeded to: 4131509126 +92: =============================================================================== +92: All tests passed (11480 assertions in 38 test cases) +92: + 82/236 Test #92: testGenericGroups ...................... Passed 0.41 sec +41: [21:37:30] testing stability w.r.t. renumbering. +test 94 + Start 94: testReactionFingerprints + +94: Test command: /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/GraphMol/ChemReactions/testReactionFingerprints +94: Working Directory: /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/GraphMol/ChemReactions +94: Test timeout computed to be: 1500 +41: [21:37:30] Finished +41: [21:37:30] testing smiles round-tripping. +94: [21:37:30] ------------------------------------- +94: [21:37:30] Test Reaction StructuralFingerprint +94: [21:37:30] ------------------------------------- +94: [21:37:30] Test Reaction DifferenceFingerprint + 83/236 Test #94: testReactionFingerprints ............... Passed 0.05 sec test 95 Start 95: testEnumeration 95: Test command: /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/GraphMol/ChemReactions/testEnumeration 95: Working Directory: /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/GraphMol/ChemReactions 95: Test timeout computed to be: 1500 -70: [12:42:37] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 1 ignored -70: [12:42:37] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 1 ignored -70: [12:42:37] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 1 ignored -70: [12:42:37] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 1 ignored -93: [12:42:37] 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 -70: [12:42:37] deprecated group abbreviation ignored on line 24 +93: [21:37:30] reactant 0 has no mapped atoms. +93: [21:37:30] product 0 has no mapped atoms. +93: [21:37:30] WARNING: neither stereo atoms nor CIP codes found for double bond. Stereochemistry info will not be propagated to product. + 84/236 Test #93: testReaction ........................... Passed 0.35 sec +test 96 + Start 96: rxnTestCatch + +96: Test command: /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/GraphMol/ChemReactions/rxnTestCatch +96: Working Directory: /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/GraphMol/ChemReactions +96: Test timeout computed to be: 1500 +89: Randomness seeded to: 1809166056 +89: [21:37:30] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [21:37:30] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [21:37:30] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [21:37:30] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [21:37:30] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [21:37:30] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [21:37:30] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [21:37:30] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [21:37:30] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [21:37:30] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [21:37:30] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [21:37:30] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [21:37:30] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [21:37:30] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [21:37:30] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [21:37:30] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [21:37:30] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [21:37:30] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [21:37:30] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [21:37:30] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [21:37:30] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [21:37:30] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [21:37:30] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [21:37:30] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [21:37:30] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [21:37:30] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [21:37:30] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [21:37:30] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [21:37:30] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [21:37:30] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [21:37:30] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [21:37:30] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [21:37:30] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [21:37:30] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [21:37:30] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [21:37:30] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [21:37:30] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [21:37:30] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [21:37:30] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [21:37:30] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [21:37:30] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [21:37:30] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [21:37:30] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [21:37:30] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [21:37:30] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [21:37:30] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [21:37:30] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [21:37:30] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [21:37:30] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [21:37:30] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [21:37:30] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +41: [21:37:30] Finished +41: [21:37:30] testing github #1567: Non-canonical result from MolFragmentToSmiles() +41: [21:37:30] Finished + 85/236 Test #41: hanoiTest .............................. Passed 3.27 sec +89: [21:37:30] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [21:37:30] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [21:37:30] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [21:37:30] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [21:37:30] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [21:37:30] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [21:37:30] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [21:37:30] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [21:37:30] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [21:37:30] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +test 97 + Start 97: pyChemReactions + +97: Test command: /usr/bin/python3 "/build/reproducible-path/rdkit-202409.4/Code/GraphMol/ChemReactions/Wrap/testReactionWrapper.py" +97: Working Directory: /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/GraphMol/ChemReactions/Wrap +97: Test timeout computed to be: 1500 +89: [21:37:30] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [21:37:30] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [21:37:30] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [21:37:30] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [21:37:30] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +96: Randomness seeded to: 3306269141 +96: [21:37:30] atom 0 in product 0 has multiple charge specifications. +96: [21:37:30] Found a SCD/SED line with missing/empty SDT specification at line 34 +96: [21:37:30] Found a SCD/SED line with missing/empty SDT specification at line 36 +96: [21:37:30] Found a SCD/SED line with missing/empty SDT specification at line 38 +96: [21:37:30] Found a SCD/SED line with missing/empty SDT specification at line 40 +96: [21:37:30] Found a SCD/SED line with missing/empty SDT specification at line 42 +96: [21:37:30] Found a SCD/SED line with missing/empty SDT specification at line 87 +96: [21:37:30] Found a SCD/SED line with missing/empty SDT specification at line 89 +96: [21:37:30] Found a SCD/SED line with missing/empty SDT specification at line 91 +96: [21:37:30] Found a SCD/SED line with missing/empty SDT specification at line 93 +96: [21:37:30] Found a SCD/SED line with missing/empty SDT specification at line 95 +96: [21:37:30] mapped atoms in the reactants were not mapped in the products. +96: unmapped numbers are: 2 +96: [21:37:30] mapped atoms in the reactants were not mapped in the products. +96: unmapped numbers are: 2 +96: [21:37:30] SMARTS Parse Error: unclosed ring for input: 'CC1' +96: [21:37:30] SMILES Parse Error: unclosed ring for input: 'CC1' +96: [21:37:30] mapped atoms in the reactants were not mapped in the products. +96: unmapped numbers are: 2 +96: [21:37:30] product atom-mapping number 2 not found in reactants. +89: [21:37:30] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [21:37:30] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [21:37:30] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [21:37:30] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [21:37:30] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +96: [21:37:30] mapped atoms in the reactants were not mapped in the products. +96: unmapped numbers are: 2 +96: [21:37:30] product atom-mapping number 2 not found in reactants. +96: [21:37:30] CX Extensions: Substance group hierarchy is not always preserved. +96: [21:37:30] CX Extensions: Substance group hierarchy is not always preserved. +89: [21:37:30] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [21:37:30] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [21:37:30] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [21:37:30] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [21:37:30] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [21:37:30] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [21:37:30] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [21:37:30] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [21:37:30] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [21:37:30] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [21:37:30] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [21:37:30] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [21:37:30] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [21:37:30] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [21:37:30] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [21:37:30] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [21:37:30] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [21:37:30] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [21:37:30] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [21:37:30] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +96: [21:37:30] reactant 0 has no mapped atoms. +96: [21:37:30] product 0 has no mapped atoms. +96: [21:37:30] Can't kekulize mol. Unkekulized atoms: 0 1 2 3 4 +96: [21:37:30] Can't kekulize mol. Unkekulized atoms: 0 1 2 3 4 +96: [21:37:30] Explicit valence for atom # 1 O, 5, is greater than permitted +89: [21:37:30] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [21:37:30] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [21:37:30] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [21:37:30] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [21:37:30] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +96: =============================================================================== +96: All tests passed (705 assertions in 29 test cases) +96: +89: [21:37:30] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [21:37:30] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [21:37:30] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [21:37:30] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [21:37:30] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. + 86/236 Test #96: rxnTestCatch ........................... Passed 0.07 sec +test 98 + Start 98: pyChemReactionEnumerations + +98: Test command: /usr/bin/python3 "/build/reproducible-path/rdkit-202409.4/Code/GraphMol/ChemReactions/Wrap/testEnumerations.py" +98: Working Directory: /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/GraphMol/ChemReactions/Wrap +98: Test timeout computed to be: 1500 +89: [21:37:30] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [21:37:30] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [21:37:30] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [21:37:30] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [21:37:30] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [21:37:30] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [21:37:30] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [21:37:30] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [21:37:30] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [21:37:30] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [21:37:30] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [21:37:30] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [21:37:30] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [21:37:30] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [21:37:30] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [21:37:30] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [21:37:30] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [21:37:30] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [21:37:30] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [21:37:30] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [21:37:30] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [21:37:30] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [21:37:30] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [21:37:30] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [21:37:30] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [21:37:30] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [21:37:30] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [21:37:30] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [21:37:30] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [21:37:30] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [21:37:30] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [21:37:30] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [21:37:30] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [21:37:30] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [21:37:30] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [21:37:30] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [21:37:30] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [21:37:30] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [21:37:30] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +95: 30000000 30000000 +89: [21:37:30] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [21:37:30] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [21:37:30] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [21:37:30] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [21:37:30] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [21:37:30] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [21:37:30] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [21:37:30] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [21:37:30] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [21:37:30] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [21:37:30] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [21:37:30] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [21:37:30] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [21:37:30] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [21:37:30] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [21:37:30] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [21:37:30] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [21:37:30] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [21:37:30] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [21:37:30] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [21:37:30] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [21:37:30] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [21:37:30] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [21:37:30] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [21:37:30] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [21:37:30] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [21:37:30] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [21:37:30] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [21:37:30] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [21:37:30] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [21:37:30] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [21:37:30] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [21:37:30] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [21:37:30] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [21:37:30] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [21:37:30] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [21:37:30] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [21:37:30] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [21:37:30] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [21:37:30] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [21:37:30] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [21:37:30] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [21:37:30] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [21:37:30] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [21:37:30] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [21:37:30] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [21:37:30] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [21:37:30] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [21:37:30] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [21:37:30] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [21:37:30] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [21:37:30] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [21:37:30] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [21:37:30] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [21:37:30] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [21:37:30] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [21:37:30] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [21:37:30] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [21:37:30] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [21:37:30] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [21:37:30] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +70: [21:37:30] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 1 ignored +70: [21:37:30] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 1 ignored +70: [21:37:30] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 1 ignored +70: [21:37:30] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 1 ignored +70: [21:37:30] deprecated group abbreviation ignored on line 24 70: smiles: [1*]c1c([2*])c([3*])c([4*])c(-c2c([9*])oc3c([8*])c([7*])c([6*])c([5*])c3c2=O)c1[10*] -70: [12:42:37] +70: [21:37:30] 70: 70: **** 70: Post-condition Violation @@ -22832,91 +22931,36 @@ 70: 0# Invar::Invariant::toString[abi:cxx11]() const in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu//lib/libRDKitRDGeneral.so.1 70: 1# Invar::operator<<(std::ostream&, Invar::Invariant const&) in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu//lib/libRDKitRDGeneral.so.1 70: 2# RDKit::PeriodicTable::getAtomicNumber(std::__cxx11::basic_string, std::allocator > const&) const in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu//lib/libRDKitFileParsers.so.1 -70: 3# 0x0000FFFF8EDC7D24 in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu//lib/libRDKitFileParsers.so.1 -70: 4# 0x0000FFFF8EDD5920 in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu//lib/libRDKitFileParsers.so.1 -70: 5# 0x0000FFFF8EDD684C in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu//lib/libRDKitFileParsers.so.1 +70: 3# 0x0000FFFFA6B97D24 in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu//lib/libRDKitFileParsers.so.1 +70: 4# 0x0000FFFFA6BA5920 in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu//lib/libRDKitFileParsers.so.1 +70: 5# 0x0000FFFFA6BA684C in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu//lib/libRDKitFileParsers.so.1 70: 6# RDKit::FileParserUtils::ParseV2000CTAB(std::istream*, unsigned int&, RDKit::RWMol*, RDKit::Conformer*&, bool&, unsigned int&, unsigned int&, bool) in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu//lib/libRDKitFileParsers.so.1 70: 7# RDKit::v2::FileParsers::MolFromMolDataStream(std::istream&, unsigned int&, RDKit::v2::FileParsers::MolFileParserParams const&) in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu//lib/libRDKitFileParsers.so.1 70: 8# RDKit::v2::FileParsers::MolFromMolFile(std::__cxx11::basic_string, std::allocator > const&, RDKit::v2::FileParsers::MolFileParserParams const&) in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu//lib/libRDKitFileParsers.so.1 -70: 9# 0x0000AAAAD6B7F21C in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersTest1 -70: 10# 0x0000AAAAD6BF4524 in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersTest1 -70: 11# 0x0000AAAAD6B656AC in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersTest1 -70: 12# 0x0000FFFF8E49229C in /lib/aarch64-linux-gnu/libc.so.6 +70: 9# 0x0000AAAAB18FF21C in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersTest1 +70: 10# 0x0000AAAAB1974524 in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersTest1 +70: 11# 0x0000AAAAB18E56AC in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersTest1 +70: 12# 0x0000FFFFA626229C in /lib/aarch64-linux-gnu/libc.so.6 70: 13# __libc_start_main in /lib/aarch64-linux-gnu/libc.so.6 -70: 14# 0x0000AAAAD6B65870 in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersTest1 +70: 14# 0x0000AAAAB18E5870 in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersTest1 70: ---------- 70: **** 70: -41: [12:42:37] Finished -41: [12:42:37] testing github #1567: Non-canonical result from MolFragmentToSmiles() -41: [12:42:37] Finished -93: [12:42:37] product atom-mapping number 17 not found in reactants. -93: [12:42:37] product atom-mapping number 18 not found in reactants. -93: [12:42:37] mapped atoms in the reactants were not mapped in the products. -93: unmapped numbers are: 12 - 84/236 Test #41: hanoiTest .............................. Passed 1.81 sec -test 96 - Start 96: rxnTestCatch - -96: Test command: /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/GraphMol/ChemReactions/rxnTestCatch -96: Working Directory: /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/GraphMol/ChemReactions -96: Test timeout computed to be: 1500 -95: 30000000 30000000 -93: [12:42:37] Reaction has explicit hydrogens, reactants will need explicit hydrogens (addHs) -93: [12:42:37] Reaction has explicit hydrogens, reactants will need explicit hydrogens (addHs) -93: -93: [12:42:37] Mismatched potential rlabels: 1 unmapped reactant dummy atom rlabels,0 unmappped product dummy atom rlabels -93: ------------- -93: CCOc1ccccc1 -96: Randomness seeded to: 2113641166 -96: [12:42:37] atom 0 in product 0 has multiple charge specifications. -96: [12:42:37] Found a SCD/SED line with missing/empty SDT specification at line 34 -96: [12:42:37] Found a SCD/SED line with missing/empty SDT specification at line 36 -96: [12:42:37] Found a SCD/SED line with missing/empty SDT specification at line 38 -96: [12:42:37] Found a SCD/SED line with missing/empty SDT specification at line 40 -96: [12:42:37] Found a SCD/SED line with missing/empty SDT specification at line 42 -96: [12:42:37] Found a SCD/SED line with missing/empty SDT specification at line 87 -96: [12:42:37] Found a SCD/SED line with missing/empty SDT specification at line 89 -96: [12:42:37] Found a SCD/SED line with missing/empty SDT specification at line 91 -96: [12:42:37] Found a SCD/SED line with missing/empty SDT specification at line 93 -96: [12:42:37] Found a SCD/SED line with missing/empty SDT specification at line 95 -96: [12:42:37] mapped atoms in the reactants were not mapped in the products. -96: unmapped numbers are: 2 -96: [12:42:37] mapped atoms in the reactants were not mapped in the products. -96: unmapped numbers are: 2 -96: [12:42:37] SMARTS Parse Error: unclosed ring for input: 'CC1' -96: [12:42:37] SMILES Parse Error: unclosed ring for input: 'CC1' -96: [12:42:37] mapped atoms in the reactants were not mapped in the products. -96: unmapped numbers are: 2 -96: [12:42:37] product atom-mapping number 2 not found in reactants. -96: [12:42:37] mapped atoms in the reactants were not mapped in the products. -96: unmapped numbers are: 2 -96: [12:42:37] product atom-mapping number 2 not found in reactants. -96: [12:42:37] CX Extensions: Substance group hierarchy is not always preserved. -96: [12:42:37] CX Extensions: Substance group hierarchy is not always preserved. -96: [12:42:37] reactant 0 has no mapped atoms. -96: [12:42:37] product 0 has no mapped atoms. -96: [12:42:37] Can't kekulize mol. Unkekulized atoms: 0 1 2 3 4 -96: [12:42:37] Can't kekulize mol. Unkekulized atoms: 0 1 2 3 4 -96: [12:42:37] Explicit valence for atom # 1 O, 5, is greater than permitted -70: [12:42:37] 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: [12:42:37] Warning: molecule is tagged as 3D, but all Z coords are zero and 2D stereo markers have been found, marking the mol as 2D. -96: =============================================================================== -96: All tests passed (705 assertions in 29 test cases) -96: - 85/236 Test #96: rxnTestCatch ........................... Passed 0.06 sec -test 97 - Start 97: pyChemReactions +29: Checking against /build/reproducible-path/rdkit-202409.4/Code/ForceField/MMFF/test_data/MMFF94_reference.log... + 87/236 Test #43: resMolSupplierTest ..................... Passed 3.49 sec +test 99 + Start 99: pyChemReactionSanitize -97: Test command: /usr/bin/python3 "/build/reproducible-path/rdkit-202409.4/Code/GraphMol/ChemReactions/Wrap/testReactionWrapper.py" -97: Working Directory: /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/GraphMol/ChemReactions/Wrap -97: Test timeout computed to be: 1500 -89: [12:42:37] Explicit valence for atom # 2 O, 4, is greater than permitted -89: [12:42:37] Explicit valence for atom # 3 Al, 6, is greater than permitted -89: [12:42:37] Explicit valence for atom # 3 Be, 4, is greater than permitted +99: Test command: /usr/bin/python3 "/build/reproducible-path/rdkit-202409.4/Code/GraphMol/ChemReactions/Wrap/testSanitize.py" +99: Working Directory: /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/GraphMol/ChemReactions/Wrap +99: Test timeout computed to be: 1500 +70: [21:37:31] 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: [21:37:31] Warning: molecule is tagged as 3D, but all Z coords are zero and 2D stereo markers have been found, marking the mol as 2D. +29: All 191 tests passed 70: ---------------------------------- 70: ---------------------------------- -70: [12:42:37] +98: [21:37:31] == testCartesianProduct +70: [21:37:31] 70: 70: **** 70: Pre-condition Violation @@ -22928,66 +22972,17 @@ 70: 0# Invar::Invariant::toString[abi:cxx11]() const in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu//lib/libRDKitRDGeneral.so.1 70: 1# Invar::operator<<(std::ostream&, Invar::Invariant const&) in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu//lib/libRDKitRDGeneral.so.1 70: 2# RDKit::setAtomRLabel(RDKit::Atom*, int) in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu//lib/libRDKitGraphMol.so.1 -70: 3# 0x0000AAAAD6B8ECE0 in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersTest1 -70: 4# 0x0000AAAAD6BF4584 in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersTest1 -70: 5# 0x0000AAAAD6B656AC in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersTest1 -70: 6# 0x0000FFFF8E49229C in /lib/aarch64-linux-gnu/libc.so.6 +70: 3# 0x0000AAAAB190ECE0 in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersTest1 +70: 4# 0x0000AAAAB1974584 in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersTest1 +70: 5# 0x0000AAAAB18E56AC in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersTest1 +70: 6# 0x0000FFFFA626229C in /lib/aarch64-linux-gnu/libc.so.6 70: 7# __libc_start_main in /lib/aarch64-linux-gnu/libc.so.6 -70: 8# 0x0000AAAAD6B65870 in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersTest1 +70: 8# 0x0000AAAAB18E5870 in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersTest1 70: ---------- 70: **** 70: -70: [12:42:37] WARNING: could not find number of expected rings. Switching to an approximate ring finding algorithm. -93: [12:42:37] reactant 0 has no mapped atoms. -93: [12:42:37] product 0 has no mapped atoms. -93: [12:42:37] WARNING: neither stereo atoms nor CIP codes found for double bond. Stereochemistry info will not be propagated to product. - 86/236 Test #93: testReaction ........................... Passed 0.21 sec -test 98 - Start 98: pyChemReactionEnumerations - -98: Test command: /usr/bin/python3 "/build/reproducible-path/rdkit-202409.4/Code/GraphMol/ChemReactions/Wrap/testEnumerations.py" -98: Working Directory: /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/GraphMol/ChemReactions/Wrap -98: Test timeout computed to be: 1500 -89: [12:42:37] Explicit valence for atom # 27 P, 6, is greater than permitted - 87/236 Test #43: resMolSupplierTest ..................... Passed 1.99 sec -test 99 - Start 99: pyChemReactionSanitize - -99: Test command: /usr/bin/python3 "/build/reproducible-path/rdkit-202409.4/Code/GraphMol/ChemReactions/Wrap/testSanitize.py" -99: Working Directory: /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/GraphMol/ChemReactions/Wrap -99: Test timeout computed to be: 1500 -29: Checking against /build/reproducible-path/rdkit-202409.4/Code/ForceField/MMFF/test_data/MMFF94_reference.log... -70: [12:42:37] SMARTS Parse Error: syntax error while parsing: MyDogHasFleas -70: [12:42:37] SMARTS Parse Error: Failed parsing SMARTS 'MyDogHasFleas' for input: 'MyDogHasFleas' -29: All 191 tests passed -70: [12:42:37] Empty atom list: 'M ALS 1 0 F' on line 8. - 88/236 Test #70: fileParsersTest1 ....................... Passed 1.54 sec -test 100 - Start 100: testChemTransforms - -100: Test command: /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/GraphMol/ChemTransforms/testChemTransforms -100: Working Directory: /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/GraphMol/ChemTransforms -100: Test timeout computed to be: 1500 -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 -100: [12:42:37] SMARTS Parse Error: syntax error while parsing: bar -100: [12:42:37] SMARTS Parse Error: Failed parsing SMARTS 'bar' for input: 'bar' -29: -29: Computing MMFF94 energies for /build/reproducible-path/rdkit-202409.4/Code/ForceField/MMFF/test_data/MMFF94_dative.smi... - 89/236 Test #100: testChemTransforms ..................... Passed 0.04 sec -test 101 - Start 101: chemTransformsTestCatch - -101: Test command: /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/GraphMol/ChemTransforms/chemTransformsTestCatch -101: Working Directory: /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/GraphMol/ChemTransforms -101: Test timeout computed to be: 1500 -97: ...[12:42:37] +70: [21:37:31] WARNING: could not find number of expected rings. Switching to an approximate ring finding algorithm. +97: ...[21:37:31] 97: 97: **** 97: Pre-condition Violation @@ -23021,7 +23016,7 @@ 97: 22# _object* RDKit::RunReactants(RDKit::ChemicalReaction*, boost::python::tuple, unsigned int) in /build/reproducible-path/rdkit-202409.4/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-202409.4/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# 0x0000FFFF94062680 in /lib/aarch64-linux-gnu/libboost_python313.so.1.83.0 +97: 25# 0x0000FFFFA1072680 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-202409.4/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-202409.4/obj-aarch64-linux-gnu/rdkit/Chem/rdDepictor.so @@ -23032,17 +23027,17 @@ 97: 33# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202409.4/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-202409.4/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-202409.4/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so -97: 36# 0x0000FFFF91B09FA0 in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so -97: 37# 0x0000FFFF91B09F38 in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so -97: 38# 0x0000FFFF91B09EC8 in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so -97: 39# 0x0000FFFF91B09E60 in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so -97: 40# 0x0000FFFF91B09DF8 in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so +97: 36# 0x0000FFFF9EB19FA0 in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so +97: 37# 0x0000FFFF9EB19F38 in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so +97: 38# 0x0000FFFF9EB19EC8 in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so +97: 39# 0x0000FFFF9EB19E60 in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so +97: 40# 0x0000FFFF9EB19DF8 in /build/reproducible-path/rdkit-202409.4/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-202409.4/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-202409.4/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-202409.4/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-202409.4/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# 0x0000FFFF9405F25C in /lib/aarch64-linux-gnu/libboost_python313.so.1.83.0 +97: 46# 0x0000FFFFA106F25C 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# 0x000000000052F1D8 in /usr/bin/python3 @@ -23074,13 +23069,13 @@ 97: 75# 0x0000000000621C6C in /usr/bin/python3 97: 76# Py_RunMain in /usr/bin/python3 97: 77# Py_BytesMain in /usr/bin/python3 -97: 78# 0x0000FFFF94B9229C in /lib/aarch64-linux-gnu/libc.so.6 +97: 78# 0x0000FFFFA1BA229C 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: [12:42:37] +97: [21:37:31] 97: 97: **** 97: Pre-condition Violation @@ -23114,7 +23109,7 @@ 97: 22# _object* RDKit::RunReactants(RDKit::ChemicalReaction*, boost::python::tuple, unsigned int) in /build/reproducible-path/rdkit-202409.4/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-202409.4/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# 0x0000FFFF94062680 in /lib/aarch64-linux-gnu/libboost_python313.so.1.83.0 +97: 25# 0x0000FFFFA1072680 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-202409.4/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-202409.4/obj-aarch64-linux-gnu/rdkit/Chem/rdDepictor.so @@ -23125,17 +23120,17 @@ 97: 33# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202409.4/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-202409.4/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-202409.4/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so -97: 36# 0x0000FFFF91B09FA0 in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so -97: 37# 0x0000FFFF91B09F38 in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so -97: 38# 0x0000FFFF91B09EC8 in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so -97: 39# 0x0000FFFF91B09E60 in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so -97: 40# 0x0000FFFF91B09DF8 in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so +97: 36# 0x0000FFFF9EB19FA0 in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so +97: 37# 0x0000FFFF9EB19F38 in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so +97: 38# 0x0000FFFF9EB19EC8 in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so +97: 39# 0x0000FFFF9EB19E60 in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so +97: 40# 0x0000FFFF9EB19DF8 in /build/reproducible-path/rdkit-202409.4/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-202409.4/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-202409.4/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-202409.4/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-202409.4/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# 0x0000FFFF9405F25C in /lib/aarch64-linux-gnu/libboost_python313.so.1.83.0 +97: 46# 0x0000FFFFA106F25C 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# 0x000000000052F1D8 in /usr/bin/python3 @@ -23167,16 +23162,132 @@ 97: 75# 0x0000000000621C6C in /usr/bin/python3 97: 76# Py_RunMain in /usr/bin/python3 97: 77# Py_BytesMain in /usr/bin/python3 -97: 78# 0x0000FFFF94B9229C in /lib/aarch64-linux-gnu/libc.so.6 +97: 78# 0x0000FFFFA1BA229C 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: -98: [12:42:37] == testCartesianProduct -101: Randomness seeded to: 3667115067 -101: [12:42:37] Incomplete atom labelling, cannot make bond -101: [12:42:37] +97: .........[21:37:31] stereo atoms in input cannot be mapped to output (atoms are no longer bonded) +97: [21:37:31] stereo atoms in input cannot be mapped to output (atoms are no longer bonded) +97: [21:37:31] stereo atoms in input cannot be mapped to output (atoms are no longer bonded) +97: [21:37:31] stereo atoms in input cannot be mapped to output (atoms are no longer bonded) +97: .[21:37:31] product atom-mapping number 1 found multiple times. +97: [21:37:31] product atom-mapping number 1 found multiple times. +98: .[21:37:31] == testEnumerateLibrary +97: ................[21:37:31] mapped atoms in the reactants were not mapped in the products. +97: unmapped numbers are: 3 +98: /build/reproducible-path/rdkit-202409.4/Code/GraphMol/ChemReactions/Wrap/testEnumerations.py:266: ResourceWarning: unclosed file <_io.BufferedReader name='/build/reproducible-path/rdkit-202409.4/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: [21:37:31] 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: :488: RuntimeWarning: to-Python converter for boost::shared_ptr already registered; second conversion method ignored. +29: +29: Computing MMFF94 energies for /build/reproducible-path/rdkit-202409.4/Code/ForceField/MMFF/test_data/MMFF94_dative.smi... +97: [21:37:31] mapped atoms in the reactants were not mapped in the products. +97: unmapped numbers are: 3 +97: ..[21:37:31] reactant 2 has no mapped atoms. +97: [21:37:31] reactant 2 has no mapped atoms. +97: [21:37:31] product 1 has no mapped atoms. +97: ........[21:37:31] SMARTS Parse Error: syntax error while parsing: [C:1](=[O:2])Q +97: [21:37:31] SMARTS Parse Error: Failed parsing SMARTS '[C:1](=[O:2])Q' for input: '[C:1](=[O:2])Q' +97: [21:37:31] SMARTS Parse Error: syntax error while parsing: [C:1](=[O:2])[N:3]Q +97: [21:37:31] SMARTS Parse Error: Failed parsing SMARTS '[C:1](=[O:2])[N:3]Q' for input: '[C:1](=[O:2])[N:3]Q' +97: .[21:37:31] reactant atom-mapping number 1 found multiple times. +97: [21:37:31] product atom-mapping number 2 not found in reactants. +97: [21:37:31] mapped atoms in the reactants were not mapped in the products. +97: unmapped numbers are: 4 +97: [21:37:31] product atom-mapping number 5 not found in reactants. +98: ..[21:37:31] == testRGroupState +97: ........./build/reproducible-path/rdkit-202409.4/Code/GraphMol/ChemReactions/Wrap/testReactionWrapper.py:745: ResourceWarning: unclosed file <_io.BufferedReader name='/build/reproducible-path/rdkit-202409.4/Code/GraphMol/ChemReactions/testData/reaction1.no_metadata.png'> +97: png = open(fname, 'rb').read() +97: ResourceWarning: Enable tracemalloc to get the object allocation traceback +97: [21:37:31] Found a SCD/SED line with missing/empty SDT specification at line 34 +97: [21:37:31] Found a SCD/SED line with missing/empty SDT specification at line 36 +97: [21:37:31] Found a SCD/SED line with missing/empty SDT specification at line 38 +97: [21:37:31] Found a SCD/SED line with missing/empty SDT specification at line 40 +97: [21:37:31] Found a SCD/SED line with missing/empty SDT specification at line 42 +97: [21:37:31] Found a SCD/SED line with missing/empty SDT specification at line 87 +97: [21:37:31] Found a SCD/SED line with missing/empty SDT specification at line 89 +97: [21:37:31] Found a SCD/SED line with missing/empty SDT specification at line 91 +97: [21:37:31] Found a SCD/SED line with missing/empty SDT specification at line 93 +97: [21:37:31] Found a SCD/SED line with missing/empty SDT specification at line 95 +98: .[21:37:31] == testRandomEnumerateAllBBsLibrary +98: ** [1, 1] +98: ** [0, 2] +98: ** [1, 0] +97: ..[21:37:31] SMARTS Parse Error: syntax error while parsing: boromicacid +97: [21:37:31] SMARTS Parse Error: Failed parsing SMARTS 'boromicacid' for input: 'boromicacid' +97: [21:37:31] SMARTS Parse Error: syntax error while parsing: carboxylicacid,acidchlroide +97: [21:37:31] SMARTS Parse Error: Failed parsing SMARTS 'carboxylicacid,acidchlroide' for input: 'carboxylicacid,acidchlroide' +97: [21:37:31] SMARTS Parse Error: syntax error while parsing: carboxyliccaid,acidchloride +97: [21:37:31] SMARTS Parse Error: Failed parsing SMARTS 'carboxyliccaid,acidchloride' for input: 'carboxyliccaid,acidchloride' +97: [21:37:31] reaction has no reactants +97: [21:37:31] reaction has no products +97: [21:37:31] initialization failed +97: [21:37:31] reaction has no reactants +97: [21:37:31] reaction has no products +98: .[21:37:31] == testRandomEnumerateLibrary +97: .[21:37:31] SMARTS Parse Error: syntax error while parsing: boromicacid +97: [21:37:31] SMARTS Parse Error: Failed parsing SMARTS 'boromicacid' for input: 'boromicacid' +97: [21:37:31] SMARTS Parse Error: syntax error while parsing: carboxylicacid,acidchlroide +97: [21:37:31] SMARTS Parse Error: Failed parsing SMARTS 'carboxylicacid,acidchlroide' for input: 'carboxylicacid,acidchlroide' +97: [21:37:31] SMARTS Parse Error: syntax error while parsing: carboxyliccaid,acidchloride +97: [21:37:31] SMARTS Parse Error: Failed parsing SMARTS 'carboxyliccaid,acidchloride' for input: 'carboxyliccaid,acidchloride' +97: [21:37:31] reaction has no reactants +97: [21:37:31] reaction has no products +97: [21:37:31] initialization failed +97: [21:37:31] reaction has no reactants +97: [21:37:31] reaction has no products +97: . +97: ---------------------------------------------------------------------- +97: Ran 54 tests in 0.111s +97: +97: OK +97: ******************************************** +97: /build/reproducible-path/rdkit-202409.4/Code/GraphMol/ChemReactions/testData/AmideBond.rxn +97: +98: .[21:37:31] == testRandomSample +98: .[21:37:31] == testRandomSampleAllBBs +98: .[21:37:31] deprecated -- please use MatchOnlyAtRgroupsAdjustParams instead +98: [21:37:31] deprecated -- please use MatchOnlyAtRgroupsAdjustParams instead +98: .[21:37:31] == testRemoveBadMatches +98: .[21:37:31] == testTimings +89: [21:37:31] Explicit valence for atom # 9 N, 6, is greater than permitted + 88/236 Test #97: pyChemReactions ........................ Passed 0.61 sec +test 100 + Start 100: testChemTransforms + +100: Test command: /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/GraphMol/ChemTransforms/testChemTransforms +100: Working Directory: /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/GraphMol/ChemTransforms +100: Test timeout computed to be: 1500 +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 +100: [21:37:31] SMARTS Parse Error: syntax error while parsing: bar +100: [21:37:31] SMARTS Parse Error: Failed parsing SMARTS 'bar' for input: 'bar' +89: [21:37:31] Explicit valence for atom # 3 Al, 6, is greater than permitted + 89/236 Test #100: testChemTransforms ..................... Passed 0.08 sec +test 101 + Start 101: chemTransformsTestCatch + +101: Test command: /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/GraphMol/ChemTransforms/chemTransformsTestCatch +101: Working Directory: /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/GraphMol/ChemTransforms +101: Test timeout computed to be: 1500 +70: [21:37:31] SMARTS Parse Error: syntax error while parsing: MyDogHasFleas +70: [21:37:31] SMARTS Parse Error: Failed parsing SMARTS 'MyDogHasFleas' for input: 'MyDogHasFleas' +89: [21:37:31] Explicit valence for atom # 4 Al, 6, is greater than permitted +89: [21:37:31] Explicit valence for atom # 10 Si, 6, is greater than permitted +101: Randomness seeded to: 108316761 +101: [21:37:31] Incomplete atom labelling, cannot make bond +101: [21:37:31] 101: 101: **** 101: Invariant Violation @@ -23189,28 +23300,21 @@ 101: 1# Invar::operator<<(std::ostream&, Invar::Invariant const&) in /build/reproducible-path/rdkit-202409.4/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-202409.4/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-202409.4/obj-aarch64-linux-gnu//lib/libRDKitChemTransforms.so.1 -101: 4# 0x0000AAAACE2D69A0 in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/GraphMol/ChemTransforms/chemTransformsTestCatch -101: 5# 0x0000AAAACE325A4C in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/GraphMol/ChemTransforms/chemTransformsTestCatch -101: 6# 0x0000AAAACE326400 in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/GraphMol/ChemTransforms/chemTransformsTestCatch -101: 7# 0x0000AAAACE326834 in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/GraphMol/ChemTransforms/chemTransformsTestCatch -101: 8# 0x0000AAAACE2FAEF8 in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/GraphMol/ChemTransforms/chemTransformsTestCatch -101: 9# 0x0000AAAACE2FB444 in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/GraphMol/ChemTransforms/chemTransformsTestCatch -101: 10# 0x0000AAAACE2CBE90 in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/GraphMol/ChemTransforms/chemTransformsTestCatch -101: 11# 0x0000FFFF843F229C in /lib/aarch64-linux-gnu/libc.so.6 +101: 4# 0x0000AAAAABA369A0 in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/GraphMol/ChemTransforms/chemTransformsTestCatch +101: 5# 0x0000AAAAABA85A4C in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/GraphMol/ChemTransforms/chemTransformsTestCatch +101: 6# 0x0000AAAAABA86400 in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/GraphMol/ChemTransforms/chemTransformsTestCatch +101: 7# 0x0000AAAAABA86834 in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/GraphMol/ChemTransforms/chemTransformsTestCatch +101: 8# 0x0000AAAAABA5AEF8 in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/GraphMol/ChemTransforms/chemTransformsTestCatch +101: 9# 0x0000AAAAABA5B444 in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/GraphMol/ChemTransforms/chemTransformsTestCatch +101: 10# 0x0000AAAAABA2BE90 in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/GraphMol/ChemTransforms/chemTransformsTestCatch +101: 11# 0x0000FFFFB351229C in /lib/aarch64-linux-gnu/libc.so.6 101: 12# __libc_start_main in /lib/aarch64-linux-gnu/libc.so.6 -101: 13# 0x0000AAAACE2CBF70 in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/GraphMol/ChemTransforms/chemTransformsTestCatch +101: 13# 0x0000AAAAABA2BF70 in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/GraphMol/ChemTransforms/chemTransformsTestCatch 101: ---------- 101: **** 101: -97: .........[12:42:37] stereo atoms in input cannot be mapped to output (atoms are no longer bonded) -97: [12:42:37] stereo atoms in input cannot be mapped to output (atoms are no longer bonded) -97: [12:42:37] stereo atoms in input cannot be mapped to output (atoms are no longer bonded) -97: [12:42:37] stereo atoms in input cannot be mapped to output (atoms are no longer bonded) -97: .[12:42:37] product atom-mapping number 1 found multiple times. -97: [12:42:37] product atom-mapping number 1 found multiple times. -98: .[12:42:37] == testEnumerateLibrary -101: [12:42:37] Incomplete atom labelling, cannot make bond -101: [12:42:37] +101: [21:37:31] Incomplete atom labelling, cannot make bond +101: [21:37:31] 101: 101: **** 101: Invariant Violation @@ -23223,24 +23327,21 @@ 101: 1# Invar::operator<<(std::ostream&, Invar::Invariant const&) in /build/reproducible-path/rdkit-202409.4/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-202409.4/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-202409.4/obj-aarch64-linux-gnu//lib/libRDKitChemTransforms.so.1 -101: 4# 0x0000AAAACE2D69A0 in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/GraphMol/ChemTransforms/chemTransformsTestCatch -101: 5# 0x0000AAAACE325A4C in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/GraphMol/ChemTransforms/chemTransformsTestCatch -101: 6# 0x0000AAAACE326400 in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/GraphMol/ChemTransforms/chemTransformsTestCatch -101: 7# 0x0000AAAACE326834 in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/GraphMol/ChemTransforms/chemTransformsTestCatch -101: 8# 0x0000AAAACE2FAEF8 in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/GraphMol/ChemTransforms/chemTransformsTestCatch -101: 9# 0x0000AAAACE2FB444 in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/GraphMol/ChemTransforms/chemTransformsTestCatch -101: 10# 0x0000AAAACE2CBE90 in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/GraphMol/ChemTransforms/chemTransformsTestCatch -101: 11# 0x0000FFFF843F229C in /lib/aarch64-linux-gnu/libc.so.6 +101: 4# 0x0000AAAAABA369A0 in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/GraphMol/ChemTransforms/chemTransformsTestCatch +101: 5# 0x0000AAAAABA85A4C in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/GraphMol/ChemTransforms/chemTransformsTestCatch +101: 6# 0x0000AAAAABA86400 in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/GraphMol/ChemTransforms/chemTransformsTestCatch +101: 7# 0x0000AAAAABA86834 in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/GraphMol/ChemTransforms/chemTransformsTestCatch +101: 8# 0x0000AAAAABA5AEF8 in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/GraphMol/ChemTransforms/chemTransformsTestCatch +101: 9# 0x0000AAAAABA5B444 in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/GraphMol/ChemTransforms/chemTransformsTestCatch +101: 10# 0x0000AAAAABA2BE90 in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/GraphMol/ChemTransforms/chemTransformsTestCatch +101: 11# 0x0000FFFFB351229C in /lib/aarch64-linux-gnu/libc.so.6 101: 12# __libc_start_main in /lib/aarch64-linux-gnu/libc.so.6 -101: 13# 0x0000AAAACE2CBF70 in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/GraphMol/ChemTransforms/chemTransformsTestCatch +101: 13# 0x0000AAAAABA2BF70 in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/GraphMol/ChemTransforms/chemTransformsTestCatch 101: ---------- 101: **** 101: -98: /build/reproducible-path/rdkit-202409.4/Code/GraphMol/ChemReactions/Wrap/testEnumerations.py:266: ResourceWarning: unclosed file <_io.BufferedReader name='/build/reproducible-path/rdkit-202409.4/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 -101: [12:42:37] Incomplete atom labelling, cannot make bond -101: [12:42:37] +101: [21:37:31] Incomplete atom labelling, cannot make bond +101: [21:37:31] 101: 101: **** 101: Invariant Violation @@ -23253,23 +23354,24 @@ 101: 1# Invar::operator<<(std::ostream&, Invar::Invariant const&) in /build/reproducible-path/rdkit-202409.4/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-202409.4/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-202409.4/obj-aarch64-linux-gnu//lib/libRDKitChemTransforms.so.1 -101: 4# 0x0000AAAACE2D69A0 in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/GraphMol/ChemTransforms/chemTransformsTestCatch -101: 5# 0x0000AAAACE325A4C in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/GraphMol/ChemTransforms/chemTransformsTestCatch -101: 6# 0x0000AAAACE326400 in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/GraphMol/ChemTransforms/chemTransformsTestCatch -101: 7# 0x0000AAAACE326834 in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/GraphMol/ChemTransforms/chemTransformsTestCatch -101: 8# 0x0000AAAACE2FAEF8 in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/GraphMol/ChemTransforms/chemTransformsTestCatch -101: 9# 0x0000AAAACE2FB444 in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/GraphMol/ChemTransforms/chemTransformsTestCatch -101: 10# 0x0000AAAACE2CBE90 in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/GraphMol/ChemTransforms/chemTransformsTestCatch -101: 11# 0x0000FFFF843F229C in /lib/aarch64-linux-gnu/libc.so.6 +101: 4# 0x0000AAAAABA369A0 in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/GraphMol/ChemTransforms/chemTransformsTestCatch +101: 5# 0x0000AAAAABA85A4C in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/GraphMol/ChemTransforms/chemTransformsTestCatch +101: 6# 0x0000AAAAABA86400 in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/GraphMol/ChemTransforms/chemTransformsTestCatch +101: 7# 0x0000AAAAABA86834 in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/GraphMol/ChemTransforms/chemTransformsTestCatch +101: 8# 0x0000AAAAABA5AEF8 in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/GraphMol/ChemTransforms/chemTransformsTestCatch +101: 9# 0x0000AAAAABA5B444 in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/GraphMol/ChemTransforms/chemTransformsTestCatch +101: 10# 0x0000AAAAABA2BE90 in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/GraphMol/ChemTransforms/chemTransformsTestCatch +101: 11# 0x0000FFFFB351229C in /lib/aarch64-linux-gnu/libc.so.6 101: 12# __libc_start_main in /lib/aarch64-linux-gnu/libc.so.6 -101: 13# 0x0000AAAACE2CBF70 in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/GraphMol/ChemTransforms/chemTransformsTestCatch +101: 13# 0x0000AAAAABA2BF70 in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/GraphMol/ChemTransforms/chemTransformsTestCatch 101: ---------- 101: **** 101: -101: [12:42:37] Incomplete atom labelling, cannot make bond -101: [12:42:37] Incomplete atom labelling, cannot make bond -101: [12:42:37] Incomplete atom labelling, cannot make bond -101: [12:42:37] +70: [21:37:31] Empty atom list: 'M ALS 1 0 F' on line 8. +101: [21:37:31] Incomplete atom labelling, cannot make bond +101: [21:37:31] Incomplete atom labelling, cannot make bond +101: [21:37:31] Incomplete atom labelling, cannot make bond +101: [21:37:31] 101: 101: **** 101: Invariant Violation @@ -23282,29 +23384,28 @@ 101: 1# Invar::operator<<(std::ostream&, Invar::Invariant const&) in /build/reproducible-path/rdkit-202409.4/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-202409.4/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-202409.4/obj-aarch64-linux-gnu//lib/libRDKitChemTransforms.so.1 -101: 4# 0x0000AAAACE2D69A0 in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/GraphMol/ChemTransforms/chemTransformsTestCatch -101: 5# 0x0000AAAACE325A4C in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/GraphMol/ChemTransforms/chemTransformsTestCatch -101: 6# 0x0000AAAACE326400 in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/GraphMol/ChemTransforms/chemTransformsTestCatch -101: 7# 0x0000AAAACE326834 in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/GraphMol/ChemTransforms/chemTransformsTestCatch -101: 8# 0x0000AAAACE2FAEF8 in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/GraphMol/ChemTransforms/chemTransformsTestCatch -101: 9# 0x0000AAAACE2FB444 in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/GraphMol/ChemTransforms/chemTransformsTestCatch -101: 10# 0x0000AAAACE2CBE90 in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/GraphMol/ChemTransforms/chemTransformsTestCatch -101: 11# 0x0000FFFF843F229C in /lib/aarch64-linux-gnu/libc.so.6 +101: 4# 0x0000AAAAABA369A0 in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/GraphMol/ChemTransforms/chemTransformsTestCatch +101: 5# 0x0000AAAAABA85A4C in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/GraphMol/ChemTransforms/chemTransformsTestCatch +101: 6# 0x0000AAAAABA86400 in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/GraphMol/ChemTransforms/chemTransformsTestCatch +101: 7# 0x0000AAAAABA86834 in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/GraphMol/ChemTransforms/chemTransformsTestCatch +101: 8# 0x0000AAAAABA5AEF8 in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/GraphMol/ChemTransforms/chemTransformsTestCatch +101: 9# 0x0000AAAAABA5B444 in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/GraphMol/ChemTransforms/chemTransformsTestCatch +101: 10# 0x0000AAAAABA2BE90 in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/GraphMol/ChemTransforms/chemTransformsTestCatch +101: 11# 0x0000FFFFB351229C in /lib/aarch64-linux-gnu/libc.so.6 101: 12# __libc_start_main in /lib/aarch64-linux-gnu/libc.so.6 -101: 13# 0x0000AAAACE2CBF70 in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/GraphMol/ChemTransforms/chemTransformsTestCatch +101: 13# 0x0000AAAAABA2BF70 in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/GraphMol/ChemTransforms/chemTransformsTestCatch 101: ---------- 101: **** 101: -97: ................[12:42:37] mapped atoms in the reactants were not mapped in the products. -97: unmapped numbers are: 3 -97: [12:42:37] 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: :488: RuntimeWarning: to-Python converter for boost::shared_ptr already registered; second conversion method ignored. -97: [12:42:37] mapped atoms in the reactants were not mapped in the products. -97: unmapped numbers are: 3 -101: [12:42:37] Incomplete atom labelling, cannot make bond -101: [12:42:37] + 90/236 Test #70: fileParsersTest1 ....................... Passed 3.08 sec +test 102 + Start 102: tautomerQueryTestCatch + +102: Test command: /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/GraphMol/TautomerQuery/tautomerQueryTestCatch +102: Working Directory: /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/GraphMol/TautomerQuery +102: Test timeout computed to be: 1500 +101: [21:37:31] Incomplete atom labelling, cannot make bond +101: [21:37:31] 101: 101: **** 101: Invariant Violation @@ -23317,23 +23418,20 @@ 101: 1# Invar::operator<<(std::ostream&, Invar::Invariant const&) in /build/reproducible-path/rdkit-202409.4/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-202409.4/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-202409.4/obj-aarch64-linux-gnu//lib/libRDKitChemTransforms.so.1 -101: 4# 0x0000AAAACE2D69A0 in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/GraphMol/ChemTransforms/chemTransformsTestCatch -101: 5# 0x0000AAAACE325A4C in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/GraphMol/ChemTransforms/chemTransformsTestCatch -101: 6# 0x0000AAAACE326400 in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/GraphMol/ChemTransforms/chemTransformsTestCatch -101: 7# 0x0000AAAACE326834 in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/GraphMol/ChemTransforms/chemTransformsTestCatch -101: 8# 0x0000AAAACE2FAEF8 in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/GraphMol/ChemTransforms/chemTransformsTestCatch -101: 9# 0x0000AAAACE2FB444 in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/GraphMol/ChemTransforms/chemTransformsTestCatch -101: 10# 0x0000AAAACE2CBE90 in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/GraphMol/ChemTransforms/chemTransformsTestCatch -101: 11# 0x0000FFFF843F229C in /lib/aarch64-linux-gnu/libc.so.6 +101: 4# 0x0000AAAAABA369A0 in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/GraphMol/ChemTransforms/chemTransformsTestCatch +101: 5# 0x0000AAAAABA85A4C in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/GraphMol/ChemTransforms/chemTransformsTestCatch +101: 6# 0x0000AAAAABA86400 in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/GraphMol/ChemTransforms/chemTransformsTestCatch +101: 7# 0x0000AAAAABA86834 in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/GraphMol/ChemTransforms/chemTransformsTestCatch +101: 8# 0x0000AAAAABA5AEF8 in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/GraphMol/ChemTransforms/chemTransformsTestCatch +101: 9# 0x0000AAAAABA5B444 in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/GraphMol/ChemTransforms/chemTransformsTestCatch +101: 10# 0x0000AAAAABA2BE90 in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/GraphMol/ChemTransforms/chemTransformsTestCatch +101: 11# 0x0000FFFFB351229C in /lib/aarch64-linux-gnu/libc.so.6 101: 12# __libc_start_main in /lib/aarch64-linux-gnu/libc.so.6 -101: 13# 0x0000AAAACE2CBF70 in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/GraphMol/ChemTransforms/chemTransformsTestCatch +101: 13# 0x0000AAAAABA2BF70 in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/GraphMol/ChemTransforms/chemTransformsTestCatch 101: ---------- 101: **** 101: -97: ..[12:42:37] reactant 2 has no mapped atoms. -97: [12:42:37] reactant 2 has no mapped atoms. -97: [12:42:37] product 1 has no mapped atoms. -101: [12:42:37] +101: [21:37:31] 101: 101: **** 101: Invariant Violation @@ -23347,120 +23445,75 @@ 101: 2# RDKit::molzip(RDKit::ROMol const&, RDKit::ROMol const&, RDKit::MolzipParams const&, std::optional, std::allocator > > >&) in /build/reproducible-path/rdkit-202409.4/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-202409.4/obj-aarch64-linux-gnu//lib/libRDKitChemTransforms.so.1 101: 4# RDKit::molzip(RDKit::ROMol const&, RDKit::MolzipParams const&) in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu//lib/libRDKitChemTransforms.so.1 -101: 5# 0x0000AAAACE2CCC58 in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/GraphMol/ChemTransforms/chemTransformsTestCatch -101: 6# 0x0000AAAACE325A4C in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/GraphMol/ChemTransforms/chemTransformsTestCatch -101: 7# 0x0000AAAACE326400 in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/GraphMol/ChemTransforms/chemTransformsTestCatch -101: 8# 0x0000AAAACE326834 in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/GraphMol/ChemTransforms/chemTransformsTestCatch -101: 9# 0x0000AAAACE2FAEF8 in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/GraphMol/ChemTransforms/chemTransformsTestCatch -101: 10# 0x0000AAAACE2FB444 in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/GraphMol/ChemTransforms/chemTransformsTestCatch -101: 11# 0x0000AAAACE2CBE90 in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/GraphMol/ChemTransforms/chemTransformsTestCatch -101: 12# 0x0000FFFF843F229C in /lib/aarch64-linux-gnu/libc.so.6 +101: 5# 0x0000AAAAABA2CC58 in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/GraphMol/ChemTransforms/chemTransformsTestCatch +101: 6# 0x0000AAAAABA85A4C in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/GraphMol/ChemTransforms/chemTransformsTestCatch +101: 7# 0x0000AAAAABA86400 in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/GraphMol/ChemTransforms/chemTransformsTestCatch +101: 8# 0x0000AAAAABA86834 in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/GraphMol/ChemTransforms/chemTransformsTestCatch +101: 9# 0x0000AAAAABA5AEF8 in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/GraphMol/ChemTransforms/chemTransformsTestCatch +101: 10# 0x0000AAAAABA5B444 in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/GraphMol/ChemTransforms/chemTransformsTestCatch +101: 11# 0x0000AAAAABA2BE90 in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/GraphMol/ChemTransforms/chemTransformsTestCatch +101: 12# 0x0000FFFFB351229C in /lib/aarch64-linux-gnu/libc.so.6 101: 13# __libc_start_main in /lib/aarch64-linux-gnu/libc.so.6 -101: 14# 0x0000AAAACE2CBF70 in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/GraphMol/ChemTransforms/chemTransformsTestCatch +101: 14# 0x0000AAAAABA2BF70 in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/GraphMol/ChemTransforms/chemTransformsTestCatch 101: ---------- 101: **** 101: 101: =============================================================================== 101: All tests passed (674 assertions in 9 test cases) 101: - 90/236 Test #101: chemTransformsTestCatch ................ Passed 0.06 sec -test 102 - Start 102: tautomerQueryTestCatch + 91/236 Test #101: chemTransformsTestCatch ................ Passed 0.11 sec +test 103 + Start 103: pyTautomerQuery -102: Test command: /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/GraphMol/TautomerQuery/tautomerQueryTestCatch -102: Working Directory: /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/GraphMol/TautomerQuery -102: Test timeout computed to be: 1500 -97: ........[12:42:37] SMARTS Parse Error: syntax error while parsing: [C:1](=[O:2])Q -97: [12:42:37] SMARTS Parse Error: Failed parsing SMARTS '[C:1](=[O:2])Q' for input: '[C:1](=[O:2])Q' -97: [12:42:37] SMARTS Parse Error: syntax error while parsing: [C:1](=[O:2])[N:3]Q -97: [12:42:37] SMARTS Parse Error: Failed parsing SMARTS '[C:1](=[O:2])[N:3]Q' for input: '[C:1](=[O:2])[N:3]Q' -97: .[12:42:37] reactant atom-mapping number 1 found multiple times. -97: [12:42:37] product atom-mapping number 2 not found in reactants. -97: [12:42:37] mapped atoms in the reactants were not mapped in the products. -97: unmapped numbers are: 4 -97: [12:42:37] product atom-mapping number 5 not found in reactants. -98: ..[12:42:37] == testRGroupState -98: .[12:42:37] == testRandomEnumerateAllBBsLibrary -98: ** [1, 1] -98: ** [0, 2] -98: ** [1, 0] -98: .[12:42:37] == testRandomEnumerateLibrary -98: .[12:42:37] == testRandomSample -98: .[12:42:37] == testRandomSampleAllBBs -98: .[12:42:37] deprecated -- please use MatchOnlyAtRgroupsAdjustParams instead -98: [12:42:37] deprecated -- please use MatchOnlyAtRgroupsAdjustParams instead -98: .[12:42:37] == testRemoveBadMatches -98: .[12:42:37] == testTimings -97: ........./build/reproducible-path/rdkit-202409.4/Code/GraphMol/ChemReactions/Wrap/testReactionWrapper.py:745: ResourceWarning: unclosed file <_io.BufferedReader name='/build/reproducible-path/rdkit-202409.4/Code/GraphMol/ChemReactions/testData/reaction1.no_metadata.png'> -97: png = open(fname, 'rb').read() -97: ResourceWarning: Enable tracemalloc to get the object allocation traceback -97: [12:42:37] Found a SCD/SED line with missing/empty SDT specification at line 34 -97: [12:42:37] Found a SCD/SED line with missing/empty SDT specification at line 36 -97: [12:42:37] Found a SCD/SED line with missing/empty SDT specification at line 38 -97: [12:42:37] Found a SCD/SED line with missing/empty SDT specification at line 40 -97: [12:42:37] Found a SCD/SED line with missing/empty SDT specification at line 42 -97: [12:42:37] Found a SCD/SED line with missing/empty SDT specification at line 87 -97: [12:42:37] Found a SCD/SED line with missing/empty SDT specification at line 89 -97: [12:42:37] Found a SCD/SED line with missing/empty SDT specification at line 91 -97: [12:42:37] Found a SCD/SED line with missing/empty SDT specification at line 93 -97: [12:42:37] Found a SCD/SED line with missing/empty SDT specification at line 95 -97: ..[12:42:37] SMARTS Parse Error: syntax error while parsing: boromicacid -97: [12:42:37] SMARTS Parse Error: Failed parsing SMARTS 'boromicacid' for input: 'boromicacid' -97: [12:42:37] SMARTS Parse Error: syntax error while parsing: carboxylicacid,acidchlroide -97: [12:42:37] SMARTS Parse Error: Failed parsing SMARTS 'carboxylicacid,acidchlroide' for input: 'carboxylicacid,acidchlroide' -99: .[12:42:37] reactant 0 has no mapped atoms. -99: [12:42:37] product 0 has no mapped atoms. -99: [12:42:37] reactant 0 has no mapped atoms. -99: [12:42:37] product 0 has no mapped atoms. -97: [12:42:37] SMARTS Parse Error: syntax error while parsing: carboxyliccaid,acidchloride -97: [12:42:37] SMARTS Parse Error: Failed parsing SMARTS 'carboxyliccaid,acidchloride' for input: 'carboxyliccaid,acidchloride' -97: [12:42:37] reaction has no reactants -97: [12:42:37] reaction has no products -97: [12:42:37] initialization failed -97: [12:42:37] reaction has no reactants -97: [12:42:37] reaction has no products -99: .[12:42:37] reactant 0 has no mapped atoms. -99: [12:42:37] reactant 1 has no mapped atoms. -99: [12:42:37] product 0 has no mapped atoms. -99: [12:42:37] reactant 0 has no mapped atoms. -99: [12:42:37] reactant 1 has no mapped atoms. -99: [12:42:37] product 0 has no mapped atoms. -99: [12:42:37] reactant 0 has no mapped atoms. -99: [12:42:37] reactant 1 has no mapped atoms. -99: [12:42:37] product 0 has no mapped atoms. -99: [12:42:37] reactant 0 has no mapped atoms. -99: [12:42:37] reactant 1 has no mapped atoms. -99: [12:42:37] product 0 has no mapped atoms. -99: [12:42:37] reactant 0 has no mapped atoms. -99: [12:42:37] reactant 1 has no mapped atoms. -99: [12:42:37] product 0 has no mapped atoms. -99: [12:42:37] reactant 0 has no mapped atoms. -99: [12:42:37] reactant 1 has no mapped atoms. -99: [12:42:37] product 0 has no mapped atoms. -99: [12:42:37] reactant 0 has no mapped atoms. -99: [12:42:37] reactant 1 has no mapped atoms. -99: [12:42:37] product 0 has no mapped atoms. -99: [12:42:37] reactant 0 has no mapped atoms. -99: [12:42:37] reactant 1 has no mapped atoms. -99: [12:42:37] product 0 has no mapped atoms. -99: [12:42:37] reactant 0 has no mapped atoms. -99: [12:42:37] reactant 1 has no mapped atoms. -99: [12:42:37] product 0 has no mapped atoms. -99: [12:42:37] reactant 0 has no mapped atoms. -99: [12:42:37] reactant 1 has no mapped atoms. -99: [12:42:37] product 0 has no mapped atoms. -99: [12:42:37] reactant 0 has no mapped atoms. -99: [12:42:37] reactant 1 has no mapped atoms. -99: [12:42:37] product 0 has no mapped atoms. -99: [12:42:37] reactant 0 has no mapped atoms. -99: [12:42:37] reactant 1 has no mapped atoms. -99: [12:42:37] product 0 has no mapped atoms. -99: [12:42:37] reactant 0 has no mapped atoms. -99: [12:42:37] reactant 1 has no mapped atoms. -99: [12:42:37] product 0 has no mapped atoms. -99: [12:42:37] reactant 0 has no mapped atoms. -99: [12:42:37] reactant 1 has no mapped atoms. -99: [12:42:37] product 0 has no mapped atoms. +103: Test command: /usr/bin/python3 "/build/reproducible-path/rdkit-202409.4/Code/GraphMol/TautomerQuery/Wrap/rough_test.py" +103: Working Directory: /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/GraphMol/TautomerQuery/Wrap +103: Test timeout computed to be: 1500 +99: .[21:37:31] reactant 0 has no mapped atoms. +99: [21:37:31] product 0 has no mapped atoms. +99: [21:37:31] reactant 0 has no mapped atoms. +99: [21:37:31] product 0 has no mapped atoms. +99: .[21:37:31] reactant 0 has no mapped atoms. +99: [21:37:31] reactant 1 has no mapped atoms. +99: [21:37:31] product 0 has no mapped atoms. +99: [21:37:31] reactant 0 has no mapped atoms. +99: [21:37:31] reactant 1 has no mapped atoms. +99: [21:37:31] product 0 has no mapped atoms. +99: [21:37:31] reactant 0 has no mapped atoms. +99: [21:37:31] reactant 1 has no mapped atoms. +99: [21:37:31] product 0 has no mapped atoms. +99: [21:37:31] reactant 0 has no mapped atoms. +99: [21:37:31] reactant 1 has no mapped atoms. +99: [21:37:31] product 0 has no mapped atoms. +99: [21:37:31] reactant 0 has no mapped atoms. +99: [21:37:31] reactant 1 has no mapped atoms. +99: [21:37:31] product 0 has no mapped atoms. +99: [21:37:31] reactant 0 has no mapped atoms. +99: [21:37:31] reactant 1 has no mapped atoms. +99: [21:37:31] product 0 has no mapped atoms. +99: [21:37:31] reactant 0 has no mapped atoms. +99: [21:37:31] reactant 1 has no mapped atoms. +99: [21:37:31] product 0 has no mapped atoms. +99: [21:37:31] reactant 0 has no mapped atoms. +99: [21:37:31] reactant 1 has no mapped atoms. +99: [21:37:31] product 0 has no mapped atoms. +99: [21:37:31] reactant 0 has no mapped atoms. +99: [21:37:31] reactant 1 has no mapped atoms. +99: [21:37:31] product 0 has no mapped atoms. +99: [21:37:31] reactant 0 has no mapped atoms. +99: [21:37:31] reactant 1 has no mapped atoms. +99: [21:37:31] product 0 has no mapped atoms. +99: [21:37:31] reactant 0 has no mapped atoms. +99: [21:37:31] reactant 1 has no mapped atoms. +99: [21:37:31] product 0 has no mapped atoms. +99: [21:37:31] reactant 0 has no mapped atoms. +99: [21:37:31] reactant 1 has no mapped atoms. +99: [21:37:31] product 0 has no mapped atoms. +99: [21:37:31] reactant 0 has no mapped atoms. +99: [21:37:31] reactant 1 has no mapped atoms. +99: [21:37:31] product 0 has no mapped atoms. +99: [21:37:31] reactant 0 has no mapped atoms. +99: [21:37:31] reactant 1 has no mapped atoms. +99: [21:37:31] product 0 has no mapped atoms. 99: () 99: ******************************************** 99: $RXN @@ -23824,16 +23877,16 @@ 99: 1 2 1 0 99: M ISO 2 1 1 2 2 99: M END -99: [12:42:37] reactant 0 has no mapped atoms. -99: [12:42:37] reactant 1 has no mapped atoms. -99: [12:42:37] product 0 has no mapped atoms. -99: [12:42:37] Could not find RLabel mapping for atom: 0 in template: 1 -99: [12:42:37] reactant 1 has no mapped atoms. -99: [12:42:37] reactant 1 has no mapped atoms. -99: [12:42:37] reactant 1 has no mapped atoms. +99: [21:37:31] reactant 0 has no mapped atoms. +99: [21:37:31] reactant 1 has no mapped atoms. +99: [21:37:31] product 0 has no mapped atoms. +99: [21:37:31] Could not find RLabel mapping for atom: 0 in template: 1 +99: [21:37:31] reactant 1 has no mapped atoms. +99: [21:37:31] reactant 1 has no mapped atoms. +99: [21:37:31] reactant 1 has no mapped atoms. 99: .. 99: ---------------------------------------------------------------------- -99: Ran 4 tests in 0.013s +99: Ran 4 tests in 0.025s 99: 99: OK 99: @@ -23890,61 +23943,38 @@ 99: M END 99: 99: $RXN Failed -97: .[12:42:37] SMARTS Parse Error: syntax error while parsing: boromicacid -97: [12:42:37] SMARTS Parse Error: Failed parsing SMARTS 'boromicacid' for input: 'boromicacid' -97: [12:42:37] SMARTS Parse Error: syntax error while parsing: carboxylicacid,acidchlroide -97: [12:42:37] SMARTS Parse Error: Failed parsing SMARTS 'carboxylicacid,acidchlroide' for input: 'carboxylicacid,acidchlroide' -97: [12:42:37] SMARTS Parse Error: syntax error while parsing: carboxyliccaid,acidchloride -97: [12:42:37] SMARTS Parse Error: Failed parsing SMARTS 'carboxyliccaid,acidchloride' for input: 'carboxyliccaid,acidchloride' -97: [12:42:37] reaction has no reactants -97: [12:42:37] reaction has no products -97: [12:42:37] initialization failed -97: [12:42:37] reaction has no reactants -97: [12:42:37] reaction has no products -97: . -97: ---------------------------------------------------------------------- -97: Ran 54 tests in 0.107s -97: -97: OK -97: ******************************************** -97: /build/reproducible-path/rdkit-202409.4/Code/GraphMol/ChemReactions/testData/AmideBond.rxn -97: -89: [12:42:37] Explicit valence for atom # 9 N, 6, is greater than permitted -102: Randomness seeded to: 2912669464 -102: =============================================================================== -102: All tests passed (93 assertions in 13 test cases) -102: - 91/236 Test #99: pyChemReactionSanitize ................. Passed 0.30 sec -test 103 - Start 103: pyTautomerQuery - -103: Test command: /usr/bin/python3 "/build/reproducible-path/rdkit-202409.4/Code/GraphMol/TautomerQuery/Wrap/rough_test.py" -103: Working Directory: /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/GraphMol/TautomerQuery/Wrap -103: Test timeout computed to be: 1500 - 92/236 Test #102: tautomerQueryTestCatch ................. Passed 0.11 sec +89: [21:37:31] Explicit valence for atom # 2 O, 4, is greater than permitted +89: [21:37:31] Explicit valence for atom # 3 Al, 6, is greater than permitted +89: [21:37:31] Explicit valence for atom # 3 Be, 4, is greater than permitted +89: [21:37:31] Explicit valence for atom # 27 P, 6, is greater than permitted + 92/236 Test #99: pyChemReactionSanitize ................. Passed 0.70 sec test 104 Start 104: testSubgraphs1 104: Test command: /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/GraphMol/Subgraphs/testSubgraphs1 104: Working Directory: /build/reproducible-path/rdkit-202409.4/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 - 93/236 Test #97: pyChemReactions ........................ Passed 0.44 sec +102: Randomness seeded to: 2414456486 +102: =============================================================================== +102: All tests passed (93 assertions in 13 test cases) +102: + 93/236 Test #102: tautomerQueryTestCatch ................. Passed 0.20 sec test 105 Start 105: testSubgraphs2 105: Test command: /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/GraphMol/Subgraphs/testSubgraphs2 105: Working Directory: /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/GraphMol/Subgraphs 105: Test timeout computed to be: 1500 +104: ----------------------- +104: Subgraph retrieval +104: Finished +104: ----------------------- +104: testSubgraphs2a 105: ----------------------- 105: Test1: pathToSubmol +104: Finished +104: ----------------------- +104: testSubgraphs2 105: Finished 105: ----------------------- 105: Test2: Atom Environments @@ -23958,19 +23988,19 @@ 105: ----------------------- 105: Testing github Issue103: more stereochemistry and pathToSubmol (path needs to be in sorted order) 105: Finished - 94/236 Test #105: testSubgraphs2 ......................... Passed 0.01 sec + 94/236 Test #105: testSubgraphs2 ......................... Passed 0.04 sec test 106 Start 106: subgraphsCatch 106: Test command: /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/GraphMol/Subgraphs/subgraphsCatch 106: Working Directory: /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/GraphMol/Subgraphs 106: Test timeout computed to be: 1500 -106: Randomness seeded to: 111186187 +106: Randomness seeded to: 2743434903 106: --------- 106: =============================================================================== 106: All tests passed (11 assertions in 1 test case) 106: - 95/236 Test #106: subgraphsCatch ......................... Passed 0.01 sec + 95/236 Test #106: subgraphsCatch ......................... Passed 0.04 sec test 107 Start 107: filterCatalogTest @@ -23989,7 +24019,11 @@ 104: Finished 104: ----------------------- 104: testUniqueSubgraphs2 -89: [12:42:37] Explicit valence for atom # 3 Al, 6, is greater than permitted +103: ..... +103: ---------------------------------------------------------------------- +103: Ran 5 tests in 0.024s +103: +103: OK 107: Warning: molecule failed filter 107: Warning: molecule failed filter: reason hzone_phenol_A(479) 107: v = { @@ -24049,6 +24083,13 @@ 107: 12,16}, 107: } 107: Warning: molecule failed filter + 96/236 Test #103: pyTautomerQuery ........................ Passed 0.37 sec +test 108 + Start 108: pyFilterCatalog + +108: Test command: /usr/bin/python3 "/build/reproducible-path/rdkit-202409.4/Code/GraphMol/FilterCatalog/Wrap/rough_test.py" +108: Working Directory: /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/GraphMol/FilterCatalog/Wrap +108: Test timeout computed to be: 1500 107: Warning: molecule failed filter: reason keto_keto_gamma(5) 107: v = { 107: 0,0}, @@ -24078,8 +24119,6 @@ 107: 10,15}, 107: 11,16}, 107: } -89: [12:42:37] Explicit valence for atom # 4 Al, 6, is greater than permitted -89: [12:42:37] Explicit valence for atom # 10 Si, 6, is greater than permitted 104: Finished 104: ----------------------- 104: testRootedSubgraphs @@ -24087,42 +24126,25 @@ 104: ----------------------- 104: testRootedPaths 104: Finished - 96/236 Test #104: testSubgraphs1 ......................... Passed 0.16 sec -test 108 - Start 108: pyFilterCatalog - -108: Test command: /usr/bin/python3 "/build/reproducible-path/rdkit-202409.4/Code/GraphMol/FilterCatalog/Wrap/rough_test.py" -108: Working Directory: /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/GraphMol/FilterCatalog/Wrap -108: Test timeout computed to be: 1500 - 97/236 Test #107: filterCatalogTest ...................... Passed 0.16 sec + 97/236 Test #104: testSubgraphs1 ......................... Passed 0.35 sec test 109 Start 109: testFragCatalog 109: Test command: /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/GraphMol/FragCatalog/testFragCatalog 109: Working Directory: /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/GraphMol/FragCatalog 109: Test timeout computed to be: 1500 -103: ..... -103: ---------------------------------------------------------------------- -103: Ran 5 tests in 0.025s -103: -103: OK 109: 21 - 98/236 Test #103: pyTautomerQuery ........................ Passed 0.28 sec +89: [21:37:32] Explicit valence for atom # 9 N, 6, is greater than permitted + 98/236 Test #107: filterCatalogTest ...................... Passed 0.31 sec test 110 Start 110: pyFragCatalog 110: Test command: /usr/bin/python3 "/build/reproducible-path/rdkit-202409.4/Code/GraphMol/FragCatalog/Wrap/rough_test.py" 110: Working Directory: /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/GraphMol/FragCatalog/Wrap 110: Test timeout computed to be: 1500 -89: [12:42:38] Explicit valence for atom # 2 O, 4, is greater than permitted -89: [12:42:38] Explicit valence for atom # 3 Al, 6, is greater than permitted -89: [12:42:38] Explicit valence for atom # 3 Be, 4, is greater than permitted -89: [12:42:38] Explicit valence for atom # 27 P, 6, is greater than permitted -108: :488: RuntimeWarning: to-Python converter for boost::shared_ptr already registered; second conversion method ignored. -108: :488: RuntimeWarning: to-Python converter for boost::shared_ptr already registered; second conversion method ignored. 98: . 98: ---------------------------------------------------------------------- -98: Ran 11 tests in 0.516s +98: Ran 11 tests in 1.039s 98: 98: OK 98: True @@ -24135,94 +24157,87 @@ 98: 0 10 out of 10 98: 1 5 out of 5 98: 2 6 out of 6 -98: Skipped 10000000 in 0.033672332763671875 seconds -98: Skipped 10000000 in 0.2597079277038574 seconds -98: Skipped 10000000 in 0.07449173927307129 seconds -89: =============================================================================== -89: All tests passed (21562 assertions in 3 test cases) -89: - 99/236 Test #89: multithreadedSupplierCatchTest ......... Passed 1.50 sec +98: Skipped 10000000 in 0.03569984436035156 seconds +98: Skipped 10000000 in 0.5625553131103516 seconds +98: Skipped 10000000 in 0.15682148933410645 seconds +89: [21:37:32] Explicit valence for atom # 3 Al, 6, is greater than permitted +108: :488: RuntimeWarning: to-Python converter for boost::shared_ptr already registered; second conversion method ignored. +108: :488: RuntimeWarning: to-Python converter for boost::shared_ptr already registered; second conversion method ignored. +89: [21:37:32] Explicit valence for atom # 4 Al, 6, is greater than permitted +89: [21:37:32] Explicit valence for atom # 10 Si, 6, is greater than permitted + 99/236 Test #98: pyChemReactionEnumerations ............. Passed 1.53 sec test 111 Start 111: testDescriptors 111: Test command: /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/GraphMol/Descriptors/testDescriptors 111: Working Directory: /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/GraphMol/Descriptors 111: Test timeout computed to be: 1500 -111: [12:42:38] ------------------------------------- -111: [12:42:38] Test Crippen parameter acquisition. -111: [12:42:38] done -111: [12:42:38] ------------------------------------- -111: [12:42:38] Test Crippen calculation. -111: [12:42:38] done -111: [12:42:38] ------------------------------------- -111: [12:42:38] Test Issue262: problems with Crippen calculation from pickles. -111: [12:42:38] done -111: [12:42:38] ------------------------------------- -111: [12:42:38] Test AMW calculation. -111: [12:42:38] done -111: [12:42:38] ------------------------------------- -111: [12:42:38] Test Exact MW calculation. -111: [12:42:38] done -111: [12:42:38] ------------------------------------- -111: [12:42:38] Test Labute ASA descriptors. -111: [12:42:38] done -111: [12:42:38] ------------------------------------- -111: [12:42:38] Test TPSA descriptors. -111: [12:42:38] done -111: [12:42:38] ------------------------------------- -111: [12:42:38] Test Lipinski parameters. -100/236 Test #98: pyChemReactionEnumerations ............. Passed 0.80 sec +111: [21:37:32] ------------------------------------- +111: [21:37:32] Test Crippen parameter acquisition. +111: [21:37:32] done +111: [21:37:32] ------------------------------------- +111: [21:37:32] Test Crippen calculation. +111: [21:37:32] done +111: [21:37:32] ------------------------------------- +111: [21:37:32] Test Issue262: problems with Crippen calculation from pickles. +111: [21:37:32] done +111: [21:37:32] ------------------------------------- +111: [21:37:32] Test AMW calculation. +111: [21:37:32] done +111: [21:37:32] ------------------------------------- +111: [21:37:32] Test Exact MW calculation. +111: [21:37:32] done +111: [21:37:32] ------------------------------------- +111: [21:37:32] Test Labute ASA descriptors. +111: [21:37:32] done +111: [21:37:32] ------------------------------------- +111: [21:37:32] Test TPSA descriptors. +111: [21:37:32] done +111: [21:37:32] ------------------------------------- +111: [21:37:32] Test Lipinski parameters. +89: [21:37:32] Explicit valence for atom # 2 O, 4, is greater than permitted +89: [21:37:32] Explicit valence for atom # 3 Al, 6, is greater than permitted +89: [21:37:32] Explicit valence for atom # 3 Be, 4, is greater than permitted +89: [21:37:32] Explicit valence for atom # 27 P, 6, is greater than permitted +89: =============================================================================== +89: All tests passed (21562 assertions in 3 test cases) +89: +100/236 Test #89: multithreadedSupplierCatchTest ......... Passed 2.54 sec test 112 Start 112: testAUTOCORR2D 112: Test command: /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/GraphMol/Descriptors/testAUTOCORR2D 112: Working Directory: /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/GraphMol/Descriptors 112: Test timeout computed to be: 1500 -112: [12:42:38] ---------------------------- -112: start test autocorr2D -111: [12:42:38] done -111: [12:42:38] ------------------------------------- -111: [12:42:38] Test VSA descriptors. -111: [12:42:38] done -111: [12:42:38] ------------------------------------- -111: [12:42:38] Test molecular formula calculation. -111: [12:42:38] done -111: [12:42:38] ------------------------------------- -111: [12:42:38] Test Issue 3415534. -111: [12:42:38] done -111: [12:42:38] ------------------------------------- -111: [12:42:38] Test Issue3433771: Bad definition for Crippen atom type O11. -111: [12:42:38] done -111: [12:42:38] ------------------------------------- -111: [12:42:38] Test multithreading +111: [21:37:32] done +111: [21:37:32] ------------------------------------- +111: [21:37:32] Test VSA descriptors. +111: [21:37:32] done +111: [21:37:32] ------------------------------------- +111: [21:37:32] Test molecular formula calculation. +111: [21:37:32] done +111: [21:37:32] ------------------------------------- +111: [21:37:32] Test Issue 3415534. +111: [21:37:32] done +111: [21:37:32] ------------------------------------- +111: [21:37:32] Test Issue3433771: Bad definition for Crippen atom type O11. +111: [21:37:32] done +111: [21:37:32] ------------------------------------- +111: [21:37:32] Test multithreading 111: reading molecules -110: ......... -110: ---------------------------------------------------------------------- -110: Ran 9 tests in 0.031s -110: -110: OK +112: [21:37:32] ---------------------------- +112: start test autocorr2D 111: processing 111: launch :0 111: launch :1 111: launch :2 111: launch :3 -101/236 Test #110: pyFragCatalog .......................... Passed 0.28 sec -test 113 - Start 113: testATF - -113: Test command: /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/GraphMol/Descriptors/testATF -113: Working Directory: /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/GraphMol/Descriptors -113: Test timeout computed to be: 1500 -102/236 Test #113: testATF ................................ Passed 0.01 sec -test 114 - Start 114: testBCUT - -114: Test command: /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/GraphMol/Descriptors/testBCUT -114: Working Directory: /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/GraphMol/Descriptors -114: Test timeout computed to be: 1500 -114: [12:42:38] ------------------------------------- -114: [12:42:38] Basic BCUT tests. -109: [12:42:38] +110: ......... +110: ---------------------------------------------------------------------- +110: Ran 9 tests in 0.072s +110: +110: OK +109: [21:37:32] 109: 109: **** 109: Invariant Violation @@ -24233,17 +24248,17 @@ 109: Stacktrace: 109: 0# Invar::Invariant::toString[abi:cxx11]() const in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu//lib/libRDKitRDGeneral.so.1 109: 1# Invar::operator<<(std::ostream&, Invar::Invariant const&) in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu//lib/libRDKitRDGeneral.so.1 -109: 2# 0x0000FFFFAC471888 in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu//lib/libRDKitFragCatalog.so.1 +109: 2# 0x0000FFFFA9DE1888 in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu//lib/libRDKitFragCatalog.so.1 109: 3# RDKit::readFuncGroups(std::istream&, int) in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu//lib/libRDKitFragCatalog.so.1 -109: 4# 0x0000AAAAB68D785C in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/GraphMol/FragCatalog/testFragCatalog -109: 5# 0x0000AAAAB68D4760 in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/GraphMol/FragCatalog/testFragCatalog -109: 6# 0x0000FFFFABA4229C in /lib/aarch64-linux-gnu/libc.so.6 +109: 4# 0x0000AAAAE414785C in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/GraphMol/FragCatalog/testFragCatalog +109: 5# 0x0000AAAAE4144760 in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/GraphMol/FragCatalog/testFragCatalog +109: 6# 0x0000FFFFA93B229C in /lib/aarch64-linux-gnu/libc.so.6 109: 7# __libc_start_main in /lib/aarch64-linux-gnu/libc.so.6 -109: 8# 0x0000AAAAB68D4930 in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/GraphMol/FragCatalog/testFragCatalog +109: 8# 0x0000AAAAE4144930 in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/GraphMol/FragCatalog/testFragCatalog 109: ---------- 109: **** 109: -109: [12:42:38] +109: [21:37:32] 109: 109: **** 109: Invariant Violation @@ -24254,17 +24269,17 @@ 109: Stacktrace: 109: 0# Invar::Invariant::toString[abi:cxx11]() const in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu//lib/libRDKitRDGeneral.so.1 109: 1# Invar::operator<<(std::ostream&, Invar::Invariant const&) in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu//lib/libRDKitRDGeneral.so.1 -109: 2# 0x0000FFFFAC471888 in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu//lib/libRDKitFragCatalog.so.1 +109: 2# 0x0000FFFFA9DE1888 in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu//lib/libRDKitFragCatalog.so.1 109: 3# RDKit::readFuncGroups(std::istream&, int) in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu//lib/libRDKitFragCatalog.so.1 -109: 4# 0x0000AAAAB68D785C in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/GraphMol/FragCatalog/testFragCatalog -109: 5# 0x0000AAAAB68D4760 in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/GraphMol/FragCatalog/testFragCatalog -109: 6# 0x0000FFFFABA4229C in /lib/aarch64-linux-gnu/libc.so.6 +109: 4# 0x0000AAAAE414785C in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/GraphMol/FragCatalog/testFragCatalog +109: 5# 0x0000AAAAE4144760 in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/GraphMol/FragCatalog/testFragCatalog +109: 6# 0x0000FFFFA93B229C in /lib/aarch64-linux-gnu/libc.so.6 109: 7# __libc_start_main in /lib/aarch64-linux-gnu/libc.so.6 -109: 8# 0x0000AAAAB68D4930 in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/GraphMol/FragCatalog/testFragCatalog +109: 8# 0x0000AAAAE4144930 in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/GraphMol/FragCatalog/testFragCatalog 109: ---------- 109: **** 109: -109: [12:42:38] +109: [21:37:32] 109: 109: **** 109: Invariant Violation @@ -24275,642 +24290,779 @@ 109: Stacktrace: 109: 0# Invar::Invariant::toString[abi:cxx11]() const in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu//lib/libRDKitRDGeneral.so.1 109: 1# Invar::operator<<(std::ostream&, Invar::Invariant const&) in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu//lib/libRDKitRDGeneral.so.1 -109: 2# 0x0000FFFFAC471888 in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu//lib/libRDKitFragCatalog.so.1 +109: 2# 0x0000FFFFA9DE1888 in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu//lib/libRDKitFragCatalog.so.1 109: 3# RDKit::readFuncGroups(std::istream&, int) in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu//lib/libRDKitFragCatalog.so.1 -109: 4# 0x0000AAAAB68D785C in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/GraphMol/FragCatalog/testFragCatalog -109: 5# 0x0000AAAAB68D4760 in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/GraphMol/FragCatalog/testFragCatalog -109: 6# 0x0000FFFFABA4229C in /lib/aarch64-linux-gnu/libc.so.6 +109: 4# 0x0000AAAAE414785C in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/GraphMol/FragCatalog/testFragCatalog +109: 5# 0x0000AAAAE4144760 in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/GraphMol/FragCatalog/testFragCatalog +109: 6# 0x0000FFFFA93B229C in /lib/aarch64-linux-gnu/libc.so.6 109: 7# __libc_start_main in /lib/aarch64-linux-gnu/libc.so.6 -109: 8# 0x0000AAAAB68D4930 in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/GraphMol/FragCatalog/testFragCatalog +109: 8# 0x0000AAAAE4144930 in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/GraphMol/FragCatalog/testFragCatalog 109: ---------- 109: **** 109: -103/236 Test #109: testFragCatalog ........................ Passed 0.38 sec +101/236 Test #109: testFragCatalog ........................ Passed 0.66 sec +test 113 + Start 113: testATF + +113: Test command: /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/GraphMol/Descriptors/testATF +113: Working Directory: /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/GraphMol/Descriptors +113: Test timeout computed to be: 1500 +102/236 Test #113: testATF ................................ Passed 0.04 sec +test 114 + Start 114: testBCUT + +114: Test command: /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/GraphMol/Descriptors/testBCUT +114: Working Directory: /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/GraphMol/Descriptors +114: Test timeout computed to be: 1500 +114: [21:37:32] ------------------------------------- +114: [21:37:32] Basic BCUT tests. +114: [21:37:32] done +114: [21:37:32] ------------------------------------- +114: [21:37:32] Larger BCUT tests. +103/236 Test #110: pyFragCatalog .......................... Passed 0.69 sec test 115 Start 115: testEEM 115: Test command: /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/GraphMol/Descriptors/testEEM 115: Working Directory: /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/GraphMol/Descriptors 115: Test timeout computed to be: 1500 -114: [12:42:38] done -114: [12:42:38] ------------------------------------- -114: [12:42:38] Larger BCUT tests. -112: [12:42:38] done -112: [12:42:38] ------------------------------------- -112: [12:42:38] Test Github #3806: NaNs from AUTOCORR2D descriptor -112: [12:42:38] done -104/236 Test #112: testAUTOCORR2D ......................... Passed 0.18 sec +115: =>start test EEM +115: [21:37:32] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: 0 +115: [21:37:32] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [21:37:32] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [21:37:32] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [21:37:32] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [21:37:32] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [21:37:32] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [21:37:32] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [21:37:32] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [21:37:32] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [21:37:32] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [21:37:32] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [21:37:32] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [21:37:32] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [21:37:32] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [21:37:32] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [21:37:32] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [21:37:32] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [21:37:32] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [21:37:32] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [21:37:32] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [21:37:32] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [21:37:32] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [21:37:32] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [21:37:32] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [21:37:32] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [21:37:32] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [21:37:32] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [21:37:32] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [21:37:32] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [21:37:32] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [21:37:32] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [21:37:32] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [21:37:32] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [21:37:32] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [21:37:32] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [21:37:32] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [21:37:32] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [21:37:32] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [21:37:32] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [21:37:32] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [21:37:32] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [21:37:32] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [21:37:32] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [21:37:32] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [21:37:32] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [21:37:32] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [21:37:32] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [21:37:32] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [21:37:32] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [21:37:32] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [21:37:32] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [21:37:32] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [21:37:32] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [21:37:32] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [21:37:32] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [21:37:32] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [21:37:32] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [21:37:32] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [21:37:32] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [21:37:32] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [21:37:32] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [21:37:32] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [21:37:32] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [21:37:32] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [21:37:33] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [21:37:33] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [21:37:33] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [21:37:33] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [21:37:33] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [21:37:33] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [21:37:33] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [21:37:33] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [21:37:33] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [21:37:33] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [21:37:33] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [21:37:33] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [21:37:33] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [21:37:33] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [21:37:33] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [21:37:33] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [21:37:33] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [21:37:33] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [21:37:33] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [21:37:33] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [21:37:33] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [21:37:33] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [21:37:33] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [21:37:33] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [21:37:33] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [21:37:33] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [21:37:33] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [21:37:33] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [21:37:33] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [21:37:33] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [21:37:33] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [21:37:33] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [21:37:33] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [21:37:33] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [21:37:33] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [21:37:33] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: 100 +115: [21:37:33] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [21:37:33] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [21:37:33] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [21:37:33] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [21:37:33] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [21:37:33] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [21:37:33] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [21:37:33] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [21:37:33] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [21:37:33] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [21:37:33] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [21:37:33] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [21:37:33] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [21:37:33] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [21:37:33] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [21:37:33] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [21:37:33] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [21:37:33] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [21:37:33] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [21:37:33] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [21:37:33] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [21:37:33] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [21:37:33] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [21:37:33] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [21:37:33] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [21:37:33] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [21:37:33] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [21:37:33] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [21:37:33] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [21:37:33] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [21:37:33] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [21:37:33] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [21:37:33] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [21:37:33] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [21:37:33] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [21:37:33] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [21:37:33] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [21:37:33] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [21:37:33] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [21:37:33] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [21:37:33] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [21:37:33] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [21:37:33] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [21:37:33] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [21:37:33] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [21:37:33] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [21:37:33] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [21:37:33] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [21:37:33] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [21:37:33] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [21:37:33] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [21:37:33] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [21:37:33] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [21:37:33] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [21:37:33] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [21:37:33] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [21:37:33] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [21:37:33] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [21:37:33] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [21:37:33] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [21:37:33] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [21:37:33] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [21:37:33] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [21:37:33] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [21:37:33] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [21:37:33] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [21:37:33] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [21:37:33] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [21:37:33] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [21:37:33] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [21:37:33] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [21:37:33] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [21:37:33] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [21:37:33] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [21:37:33] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [21:37:33] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [21:37:33] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [21:37:33] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [21:37:33] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [21:37:33] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [21:37:33] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [21:37:33] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [21:37:33] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [21:37:33] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [21:37:33] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [21:37:33] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [21:37:33] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [21:37:33] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [21:37:33] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [21:37:33] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [21:37:33] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [21:37:33] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [21:37:33] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [21:37:33] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [21:37:33] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [21:37:33] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [21:37:33] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [21:37:33] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [21:37:33] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +112: [21:37:33] done +115: [21:37:33] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: 200 +115: [21:37:33] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [21:37:33] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [21:37:33] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [21:37:33] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [21:37:33] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [21:37:33] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [21:37:33] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [21:37:33] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [21:37:33] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [21:37:33] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [21:37:33] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [21:37:33] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [21:37:33] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [21:37:33] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [21:37:33] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +112: [21:37:33] ------------------------------------- +112: [21:37:33] Test Github #3806: NaNs from AUTOCORR2D descriptor +112: [21:37:33] done +104/236 Test #112: testAUTOCORR2D ......................... Passed 0.55 sec test 116 Start 116: testPBF 116: Test command: /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/GraphMol/Descriptors/testPBF 116: Working Directory: /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/GraphMol/Descriptors 116: Test timeout computed to be: 1500 -115: =>start test EEM -115: [12:42:38] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: 0 -115: [12:42:38] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [12:42:38] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [12:42:38] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [12:42:38] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [12:42:38] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [12:42:38] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [12:42:38] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [12:42:38] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [12:42:38] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [12:42:38] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [12:42:38] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [12:42:38] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [12:42:38] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [12:42:38] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [12:42:38] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [12:42:38] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [12:42:38] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [12:42:38] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [12:42:38] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [12:42:38] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [12:42:38] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [12:42:38] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [12:42:38] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -116: [12:42:38] ------------------------------------- -116: [12:42:38] Basic PBF tests. -115: [12:42:38] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [12:42:38] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [12:42:38] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [12:42:38] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [12:42:38] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [12:42:38] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [12:42:38] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [12:42:38] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [12:42:38] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [12:42:38] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [12:42:38] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [12:42:38] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [12:42:38] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [12:42:38] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [12:42:38] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [12:42:38] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [12:42:38] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [12:42:38] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [12:42:38] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [12:42:38] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [12:42:38] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [12:42:38] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [12:42:38] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [12:42:38] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [12:42:38] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [12:42:38] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [12:42:38] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [12:42:38] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [12:42:38] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [12:42:38] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [12:42:38] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [12:42:38] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [12:42:38] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [12:42:38] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [12:42:38] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [12:42:38] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [12:42:38] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [12:42:38] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [12:42:38] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [12:42:38] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [12:42:38] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [12:42:38] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [12:42:38] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [12:42:38] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [12:42:38] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [12:42:38] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [12:42:38] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [12:42:38] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [12:42:38] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [12:42:38] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [12:42:38] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [12:42:38] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [12:42:38] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [12:42:38] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [12:42:38] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [12:42:38] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [12:42:38] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [12:42:38] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [12:42:38] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [12:42:38] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [12:42:38] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [12:42:38] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [12:42:38] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [12:42:38] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [12:42:38] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [12:42:38] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [12:42:38] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [12:42:38] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [12:42:38] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -116: [12:42:38] done -116: [12:42:38] ------------------------------------- -116: [12:42:38] PBF edge cases. -116: [12:42:38] done -105/236 Test #116: testPBF ................................ Passed 0.13 sec +115: [21:37:33] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [21:37:33] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [21:37:33] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [21:37:33] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [21:37:33] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [21:37:33] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [21:37:33] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [21:37:33] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [21:37:33] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [21:37:33] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [21:37:33] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [21:37:33] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [21:37:33] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [21:37:33] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [21:37:33] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [21:37:33] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [21:37:33] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [21:37:33] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [21:37:33] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [21:37:33] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [21:37:33] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [21:37:33] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [21:37:33] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [21:37:33] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [21:37:33] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [21:37:33] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [21:37:33] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [21:37:33] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [21:37:33] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [21:37:33] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [21:37:33] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [21:37:33] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [21:37:33] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [21:37:33] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [21:37:33] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [21:37:33] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [21:37:33] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [21:37:33] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [21:37:33] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [21:37:33] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [21:37:33] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [21:37:33] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [21:37:33] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [21:37:33] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [21:37:33] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [21:37:33] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [21:37:33] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [21:37:33] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [21:37:33] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +116: [21:37:33] ------------------------------------- +116: [21:37:33] Basic PBF tests. +115: [21:37:33] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [21:37:33] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [21:37:33] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [21:37:33] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [21:37:33] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [21:37:33] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [21:37:33] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [21:37:33] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [21:37:33] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [21:37:33] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [21:37:33] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [21:37:33] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [21:37:33] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [21:37:33] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [21:37:33] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [21:37:33] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [21:37:33] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [21:37:33] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [21:37:33] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [21:37:33] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [21:37:33] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [21:37:33] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [21:37:33] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [21:37:33] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [21:37:33] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [21:37:33] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [21:37:33] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [21:37:33] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [21:37:33] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [21:37:33] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [21:37:33] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [21:37:33] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [21:37:33] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [21:37:33] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [21:37:33] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [21:37:33] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: 300 +115: [21:37:33] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [21:37:33] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [21:37:33] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [21:37:33] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [21:37:33] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [21:37:33] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [21:37:33] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [21:37:33] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [21:37:33] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [21:37:33] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [21:37:33] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [21:37:33] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [21:37:33] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [21:37:33] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [21:37:33] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [21:37:33] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [21:37:33] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [21:37:33] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [21:37:33] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [21:37:33] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [21:37:33] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [21:37:33] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [21:37:33] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [21:37:33] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [21:37:33] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [21:37:33] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [21:37:33] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [21:37:33] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [21:37:33] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [21:37:33] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [21:37:33] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [21:37:33] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [21:37:33] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [21:37:33] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [21:37:33] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [21:37:33] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [21:37:33] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [21:37:33] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [21:37:33] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [21:37:33] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [21:37:33] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [21:37:33] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [21:37:33] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [21:37:33] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [21:37:33] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [21:37:33] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [21:37:33] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [21:37:33] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [21:37:33] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [21:37:33] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [21:37:33] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [21:37:33] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [21:37:33] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [21:37:33] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [21:37:33] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [21:37:33] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [21:37:33] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [21:37:33] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [21:37:33] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [21:37:33] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [21:37:33] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [21:37:33] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [21:37:33] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [21:37:33] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +108: .............[21:37:33] SMILES Parse Error: syntax error while parsing: --- +108: [21:37:33] SMILES Parse Error: check for mistakes around position 1: +108: [21:37:33] --- +108: [21:37:33] ^ +108: [21:37:33] SMILES Parse Error: Failed parsing SMILES '---' for input: '---' +108: [21:37:33] dasfsadf +108: [21:37:33] SMILES Parse Error: syntax error while parsing: --- +108: [21:37:33] SMILES Parse Error: check for mistakes around position 1: +108: [21:37:33] --- +108: [21:37:33] ^ +108: [21:37:33] SMILES Parse Error: Failed parsing SMILES '---' for input: '---' +108: [21:37:33] dasfsadf +108: [21:37:33] SMILES Parse Error: syntax error while parsing: --- +108: [21:37:33] SMILES Parse Error: check for mistakes around position 1: +108: [21:37:33] --- +108: [21:37:33] ^ +108: [21:37:33] SMILES Parse Error: Failed parsing SMILES '---' for input: '---' +108: [21:37:33] dasfsadf +108: [21:37:33] SMILES Parse Error: syntax error while parsing: --- +108: [21:37:33] SMILES Parse Error: check for mistakes around position 1: +108: [21:37:33] --- +108: [21:37:33] ^ +108: [21:37:33] SMILES Parse Error: Failed parsing SMILES '---' for input: '---' +108: [21:37:33] dasfsadf +108: [21:37:33] SMILES Parse Error: syntax error while parsing: --- +108: [21:37:33] SMILES Parse Error: check for mistakes around position 1: +108: [21:37:33] --- +108: [21:37:33] ^ +108: [21:37:33] SMILES Parse Error: Failed parsing SMILES '---' for input: '---' +108: [21:37:33] dasfsadf +108: [21:37:33] SMILES Parse Error: syntax error while parsing: --- +108: [21:37:33] SMILES Parse Error: check for mistakes around position 1: +108: [21:37:33] --- +108: [21:37:33] ^ +108: [21:37:33] SMILES Parse Error: Failed parsing SMILES '---' for input: '---' +108: [21:37:33] dasfsadf +108: [21:37:33] SMILES Parse Error: syntax error while parsing: --- +108: [21:37:33] SMILES Parse Error: check for mistakes around position 1: +108: [21:37:33] --- +108: [21:37:33] ^ +108: [21:37:33] SMILES Parse Error: Failed parsing SMILES '---' for input: '---' +108: [21:37:33] dasfsadf +108: [21:37:33] SMILES Parse Error: syntax error while parsing: --- +108: [21:37:33] SMILES Parse Error: check for mistakes around position 1: +108: [21:37:33] --- +108: [21:37:33] ^ +108: [21:37:33] SMILES Parse Error: Failed parsing SMILES '---' for input: '---' +108: [21:37:33] dasfsadf +108: [21:37:33] SMILES Parse Error: syntax error while parsing: --- +108: [21:37:33] SMILES Parse Error: check for mistakes around position 1: +108: [21:37:33] --- +108: [21:37:33] ^ +108: [21:37:33] SMILES Parse Error: Failed parsing SMILES '---' for input: '---' +108: [21:37:33] dasfsadf +108: [21:37:33] SMILES Parse Error: syntax error while parsing: --- +108: [21:37:33] SMILES Parse Error: check for mistakes around position 1: +108: [21:37:33] --- +108: [21:37:33] ^ +108: [21:37:33] SMILES Parse Error: Failed parsing SMILES '---' for input: '---' +108: [21:37:33] dasfsadf +115: [21:37:33] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [21:37:33] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +114: [21:37:33] ------------------------------------- +114: [21:37:33] Test empty molecule BCUT. +108: [21:37:33] SMILES Parse Error: syntax error while parsing: --- +108: [21:37:33] SMILES Parse Error: check for mistakes around position 1: +108: [21:37:33] --- +108: [21:37:33] ^ +108: [21:37:33] SMILES Parse Error: Failed parsing SMILES '---' for input: '---' +108: [21:37:33] dasfsadf +108: [21:37:33] SMILES Parse Error: syntax error while parsing: --- +108: [21:37:33] SMILES Parse Error: check for mistakes around position 1: +108: [21:37:33] --- +108: [21:37:33] ^ +108: [21:37:33] SMILES Parse Error: Failed parsing SMILES '---' for input: '---' +108: [21:37:33] dasfsadf +108: [21:37:33] SMILES Parse Error: syntax error while parsing: --- +108: [21:37:33] SMILES Parse Error: check for mistakes around position 1: +108: [21:37:33] --- +108: [21:37:33] ^ +108: [21:37:33] SMILES Parse Error: Failed parsing SMILES '---' for input: '---' +108: [21:37:33] dasfsadf +108: [21:37:33] SMILES Parse Error: syntax error while parsing: --- +108: [21:37:33] SMILES Parse Error: check for mistakes around position 1: +108: [21:37:33] --- +108: [21:37:33] ^ +108: [21:37:33] SMILES Parse Error: Failed parsing SMILES '---' for input: '---' +108: [21:37:33] dasfsadf +108: [21:37:33] SMILES Parse Error: syntax error while parsing: --- +108: [21:37:33] SMILES Parse Error: check for mistakes around position 1: +108: [21:37:33] --- +108: [21:37:33] ^ +108: [21:37:33] SMILES Parse Error: Failed parsing SMILES '---' for input: '---' +108: [21:37:33] dasfsadf +108: [21:37:33] SMILES Parse Error: syntax error while parsing: --- +108: [21:37:33] SMILES Parse Error: check for mistakes around position 1: +108: [21:37:33] --- +108: [21:37:33] ^ +108: [21:37:33] SMILES Parse Error: Failed parsing SMILES '---' for input: '---' +108: [21:37:33] dasfsadf +108: [21:37:33] SMILES Parse Error: syntax error while parsing: --- +108: [21:37:33] SMILES Parse Error: check for mistakes around position 1: +108: [21:37:33] --- +108: [21:37:33] ^ +108: [21:37:33] SMILES Parse Error: Failed parsing SMILES '---' for input: '---' +108: [21:37:33] dasfsadf +108: [21:37:33] SMILES Parse Error: syntax error while parsing: --- +108: [21:37:33] SMILES Parse Error: check for mistakes around position 1: +108: [21:37:33] --- +108: [21:37:33] ^ +108: [21:37:33] SMILES Parse Error: Failed parsing SMILES '---' for input: '---' +108: [21:37:33] dasfsadf +108: [21:37:33] SMILES Parse Error: syntax error while parsing: --- +108: [21:37:33] SMILES Parse Error: check for mistakes around position 1: +108: [21:37:33] --- +108: [21:37:33] ^ +108: [21:37:33] SMILES Parse Error: Failed parsing SMILES '---' for input: '---' +108: [21:37:33] dasfsadf +108: [21:37:33] SMILES Parse Error: syntax error while parsing: --- +108: [21:37:33] SMILES Parse Error: check for mistakes around position 1: +108: [21:37:33] --- +108: [21:37:33] ^ +108: [21:37:33] SMILES Parse Error: Failed parsing SMILES '---' for input: '---' +108: [21:37:33] dasfsadf +115: [21:37:33] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +105/236 Test #114: testBCUT ............................... Passed 0.41 sec test 117 Start 117: testRDFcustom 117: Test command: /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/GraphMol/Descriptors/testRDFcustom 117: Working Directory: /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/GraphMol/Descriptors 117: Test timeout computed to be: 1500 -115: [12:42:38] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [12:42:38] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [12:42:38] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [12:42:38] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [12:42:38] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [12:42:38] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [12:42:38] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [12:42:38] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: 100 -115: [12:42:38] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [12:42:38] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [12:42:38] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [12:42:38] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [12:42:38] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [12:42:38] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [12:42:38] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [12:42:38] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [12:42:38] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -108: .............[12:42:38] SMILES Parse Error: syntax error while parsing: --- -108: [12:42:38] SMILES Parse Error: check for mistakes around position 1: -108: [12:42:38] --- -108: [12:42:38] ^ -108: [12:42:38] SMILES Parse Error: Failed parsing SMILES '---' for input: '---' -108: [12:42:38] dasfsadf -108: [12:42:38] SMILES Parse Error: syntax error while parsing: --- -108: [12:42:38] SMILES Parse Error: check for mistakes around position 1: -108: [12:42:38] --- -108: [12:42:38] ^ -108: [12:42:38] SMILES Parse Error: Failed parsing SMILES '---' for input: '---' -108: [12:42:38] dasfsadf -115: [12:42:38] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [12:42:38] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -108: [12:42:38] SMILES Parse Error: syntax error while parsing: --- -108: [12:42:38] SMILES Parse Error: check for mistakes around position 1: -108: [12:42:38] --- -108: [12:42:38] ^ -108: [12:42:38] SMILES Parse Error: Failed parsing SMILES '---' for input: '---' -108: [12:42:38] dasfsadf -108: [12:42:38] SMILES Parse Error: syntax error while parsing: --- -108: [12:42:38] SMILES Parse Error: check for mistakes around position 1: -108: [12:42:38] --- -108: [12:42:38] ^ -108: [12:42:38] SMILES Parse Error: Failed parsing SMILES '---' for input: '---' -108: [12:42:38] dasfsadf -108: [12:42:38] SMILES Parse Error: syntax error while parsing: --- -108: [12:42:38] SMILES Parse Error: check for mistakes around position 1: -108: [12:42:38] --- -108: [12:42:38] ^ -108: [12:42:38] SMILES Parse Error: Failed parsing SMILES '---' for input: '---' -108: [12:42:38] dasfsadf -108: [12:42:38] SMILES Parse Error: syntax error while parsing: --- -108: [12:42:38] SMILES Parse Error: check for mistakes around position 1: -108: [12:42:38] --- -108: [12:42:38] ^ -108: [12:42:38] SMILES Parse Error: Failed parsing SMILES '---' for input: '---' -108: [12:42:38] dasfsadf -115: [12:42:38] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -108: [12:42:38] SMILES Parse Error: syntax error while parsing: --- -108: [12:42:38] SMILES Parse Error: check for mistakes around position 1: -108: [12:42:38] --- -108: [12:42:38] ^ -108: [12:42:38] SMILES Parse Error: Failed parsing SMILES '---' for input: '---' -108: [12:42:38] dasfsadf -108: [12:42:38] SMILES Parse Error: syntax error while parsing: --- -108: [12:42:38] SMILES Parse Error: check for mistakes around position 1: -108: [12:42:38] --- -108: [12:42:38] ^ -108: [12:42:38] SMILES Parse Error: Failed parsing SMILES '---' for input: '---' -108: [12:42:38] dasfsadf -108: [12:42:38] SMILES Parse Error: syntax error while parsing: --- -108: [12:42:38] SMILES Parse Error: check for mistakes around position 1: -108: [12:42:38] --- -108: [12:42:38] ^ -108: [12:42:38] SMILES Parse Error: Failed parsing SMILES '---' for input: '---' -108: [12:42:38] dasfsadf -108: [12:42:38] SMILES Parse Error: syntax error while parsing: --- -108: [12:42:38] SMILES Parse Error: check for mistakes around position 1: -108: [12:42:38] --- -108: [12:42:38] ^ -108: [12:42:38] SMILES Parse Error: Failed parsing SMILES '---' for input: '---' -108: [12:42:38] dasfsadf -115: [12:42:38] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [12:42:38] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [12:42:38] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [12:42:38] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [12:42:38] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [12:42:38] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [12:42:38] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [12:42:38] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [12:42:38] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [12:42:38] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [12:42:38] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [12:42:38] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [12:42:38] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [12:42:38] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [12:42:38] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -108: [12:42:38] SMILES Parse Error: syntax error while parsing: --- -108: [12:42:38] SMILES Parse Error: check for mistakes around position 1: -108: [12:42:38] --- -108: [12:42:38] ^ -108: [12:42:38] SMILES Parse Error: Failed parsing SMILES '---' for input: '---' -108: [12:42:38] dasfsadf -108: [12:42:38] SMILES Parse Error: syntax error while parsing: --- -108: [12:42:38] SMILES Parse Error: check for mistakes around position 1: -108: [12:42:38] --- -108: [12:42:38] ^ -108: [12:42:38] SMILES Parse Error: Failed parsing SMILES '---' for input: '---' -108: [12:42:38] dasfsadf -108: [12:42:38] SMILES Parse Error: syntax error while parsing: --- -108: [12:42:38] SMILES Parse Error: check for mistakes around position 1: -108: [12:42:38] --- -108: [12:42:38] ^ -108: [12:42:38] SMILES Parse Error: Failed parsing SMILES '---' for input: '---' -108: [12:42:38] dasfsadf -108: [12:42:38] SMILES Parse Error: syntax error while parsing: --- -108: [12:42:38] SMILES Parse Error: check for mistakes around position 1: -108: [12:42:38] --- -108: [12:42:38] ^ -108: [12:42:38] SMILES Parse Error: Failed parsing SMILES '---' for input: '---' -108: [12:42:38] dasfsadf -108: [12:42:38] SMILES Parse Error: syntax error while parsing: --- -108: [12:42:38] SMILES Parse Error: check for mistakes around position 1: -108: [12:42:38] --- -108: [12:42:38] ^ -108: [12:42:38] SMILES Parse Error: Failed parsing SMILES '---' for input: '---' -108: [12:42:38] dasfsadf -108: [12:42:38] SMILES Parse Error: syntax error while parsing: --- -108: [12:42:38] SMILES Parse Error: check for mistakes around position 1: -108: [12:42:38] --- -108: [12:42:38] ^ -108: [12:42:38] SMILES Parse Error: Failed parsing SMILES '---' for input: '---' -108: [12:42:38] dasfsadf -108: [12:42:38] SMILES Parse Error: syntax error while parsing: --- -108: [12:42:38] SMILES Parse Error: check for mistakes around position 1: -108: [12:42:38] --- -108: [12:42:38] ^ -108: [12:42:38] SMILES Parse Error: Failed parsing SMILES '---' for input: '---' -108: [12:42:38] dasfsadf -108: [12:42:38] SMILES Parse Error: syntax error while parsing: --- -108: [12:42:38] SMILES Parse Error: check for mistakes around position 1: -108: [12:42:38] --- -108: [12:42:38] ^ -108: [12:42:38] SMILES Parse Error: Failed parsing SMILES '---' for input: '---' -108: [12:42:38] dasfsadf -108: [12:42:38] SMILES Parse Error: syntax error while parsing: --- -108: [12:42:38] SMILES Parse Error: check for mistakes around position 1: -108: [12:42:38] --- -108: [12:42:38] ^ -108: [12:42:38] SMILES Parse Error: Failed parsing SMILES '---' for input: '---' -108: [12:42:38] dasfsadf -108: [12:42:38] SMILES Parse Error: syntax error while parsing: --- -108: [12:42:38] SMILES Parse Error: check for mistakes around position 1: -108: [12:42:38] --- -108: [12:42:38] ^ -108: [12:42:38] SMILES Parse Error: Failed parsing SMILES '---' for input: '---' -108: [12:42:38] dasfsadf -115: [12:42:38] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [12:42:38] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [12:42:38] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [12:42:38] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [12:42:38] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [12:42:38] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [12:42:38] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [12:42:38] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [12:42:38] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -108: [12:42:38] SMILES Parse Error: syntax error while parsing: --- -108: [12:42:38] SMILES Parse Error: check for mistakes around position 1: -108: [12:42:38] --- -108: [12:42:38] ^ -108: [12:42:38] SMILES Parse Error: Failed parsing SMILES '---' for input: '---' -108: [12:42:38] dasfsadf -108: [12:42:38] SMILES Parse Error: syntax error while parsing: --- -108: [12:42:38] SMILES Parse Error: check for mistakes around position 1: -108: [12:42:38] --- -108: [12:42:38] ^ -108: [12:42:38] SMILES Parse Error: Failed parsing SMILES '---' for input: '---' -108: [12:42:38] dasfsadf -108: [12:42:38] SMILES Parse Error: syntax error while parsing: --- -108: [12:42:38] SMILES Parse Error: check for mistakes around position 1: -108: [12:42:38] --- -108: [12:42:38] ^ -108: [12:42:38] SMILES Parse Error: Failed parsing SMILES '---' for input: '---' -108: [12:42:38] dasfsadf -108: [12:42:38] SMILES Parse Error: syntax error while parsing: --- -108: [12:42:38] SMILES Parse Error: check for mistakes around position 1: -108: [12:42:38] --- -108: [12:42:38] ^ -108: [12:42:38] SMILES Parse Error: Failed parsing SMILES '---' for input: '---' -108: [12:42:38] dasfsadf -108: [12:42:38] SMILES Parse Error: syntax error while parsing: --- -108: [12:42:38] SMILES Parse Error: check for mistakes around position 1: -108: [12:42:38] --- -108: [12:42:38] ^ -108: [12:42:38] SMILES Parse Error: Failed parsing SMILES '---' for input: '---' -108: [12:42:38] dasfsadf -108: [12:42:38] SMILES Parse Error: syntax error while parsing: --- -108: [12:42:38] SMILES Parse Error: check for mistakes around position 1: -108: [12:42:38] --- -108: [12:42:38] ^ -108: [12:42:38] SMILES Parse Error: Failed parsing SMILES '---' for input: '---' -108: [12:42:38] dasfsadf -108: [12:42:38] SMILES Parse Error: syntax error while parsing: --- -108: [12:42:38] SMILES Parse Error: check for mistakes around position 1: -108: [12:42:38] --- -108: [12:42:38] ^ -108: [12:42:38] SMILES Parse Error: Failed parsing SMILES '---' for input: '---' -108: [12:42:38] dasfsadf -108: [12:42:38] SMILES Parse Error: syntax error while parsing: --- -108: [12:42:38] SMILES Parse Error: check for mistakes around position 1: -108: [12:42:38] --- -108: [12:42:38] ^ -108: [12:42:38] SMILES Parse Error: Failed parsing SMILES '---' for input: '---' -108: [12:42:38] dasfsadf -108: [12:42:38] SMILES Parse Error: syntax error while parsing: --- -108: [12:42:38] SMILES Parse Error: check for mistakes around position 1: -108: [12:42:38] --- -108: [12:42:38] ^ -108: [12:42:38] SMILES Parse Error: Failed parsing SMILES '---' for input: '---' -108: [12:42:38] dasfsadf -108: [12:42:38] SMILES Parse Error: syntax error while parsing: --- -108: [12:42:38] SMILES Parse Error: check for mistakes around position 1: -108: [12:42:38] --- -108: [12:42:38] ^ -108: [12:42:38] SMILES Parse Error: Failed parsing SMILES '---' for input: '---' -108: [12:42:38] dasfsadf -115: [12:42:38] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [12:42:38] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [12:42:38] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [12:42:38] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [12:42:38] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [12:42:38] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [12:42:38] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [12:42:38] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [12:42:38] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [12:42:38] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [12:42:38] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [12:42:38] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [12:42:38] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [12:42:38] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [12:42:38] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [12:42:38] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [12:42:38] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [12:42:38] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [12:42:38] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [12:42:38] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [12:42:38] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [12:42:38] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [12:42:38] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [12:42:38] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [12:42:38] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [12:42:38] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [12:42:38] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [12:42:38] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [12:42:38] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [12:42:38] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [12:42:38] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [12:42:38] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [12:42:38] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [12:42:38] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [12:42:38] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [12:42:38] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [12:42:38] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [12:42:38] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [12:42:38] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [12:42:38] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [12:42:38] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [12:42:38] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [12:42:38] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [12:42:38] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [12:42:38] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [12:42:38] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [12:42:38] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [12:42:38] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [12:42:38] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [12:42:38] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [12:42:38] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [12:42:38] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [12:42:38] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [12:42:38] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [12:42:38] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [12:42:38] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [12:42:38] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [12:42:38] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [12:42:38] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [12:42:38] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [12:42:38] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [12:42:38] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [12:42:38] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [12:42:38] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: 200 -115: [12:42:38] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [12:42:38] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [12:42:38] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [12:42:38] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [12:42:38] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [12:42:38] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [12:42:38] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [12:42:38] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [12:42:38] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [12:42:38] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [12:42:38] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [12:42:38] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [12:42:38] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [12:42:38] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [12:42:38] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [12:42:38] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [12:42:38] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [12:42:38] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [12:42:38] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [12:42:38] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [12:42:38] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [12:42:38] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [12:42:38] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [12:42:38] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [12:42:38] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [12:42:38] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [12:42:38] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [12:42:38] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [12:42:38] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [12:42:38] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [12:42:38] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [12:42:38] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [12:42:38] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [12:42:38] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [12:42:38] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [12:42:38] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [12:42:38] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [12:42:38] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [12:42:38] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -114: [12:42:38] ------------------------------------- -114: [12:42:38] Test empty molecule BCUT. -115: [12:42:38] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [12:42:38] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [12:42:38] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [12:42:38] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [12:42:38] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [12:42:38] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [12:42:38] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [12:42:38] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [12:42:38] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [12:42:38] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [12:42:38] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [12:42:38] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [12:42:38] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -106/236 Test #114: testBCUT ............................... Passed 0.28 sec +115: [21:37:33] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [21:37:33] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [21:37:33] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [21:37:33] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [21:37:33] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [21:37:33] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +108: [21:37:33] SMILES Parse Error: syntax error while parsing: --- +108: [21:37:33] SMILES Parse Error: check for mistakes around position 1: +108: [21:37:33] --- +108: [21:37:33] ^ +108: [21:37:33] SMILES Parse Error: Failed parsing SMILES '---' for input: '---' +108: [21:37:33] dasfsadf +108: [21:37:33] SMILES Parse Error: syntax error while parsing: --- +108: [21:37:33] SMILES Parse Error: check for mistakes around position 1: +108: [21:37:33] --- +108: [21:37:33] ^ +108: [21:37:33] SMILES Parse Error: Failed parsing SMILES '---' for input: '---' +108: [21:37:33] dasfsadf +108: [21:37:33] SMILES Parse Error: syntax error while parsing: --- +108: [21:37:33] SMILES Parse Error: check for mistakes around position 1: +108: [21:37:33] --- +108: [21:37:33] ^ +108: [21:37:33] SMILES Parse Error: Failed parsing SMILES '---' for input: '---' +108: [21:37:33] dasfsadf +108: [21:37:33] SMILES Parse Error: syntax error while parsing: --- +108: [21:37:33] SMILES Parse Error: check for mistakes around position 1: +108: [21:37:33] --- +108: [21:37:33] ^ +108: [21:37:33] SMILES Parse Error: Failed parsing SMILES '---' for input: '---' +108: [21:37:33] dasfsadf +108: [21:37:33] SMILES Parse Error: syntax error while parsing: --- +108: [21:37:33] SMILES Parse Error: check for mistakes around position 1: +108: [21:37:33] --- +108: [21:37:33] ^ +108: [21:37:33] SMILES Parse Error: Failed parsing SMILES '---' for input: '---' +108: [21:37:33] dasfsadf +108: [21:37:33] SMILES Parse Error: syntax error while parsing: --- +108: [21:37:33] SMILES Parse Error: check for mistakes around position 1: +108: [21:37:33] --- +108: [21:37:33] ^ +108: [21:37:33] SMILES Parse Error: Failed parsing SMILES '---' for input: '---' +108: [21:37:33] dasfsadf +108: [21:37:33] SMILES Parse Error: syntax error while parsing: --- +108: [21:37:33] SMILES Parse Error: check for mistakes around position 1: +108: [21:37:33] --- +108: [21:37:33] ^ +108: [21:37:33] SMILES Parse Error: Failed parsing SMILES '---' for input: '---' +108: [21:37:33] dasfsadf +108: [21:37:33] SMILES Parse Error: syntax error while parsing: --- +108: [21:37:33] SMILES Parse Error: check for mistakes around position 1: +108: [21:37:33] --- +108: [21:37:33] ^ +108: [21:37:33] SMILES Parse Error: Failed parsing SMILES '---' for input: '---' +108: [21:37:33] dasfsadf +108: [21:37:33] SMILES Parse Error: syntax error while parsing: --- +108: [21:37:33] SMILES Parse Error: check for mistakes around position 1: +108: [21:37:33] --- +108: [21:37:33] ^ +108: [21:37:33] SMILES Parse Error: Failed parsing SMILES '---' for input: '---' +108: [21:37:33] dasfsadf +108: [21:37:33] SMILES Parse Error: syntax error while parsing: --- +108: [21:37:33] SMILES Parse Error: check for mistakes around position 1: +108: [21:37:33] --- +108: [21:37:33] ^ +108: [21:37:33] SMILES Parse Error: Failed parsing SMILES '---' for input: '---' +108: [21:37:33] dasfsadf +115: [21:37:33] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [21:37:33] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [21:37:33] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [21:37:33] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [21:37:33] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [21:37:33] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [21:37:33] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [21:37:33] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [21:37:33] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [21:37:33] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [21:37:33] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [21:37:33] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [21:37:33] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [21:37:33] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [21:37:33] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [21:37:33] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [21:37:33] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [21:37:33] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [21:37:33] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [21:37:33] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [21:37:33] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [21:37:33] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [21:37:33] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [21:37:33] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [21:37:33] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [21:37:33] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [21:37:33] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: 400 +115: [21:37:33] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [21:37:33] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [21:37:33] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [21:37:33] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [21:37:33] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [21:37:33] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [21:37:33] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [21:37:33] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [21:37:33] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [21:37:33] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [21:37:33] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [21:37:33] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [21:37:33] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [21:37:33] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [21:37:33] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [21:37:33] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [21:37:33] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [21:37:33] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [21:37:33] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [21:37:33] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [21:37:33] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [21:37:33] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [21:37:33] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [21:37:33] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [21:37:33] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [21:37:33] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [21:37:33] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [21:37:33] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [21:37:33] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [21:37:33] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [21:37:33] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [21:37:33] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [21:37:33] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [21:37:33] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [21:37:33] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [21:37:33] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [21:37:33] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [21:37:33] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [21:37:33] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [21:37:33] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [21:37:33] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [21:37:33] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [21:37:33] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [21:37:33] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [21:37:33] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [21:37:33] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [21:37:33] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [21:37:33] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [21:37:33] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [21:37:33] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [21:37:33] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [21:37:33] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [21:37:33] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [21:37:33] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [21:37:33] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [21:37:33] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [21:37:33] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [21:37:33] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [21:37:33] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [21:37:33] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [21:37:33] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [21:37:33] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [21:37:33] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [21:37:33] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [21:37:33] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [21:37:33] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [21:37:33] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [21:37:33] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [21:37:33] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [21:37:33] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [21:37:33] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [21:37:33] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [21:37:33] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [21:37:33] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [21:37:33] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [21:37:33] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [21:37:33] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [21:37:33] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [21:37:33] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [21:37:33] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [21:37:33] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [21:37:33] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [21:37:33] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [21:37:33] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [21:37:33] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [21:37:33] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [21:37:33] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +108: .[21:37:33] SMILES Parse Error: syntax error while parsing: mydoghasfleas +108: [21:37:33] SMILES Parse Error: check for mistakes around position 1: +108: [21:37:33] mydoghasfleas +108: [21:37:33] ^ +108: [21:37:33] SMILES Parse Error: Failed parsing SMILES 'mydoghasfleas' for input: 'mydoghasfleas' +116: [21:37:33] done +116: [21:37:33] ------------------------------------- +116: [21:37:33] PBF edge cases. +116: [21:37:33] done +115: [21:37:33] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [21:37:33] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [21:37:33] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [21:37:33] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [21:37:33] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [21:37:33] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +106/236 Test #116: testPBF ................................ Passed 0.24 sec test 118 Start 118: testRDF 118: Test command: /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/GraphMol/Descriptors/testRDF 118: Working Directory: /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/GraphMol/Descriptors 118: Test timeout computed to be: 1500 -115: [12:42:38] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [12:42:38] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [12:42:38] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [12:42:38] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [12:42:38] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [12:42:38] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [12:42:38] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [12:42:38] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [12:42:38] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [12:42:38] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [12:42:38] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [12:42:38] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -108: .[12:42:38] SMILES Parse Error: syntax error while parsing: mydoghasfleas -108: [12:42:38] SMILES Parse Error: check for mistakes around position 1: -108: [12:42:38] mydoghasfleas -108: [12:42:38] ^ -108: [12:42:38] SMILES Parse Error: Failed parsing SMILES 'mydoghasfleas' for input: 'mydoghasfleas' -115: [12:42:38] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [12:42:38] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [12:42:38] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [12:42:38] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [12:42:38] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [12:42:38] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [12:42:38] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [12:42:38] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [12:42:38] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [12:42:38] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [12:42:38] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [12:42:38] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [12:42:38] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [12:42:38] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [12:42:38] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [12:42:38] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [12:42:38] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [12:42:38] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [12:42:38] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [12:42:38] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [12:42:38] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [12:42:38] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [12:42:38] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [12:42:38] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [12:42:38] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [12:42:38] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [12:42:38] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [12:42:38] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [12:42:38] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [12:42:38] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [12:42:38] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [12:42:38] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [12:42:38] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [12:42:38] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [12:42:38] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [12:42:38] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: 300 -115: [12:42:38] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [12:42:38] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [12:42:38] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [12:42:38] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [12:42:38] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [12:42:38] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [12:42:38] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [12:42:38] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [12:42:38] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [12:42:38] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [12:42:38] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [12:42:38] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [12:42:38] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [12:42:38] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [12:42:38] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [12:42:38] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [12:42:38] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [12:42:38] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [12:42:38] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [12:42:38] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [12:42:38] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [12:42:38] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [12:42:38] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [12:42:38] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [12:42:38] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [12:42:38] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [12:42:38] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [12:42:38] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [12:42:38] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [12:42:38] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [12:42:38] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [12:42:38] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [12:42:38] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [12:42:38] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [12:42:38] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [12:42:38] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [12:42:38] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [12:42:38] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [12:42:38] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [12:42:38] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [12:42:38] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [12:42:38] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [12:42:38] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [12:42:38] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [12:42:38] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [12:42:38] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [12:42:38] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [12:42:38] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [12:42:38] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [12:42:38] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [12:42:38] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [12:42:38] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [12:42:38] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [12:42:38] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [12:42:38] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [12:42:38] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [12:42:38] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [12:42:38] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [12:42:38] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [12:42:38] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [12:42:38] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [12:42:38] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [12:42:38] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [12:42:38] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [12:42:38] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [12:42:38] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [12:42:38] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [12:42:38] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [12:42:38] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [12:42:38] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [12:42:38] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [12:42:38] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [12:42:38] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [12:42:38] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [12:42:38] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [12:42:38] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [12:42:38] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [12:42:38] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [12:42:38] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [12:42:38] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [12:42:38] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [12:42:38] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [12:42:38] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [12:42:38] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [12:42:38] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [12:42:38] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [12:42:38] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [12:42:38] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [12:42:38] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [21:37:33] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [21:37:33] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [21:37:33] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [21:37:33] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [21:37:33] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [21:37:33] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: Elapsed time: 0.425258 s +115: Errors:0 +115: [21:37:33] test on : 500 molecules done +107/236 Test #115: testEEM ................................ Passed 0.49 sec +test 119 + Start 119: testMORSE + +119: Test command: /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/GraphMol/Descriptors/testMORSE +119: Working Directory: /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/GraphMol/Descriptors +119: Test timeout computed to be: 1500 108: ....... 108: ---------------------------------------------------------------------- -108: Ran 21 tests in 0.578s +108: Ran 21 tests in 1.116s 108: 108: OK 108: (Five aromatic carbons And (Not any of Five aromatic carbons)) @@ -24932,139 +25084,18 @@ 108: 1 108: 2 108: running -115: [12:42:38] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [12:42:38] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [12:42:38] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [12:42:38] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [12:42:38] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [12:42:38] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [12:42:38] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [12:42:38] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [12:42:38] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [12:42:38] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [12:42:38] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: 400 -115: [12:42:38] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [12:42:38] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [12:42:38] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [12:42:38] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [12:42:38] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [12:42:38] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [12:42:38] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [12:42:38] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [12:42:38] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [12:42:38] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [12:42:38] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [12:42:38] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [12:42:38] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [12:42:38] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [12:42:38] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [12:42:38] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [12:42:38] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [12:42:38] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [12:42:38] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [12:42:38] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [12:42:38] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [12:42:38] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [12:42:38] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [12:42:38] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [12:42:38] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [12:42:38] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [12:42:38] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [12:42:38] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [12:42:38] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [12:42:38] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [12:42:38] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [12:42:38] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [12:42:38] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [12:42:38] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [12:42:38] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [12:42:38] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [12:42:38] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [12:42:38] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [12:42:38] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [12:42:38] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [12:42:38] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [12:42:38] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [12:42:38] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [12:42:38] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [12:42:38] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [12:42:38] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [12:42:38] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [12:42:38] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [12:42:38] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [12:42:38] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [12:42:38] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [12:42:38] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [12:42:38] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [12:42:38] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [12:42:38] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [12:42:38] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [12:42:38] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [12:42:38] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [12:42:38] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [12:42:38] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [12:42:38] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [12:42:38] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [12:42:38] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [12:42:38] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [12:42:38] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [12:42:38] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [12:42:38] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [12:42:38] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [12:42:38] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [12:42:38] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [12:42:38] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [12:42:38] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -107/236 Test #108: pyFilterCatalog ........................ Passed 0.84 sec -115: [12:42:38] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -test 119 - Start 119: testMORSE - -119: Test command: /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/GraphMol/Descriptors/testMORSE -119: Working Directory: /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/GraphMol/Descriptors -119: Test timeout computed to be: 1500 -115: [12:42:38] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [12:42:38] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [12:42:38] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [12:42:38] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [12:42:38] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [12:42:38] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [12:42:38] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [12:42:38] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [12:42:38] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [12:42:38] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [12:42:38] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [12:42:38] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [12:42:38] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [12:42:38] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [12:42:38] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [12:42:38] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [12:42:38] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [12:42:38] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [12:42:38] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [12:42:38] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [12:42:38] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [12:42:38] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [12:42:38] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [12:42:38] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [12:42:38] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [12:42:38] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: Elapsed time: 0.409412 s -115: Errors:0 -115: [12:42:38] test on : 500 molecules done -108/236 Test #115: testEEM ................................ Passed 0.44 sec +108/236 Test #108: pyFilterCatalog ........................ Passed 1.63 sec test 120 Start 120: test3D 120: Test command: /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/GraphMol/Descriptors/test3D 120: Working Directory: /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/GraphMol/Descriptors 120: Test timeout computed to be: 1500 -120: [12:42:38] ------------------------------------- -120: [12:42:38] Basic PMI tests. +120: [21:37:33] ------------------------------------- +120: [21:37:33] Basic PMI tests. 118: =>start test rdf -118: [12:42:38] test on : 365 molecules done -109/236 Test #118: testRDF ................................ Passed 0.25 sec +118: [21:37:33] test on : 365 molecules done +109/236 Test #118: testRDF ................................ Passed 0.34 sec test 121 Start 121: testWHIM @@ -25072,49 +25103,49 @@ 121: Working Directory: /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/GraphMol/Descriptors 121: Test timeout computed to be: 1500 117: =>start test rdf custom -117: [12:42:38] test on : 365 molecules done -120: [12:42:38] done -120: [12:42:38] ------------------------------------- -120: [12:42:38] More PMI/NPR tests. -120: [12:42:38] done -120: [12:42:38] ------------------------------------- -120: [12:42:38] Basic NPR tests. -120: [12:42:39] done -120: [12:42:39] ------------------------------------- -120: [12:42:39] PMI edge cases. -120: [12:42:39] done -120: [12:42:39] ------------------------------------- -120: [12:42:39] NPR edge cases. -120: [12:42:39] done -120: [12:42:39] ------------------------------------- -120: [12:42:39] 3D descriptors. -120: [12:42:39] done -120: [12:42:39] ------------------------------------- -120: [12:42:39] 3D descriptor edge cases. -120: [12:42:39] done -120: [12:42:39] ------------------------------------- -120: [12:42:39] Inertial shape factor. -120: [12:42:39] done -110/236 Test #120: test3D ................................. Passed 0.23 sec +117: [21:37:33] test on : 365 molecules done +120: [21:37:33] done +120: [21:37:33] ------------------------------------- +120: [21:37:33] More PMI/NPR tests. +120: [21:37:33] done +120: [21:37:33] ------------------------------------- +120: [21:37:33] Basic NPR tests. +121: =>start test WHIM +121: [21:37:33] test on : 365 molecules done +110/236 Test #121: testWHIM ............................... Passed 0.20 sec test 122 Start 122: testGETAWAY 122: Test command: /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/GraphMol/Descriptors/testGETAWAY 122: Working Directory: /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/GraphMol/Descriptors 122: Test timeout computed to be: 1500 -121: =>start test WHIM -121: [12:42:39] test on : 365 molecules done -111/236 Test #121: testWHIM ............................... Passed 0.18 sec +119: =>start test MORSE +119: =>read file +119: [21:37:33] test on : 365 molecules done +111/236 Test #119: testMORSE .............................. Passed 0.58 sec test 123 Start 123: testAUTOCORR3D 123: Test command: /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/GraphMol/Descriptors/testAUTOCORR3D 123: Working Directory: /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/GraphMol/Descriptors 123: Test timeout computed to be: 1500 -119: =>start test MORSE -119: =>read file -119: [12:42:39] test on : 365 molecules done -112/236 Test #119: testMORSE .............................. Passed 0.39 sec +120: [21:37:34] done +120: [21:37:34] ------------------------------------- +120: [21:37:34] PMI edge cases. +120: [21:37:34] done +120: [21:37:34] ------------------------------------- +120: [21:37:34] NPR edge cases. +120: [21:37:34] done +120: [21:37:34] ------------------------------------- +120: [21:37:34] 3D descriptors. +120: [21:37:34] done +120: [21:37:34] ------------------------------------- +120: [21:37:34] 3D descriptor edge cases. +120: [21:37:34] done +120: [21:37:34] ------------------------------------- +120: [21:37:34] Inertial shape factor. +120: [21:37:34] done +112/236 Test #120: test3D ................................. Passed 0.48 sec test 124 Start 124: testCoulombMat @@ -25123,14 +25154,14 @@ 124: Test timeout computed to be: 1500 124: ===================== Testing CoulombMat ======================= 124: CM test 1 mat Done -113/236 Test #124: testCoulombMat ......................... Passed 0.02 sec +113/236 Test #124: testCoulombMat ......................... Passed 0.04 sec test 125 Start 125: descriptorsTestCatch 125: Test command: /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/GraphMol/Descriptors/descriptorsTestCatch 125: Working Directory: /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/GraphMol/Descriptors 125: Test timeout computed to be: 1500 -125: Randomness seeded to: 3575580978 +125: Randomness seeded to: 3810810653 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 @@ -25138,53 +25169,154 @@ 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 +117: =>start test morse custom +117: [21:37:34] test on : 365 molecules done +125: Warning: Atom Count for residue GLU5A does not match expected count 123: =>start test autocorr3D -123: [12:42:39] test on : 365 molecules done -114/236 Test #123: testAUTOCORR3D ......................... Passed 0.20 sec +123: [21:37:34] test on : 365 molecules done +114/236 Test #123: testAUTOCORR3D ......................... Passed 0.40 sec test 126 Start 126: pyMolDescriptors 126: Test command: /usr/bin/python3 "/build/reproducible-path/rdkit-202409.4/Code/GraphMol/Descriptors/Wrap/testMolDescriptors.py" 126: Working Directory: /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/GraphMol/Descriptors/Wrap 126: Test timeout computed to be: 1500 -125: Warning: Atom Count for residue GLU5A does not match expected count -117: =>start test morse custom -117: [12:42:39] test on : 365 molecules done +111: [21:37:34] done +111: [21:37:34] ------------------------------------- +111: [21:37:34] Test Issue252: Bad definitions for Crippen atom types. +111: [21:37:34] done +111: [21:37:34] ------------------------------------- +111: [21:37:34] Test calculation of ChiVs. +111: [21:37:34] done +111: [21:37:34] ------------------------------------- +111: [21:37:34] Test calculation of ChiNs. +111: [21:37:34] done +111: [21:37:34] ------------------------------------- +111: [21:37:34] Test calculation of HallKierAlpha. +111: [21:37:34] done +111: [21:37:34] ------------------------------------- +111: [21:37:34] Test calculation of Kappa1. +111: [21:37:34] done +111: [21:37:34] ------------------------------------- +111: [21:37:34] Test calculation of Kappa2. +111: [21:37:34] done +111: [21:37:34] ------------------------------------- +111: [21:37:34] Test calculation of Kappa3. +111: [21:37:34] done +111: [21:37:34] ------------------------------------- +111: [21:37:34] Test Crippen atom type calculations. +111: [21:37:34] done +111: [21:37:34] ------------------------------------- +111: [21:37:34] Test ring descriptors +111: [21:37:34] done +111: [21:37:34] ------------------------------------- +111: [21:37:34] Test other count descriptors. +111: [21:37:34] done +111: [21:37:34] ------------------------------------- +111: [21:37:34] Test MQN +111: [21:37:34] done +111: [21:37:34] ------------------------------------- +111: [21:37:34] Test GitHub Issue 56. +111: [21:37:34] WARNING: not removing hydrogen atom without neighbors +111: [21:37:34] WARNING: not removing hydrogen atom without neighbors +111: [21:37:34] WARNING: not removing hydrogen atom without neighbors +111: [21:37:34] WARNING: not removing hydrogen atom without neighbors +111: [21:37:34] done +111: [21:37:34] ------------------------------------- +111: [21:37:34] Test Github92: Bad Crippen atom type for pyrrole H. +111: [21:37:34] done +111: [21:37:34] ------------------------------------- +111: [21:37:34] Test Github362: order dependence in Kier-Hall descriptors. +111: [21:37:34] done +111: [21:37:34] ------------------------------------- +111: [21:37:34] Test calculation of spiro and bridgehead counts. +111: [21:37:34] done +111: [21:37:34] ------------------------------------- +111: [21:37:34] Test Github694: ExactMolWt ignoring the mass of the electron +111: [21:37:34] done +111: [21:37:34] ------------------------------------- +111: [21:37:34] Testing Properties and KitchenSink +111: [21:37:34] ---Caught keyerror (bad property name)--- +111: [21:37:34] ------------------------------------- +111: [21:37:34] Test USR Descriptor +111: [21:37:34] done +111: [21:37:34] ------------------------------------- +111: [21:37:34] Test Github #1702: AUTOCORR2D.h not installed unless RDK_BUILD_DESCRIPTORS3D but is required +111: [21:37:34] done +111: [21:37:34] ------------------------------------- +111: [21:37:34] Test Github #1973: support P and S terms for TPSA calculation +111: [21:37:34] done +111: [21:37:34] ------------------------------------- +111: [21:37:34] Test Github #2948: Empty molecule has non-zero LabuteASA +111: [21:37:34] done +115/236 Test #111: testDescriptors ........................ Passed 2.01 sec +test 127 + Start 127: pyMolDescriptors3D + +127: Test command: /usr/bin/python3 "/build/reproducible-path/rdkit-202409.4/Code/GraphMol/Descriptors/Wrap/test3D.py" +127: Working Directory: /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/GraphMol/Descriptors/Wrap +127: Test timeout computed to be: 1500 +117: =>start test AUTOCORR3D custom +117: [21:37:34] test on : 365 molecules done 125: Warning: Atom Count for residue ASN39A does not match expected count -126: [12:42:39] DEPRECATION WARNING: please use AtomPairGenerator -126: [12:42:39] DEPRECATION WARNING: please use AtomPairGenerator -126: [12:42:39] DEPRECATION WARNING: please use AtomPairGenerator -126: [12:42:39] DEPRECATION WARNING: please use AtomPairGenerator -126: [12:42:39] DEPRECATION WARNING: please use AtomPairGenerator -126: [12:42:39] DEPRECATION WARNING: please use AtomPairGenerator -126: [12:42:39] DEPRECATION WARNING: please use AtomPairGenerator -126: [12:42:39] DEPRECATION WARNING: please use AtomPairGenerator -126: [12:42:39] DEPRECATION WARNING: please use AtomPairGenerator -126: [12:42:39] DEPRECATION WARNING: please use AtomPairGenerator -126: [12:42:39] DEPRECATION WARNING: please use AtomPairGenerator -126: [12:42:39] DEPRECATION WARNING: please use AtomPairGenerator -126: [12:42:39] DEPRECATION WARNING: please use TopologicalTorsionGenerator -126: [12:42:39] DEPRECATION WARNING: please use TopologicalTorsionGenerator -126: [12:42:39] DEPRECATION WARNING: please use TopologicalTorsionGenerator -126: [12:42:39] DEPRECATION WARNING: please use TopologicalTorsionGenerator -126: [12:42:39] DEPRECATION WARNING: please use TopologicalTorsionGenerator -126: [12:42:39] DEPRECATION WARNING: please use TopologicalTorsionGenerator -126: [12:42:39] DEPRECATION WARNING: please use TopologicalTorsionGenerator -126: [12:42:39] DEPRECATION WARNING: please use TopologicalTorsionGenerator -126: [12:42:39] DEPRECATION WARNING: please use TopologicalTorsionGenerator -126: [12:42:39] DEPRECATION WARNING: please use TopologicalTorsionGenerator -126: [12:42:39] DEPRECATION WARNING: please use TopologicalTorsionGenerator -126: [12:42:39] DEPRECATION WARNING: please use TopologicalTorsionGenerator -126: ..[12:42:39] DEPRECATION WARNING: please use AtomPairGenerator -126: [12:42:39] DEPRECATION WARNING: please use AtomPairGenerator -126: [12:42:39] DEPRECATION WARNING: please use AtomPairGenerator -126: [12:42:39] DEPRECATION WARNING: please use AtomPairGenerator -126: [12:42:39] DEPRECATION WARNING: please use AtomPairGenerator -126: [12:42:39] DEPRECATION WARNING: please use AtomPairGenerator -126: .[12:42:39] DEPRECATION WARNING: please use AtomPairGenerator -126: [12:42:39] DEPRECATION WARNING: please use AtomPairGenerator -126: [12:42:39] DEPRECATION WARNING: please use AtomPairGenerator -126: ..[12:42:39] +117: =>start test 2 WHIM custom +117: [21:37:34] test on : 365 molecules done +29: Checking against /build/reproducible-path/rdkit-202409.4/Code/ForceField/MMFF/test_data/MMFF94_reference.log... +125: Warning: Atom Count for residue GLU53A does not match expected count +29: All 191 tests passed +75: [21:37:34] Finished: testSmiCorrectness() +75: [21:37:34] ----------------------------------------- +75: +75: [21:37:34] +75: ----------------------------------------- +125: Warning: Atom Count for residue ARG64A does not match expected count +117: =>start test 1 WHIM custom +117: [21:37:34] test on : 365 molecules done +29: +29: Computing MMFF94 energies for /build/reproducible-path/rdkit-202409.4/Code/ForceField/MMFF/test_data/MMFF94_hypervalent.smi... +127: ........ +127: ---------------------------------------------------------------------- +127: Ran 8 tests in 0.098s +127: +127: OK +75: [21:37:34] Spurious data before the first property will be ignored +75: [21:37:34] Property will be truncated after the first blank line +75: [21:37:34] Property will be truncated after the first blank line +75: [21:37:34] Property will be truncated after the first blank line +126: [21:37:34] DEPRECATION WARNING: please use AtomPairGenerator +126: [21:37:34] DEPRECATION WARNING: please use AtomPairGenerator +126: [21:37:34] DEPRECATION WARNING: please use AtomPairGenerator +126: [21:37:34] DEPRECATION WARNING: please use AtomPairGenerator +126: [21:37:34] DEPRECATION WARNING: please use AtomPairGenerator +126: [21:37:34] DEPRECATION WARNING: please use AtomPairGenerator +126: [21:37:34] DEPRECATION WARNING: please use AtomPairGenerator +126: [21:37:34] DEPRECATION WARNING: please use AtomPairGenerator +126: [21:37:34] DEPRECATION WARNING: please use AtomPairGenerator +126: [21:37:34] DEPRECATION WARNING: please use AtomPairGenerator +126: [21:37:34] DEPRECATION WARNING: please use AtomPairGenerator +126: [21:37:34] DEPRECATION WARNING: please use AtomPairGenerator +126: [21:37:34] DEPRECATION WARNING: please use TopologicalTorsionGenerator +126: [21:37:34] DEPRECATION WARNING: please use TopologicalTorsionGenerator +126: [21:37:34] DEPRECATION WARNING: please use TopologicalTorsionGenerator +126: [21:37:34] DEPRECATION WARNING: please use TopologicalTorsionGenerator +126: [21:37:34] DEPRECATION WARNING: please use TopologicalTorsionGenerator +126: [21:37:34] DEPRECATION WARNING: please use TopologicalTorsionGenerator +126: [21:37:34] DEPRECATION WARNING: please use TopologicalTorsionGenerator +126: [21:37:34] DEPRECATION WARNING: please use TopologicalTorsionGenerator +126: [21:37:34] DEPRECATION WARNING: please use TopologicalTorsionGenerator +126: [21:37:34] DEPRECATION WARNING: please use TopologicalTorsionGenerator +126: [21:37:34] DEPRECATION WARNING: please use TopologicalTorsionGenerator +126: [21:37:34] DEPRECATION WARNING: please use TopologicalTorsionGenerator +126: ..[21:37:34] DEPRECATION WARNING: please use AtomPairGenerator +126: [21:37:34] DEPRECATION WARNING: please use AtomPairGenerator +126: [21:37:34] DEPRECATION WARNING: please use AtomPairGenerator +126: [21:37:34] DEPRECATION WARNING: please use AtomPairGenerator +126: [21:37:34] DEPRECATION WARNING: please use AtomPairGenerator +126: [21:37:34] DEPRECATION WARNING: please use AtomPairGenerator +126: .[21:37:34] DEPRECATION WARNING: please use AtomPairGenerator +126: [21:37:34] DEPRECATION WARNING: please use AtomPairGenerator +126: [21:37:34] DEPRECATION WARNING: please use AtomPairGenerator +126: ..[21:37:34] 126: 126: **** 126: Pre-condition Violation @@ -25196,10 +25328,10 @@ 126: 0# Invar::Invariant::toString[abi:cxx11]() const in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu//lib/libRDKitRDGeneral.so.1 126: 1# Invar::operator<<(std::ostream&, Invar::Invariant const&) in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu//lib/libRDKitRDGeneral.so.1 126: 2# RDKit::Descriptors::BCUT2D(RDKit::ROMol const&, std::vector > const&) in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu//lib/libRDKitDescriptors.so.1 -126: 3# 0x0000FFFF7B22C4FC in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/rdkit/Chem/rdMolDescriptors.so -126: 4# 0x0000FFFF7B23F390 in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/rdkit/Chem/rdMolDescriptors.so +126: 3# 0x0000FFFFA5B2C4FC in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/rdkit/Chem/rdMolDescriptors.so +126: 4# 0x0000FFFFA5B3F390 in /build/reproducible-path/rdkit-202409.4/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# 0x0000FFFF7FAD2680 in /lib/aarch64-linux-gnu/libboost_python313.so.1.83.0 +126: 6# 0x0000FFFFAA3D2680 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-202409.4/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-202409.4/obj-aarch64-linux-gnu/rdkit/Chem/rdDepictor.so @@ -25210,17 +25342,17 @@ 126: 14# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202409.4/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-202409.4/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-202409.4/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so -126: 17# 0x0000FFFF7D549FA0 in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so -126: 18# 0x0000FFFF7D549F38 in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so -126: 19# 0x0000FFFF7D549EC8 in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so -126: 20# 0x0000FFFF7D549E60 in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so -126: 21# 0x0000FFFF7D549DF8 in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so +126: 17# 0x0000FFFFA7E49FA0 in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so +126: 18# 0x0000FFFFA7E49F38 in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so +126: 19# 0x0000FFFFA7E49EC8 in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so +126: 20# 0x0000FFFFA7E49E60 in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so +126: 21# 0x0000FFFFA7E49DF8 in /build/reproducible-path/rdkit-202409.4/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-202409.4/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-202409.4/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-202409.4/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-202409.4/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# 0x0000FFFF7FACF25C in /lib/aarch64-linux-gnu/libboost_python313.so.1.83.0 +126: 27# 0x0000FFFFAA3CF25C 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# 0x000000000052F1D8 in /usr/bin/python3 @@ -25252,13 +25384,12 @@ 126: 56# 0x0000000000621C6C in /usr/bin/python3 126: 57# Py_RunMain in /usr/bin/python3 126: 58# Py_BytesMain in /usr/bin/python3 -126: 59# 0x0000FFFF803D229C in /lib/aarch64-linux-gnu/libc.so.6 +126: 59# 0x0000FFFFAACD229C 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: -125: Warning: Atom Count for residue GLU53A does not match expected count 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 @@ -25266,103 +25397,15 @@ 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: Warning: Atom Count for residue GLU5A does not match expected count -125: Warning: Atom Count for residue ARG64A does not match expected count -117: =>start test AUTOCORR3D custom -117: [12:42:39] test on : 365 molecules done -111: [12:42:39] done -111: [12:42:39] ------------------------------------- -111: [12:42:39] Test Issue252: Bad definitions for Crippen atom types. -111: [12:42:39] done -111: [12:42:39] ------------------------------------- -111: [12:42:39] Test calculation of ChiVs. -111: [12:42:39] done -111: [12:42:39] ------------------------------------- -111: [12:42:39] Test calculation of ChiNs. -111: [12:42:39] done -111: [12:42:39] ------------------------------------- -111: [12:42:39] Test calculation of HallKierAlpha. -111: [12:42:39] done -111: [12:42:39] ------------------------------------- -111: [12:42:39] Test calculation of Kappa1. -111: [12:42:39] done -111: [12:42:39] ------------------------------------- -111: [12:42:39] Test calculation of Kappa2. -111: [12:42:39] done -111: [12:42:39] ------------------------------------- -111: [12:42:39] Test calculation of Kappa3. -111: [12:42:39] done -111: [12:42:39] ------------------------------------- -111: [12:42:39] Test Crippen atom type calculations. -111: [12:42:39] done -111: [12:42:39] ------------------------------------- -111: [12:42:39] Test ring descriptors -111: [12:42:39] done -111: [12:42:39] ------------------------------------- -111: [12:42:39] Test other count descriptors. -111: [12:42:39] done -111: [12:42:39] ------------------------------------- -111: [12:42:39] Test MQN -111: [12:42:39] done -111: [12:42:39] ------------------------------------- -111: [12:42:39] Test GitHub Issue 56. -111: [12:42:39] WARNING: not removing hydrogen atom without neighbors -111: [12:42:39] WARNING: not removing hydrogen atom without neighbors -111: [12:42:39] WARNING: not removing hydrogen atom without neighbors -111: [12:42:39] WARNING: not removing hydrogen atom without neighbors -111: [12:42:39] done -111: [12:42:39] ------------------------------------- -111: [12:42:39] Test Github92: Bad Crippen atom type for pyrrole H. -111: [12:42:39] done -111: [12:42:39] ------------------------------------- -111: [12:42:39] Test Github362: order dependence in Kier-Hall descriptors. -111: [12:42:39] done -111: [12:42:39] ------------------------------------- -111: [12:42:39] Test calculation of spiro and bridgehead counts. -111: [12:42:39] done -111: [12:42:39] ------------------------------------- -111: [12:42:39] Test Github694: ExactMolWt ignoring the mass of the electron -111: [12:42:39] done -111: [12:42:39] ------------------------------------- -111: [12:42:39] Testing Properties and KitchenSink -111: [12:42:39] ---Caught keyerror (bad property name)--- -111: [12:42:39] ------------------------------------- -111: [12:42:39] Test USR Descriptor -111: [12:42:39] done -111: [12:42:39] ------------------------------------- -111: [12:42:39] Test Github #1702: AUTOCORR2D.h not installed unless RDK_BUILD_DESCRIPTORS3D but is required -111: [12:42:39] done -111: [12:42:39] ------------------------------------- -111: [12:42:39] Test Github #1973: support P and S terms for TPSA calculation -111: [12:42:39] done -111: [12:42:39] ------------------------------------- -111: [12:42:39] Test Github #2948: Empty molecule has non-zero LabuteASA -111: [12:42:39] done -115/236 Test #111: testDescriptors ........................ Passed 1.50 sec -test 127 - Start 127: pyMolDescriptors3D - -127: Test command: /usr/bin/python3 "/build/reproducible-path/rdkit-202409.4/Code/GraphMol/Descriptors/Wrap/test3D.py" -127: Working Directory: /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/GraphMol/Descriptors/Wrap -127: Test timeout computed to be: 1500 125: Warning: Atom Count for residue LYS80A does not match expected count -117: =>start test 2 WHIM custom -117: [12:42:39] test on : 365 molecules done -126: Warning: Atom Count for residue ASN39A does not match expected count -117: =>start test 1 WHIM custom -117: [12:42:39] test on : 365 molecules done -126: Warning: Atom Count for residue GLU53A does not match expected count -126: Warning: Atom Count for residue ARG64A does not match expected count -29: Checking against /build/reproducible-path/rdkit-202409.4/Code/ForceField/MMFF/test_data/MMFF94_reference.log... -122: =>start test GETAWAY -122: [12:42:39] test on : 365 molecules done -116/236 Test #122: testGETAWAY ............................ Passed 0.90 sec +116/236 Test #127: pyMolDescriptors3D ..................... Passed 0.42 sec test 128 Start 128: testFingerprints 128: Test command: /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/GraphMol/Fingerprints/testFingerprints 128: Working Directory: /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/GraphMol/Fingerprints 128: Test timeout computed to be: 1500 +126: Warning: Atom Count for residue GLU5A does not match expected count 128: 128: 128: @@ -25846,621 +25889,628 @@ 128: 128: ------------------- 128: -128: [12:42:39] ------------------------------------- -128: [12:42:39] Test Morgan Fingerprints. -128: [12:42:39] done -128: [12:42:39] ------------------------------------- -128: [12:42:39] Test Morgan Fingerprints using fromAtoms argument. -128: [12:42:39] done -128: [12:42:39] ------------------------------------- -128: [12:42:39] Test Morgan Fingerprints as bit vects. -128: [12:42:39] done -128: [12:42:39] ------------------------------------- -128: [12:42:39] Test Morgan Fingerprints with feature invariants. -128: [12:42:39] done -128: [12:42:39] ------------------------------------- -128: [12:42:39] Test additional Morgan fingerprints options. -128: [12:42:39] done -128: [12:42:39] ------------------------------------- -128: [12:42:39] Test Atom Codes. -128: [12:42:39] done -128: [12:42:39] ------------------------------------- -128: [12:42:39] Test Atom Pairs. -128: [12:42:39] DEPRECATION WARNING: please use AtomPairGenerator -128: [12:42:39] DEPRECATION WARNING: please use AtomPairGenerator -128: [12:42:39] done -128: [12:42:39] ------------------------------------- -128: [12:42:39] Test Atom Pairs part 2. -128: [12:42:39] DEPRECATION WARNING: please use AtomPairGenerator -128: [12:42:39] DEPRECATION WARNING: please use AtomPairGenerator -128: [12:42:39] done -128: [12:42:39] ------------------------------------- -128: [12:42:39] Test Topological Torsions. -128: [12:42:39] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [12:42:39] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [12:42:39] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [12:42:39] done -128: [12:42:39] ------------------------------------- -128: [12:42:39] Test Bulk Topological Torsions. -128: [12:42:39] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [12:42:39] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [12:42:39] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [12:42:39] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [12:42:39] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [12:42:39] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [12:42:39] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [12:42:39] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [12:42:39] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [12:42:39] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [12:42:39] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [12:42:39] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [12:42:39] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [12:42:39] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [12:42:39] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [12:42:39] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [12:42:39] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [12:42:39] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [12:42:39] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [12:42:39] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [12:42:39] DEPRECATION WARNING: please use TopologicalTorsionGenerator -127: ........ -127: ---------------------------------------------------------------------- -127: Ran 8 tests in 0.094s -127: -127: OK -29: All 191 tests passed -128: [12:42:39] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [12:42:39] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [12:42:39] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [12:42:39] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [12:42:39] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [12:42:39] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [12:42:39] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [12:42:39] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [12:42:39] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [12:42:39] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [12:42:39] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [12:42:39] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [12:42:39] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [12:42:39] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [12:42:39] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [12:42:39] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [12:42:39] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [12:42:39] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [12:42:39] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [12:42:39] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [12:42:39] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [12:42:39] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [12:42:39] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [12:42:39] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [12:42:39] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [12:42:39] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [12:42:39] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [12:42:39] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [12:42:39] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [12:42:39] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [12:42:39] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [12:42:39] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [12:42:39] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [12:42:39] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [12:42:39] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [12:42:39] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [12:42:39] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [12:42:39] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [12:42:39] DEPRECATION WARNING: please use TopologicalTorsionGenerator -126: Warning: Atom Count for residue LYS80A does not match expected count -128: [12:42:39] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [12:42:39] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [12:42:39] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [12:42:39] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [12:42:39] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [12:42:39] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [12:42:39] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [12:42:39] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [12:42:39] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [12:42:39] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [12:42:40] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [12:42:40] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [12:42:40] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [12:42:40] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [12:42:40] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [12:42:40] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [12:42:40] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [12:42:40] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [12:42:40] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [12:42:40] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [12:42:40] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [12:42:40] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [12:42:40] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [12:42:40] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [12:42:40] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [12:42:40] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [12:42:40] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [12:42:40] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [12:42:40] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [12:42:40] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [12:42:40] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [12:42:40] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [12:42:40] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [12:42:40] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [12:42:40] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [12:42:40] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [12:42:40] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [12:42:40] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [12:42:40] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [12:42:40] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [12:42:40] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [12:42:40] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [12:42:40] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [12:42:40] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [12:42:40] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [12:42:40] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [12:42:40] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [12:42:40] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [12:42:40] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [12:42:40] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [12:42:40] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [12:42:40] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [12:42:40] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [12:42:40] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [12:42:40] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [12:42:40] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [12:42:40] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [12:42:40] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [12:42:40] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [12:42:40] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [12:42:40] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [12:42:40] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [12:42:40] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [12:42:40] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [12:42:40] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [12:42:40] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [12:42:40] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [12:42:40] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [12:42:40] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [12:42:40] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [12:42:40] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [12:42:40] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [12:42:40] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [12:42:40] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [12:42:40] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [12:42:40] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [12:42:40] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [12:42:40] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [12:42:40] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [12:42:40] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [12:42:40] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [12:42:40] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [12:42:40] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [12:42:40] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [12:42:40] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [12:42:40] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [12:42:40] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [12:42:40] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [12:42:40] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [12:42:40] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [12:42:40] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [12:42:40] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [12:42:40] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [12:42:40] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [12:42:40] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [12:42:40] DEPRECATION WARNING: please use TopologicalTorsionGenerator -29: -29: Computing MMFF94 energies for /build/reproducible-path/rdkit-202409.4/Code/ForceField/MMFF/test_data/MMFF94_hypervalent.smi... -128: [12:42:40] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [12:42:40] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [12:42:40] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [12:42:40] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [12:42:40] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [12:42:40] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [12:42:40] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [12:42:40] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [12:42:40] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [12:42:40] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [12:42:40] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [12:42:40] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [12:42:40] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [12:42:40] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [12:42:40] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [12:42:40] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [12:42:40] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [12:42:40] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [12:42:40] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [12:42:40] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [12:42:40] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [12:42:40] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [12:42:40] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [12:42:40] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [12:42:40] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [12:42:40] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [12:42:40] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [12:42:40] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [12:42:40] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [12:42:40] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [12:42:40] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [12:42:40] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [12:42:40] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [12:42:40] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [12:42:40] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [12:42:40] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [12:42:40] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [12:42:40] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [12:42:40] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [12:42:40] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [12:42:40] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [12:42:40] DEPRECATION WARNING: please use TopologicalTorsionGenerator -117/236 Test #127: pyMolDescriptors3D ..................... Passed 0.39 sec -128: [12:42:40] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [21:37:34] ------------------------------------- +128: [21:37:34] Test Morgan Fingerprints. +128: [21:37:34] done +128: [21:37:34] ------------------------------------- +128: [21:37:34] Test Morgan Fingerprints using fromAtoms argument. +128: [21:37:34] done +128: [21:37:34] ------------------------------------- +128: [21:37:34] Test Morgan Fingerprints as bit vects. +128: [21:37:34] done +128: [21:37:34] ------------------------------------- +128: [21:37:34] Test Morgan Fingerprints with feature invariants. +128: [21:37:34] done +128: [21:37:34] ------------------------------------- +128: [21:37:34] Test additional Morgan fingerprints options. +128: [21:37:34] done +128: [21:37:34] ------------------------------------- +128: [21:37:34] Test Atom Codes. +128: [21:37:34] done +128: [21:37:34] ------------------------------------- +128: [21:37:34] Test Atom Pairs. +128: [21:37:34] DEPRECATION WARNING: please use AtomPairGenerator +128: [21:37:34] DEPRECATION WARNING: please use AtomPairGenerator +128: [21:37:34] done +128: [21:37:34] ------------------------------------- +128: [21:37:34] Test Atom Pairs part 2. +128: [21:37:34] DEPRECATION WARNING: please use AtomPairGenerator +128: [21:37:34] DEPRECATION WARNING: please use AtomPairGenerator +128: [21:37:34] done +128: [21:37:34] ------------------------------------- +128: [21:37:34] Test Topological Torsions. +128: [21:37:34] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [21:37:34] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [21:37:34] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [21:37:34] done +128: [21:37:34] ------------------------------------- +128: [21:37:34] Test Bulk Topological Torsions. +128: [21:37:34] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [21:37:34] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [21:37:34] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [21:37:34] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [21:37:34] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [21:37:34] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [21:37:34] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [21:37:34] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [21:37:34] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [21:37:34] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [21:37:34] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [21:37:34] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [21:37:34] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [21:37:34] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [21:37:34] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [21:37:34] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [21:37:34] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [21:37:34] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [21:37:34] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [21:37:34] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [21:37:34] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [21:37:34] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [21:37:34] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [21:37:34] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [21:37:34] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [21:37:34] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [21:37:34] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [21:37:34] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [21:37:34] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [21:37:34] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [21:37:34] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [21:37:34] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [21:37:34] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [21:37:34] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [21:37:34] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [21:37:34] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [21:37:34] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [21:37:34] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [21:37:34] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [21:37:34] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [21:37:34] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [21:37:34] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [21:37:34] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [21:37:34] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [21:37:34] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [21:37:34] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [21:37:34] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [21:37:34] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [21:37:34] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [21:37:34] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [21:37:34] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [21:37:34] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [21:37:34] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [21:37:34] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [21:37:34] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [21:37:34] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [21:37:34] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [21:37:34] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [21:37:34] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [21:37:34] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [21:37:34] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [21:37:34] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [21:37:34] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [21:37:34] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [21:37:34] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [21:37:34] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [21:37:34] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [21:37:34] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [21:37:34] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [21:37:34] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [21:37:34] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [21:37:34] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [21:37:34] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [21:37:34] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [21:37:34] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [21:37:34] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [21:37:34] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [21:37:34] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [21:37:34] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [21:37:34] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [21:37:34] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [21:37:34] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [21:37:34] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [21:37:34] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [21:37:34] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [21:37:34] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [21:37:34] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [21:37:34] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [21:37:34] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [21:37:34] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [21:37:34] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [21:37:34] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [21:37:34] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [21:37:34] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [21:37:34] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [21:37:34] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [21:37:34] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [21:37:34] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [21:37:34] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [21:37:34] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [21:37:34] DEPRECATION WARNING: please use TopologicalTorsionGenerator +122: =>start test GETAWAY +122: [21:37:34] test on : 365 molecules done +128: [21:37:34] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [21:37:34] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [21:37:34] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [21:37:34] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [21:37:34] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [21:37:34] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [21:37:34] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [21:37:34] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [21:37:34] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [21:37:34] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [21:37:34] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [21:37:34] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [21:37:34] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [21:37:34] DEPRECATION WARNING: please use TopologicalTorsionGenerator +117/236 Test #122: testGETAWAY ............................ Passed 1.02 sec test 129 Start 129: testMHFPFingerprint 129: Test command: /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/GraphMol/Fingerprints/testMHFPFingerprint 129: Working Directory: /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/GraphMol/Fingerprints 129: Test timeout computed to be: 1500 -128: [12:42:40] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [12:42:40] done -128: [12:42:40] ------------------------------------- -128: [12:42:40] Test Hashed Atom Pairs. -128: [12:42:40] DEPRECATION WARNING: please use AtomPairGenerator -128: [12:42:40] DEPRECATION WARNING: please use AtomPairGenerator -128: [12:42:40] DEPRECATION WARNING: please use AtomPairGenerator -128: [12:42:40] DEPRECATION WARNING: please use AtomPairGenerator -128: [12:42:40] DEPRECATION WARNING: please use AtomPairGenerator -128: [12:42:40] DEPRECATION WARNING: please use AtomPairGenerator -128: [12:42:40] done -128: [12:42:40] ------------------------------------- -128: [12:42:40] Test Hashed torsions. -128: [12:42:40] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [12:42:40] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [12:42:40] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [12:42:40] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [12:42:40] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [12:42:40] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [12:42:40] done -128: [12:42:40] ------------------------------------- -128: [12:42:40] Test Rooted Atom Pairs. -128: [12:42:40] DEPRECATION WARNING: please use AtomPairGenerator -128: [12:42:40] DEPRECATION WARNING: please use AtomPairGenerator -128: [12:42:40] done -128: [12:42:40] ------------------------------------- -128: [12:42:40] Test ignoring atoms in Atom Pairs. -128: [12:42:40] DEPRECATION WARNING: please use AtomPairGenerator -128: [12:42:40] DEPRECATION WARNING: please use AtomPairGenerator -128: [12:42:40] DEPRECATION WARNING: please use AtomPairGenerator -128: [12:42:40] DEPRECATION WARNING: please use AtomPairGenerator -128: [12:42:40] DEPRECATION WARNING: please use AtomPairGenerator -128: [12:42:40] done -128: [12:42:40] ------------------------------------- -128: [12:42:40] Test Rooted Topological Torsions. -128: [12:42:40] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [12:42:40] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [12:42:40] done -128: [12:42:40] ------------------------------------- -128: [12:42:40] Test ignoring atoms in Topological Torsions. -128: [12:42:40] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [12:42:40] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [12:42:40] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [12:42:40] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [12:42:40] done -128: [12:42:40] ------------------------------------- -128: [12:42:40] Test atom info from morgan fingerprints. -128: [12:42:40] done -128: [12:42:40] ------------------------------------- -128: [12:42:40] Test atom info from morgan fingerprints including Info Redundant Environments. -128: [12:42:40] done -128: [12:42:40] ------------------------------------- -128: [12:42:40] ------------------------------------- -128: [12:42:40] DEPRECATION WARNING: please use AtomPairGenerator -128: [12:42:40] DEPRECATION WARNING: please use AtomPairGenerator -128: [12:42:40] DEPRECATION WARNING: please use AtomPairGenerator -128: [12:42:40] DEPRECATION WARNING: please use AtomPairGenerator -128: [12:42:40] DEPRECATION WARNING: please use AtomPairGenerator -128: [12:42:40] DEPRECATION WARNING: please use AtomPairGenerator -128: [12:42:40] DEPRECATION WARNING: please use AtomPairGenerator -128: [12:42:40] DEPRECATION WARNING: please use AtomPairGenerator -128: [12:42:40] DEPRECATION WARNING: please use AtomPairGenerator -128: [12:42:40] DEPRECATION WARNING: please use AtomPairGenerator -128: [12:42:40] DEPRECATION WARNING: please use AtomPairGenerator -128: [12:42:40] DEPRECATION WARNING: please use AtomPairGenerator -128: [12:42:40] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [12:42:40] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [12:42:40] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [12:42:40] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [12:42:40] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [12:42:40] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [12:42:40] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [12:42:40] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [12:42:40] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [12:42:40] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [12:42:40] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [12:42:40] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [12:42:40] ------------------------------------- -128: [12:42:40] ------------------------------------- -128: [12:42:40] ------------------------------------- -128: [12:42:40] ------------------------------------- -128: [12:42:40] Test Atom Pairs including info about chirality. -128: [12:42:40] DEPRECATION WARNING: please use AtomPairGenerator -128: [12:42:40] DEPRECATION WARNING: please use AtomPairGenerator -128: [12:42:40] DEPRECATION WARNING: please use AtomPairGenerator -128: [12:42:40] DEPRECATION WARNING: please use AtomPairGenerator -128: [12:42:40] DEPRECATION WARNING: please use AtomPairGenerator -128: [12:42:40] DEPRECATION WARNING: please use AtomPairGenerator -128: [12:42:40] DEPRECATION WARNING: please use AtomPairGenerator -128: [12:42:40] DEPRECATION WARNING: please use AtomPairGenerator -128: [12:42:40] DEPRECATION WARNING: please use AtomPairGenerator -128: [12:42:40] DEPRECATION WARNING: please use AtomPairGenerator -128: [12:42:40] DEPRECATION WARNING: please use AtomPairGenerator -128: [12:42:40] DEPRECATION WARNING: please use AtomPairGenerator -128: [12:42:40] done -128: [12:42:40] ------------------------------------- -128: [12:42:40] Test Topological Torsions including info about chirality. -128: [12:42:40] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [12:42:40] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [12:42:40] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [12:42:40] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [12:42:40] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [12:42:40] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [12:42:40] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [12:42:40] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [12:42:40] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [12:42:40] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [12:42:40] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [12:42:40] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [12:42:40] done -128: [12:42:40] ------------------------------------- -128: [12:42:40] Test GitHub Issue 25: fingerprint backwards compatibility. -128: [12:42:40] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [12:42:40] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [12:42:40] DEPRECATION WARNING: please use AtomPairGenerator -128: [12:42:40] DEPRECATION WARNING: please use AtomPairGenerator -128: [12:42:40] done -128: [12:42:40] ------------------------------------- -128: [12:42:40] Test GitHub Issue 151: PatternFingerprint problems -128: [12:42:40] done -128: [12:42:40] ------------------------------------- -128: [12:42:40] Test 3D atom pairs. -128: [12:42:40] DEPRECATION WARNING: please use AtomPairGenerator -128: [12:42:40] DEPRECATION WARNING: please use AtomPairGenerator -128: [12:42:40] DEPRECATION WARNING: please use AtomPairGenerator -128: [12:42:40] DEPRECATION WARNING: please use AtomPairGenerator -128: [12:42:40] DEPRECATION WARNING: please use AtomPairGenerator -128: [12:42:40] done -128: [12:42:40] ------------------------------------- -128: [12:42:40] Test GitHub Issue 195: GenMACCSKeys() raises an exception with an empty molecule -128: [12:42:40] done -128: [12:42:40] ------------------------------------- -128: [12:42:40] Test multithreading with the pattern FP +128: [21:37:34] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [21:37:34] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [21:37:34] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [21:37:34] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [21:37:34] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [21:37:34] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [21:37:34] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [21:37:34] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [21:37:34] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [21:37:34] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [21:37:34] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [21:37:34] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [21:37:34] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [21:37:34] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [21:37:34] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [21:37:34] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [21:37:34] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [21:37:34] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [21:37:34] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [21:37:34] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [21:37:34] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [21:37:34] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [21:37:34] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [21:37:34] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [21:37:34] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [21:37:34] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [21:37:34] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [21:37:34] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [21:37:34] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [21:37:34] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [21:37:34] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [21:37:34] DEPRECATION WARNING: please use TopologicalTorsionGenerator +129: [21:37:34] ------------------------------------- +129: [21:37:34] Test MHFP fingerprint encoder initialization +128: [21:37:34] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [21:37:34] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [21:37:34] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [21:37:34] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [21:37:34] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [21:37:34] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [21:37:34] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [21:37:34] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [21:37:34] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [21:37:34] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [21:37:34] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [21:37:34] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [21:37:34] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [21:37:34] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [21:37:34] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [21:37:34] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [21:37:34] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [21:37:34] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [21:37:34] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [21:37:34] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [21:37:34] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [21:37:34] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [21:37:34] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [21:37:34] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [21:37:34] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [21:37:34] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [21:37:34] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [21:37:34] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [21:37:34] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [21:37:34] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [21:37:34] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [21:37:34] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [21:37:34] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [21:37:34] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [21:37:34] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [21:37:34] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [21:37:34] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [21:37:34] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [21:37:34] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [21:37:34] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [21:37:34] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [21:37:34] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [21:37:34] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [21:37:34] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [21:37:34] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [21:37:34] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [21:37:34] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [21:37:34] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [21:37:34] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [21:37:34] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [21:37:34] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [21:37:34] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [21:37:34] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [21:37:34] done +128: [21:37:34] ------------------------------------- +128: [21:37:34] Test Hashed Atom Pairs. +128: [21:37:34] DEPRECATION WARNING: please use AtomPairGenerator +128: [21:37:34] DEPRECATION WARNING: please use AtomPairGenerator +128: [21:37:34] DEPRECATION WARNING: please use AtomPairGenerator +128: [21:37:34] DEPRECATION WARNING: please use AtomPairGenerator +128: [21:37:34] DEPRECATION WARNING: please use AtomPairGenerator +128: [21:37:34] DEPRECATION WARNING: please use AtomPairGenerator +128: [21:37:34] done +128: [21:37:34] ------------------------------------- +128: [21:37:34] Test Hashed torsions. +128: [21:37:34] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [21:37:34] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [21:37:34] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [21:37:34] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [21:37:34] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [21:37:34] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [21:37:34] done +128: [21:37:34] ------------------------------------- +128: [21:37:34] Test Rooted Atom Pairs. +128: [21:37:34] DEPRECATION WARNING: please use AtomPairGenerator +128: [21:37:34] DEPRECATION WARNING: please use AtomPairGenerator +128: [21:37:34] done +128: [21:37:34] ------------------------------------- +128: [21:37:34] Test ignoring atoms in Atom Pairs. +128: [21:37:34] DEPRECATION WARNING: please use AtomPairGenerator +128: [21:37:34] DEPRECATION WARNING: please use AtomPairGenerator +128: [21:37:34] DEPRECATION WARNING: please use AtomPairGenerator +128: [21:37:34] DEPRECATION WARNING: please use AtomPairGenerator +128: [21:37:34] DEPRECATION WARNING: please use AtomPairGenerator +128: [21:37:34] done +128: [21:37:34] ------------------------------------- +128: [21:37:34] Test Rooted Topological Torsions. +128: [21:37:34] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [21:37:34] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [21:37:34] done +128: [21:37:34] ------------------------------------- +128: [21:37:34] Test ignoring atoms in Topological Torsions. +128: [21:37:34] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [21:37:34] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [21:37:34] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [21:37:34] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [21:37:34] done +128: [21:37:34] ------------------------------------- +128: [21:37:34] Test atom info from morgan fingerprints. +128: [21:37:34] done +128: [21:37:34] ------------------------------------- +128: [21:37:34] Test atom info from morgan fingerprints including Info Redundant Environments. +128: [21:37:34] done +128: [21:37:34] ------------------------------------- +128: [21:37:34] ------------------------------------- +128: [21:37:34] DEPRECATION WARNING: please use AtomPairGenerator +128: [21:37:34] DEPRECATION WARNING: please use AtomPairGenerator +128: [21:37:34] DEPRECATION WARNING: please use AtomPairGenerator +128: [21:37:34] DEPRECATION WARNING: please use AtomPairGenerator +128: [21:37:34] DEPRECATION WARNING: please use AtomPairGenerator +128: [21:37:34] DEPRECATION WARNING: please use AtomPairGenerator +128: [21:37:34] DEPRECATION WARNING: please use AtomPairGenerator +128: [21:37:34] DEPRECATION WARNING: please use AtomPairGenerator +128: [21:37:34] DEPRECATION WARNING: please use AtomPairGenerator +128: [21:37:34] DEPRECATION WARNING: please use AtomPairGenerator +128: [21:37:34] DEPRECATION WARNING: please use AtomPairGenerator +128: [21:37:34] DEPRECATION WARNING: please use AtomPairGenerator +128: [21:37:34] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [21:37:34] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [21:37:34] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [21:37:34] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [21:37:34] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [21:37:34] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [21:37:34] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [21:37:34] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [21:37:34] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [21:37:34] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [21:37:34] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [21:37:34] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [21:37:34] ------------------------------------- +129: [21:37:34] done +129: [21:37:34] ------------------------------------- +129: [21:37:34] Test MHFP shingling creation +128: [21:37:34] ------------------------------------- +128: [21:37:34] ------------------------------------- +128: [21:37:34] ------------------------------------- +128: [21:37:34] Test Atom Pairs including info about chirality. +128: [21:37:34] DEPRECATION WARNING: please use AtomPairGenerator +128: [21:37:34] DEPRECATION WARNING: please use AtomPairGenerator +128: [21:37:34] DEPRECATION WARNING: please use AtomPairGenerator +128: [21:37:34] DEPRECATION WARNING: please use AtomPairGenerator +128: [21:37:34] DEPRECATION WARNING: please use AtomPairGenerator +128: [21:37:34] DEPRECATION WARNING: please use AtomPairGenerator +128: [21:37:34] DEPRECATION WARNING: please use AtomPairGenerator +128: [21:37:34] DEPRECATION WARNING: please use AtomPairGenerator +128: [21:37:34] DEPRECATION WARNING: please use AtomPairGenerator +128: [21:37:34] DEPRECATION WARNING: please use AtomPairGenerator +128: [21:37:34] DEPRECATION WARNING: please use AtomPairGenerator +128: [21:37:34] DEPRECATION WARNING: please use AtomPairGenerator +128: [21:37:34] done +128: [21:37:34] ------------------------------------- +128: [21:37:34] Test Topological Torsions including info about chirality. +128: [21:37:34] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [21:37:34] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [21:37:34] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [21:37:34] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [21:37:34] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [21:37:34] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [21:37:34] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [21:37:34] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [21:37:34] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [21:37:34] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [21:37:34] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [21:37:34] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [21:37:34] done +128: [21:37:34] ------------------------------------- +128: [21:37:34] Test GitHub Issue 25: fingerprint backwards compatibility. +128: [21:37:34] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [21:37:34] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [21:37:34] DEPRECATION WARNING: please use AtomPairGenerator +128: [21:37:34] DEPRECATION WARNING: please use AtomPairGenerator +128: [21:37:34] done +128: [21:37:34] ------------------------------------- +128: [21:37:34] Test GitHub Issue 151: PatternFingerprint problems +128: [21:37:34] done +128: [21:37:34] ------------------------------------- +128: [21:37:34] Test 3D atom pairs. +128: [21:37:34] DEPRECATION WARNING: please use AtomPairGenerator +128: [21:37:34] DEPRECATION WARNING: please use AtomPairGenerator +128: [21:37:34] DEPRECATION WARNING: please use AtomPairGenerator +128: [21:37:34] DEPRECATION WARNING: please use AtomPairGenerator +128: [21:37:34] DEPRECATION WARNING: please use AtomPairGenerator +128: [21:37:34] done +128: [21:37:34] ------------------------------------- +128: [21:37:34] Test GitHub Issue 195: GenMACCSKeys() raises an exception with an empty molecule +128: [21:37:34] done +128: [21:37:34] ------------------------------------- +128: [21:37:34] Test multithreading with the pattern FP 128: reading molecules -125: Warning: Atom Count for residue GLU150A does not match expected count -129: [12:42:40] ------------------------------------- -129: [12:42:40] Test MHFP fingerprint encoder initialization -128: pass 1 -128: launch :0 -128: launch :1 -128: launch :2 -128: launch :3 -129: [12:42:40] done -129: [12:42:40] ------------------------------------- -129: [12:42:40] Test MHFP shingling creation -125: Warning: Atom Count for residue ASN157A does not match expected count -129: [12:42:40] done -129: [12:42:40] ------------------------------------- -129: [12:42:40] Test MHFP hashing of string and uint arrays -129: [12:42:40] done -129: [12:42:40] ------------------------------------- -129: [12:42:40] Test SECFP fingerprint functionality -129: [12:42:40] done -118/236 Test #129: testMHFPFingerprint .................... Passed 0.07 sec +129: [21:37:34] done +129: [21:37:34] ------------------------------------- +129: [21:37:34] Test MHFP hashing of string and uint arrays +129: [21:37:34] done +129: [21:37:34] ------------------------------------- +129: [21:37:34] Test SECFP fingerprint functionality +129: [21:37:34] done +118/236 Test #129: testMHFPFingerprint .................... Passed 0.05 sec test 130 Start 130: testFingerprintGenerators 130: Test command: /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/GraphMol/Fingerprints/testFingerprintGenerators 130: Working Directory: /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/GraphMol/Fingerprints 130: Test timeout computed to be: 1500 -130: [12:42:40] ------------------------------------- -130: [12:42:40] Test atom-pair fp generator -130: [12:42:40] done -130: [12:42:40] ------------------------------------- -130: [12:42:40] Test atom-pair fp generator with different arguments -130: [12:42:40] done -130: [12:42:40] ------------------------------------- -130: [12:42:40] Test compatibility between atom pair implementation for FingerprintGenerator and old atom pairs implementation -130: [12:42:40] DEPRECATION WARNING: please use AtomPairGenerator -130: [12:42:40] DEPRECATION WARNING: please use AtomPairGenerator -130: [12:42:40] DEPRECATION WARNING: please use AtomPairGenerator -130: [12:42:40] DEPRECATION WARNING: please use AtomPairGenerator -130: [12:42:40] DEPRECATION WARNING: please use AtomPairGenerator -130: [12:42:40] DEPRECATION WARNING: please use AtomPairGenerator -130: [12:42:40] DEPRECATION WARNING: please use AtomPairGenerator -130: [12:42:40] DEPRECATION WARNING: please use AtomPairGenerator -130: [12:42:40] DEPRECATION WARNING: please use AtomPairGenerator -130: [12:42:40] DEPRECATION WARNING: please use AtomPairGenerator -130: [12:42:40] done -130: [12:42:40] ------------------------------------- -130: [12:42:40] Test atom-pair additional output -130: [12:42:40] done -130: [12:42:40] ------------------------------------- -130: [12:42:40] Test Folded Atom Pairs. -130: [12:42:40] done -130: [12:42:40] ------------------------------------- -130: [12:42:40] Test Rooted Atom Pairs. -130: [12:42:40] done -130: [12:42:40] ------------------------------------- -130: [12:42:40] Test ignoring atoms in Atom Pairs. -130: [12:42:40] done -130: [12:42:40] ------------------------------------- -130: [12:42:40] Test Atom Pairs including info about chirality. -130: [12:42:40] done -130: [12:42:40] ------------------------------------- -130: [12:42:40] Test Morgan Fingerprints. -130: [12:42:40] done -130: [12:42:40] ------------------------------------- -130: [12:42:40] Test morgan fp generator -130: [12:42:40] done -130: [12:42:40] ------------------------------------- -130: [12:42:40] Test Morgan Fingerprints using fromAtoms argument. -130: [12:42:40] done -130: [12:42:40] ------------------------------------- -130: [12:42:40] Test Morgan Fingerprints as bit vects. -130: [12:42:40] done -130: [12:42:40] ------------------------------------- -130: [12:42:40] Test Morgan Fingerprints with feature invariants. -130: [12:42:40] done -130: [12:42:40] ------------------------------------- -130: [12:42:40] Test additional Morgan fingerprints options. -130: [12:42:40] done -130: [12:42:40] ------------------------------------- -130: [12:42:40] Test GitHub Issue 695: Include cis/trans stereochemistry when useChirality=true with the morgan fingerprints -130: [12:42:40] done -130: [12:42:40] ------------------------------------- -130: [12:42:40] Single atoms setting radius 1 bits in Morgan fingerprints -130: [12:42:40] done -130: [12:42:40] ------------------------------------- -130: [12:42:40] Test different invariant generator combinations -130: [12:42:40] done -130: [12:42:40] ------------------------------------- -130: [12:42:40] Test invariant overriding -130: [12:42:40] done -130: [12:42:40] ------------------------------------- -130: [12:42:40] Test RDKit fp generator -128: pass 2 +128: pass 1 128: launch :0 128: launch :1 128: launch :2 128: launch :3 -130: [12:42:40] done -130: [12:42:40] ------------------------------------- -130: [12:42:40] Test unfolded version of RDKFP -130: [12:42:40] ------------------------------------- -130: [12:42:40] Test topological torsion fp generator -130: [12:42:40] DEPRECATION WARNING: please use TopologicalTorsionGenerator -130: [12:42:40] DEPRECATION WARNING: please use TopologicalTorsionGenerator -130: [12:42:40] DEPRECATION WARNING: please use TopologicalTorsionGenerator -130: [12:42:40] DEPRECATION WARNING: please use TopologicalTorsionGenerator -130: [12:42:40] DEPRECATION WARNING: please use TopologicalTorsionGenerator -130: [12:42:40] DEPRECATION WARNING: please use TopologicalTorsionGenerator -130: [12:42:40] DEPRECATION WARNING: please use TopologicalTorsionGenerator -130: [12:42:40] DEPRECATION WARNING: please use TopologicalTorsionGenerator -126: Warning: Atom Count for residue GLU150A does not match expected count -130: [12:42:40] DEPRECATION WARNING: please use TopologicalTorsionGenerator -130: [12:42:40] DEPRECATION WARNING: please use TopologicalTorsionGenerator -130: [12:42:40] done -130: [12:42:40] ------------------------------------- -130: [12:42:40] Test Topological Torsions. -130: [12:42:40] done -130: [12:42:40] ------------------------------------- -130: [12:42:40] Test Folded torsions. -130: [12:42:40] done -130: [12:42:40] ------------------------------------- -130: [12:42:40] Test Bulk Topological Torsions. -126: Warning: Atom Count for residue ASN157A does not match expected count -130: [12:42:40] done -130: [12:42:40] ------------------------------------- -130: [12:42:40] Test Rooted Topological Torsions. -130: [12:42:40] done -130: [12:42:40] ------------------------------------- -130: [12:42:40] Test ignoring atoms in Topological Torsions. -130: [12:42:40] done -130: [12:42:40] ------------------------------------- -130: [12:42:40] ------------------------------------- -130: [12:42:40] Test Topological Torsions including info about chirality. -130: [12:42:40] done -130: [12:42:40] ------------------------------------- -130: [12:42:40] Test GitHub Issue 25: fingerprint backwards compatibility. -130: [12:42:40] done -130: [12:42:40] ------------------------------------- -130: [12:42:40] Test GitHub Issue 334: explicit Hs in SMILES modifies atom pair (and topological torsion) FP. -130: [12:42:40] done -130: [12:42:40] ------------------------------------- -130: [12:42:40] Test GitHub Issue 811: rooted atom fingerprint non identical for the same molecules #811 -130: [12:42:40] done -130: [12:42:40] ------------------------------------- -130: [12:42:40] Test convenience and bulk fp calculation functions -130: [12:42:40] done -130: [12:42:40] ------------------------------------- -130: [12:42:40] Test GitHub Issue #6958 -130: [12:42:40] DEPRECATION WARNING: please use AtomPairGenerator -119/236 Test #130: testFingerprintGenerators .............. Passed 0.50 sec +130: [21:37:34] ------------------------------------- +130: [21:37:34] Test atom-pair fp generator +130: [21:37:34] done +130: [21:37:34] ------------------------------------- +130: [21:37:34] Test atom-pair fp generator with different arguments +130: [21:37:34] done +130: [21:37:34] ------------------------------------- +130: [21:37:34] Test compatibility between atom pair implementation for FingerprintGenerator and old atom pairs implementation +130: [21:37:34] DEPRECATION WARNING: please use AtomPairGenerator +130: [21:37:34] DEPRECATION WARNING: please use AtomPairGenerator +130: [21:37:34] DEPRECATION WARNING: please use AtomPairGenerator +130: [21:37:34] DEPRECATION WARNING: please use AtomPairGenerator +130: [21:37:34] DEPRECATION WARNING: please use AtomPairGenerator +130: [21:37:34] DEPRECATION WARNING: please use AtomPairGenerator +130: [21:37:34] DEPRECATION WARNING: please use AtomPairGenerator +130: [21:37:34] DEPRECATION WARNING: please use AtomPairGenerator +130: [21:37:34] DEPRECATION WARNING: please use AtomPairGenerator +130: [21:37:34] DEPRECATION WARNING: please use AtomPairGenerator +130: [21:37:34] done +130: [21:37:34] ------------------------------------- +130: [21:37:34] Test atom-pair additional output +130: [21:37:34] done +130: [21:37:34] ------------------------------------- +130: [21:37:34] Test Folded Atom Pairs. +130: [21:37:34] done +130: [21:37:34] ------------------------------------- +130: [21:37:34] Test Rooted Atom Pairs. +130: [21:37:34] done +130: [21:37:34] ------------------------------------- +130: [21:37:34] Test ignoring atoms in Atom Pairs. +130: [21:37:34] done +130: [21:37:34] ------------------------------------- +130: [21:37:34] Test Atom Pairs including info about chirality. +130: [21:37:34] done +130: [21:37:34] ------------------------------------- +130: [21:37:34] Test Morgan Fingerprints. +130: [21:37:34] done +130: [21:37:34] ------------------------------------- +130: [21:37:34] Test morgan fp generator +130: [21:37:34] done +130: [21:37:34] ------------------------------------- +130: [21:37:34] Test Morgan Fingerprints using fromAtoms argument. +130: [21:37:34] done +130: [21:37:34] ------------------------------------- +130: [21:37:34] Test Morgan Fingerprints as bit vects. +130: [21:37:34] done +130: [21:37:34] ------------------------------------- +130: [21:37:34] Test Morgan Fingerprints with feature invariants. +130: [21:37:34] done +130: [21:37:34] ------------------------------------- +130: [21:37:34] Test additional Morgan fingerprints options. +130: [21:37:34] done +130: [21:37:34] ------------------------------------- +130: [21:37:34] Test GitHub Issue 695: Include cis/trans stereochemistry when useChirality=true with the morgan fingerprints +130: [21:37:34] done +130: [21:37:34] ------------------------------------- +130: [21:37:34] Single atoms setting radius 1 bits in Morgan fingerprints +130: [21:37:34] done +130: [21:37:34] ------------------------------------- +130: [21:37:34] Test different invariant generator combinations +130: [21:37:35] done +130: [21:37:35] ------------------------------------- +130: [21:37:35] Test invariant overriding +130: [21:37:35] done +130: [21:37:35] ------------------------------------- +130: [21:37:35] Test RDKit fp generator +126: Warning: Atom Count for residue ASN39A does not match expected count +75: [21:37:35] Finished: testSDCorrectness() +75: [21:37:35] ----------------------------------------- +75: +119/236 Test #75: testMultithreadedMolSupplier ........... Passed 5.63 sec test 131 Start 131: fpTestCatch 131: Test command: /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/GraphMol/Fingerprints/fpTestCatch 131: Working Directory: /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/GraphMol/Fingerprints 131: Test timeout computed to be: 1500 -131: Randomness seeded to: 932554694 +131: Randomness seeded to: 877927249 131: =============================================================================== 131: All tests passed (188 assertions in 16 test cases) 131: -120/236 Test #131: fpTestCatch ............................ Passed 0.02 sec +120/236 Test #131: fpTestCatch ............................ Passed 0.04 sec test 132 Start 132: fpGenTestCatch 132: Test command: /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/GraphMol/Fingerprints/fpGenTestCatch 132: Working Directory: /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/GraphMol/Fingerprints 132: Test timeout computed to be: 1500 -132: Randomness seeded to: 3202054555 +128: pass 2 +128: launch :0 +128: launch :1 +128: launch :2 +128: launch :3 +126: Warning: Atom Count for residue GLU53A does not match expected count +126: Warning: Atom Count for residue ARG64A does not match expected count +125: Warning: Atom Count for residue GLU150A does not match expected count +130: [21:37:35] done +130: [21:37:35] ------------------------------------- +130: [21:37:35] Test unfolded version of RDKFP +130: [21:37:35] ------------------------------------- +130: [21:37:35] Test topological torsion fp generator +130: [21:37:35] DEPRECATION WARNING: please use TopologicalTorsionGenerator +130: [21:37:35] DEPRECATION WARNING: please use TopologicalTorsionGenerator +130: [21:37:35] DEPRECATION WARNING: please use TopologicalTorsionGenerator +130: [21:37:35] DEPRECATION WARNING: please use TopologicalTorsionGenerator +130: [21:37:35] DEPRECATION WARNING: please use TopologicalTorsionGenerator +130: [21:37:35] DEPRECATION WARNING: please use TopologicalTorsionGenerator +130: [21:37:35] DEPRECATION WARNING: please use TopologicalTorsionGenerator +130: [21:37:35] DEPRECATION WARNING: please use TopologicalTorsionGenerator +132: Randomness seeded to: 3228018567 132: =============================================================================== 132: All tests passed (2707 assertions in 6 test cases) 132: -121/236 Test #132: fpGenTestCatch ......................... Passed 0.10 sec +121/236 Test #132: fpGenTestCatch ......................... Passed 0.14 sec test 133 Start 133: pyTestGenerator 133: Test command: /usr/bin/python3 "/build/reproducible-path/rdkit-202409.4/Code/GraphMol/Fingerprints/Wrap/testGenerators.py" 133: Working Directory: /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/GraphMol/Fingerprints/Wrap 133: Test timeout computed to be: 1500 -117: =>start test GETAWAY custom -117: [12:42:40] test on : 365 molecules done -122/236 Test #117: testRDFcustom .......................... Passed 2.22 sec +130: [21:37:35] DEPRECATION WARNING: please use TopologicalTorsionGenerator +130: [21:37:35] DEPRECATION WARNING: please use TopologicalTorsionGenerator +130: [21:37:35] done +130: [21:37:35] ------------------------------------- +130: [21:37:35] Test Topological Torsions. +130: [21:37:35] done +130: [21:37:35] ------------------------------------- +130: [21:37:35] Test Folded torsions. +130: [21:37:35] done +130: [21:37:35] ------------------------------------- +130: [21:37:35] Test Bulk Topological Torsions. +125: Warning: Atom Count for residue ASN157A does not match expected count +126: Warning: Atom Count for residue LYS80A does not match expected count +130: [21:37:35] done +130: [21:37:35] ------------------------------------- +130: [21:37:35] Test Rooted Topological Torsions. +130: [21:37:35] done +130: [21:37:35] ------------------------------------- +130: [21:37:35] Test ignoring atoms in Topological Torsions. +130: [21:37:35] done +130: [21:37:35] ------------------------------------- +130: [21:37:35] ------------------------------------- +130: [21:37:35] Test Topological Torsions including info about chirality. +130: [21:37:35] done +130: [21:37:35] ------------------------------------- +130: [21:37:35] Test GitHub Issue 25: fingerprint backwards compatibility. +130: [21:37:35] done +130: [21:37:35] ------------------------------------- +130: [21:37:35] Test GitHub Issue 334: explicit Hs in SMILES modifies atom pair (and topological torsion) FP. +130: [21:37:35] done +130: [21:37:35] ------------------------------------- +130: [21:37:35] Test GitHub Issue 811: rooted atom fingerprint non identical for the same molecules #811 +130: [21:37:35] done +130: [21:37:35] ------------------------------------- +130: [21:37:35] Test convenience and bulk fp calculation functions +130: [21:37:35] done +130: [21:37:35] ------------------------------------- +130: [21:37:35] Test GitHub Issue #6958 +130: [21:37:35] DEPRECATION WARNING: please use AtomPairGenerator +122/236 Test #130: testFingerprintGenerators .............. Passed 0.53 sec test 134 Start 134: pyTestMHFP 134: Test command: /usr/bin/python3 "/build/reproducible-path/rdkit-202409.4/Code/GraphMol/Fingerprints/Wrap/testMHFP.py" 134: Working Directory: /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/GraphMol/Fingerprints/Wrap 134: Test timeout computed to be: 1500 -75: [12:42:40] Finished: testSmiCorrectness() -75: [12:42:40] ----------------------------------------- -75: -75: [12:42:40] -75: ----------------------------------------- -75: [12:42:41] Spurious data before the first property will be ignored -75: [12:42:41] Property will be truncated after the first blank line -75: [12:42:41] Property will be truncated after the first blank line -75: [12:42:41] Property will be truncated after the first blank line +126: Warning: Atom Count for residue GLU150A does not match expected count +126: Warning: Atom Count for residue ASN157A does not match expected count 134: .. 134: ---------------------------------------------------------------------- 134: Ran 2 tests in 0.018s 134: 134: OK -123/236 Test #134: pyTestMHFP ............................. Passed 0.39 sec +133: .............. +133: ---------------------------------------------------------------------- +133: Ran 14 tests in 0.144s +133: +133: OK +123/236 Test #134: pyTestMHFP ............................. Passed 0.30 sec test 135 Start 135: testPartialCharges 135: Test command: /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/GraphMol/PartialCharges/testPartialCharges 135: Working Directory: /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/GraphMol/PartialCharges 135: Test timeout computed to be: 1500 -124/236 Test #135: testPartialCharges ..................... Passed 0.02 sec +124/236 Test #135: testPartialCharges ..................... Passed 0.04 sec test 136 Start 136: pyPartialCharges 136: Test command: /usr/bin/python3 "/build/reproducible-path/rdkit-202409.4/Code/GraphMol/PartialCharges/Wrap/testPartialCharges.py" 136: Working Directory: /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/GraphMol/PartialCharges/Wrap 136: Test timeout computed to be: 1500 -133: .............. -133: ---------------------------------------------------------------------- -133: Ran 14 tests in 0.130s -133: -133: OK -81: =============================================================================== -81: All tests passed (1601 assertions in 100 test cases) -81: -125/236 Test #81: fileParsersCatchTest ................... Passed 4.71 sec +125/236 Test #133: pyTestGenerator ........................ Passed 0.68 sec test 137 Start 137: testMolTransforms 137: Test command: /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/GraphMol/MolTransforms/testMolTransforms 137: Working Directory: /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/GraphMol/MolTransforms 137: Test timeout computed to be: 1500 +81: =============================================================================== +81: All tests passed (1601 assertions in 100 test cases) +81: +126/236 Test #81: fileParsersCatchTest ................... Passed 6.24 sec +test 138 + Start 138: molTransformsTestCatch + +138: Test command: /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/GraphMol/MolTransforms/molTransformsTestCatch +138: Working Directory: /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/GraphMol/MolTransforms +138: Test timeout computed to be: 1500 +138: Randomness seeded to: 572564116 +138: =============================================================================== +138: All tests passed (4 assertions in 1 test case) +138: +127/236 Test #138: molTransformsTestCatch ................. Passed 0.02 sec +test 139 + Start 139: pyMolTransforms + +139: Test command: /usr/bin/python3 "/build/reproducible-path/rdkit-202409.4/Code/GraphMol/MolTransforms/Wrap/testMolTransforms.py" +139: Working Directory: /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/GraphMol/MolTransforms/Wrap +139: Test timeout computed to be: 1500 137: *********************************************************** 137: Testing MolTransforms 137: --------------------------------- @@ -26491,70 +26541,97 @@ 137: testWeightedCentroid 137: 137: *********************************************************** -126/236 Test #137: testMolTransforms ...................... Passed 0.02 sec -test 138 - Start 138: molTransformsTestCatch - -138: Test command: /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/GraphMol/MolTransforms/molTransformsTestCatch -138: Working Directory: /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/GraphMol/MolTransforms -138: Test timeout computed to be: 1500 -138: Randomness seeded to: 588924664 -138: =============================================================================== -138: All tests passed (4 assertions in 1 test case) -138: -127/236 Test #133: pyTestGenerator ........................ Passed 0.55 sec -128/236 Test #138: molTransformsTestCatch ................. Passed 0.02 sec -test 139 - Start 139: pyMolTransforms - -139: Test command: /usr/bin/python3 "/build/reproducible-path/rdkit-202409.4/Code/GraphMol/MolTransforms/Wrap/testMolTransforms.py" -139: Working Directory: /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/GraphMol/MolTransforms/Wrap -139: Test timeout computed to be: 1500 +128/236 Test #137: testMolTransforms ...................... Passed 0.05 sec test 140 Start 140: forceFieldHelpersCatch 140: Test command: /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/GraphMol/ForceFieldHelpers/forceFieldHelpersCatch 140: Working Directory: /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/GraphMol/ForceFieldHelpers 140: Test timeout computed to be: 1500 -140: Randomness seeded to: 1442041808 +140: Randomness seeded to: 3851998745 140: =============================================================================== 140: All tests passed (11 assertions in 1 test case) 140: -129/236 Test #140: forceFieldHelpersCatch ................. Passed 0.03 sec +129/236 Test #140: forceFieldHelpersCatch ................. Passed 0.04 sec test 141 Start 141: testMMFFForceFieldHelpers 141: Test command: /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/GraphMol/ForceFieldHelpers/MMFF/testMMFFForceFieldHelpers 141: Working Directory: /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/GraphMol/ForceFieldHelpers/MMFF 141: Test timeout computed to be: 1500 -141: [12:42:41] ------------------------------------- -141: [12:42:41] Test MMFF atom types. -141: [12:42:41] done -141: [12:42:41] ------------------------------------- -141: [12:42:41] Testing MMFF builder tools. +141: [21:37:36] ------------------------------------- +141: [21:37:36] Test MMFF atom types. +141: [21:37:36] done +141: [21:37:36] ------------------------------------- +141: [21:37:36] Testing MMFF builder tools. +141: [21:37:36] done +141: [21:37:36] ------------------------------------- +141: [21:37:36] Testing MMFF builder+minimization. +141: [21:37:36] done +141: [21:37:36] ------------------------------------- +141: [21:37:36] Testing Issue239. +141: [21:37:36] done +141: [21:37:36] ------------------------------------- +141: [21:37:36] Testing calcEnergy with passed coords. +141: [21:37:36] done +141: [21:37:36] ------------------------------------- +141: [21:37:36] Testing calcGrad. +141: [21:37:36] done +141: [21:37:36] ------------------------------------- +141: [21:37:36] Testing Issue242. +141: [21:37:36] done +141: [21:37:36] ------------------------------------- +141: [21:37:36] Testing github 308: crash during MMFF parameterization . +141: [21:37:36] ------------------------------------- +141: [21:37:36] Testing SFIssue1653802. +141: [21:37:36] done +141: [21:37:36] ------------------------------------- +141: [21:37:36] Testing SFIssue2378119. +141: [21:37:36] done +141: [21:37:36] ------------------------------------- +141: [21:37:36] Test MMFF force-field parameter getters. +141: [21:37:36] ------------------------------------- +141: [21:37:36] Test MMFF multithreading +141: generating reference data 136: ....... 136: ---------------------------------------------------------------------- -136: Ran 7 tests in 0.051s +136: Ran 7 tests in 0.063s 136: 136: OK -141: [12:42:41] done -141: [12:42:41] ------------------------------------- -141: [12:42:41] Testing MMFF builder+minimization. -130/236 Test #136: pyPartialCharges ....................... Passed 0.30 sec +139: ........ +139: ---------------------------------------------------------------------- +139: Ran 8 tests in 0.025s +139: +139: OK +130/236 Test #136: pyPartialCharges ....................... Passed 0.39 sec test 142 Start 142: testMMFFForceFieldHelpersMultiThread 142: Test command: /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/GraphMol/ForceFieldHelpers/MMFF/testMMFFForceFieldHelpersMultiThread 142: Working Directory: /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/GraphMol/ForceFieldHelpers/MMFF 142: Test timeout computed to be: 1500 -141: [12:42:41] done -141: [12:42:41] ------------------------------------- -141: [12:42:41] Testing Issue239. -142: [12:42:41] ------------------------------------- -142: [12:42:41] Test MMFF multithreading -141: [12:42:41] done -141: [12:42:41] ------------------------------------- -141: [12:42:41] Testing calcEnergy with passed coords. +117: =>start test GETAWAY custom +117: [21:37:36] test on : 365 molecules done +131/236 Test #117: testRDFcustom .......................... Passed 3.01 sec +132/236 Test #139: pyMolTransforms ........................ Passed 0.33 sec +test 143 + Start 143: testUFFForceFieldHelpers + +143: Test command: /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/GraphMol/ForceFieldHelpers/UFF/testUFFForceFieldHelpers +143: Working Directory: /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/GraphMol/ForceFieldHelpers/UFF +143: Test timeout computed to be: 1500 +test 144 + Start 144: testCrystalForceField + +144: Test command: /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/GraphMol/ForceFieldHelpers/CrystalFF/testCrystalForceField +144: Working Directory: /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/GraphMol/ForceFieldHelpers/CrystalFF +144: Test timeout computed to be: 1500 +142: [21:37:36] ------------------------------------- +142: [21:37:36] Test MMFF multithreading +143: [21:37:36] ------------------------------------- +143: [21:37:36] Test UFF atom labels. +144: ------------------------------------- +144: Test CrystalFF torsional term. 142: processing 142: launch :0 142: launch :1 @@ -26580,224 +26657,533 @@ 142: launch :21 142: launch :22 142: launch :23 -139: ........ -139: ---------------------------------------------------------------------- -139: Ran 8 tests in 0.023s -139: -139: OK -141: [12:42:41] done -141: [12:42:41] ------------------------------------- -141: [12:42:41] Testing calcGrad. -141: [12:42:41] done -141: [12:42:41] ------------------------------------- -141: [12:42:41] Testing Issue242. -141: [12:42:41] done -141: [12:42:41] ------------------------------------- -141: [12:42:41] Testing github 308: crash during MMFF parameterization . -141: [12:42:41] ------------------------------------- -141: [12:42:41] Testing SFIssue1653802. -141: [12:42:41] done -141: [12:42:41] ------------------------------------- -141: [12:42:41] Testing SFIssue2378119. -141: [12:42:41] done -141: [12:42:41] ------------------------------------- -141: [12:42:41] Test MMFF force-field parameter getters. -141: [12:42:41] ------------------------------------- -141: [12:42:41] Test MMFF multithreading -141: generating reference data -131/236 Test #139: pyMolTransforms ........................ Passed 0.28 sec -test 143 - Start 143: testUFFForceFieldHelpers - -143: Test command: /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/GraphMol/ForceFieldHelpers/UFF/testUFFForceFieldHelpers -143: Working Directory: /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/GraphMol/ForceFieldHelpers/UFF -143: Test timeout computed to be: 1500 -143: [12:42:41] ------------------------------------- -143: [12:42:41] Test UFF atom labels. -143: [12:42:41] done -143: [12:42:41] ------------------------------------- -143: [12:42:41] Test UFF atom typer. -143: [12:42:41] done -143: [12:42:41] ------------------------------------- -143: [12:42:41] Testing UFF builder tools. -143: [12:42:41] done -143: [12:42:41] ------------------------------------- -143: [12:42:41] Testing UFF builder+minimization. -143: [12:42:41] done -143: [12:42:41] ------------------------------------- -143: [12:42:41] Testing UFF special cases. -143: [12:42:41] UFFTYPER: Unrecognized charge state for atom: 0 -143: [12:42:41] done -143: [12:42:41] ------------------------------------- -143: [12:42:41] Testing Issue239. -143: [12:42:41] done -143: [12:42:41] ------------------------------------- -143: [12:42:41] Testing calcEnergy with passed coords. -143: [12:42:41] done -143: [12:42:41] ------------------------------------- -143: [12:42:41] Testing calcGrad. -143: [12:42:41] done -143: [12:42:41] ------------------------------------- -143: [12:42:41] Testing SFIssue1653802. -143: [12:42:41] done -143: [12:42:41] ------------------------------------- -143: [12:42:41] Testing SFIssue2378119. -143: [12:42:41] done -143: [12:42:41] ------------------------------------- -143: [12:42:41] Test UFF force-field parameter getters. -143: [12:42:41] ------------------------------------- -143: [12:42:41] Testing handling missing parameters. -143: [12:42:41] UFFTYPER: Unrecognized hybridization for atom: 0 -143: [12:42:41] UFFTYPER: Unrecognized atom type: Cu+1 (0) -143: [12:42:41] UFFTYPER: Unrecognized hybridization for atom: 0 -143: [12:42:41] UFFTYPER: Unrecognized atom type: Cu+1 (0) -143: [12:42:41] done -143: [12:42:41] ------------------------------------- -143: [12:42:41] Testing SFIssue3009337. -143: [12:42:41] done -143: [12:42:41] ------------------------------------- -143: [12:42:41] Test UFF multithreading -143: generating reference data -75: [12:42:41] Finished: testSDCorrectness() -75: [12:42:41] ----------------------------------------- -75: -132/236 Test #75: testMultithreadedMolSupplier ........... Passed 5.42 sec -test 144 - Start 144: testCrystalForceField - -144: Test command: /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/GraphMol/ForceFieldHelpers/CrystalFF/testCrystalForceField -144: Working Directory: /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/GraphMol/ForceFieldHelpers/CrystalFF -144: Test timeout computed to be: 1500 -144: ------------------------------------- -144: Test CrystalFF torsional term. +143: [21:37:36] done +143: [21:37:36] ------------------------------------- +143: [21:37:36] Test UFF atom typer. +143: [21:37:36] done +143: [21:37:36] ------------------------------------- +143: [21:37:36] Testing UFF builder tools. +143: [21:37:36] done +143: [21:37:36] ------------------------------------- +143: [21:37:36] Testing UFF builder+minimization. 141: processing 141: launch :0 141: launch :1 141: launch :2 141: launch :3 -141: [12:42:41] Rep: 0 Mol:0 -141: [12:42:41] Rep: 0 Mol:1 -141: [12:42:41] Rep: 0 Mol:5 -141: [12:42:41] Rep: 0 Mol:9 -141: [12:42:41] Rep: 0 Mol:13 -141: [12:42:41] Rep: 0 Mol:2 -142: done -141: [12:42:41] Rep: 0 Mol:17 -141: [12:42:41] Rep: 0 Mol:3 -142: [12:42:41] done -141: [12:42:41] Rep: 0 Mol:4 -141: [12:42:41] Rep: 0 Mol:21 -141: [12:42:41] Rep: 0 Mol:6 -141: [12:42:41] Rep: 0 Mol:25 -141: [12:42:41] Rep: 0 Mol:8 -141: [12:42:41] Rep: 0 Mol:10 -141: [12:42:41] Rep: 0 Mol:29 -141: [12:42:41] Rep: 0 Mol:12 -141: [12:42:41] Rep: 0 Mol:16 -133/236 Test #142: testMMFFForceFieldHelpersMultiThread ... Passed 0.36 sec -141: [12:42:41] Rep: 0 Mol:7 +141: [21:37:36] Rep: 0 Mol:0 +141: [21:37:36] Rep: 0 Mol:2 +141: [21:37:36] Rep: 0 Mol:3 +141: [21:37:36] Rep: 0 Mol:1 +141: [21:37:36] Rep: 0 Mol:4 +141: [21:37:36] Rep: 0 Mol:5 +141: [21:37:36] Rep: 0 Mol:9 +141: [21:37:36] Rep: 0 Mol:13 +141: [21:37:36] Rep: 0 Mol:8 +141: [21:37:36] Rep: 0 Mol:17 +141: [21:37:36] Rep: 0 Mol:6 +141: [21:37:36] Rep: 0 Mol:10 +141: [21:37:36] Rep: 0 Mol:12 +141: [21:37:36] Rep: 0 Mol:21 +141: [21:37:36] Rep: 0 Mol:16 +143: [21:37:36] done +143: [21:37:36] ------------------------------------- +143: [21:37:36] Testing UFF special cases. +143: [21:37:36] UFFTYPER: Unrecognized charge state for atom: 0 +143: [21:37:36] done +143: [21:37:36] ------------------------------------- +143: [21:37:36] Testing Issue239. +141: [21:37:36] Rep: 0 Mol:7 +141: [21:37:36] Rep: 0 Mol:11 +141: [21:37:36] Rep: 0 Mol:25 +141: [21:37:36] Rep: 0 Mol:15 +141: [21:37:36] Rep: 0 Mol:20 +141: [21:37:36] Rep: 0 Mol:19 +143: [21:37:36] done +143: [21:37:36] ------------------------------------- +143: [21:37:36] Testing calcEnergy with passed coords. +141: [21:37:36] Rep: 0 Mol:29 +141: [21:37:36] Rep: 0 Mol:24 +141: [21:37:36] Rep: 0 Mol:23 +141: [21:37:36] Rep: 0 Mol:27 +133/236 Test #144: testCrystalForceField .................. Passed 0.21 sec +141: [21:37:36] Rep: 0 Mol:31 test 145 Start 145: pyForceFieldHelpers 145: Test command: /usr/bin/python3 "/build/reproducible-path/rdkit-202409.4/Code/GraphMol/ForceFieldHelpers/Wrap/testHelpers.py" 145: Working Directory: /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/GraphMol/ForceFieldHelpers/Wrap 145: Test timeout computed to be: 1500 -141: [12:42:41] Rep: 0 Mol:11 -141: [12:42:41] Rep: 0 Mol:20 -141: [12:42:41] Rep: 0 Mol:24 -141: [12:42:41] Rep: 0 Mol:15 -134/236 Test #144: testCrystalForceField .................. Passed 0.08 sec +141: [21:37:36] Rep: 0 Mol:28 +141: [21:37:36] Rep: 0 Mol:14 +143: [21:37:36] done +143: [21:37:36] ------------------------------------- +143: [21:37:36] Testing calcGrad. +143: [21:37:36] done +143: [21:37:36] ------------------------------------- +143: [21:37:36] Testing SFIssue1653802. +143: [21:37:36] done +143: [21:37:36] ------------------------------------- +143: [21:37:36] Testing SFIssue2378119. +143: [21:37:36] done +143: [21:37:36] ------------------------------------- +143: [21:37:36] Test UFF force-field parameter getters. +143: [21:37:36] ------------------------------------- +143: [21:37:36] Testing handling missing parameters. +143: [21:37:36] UFFTYPER: Unrecognized hybridization for atom: 0 +143: [21:37:36] UFFTYPER: Unrecognized atom type: Cu+1 (0) +143: [21:37:36] UFFTYPER: Unrecognized hybridization for atom: 0 +143: [21:37:36] UFFTYPER: Unrecognized atom type: Cu+1 (0) +143: [21:37:36] done +143: [21:37:36] ------------------------------------- +143: [21:37:36] Testing SFIssue3009337. +143: [21:37:36] done +143: [21:37:36] ------------------------------------- +143: [21:37:36] Test UFF multithreading +141: [21:37:36] Rep: 0 Mol:18 +143: generating reference data +141: [21:37:36] Rep: 0 Mol:22 +141: [21:37:36] Rep: 0 Mol:26 +141: [21:37:36] Rep: 0 Mol:30 +142: done +142: [21:37:36] done +141: [21:37:36] Rep: 20 Mol:0 +141: [21:37:36] Rep: 20 Mol:4 +141: [21:37:36] Rep: 20 Mol:8 +141: [21:37:36] Rep: 20 Mol:12 +141: [21:37:36] Rep: 20 Mol:16 +141: [21:37:36] Rep: 20 Mol:20 +141: [21:37:36] Rep: 20 Mol:24 +141: [21:37:36] Rep: 20 Mol:28 +141: [21:37:36] Rep: 20 Mol:3 +141: [21:37:36] Rep: 20 Mol:7 +141: [21:37:36] Rep: 20 Mol:11 +141: [21:37:36] Rep: 20 Mol:15 +141: [21:37:36] Rep: 20 Mol:19 +141: [21:37:36] Rep: 20 Mol:23 +141: [21:37:36] Rep: 20 Mol:27 +141: [21:37:36] Rep: 20 Mol:31 +141: [21:37:36] Rep: 20 Mol:1 +141: [21:37:36] Rep: 20 Mol:5 +141: [21:37:36] Rep: 20 Mol:9 +141: [21:37:36] Rep: 20 Mol:13 +141: [21:37:36] Rep: 20 Mol:17 +141: [21:37:36] Rep: 20 Mol:21 +141: [21:37:36] Rep: 20 Mol:25 +141: [21:37:36] Rep: 20 Mol:29 +134/236 Test #142: testMMFFForceFieldHelpersMultiThread ... Passed 0.51 sec test 146 Start 146: testDistGeomHelpers 146: Test command: /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/GraphMol/DistGeomHelpers/testDistGeomHelpers 146: Working Directory: /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/GraphMol/DistGeomHelpers 146: Test timeout computed to be: 1500 -141: [12:42:41] Rep: 0 Mol:19 -141: [12:42:41] Rep: 0 Mol:28 -141: [12:42:41] Rep: 0 Mol:23 -141: [12:42:41] Rep: 0 Mol:27 -141: [12:42:41] Rep: 0 Mol:31 -146: [12:42:41] ******************************************************** -146: [12:42:41] Testing DistGeomHelpers -146: [12:42:41] --------------------------------- -146: [12:42:41] test2 +95: 0,0 0 +95: 0,1 0 +95: 1,0 0 +95: 1,1 0 +95: 2,0 0 +95: 2,1 0 +135/236 Test #95: testEnumeration ........................ Passed 6.02 sec +test 147 + Start 147: distGeomHelpersCatch + +147: Test command: /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/GraphMol/DistGeomHelpers/distGeomHelpersCatch +147: Working Directory: /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/GraphMol/DistGeomHelpers +147: Test timeout computed to be: 1500 +147: Randomness seeded to: 1057546889 +146: [21:37:36] ******************************************************** +146: [21:37:36] Testing DistGeomHelpers +146: [21:37:36] --------------------------------- +146: [21:37:36] test2 146: 146: go 146: ------------------------------------- 146: -141: [12:42:41] Rep: 0 Mol:14 -141: [12:42:41] Rep: 0 Mol:18 -141: [12:42:41] Rep: 0 Mol:22 143: processing 143: launch :0 143: launch :1 143: launch :2 143: launch :3 -143: [12:42:41] Rep: 0 Mol:3 -141: [12:42:41] Rep: 0 Mol:26 -143: [12:42:41] Rep: [12:42:41] Rep: 0 Mol:0 -143: 0 Mol:1 -143: [12:42:41] Rep: 0 Mol:5 -143: [12:42:41] Rep: 0 Mol:9 -143: [12:42:41] Rep: 0 Mol:4 -141: [12:42:41] Rep: 20 Mol:1 -141: [12:42:41] Rep: 20 Mol:5 -141: [12:42:41] Rep: 20 Mol:9 -141: [12:42:41] Rep: 20 Mol:13 -141: [12:42:41] Rep: 20 Mol:17 -143: [12:42:41] Rep: 0 Mol:2 -141: [12:42:41] Rep: 20 Mol:21 -141: [12:42:41] Rep: 20 Mol:25 -141: [12:42:41] Rep: 20 Mol:29 -143: [12:42:41] Rep: 0 Mol:7 -143: [12:42:41] Rep: 0 Mol:11 -143: [12:42:41] Rep: 0 Mol:13 -143: [12:42:41] Rep: 0 Mol:15 -143: [12:42:41] Rep: 0 Mol:19 -143: [12:42:41] Rep: 0 Mol:23 -143: [12:42:41] Rep: 0 Mol:27 -143: [12:42:41] Rep: 0 Mol:31 -141: [12:42:41] Rep: 0 Mol:30 -143: [12:42:41] Rep: 0 Mol:17 -143: [12:42:41] Rep: 0 Mol:6 -143: [12:42:41] Rep: 0 Mol:10 -143: [12:42:41] Rep: 0 Mol:8 -141: [12:42:41] Rep: 20 Mol:0 -141: [12:42:41] Rep: 20 Mol:4 -143: [12:42:41] Rep: 0 Mol:12 -143: [12:42:41] Rep: 0 Mol:16 -143: [12:42:41] Rep: 0 Mol:21 -141: [12:42:41] Rep: 20 Mol:8 -141: [12:42:41] Rep: 20 Mol:12 -141: [12:42:41] Rep: 20 Mol:16 -141: [12:42:41] Rep: 20 Mol:20 -141: [12:42:41] Rep: 20 Mol:24 -141: [12:42:41] Rep: 20 Mol:28 -128: [12:42:41] done -128: [12:42:41] ------------------------------------- -128: [12:42:41] Test GitHub Issue 258: Bad pattern fingerprint for query molecule -128: [12:42:41] done -128: [12:42:41] ------------------------------------- -128: [12:42:41] Test GitHub Issue 334: explicit Hs in SMILES modifies atom pair (and topological torsion) FP. -128: [12:42:41] DEPRECATION WARNING: please use AtomPairGenerator -128: [12:42:41] DEPRECATION WARNING: please use AtomPairGenerator -128: [12:42:41] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [12:42:41] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [12:42:41] done -128: [12:42:41] ------------------------------------- -128: [12:42:41] Test GitHub Issue 695: Include cis/trans stereochemistry when useChirality=true with the morgan fingerprints -128: [12:42:41] done -128: [12:42:41] ------------------------------------- -128: [12:42:41] Test GitHub Issue 811: rooted atom fingerprint non identical for the same molecules #811 -128: [12:42:41] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [12:42:41] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [12:42:41] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [12:42:41] done -128: [12:42:41] ------------------------------------- -128: [12:42:41] Test unfolded version of RDKFP -128: [12:42:41] ------------------------------------- -128: [12:42:41] Test bitinfo of RDKFP +147: [21:37:36] [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)] +143: [21:37:36] Rep: 0 Mol:2 +147: [21:37:36] [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: [21:37:36] [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: [21:37:36] [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: [21:37:36] [!#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: [21:37:36] [!#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: [21:37:36] [!#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: [21:37:36] [!#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: [21:37:36] [!#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: [21:37:36] [!#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: [21:37:36] [!#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: [21:37:36] [!#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: [21:37:36] [!#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: [21:37:36] [!#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: [21:37:36] [!#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: [21:37:36] [!#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: [21:37:36] [!#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: [21:37:36] [C:1][CX4H2:2]!@;-[CX3:3]=[O:4]: 85 86 87 88, [(1 -1), (1 -0.5), (1 -0.2), (1 -0.3), (1 0), (1 -0.3)] +143: [21:37:36] Rep: 0 Mol:0 +143: [21:37:36] Rep: 0 Mol:4 +143: [21:37:36] Rep: 0 Mol:3 +147: [21:37:36] [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: [21:37:36] [*: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: [21:37:36] [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: [21:37:36] [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: [21:37:36] [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: [21:37:36] [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: [21:37:36] [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: [21:37:36] [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: [21:37:36] [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: [21:37:36] [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: [21:37:36] [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: [21:37:36] [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: [21:37:36] [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: [21:37:36] [$([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: [21:37:36] [$(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: [21:37:36] [$(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: [21:37:36] [$(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: [21:37:36] [$(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: [21:37:36] [$(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: [21:37:36] [$(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: [21:37:36] [$(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: [21:37:36] [$(C=O):1][NX3H1;r{9-}:2]@;-[CX4H1;r{9-}:3][H:4]: 105 107 52 171, [(-1 5), (1 0), (1 0), (1 0), (1 0), (1 0)] +143: [21:37:36] Rep: 0 Mol:1 +143: [21:37:36] Rep: 0 Mol:5 +143: [21:37:36] Rep: 0 Mol:6 +143: [21:37:36] Rep: 0 Mol:9 +141: [21:37:36] Rep: 40 Mol:3 +141: [21:37:36] Rep: 40 Mol:7 +141: [21:37:36] Rep: 40 Mol:11 +141: [21:37:36] Rep: 40 Mol:15 +141: [21:37:36] Rep: 40 Mol:19 +141: [21:37:36] Rep: 40 Mol:23 +141: [21:37:36] Rep: 40 Mol:27 +141: [21:37:36] Rep: 40 Mol:31 +147: [21:37:36] [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: [21:37:36] [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: [21:37:36] [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: [21:37:36] [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: [21:37:36] [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: [21:37:36] 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: [21:37:36] [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: [21:37:36] [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: [21:37:36] [!#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: [21:37:36] [!#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: [21:37:36] [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: [21:37:36] [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: [21:37:36] [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: [21:37:36] [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: [21:37:36] [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: [21:37:36] [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: [21:37:36] [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: [21:37:36] [NH1:1][CX4;r{9-}:2]@;-[CX3;r{9-}:3]=[O:4]: 96 97 105 106, [(1 0), (-1 3), (1 0), (1 0), (1 0), (1 0)] +143: [21:37:36] Rep: 0 Mol:10 +147: ----------- +147: [21:37:36] [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: [21:37:36] [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: [21:37:36] [$([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: [21:37:36] [$([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: [21:37:36] [$(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: [21:37:36] [$(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: [21:37:36] [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: [21:37:36] [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: [21:37:36] 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: [21:37:36] 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)] +143: [21:37:36] Rep: 0 Mol:13 +143: [21:37:36] Rep: 0 Mol:8 +147: [21:37:36] [!#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: [21:37:36] [!#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: [21:37:36] [!#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: [21:37:36] [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: [21:37:36] [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: [21:37:36] [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: [21:37:36] [$([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: [21:37:36] [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: [21:37:36] 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)] +143: [21:37:36] Rep: 0 Mol:17 +143: [21:37:36] Rep: 0 Mol:12 +143: [21:37:36] Rep: 0 Mol:7 +143: [21:37:36] Rep: 0 Mol:16 +143: [21:37:36] Rep: 0 Mol:11 +143: [21:37:36] Rep: 0 Mol:15 +143: [21:37:36] Rep: 0 Mol:19 +147: ----------- +143: [21:37:36] Rep: 0 Mol:14 +147: ----------- +147: [21:37:36] [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: [21:37:36] [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: [21:37:36] [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: [21:37:36] [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: [21:37:36] [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: [21:37:36] [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: [21:37:36] [$(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: [21:37:36] [$(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: [21:37:36] [$(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: [21:37:36] [$(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: [21:37:36] [$(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: [21:37:36] [$(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: [21:37:36] [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: [21:37:36] [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: [21:37:36] [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: [21:37:36] [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: [21:37:36] [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: [21:37:36] [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: [21:37:36] Rep: 40 Mol:0 +141: [21:37:36] Rep: 40 Mol:4 +143: [21:37:36] Rep: 0 Mol:20 +143: [21:37:36] Rep: 0 Mol:18 +141: [21:37:36] Rep: 40 Mol:8 +141: [21:37:36] Rep: 40 Mol:12 +141: [21:37:36] Rep: 40 Mol:16 +141: [21:37:36] Rep: 40 Mol:20 +141: [21:37:36] Rep: 40 Mol:24 +141: [21:37:36] Rep: 40 Mol:28 +143: [21:37:36] Rep: 0 Mol:23 +143: [21:37:36] Rep: 0 Mol:27 +143: [21:37:36] Rep: 0 Mol:31 +143: [21:37:36] Rep: 0 Mol:22 +143: [21:37:36] Rep: 0 Mol:24 +143: [21:37:36] Rep: 0 Mol:28 +143: [21:37:36] Rep: 0 Mol:21 +143: [21:37:36] Rep: 0 Mol:26 +141: [21:37:36] Rep: 20 Mol:2 +141: [21:37:36] Rep: 20 Mol:6 +141: [21:37:36] Rep: 20 Mol:10 +141: [21:37:36] Rep: 20 Mol:14 +141: [21:37:36] Rep: 20 Mol:18 +141: [21:37:36] Rep: 20 Mol:22 +141: [21:37:36] Rep: 20 Mol:26 +141: [21:37:36] Rep: 20 Mol:30 +143: [21:37:36] Rep: 0 Mol:25 +143: [21:37:36] Rep: 0 Mol:30 +143: [21:37:36] Rep: 0 Mol:29 +141: [21:37:36] Rep: 40 Mol:1 +141: [21:37:36] Rep: 40 Mol:5 +141: [21:37:36] Rep: 40 Mol:9 +141: [21:37:36] Rep: 40 Mol:13 +141: [21:37:36] Rep: 40 Mol:17 +141: [21:37:36] Rep: 40 Mol:21 +141: [21:37:36] Rep: 40 Mol:25 +141: [21:37:36] Rep: 40 Mol:29 +147: [21:37:36] UFFTYPER: Unrecognized atom type: Pt5+2 (1) +141: [21:37:36] Rep: 60 Mol:3 +141: [21:37:36] Rep: 60 Mol:7 +141: [21:37:36] Rep: 60 Mol:11 +141: [21:37:36] Rep: 60 Mol:15 +141: [21:37:36] Rep: 60 Mol:19 +141: [21:37:36] Rep: 60 Mol:23 +141: [21:37:36] Rep: 60 Mol:27 +141: [21:37:36] Rep: 60 Mol:31 +147: [21:37:36] UFFTYPER: Unrecognized charge state for atom: 1 +145: [21:37:36] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +145: [21:37:36] Molecule does not have explicit Hs. Consider calling AddHs() +145: [21:37:36] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +145: [21:37:36] Molecule does not have explicit Hs. Consider calling AddHs() +145: [21:37:36] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +145: [21:37:36] Molecule does not have explicit Hs. Consider calling AddHs() +145: [21:37:36] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +145: [21:37:36] Molecule does not have explicit Hs. Consider calling AddHs() +145: [21:37:36] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +145: [21:37:36] Molecule does not have explicit Hs. Consider calling AddHs() +145: ..[21:37:36] Molecule does not have explicit Hs. Consider calling AddHs() +145: [21:37:37] Molecule does not have explicit Hs. Consider calling AddHs() +145: .[21:37:37] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +145: [21:37:37] Molecule does not have explicit Hs. Consider calling AddHs() +147: [21:37:37] UFFTYPER: Unrecognized charge state for atom: 1 +147: [21:37:37] UFFTYPER: Unrecognized charge state for atom: 1 +145: .[21:37:37] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +145: [21:37:37] Molecule does not have explicit Hs. Consider calling AddHs() +145: .[21:37:37] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +145: [21:37:37] Molecule does not have explicit Hs. Consider calling AddHs() +145: .[21:37:37] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +145: [21:37:37] Molecule does not have explicit Hs. Consider calling AddHs() +145: .[21:37:37] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +145: [21:37:37] Molecule does not have explicit Hs. Consider calling AddHs() +145: .[21:37:37] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +145: [21:37:37] Molecule does not have explicit Hs. Consider calling AddHs() +145: .[21:37:37] UFFTYPER: Unrecognized hybridization for atom: 0 +145: [21:37:37] UFFTYPER: Unrecognized atom type: Cu+1 (0) +145: .[21:37:37] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +145: [21:37:37] Molecule does not have explicit Hs. Consider calling AddHs() +145: [21:37:37] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +145: [21:37:37] Molecule does not have explicit Hs. Consider calling AddHs() +145: [21:37:37] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +145: [21:37:37] Molecule does not have explicit Hs. Consider calling AddHs() +145: [21:37:37] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +145: [21:37:37] Molecule does not have explicit Hs. Consider calling AddHs() +145: [21:37:37] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +145: [21:37:37] Molecule does not have explicit Hs. Consider calling AddHs() +145: .[21:37:37] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +145: [21:37:37] Molecule does not have explicit Hs. Consider calling AddHs() +145: .[21:37:37] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +145: [21:37:37] Molecule does not have explicit Hs. Consider calling AddHs() +145: .[21:37:37] Molecule does not have explicit Hs. Consider calling AddHs() +145: [21:37:37] Molecule does not have explicit Hs. Consider calling AddHs() +147: [21:37:37] UFFTYPER: Unrecognized charge state for atom: 5 +145: ...[21:37:37] Molecule does not have explicit Hs. Consider calling AddHs() +145: [21:37:37] Molecule does not have explicit Hs. Consider calling AddHs() +147: [21:37:37] UFFTYPER: Unrecognized charge state for atom: 5 +141: [21:37:37] Rep: 60 Mol:0 +141: [21:37:37] Rep: 60 Mol:4 +141: [21:37:37] Rep: 60 Mol:8 +141: [21:37:37] Rep: 60 Mol:12 +141: [21:37:37] Rep: 60 Mol:16 +141: [21:37:37] Rep: 60 Mol:20 +141: [21:37:37] Rep: 60 Mol:24 +141: [21:37:37] Rep: 60 Mol:28 +147: [21:37:37] UFFTYPER: Unrecognized charge state for atom: 5 +141: [21:37:37] Rep: 80 Mol:3 +141: [21:37:37] Rep: 80 Mol:7 +141: [21:37:37] Rep: 80 Mol:11 +141: [21:37:37] Rep: 80 Mol:15 +141: [21:37:37] Rep: 80 Mol:19 +141: [21:37:37] Rep: 80 Mol:23 +141: [21:37:37] Rep: 80 Mol:27 +141: [21:37:37] Rep: 80 Mol:31 +145: [21:37:37] Molecule does not have explicit Hs. Consider calling AddHs() +141: [21:37:37] Rep: 60 Mol:1 +141: [21:37:37] Rep: 60 Mol:5 +141: [21:37:37] Rep: 60 Mol:9 +141: [21:37:37] Rep: 60 Mol:13 +141: [21:37:37] Rep: 60 Mol:17 +141: [21:37:37] Rep: 60 Mol:21 +141: [21:37:37] Rep: 60 Mol:25 +141: [21:37:37] Rep: 60 Mol:29 +141: [21:37:37] Rep: 40 Mol:2 +141: [21:37:37] Rep: 40 Mol:6 +141: [21:37:37] Rep: 40 Mol:10 +141: [21:37:37] Rep: 40 Mol:14 +141: [21:37:37] Rep: 40 Mol:18 +141: [21:37:37] Rep: 40 Mol:22 +141: [21:37:37] Rep: 40 Mol:26 +141: [21:37:37] Rep: 40 Mol:30 +145: ... +145: ---------------------------------------------------------------------- +145: Ran 19 tests in 0.205s +145: +145: OK +147: [21:37:37] UFFTYPER: Unrecognized charge state for atom: 6 +147: [21:37:37] UFFTYPER: Unrecognized charge state for atom: 6 +147: [21:37:37] UFFTYPER: Unrecognized charge state for atom: 6 +141: [21:37:37] Rep: 80 Mol:0 +141: [21:37:37] Rep: 80 Mol:4 +141: [21:37:37] Rep: 80 Mol:8 +141: [21:37:37] Rep: 80 Mol:12 +141: [21:37:37] Rep: 80 Mol:16 +141: [21:37:37] Rep: 80 Mol:20 +141: [21:37:37] Rep: 80 Mol:24 +141: [21:37:37] Rep: 80 Mol:28 +141: [21:37:37] Rep: 80 Mol:1 +141: [21:37:37] Rep: 80 Mol:5 +141: [21:37:37] Rep: 80 Mol:9 +141: [21:37:37] Rep: 80 Mol:13 +141: [21:37:37] Rep: 80 Mol:17 +141: [21:37:37] Rep: 80 Mol:21 +136/236 Test #145: pyForceFieldHelpers .................... Passed 0.84 sec +test 148 + Start 148: pyDistGeomHelpers + +148: Test command: /usr/bin/python3 "/build/reproducible-path/rdkit-202409.4/Code/GraphMol/DistGeomHelpers/Wrap/testDistGeom.py" +148: Working Directory: /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/GraphMol/DistGeomHelpers/Wrap +148: Test timeout computed to be: 1500 +141: [21:37:37] Rep: 80 Mol:25 +141: [21:37:37] Rep: 80 Mol:29 +141: [21:37:37] Rep: 60 Mol:2 +141: [21:37:37] Rep: 60 Mol:6 +141: [21:37:37] Rep: 60 Mol:10 +143: [21:37:37] Rep: 100 Mol:3 +143: [21:37:37] Rep: 100 Mol:7 +143: [21:37:37] Rep: 100 Mol:11 +143: [21:37:37] Rep: 100 Mol:15 +143: [21:37:37] Rep: 100 Mol:19 +143: [21:37:37] Rep: 100 Mol:23 +143: [21:37:37] Rep: 100 Mol:27 +143: [21:37:37] Rep: 100 Mol:31 +141: [21:37:37] Rep: 60 Mol:14 +141: [21:37:37] Rep: 60 Mol:18 +141: [21:37:37] Rep: 60 Mol:22 +141: [21:37:37] Rep: 60 Mol:26 +141: [21:37:37] Rep: 60 Mol:30 +143: [21:37:37] Rep: 100 Mol:0 +143: [21:37:37] Rep: 100 Mol:4 +143: [21:37:37] Rep: 100 Mol:8 +143: [21:37:37] Rep: 100 Mol:12 +143: [21:37:37] Rep: 100 Mol:16 +143: [21:37:37] Rep: 100 Mol:20 +143: [21:37:37] Rep: 100 Mol:24 +143: [21:37:37] Rep: 100 Mol:28 +143: [21:37:37] Rep: 100 Mol:2 +143: [21:37:37] Rep: 100 Mol:6 +143: [21:37:37] Rep: 100 Mol:10 +143: [21:37:37] Rep: 100 Mol:14 +143: [21:37:37] Rep: 100 Mol:18 +143: [21:37:37] Rep: 100 Mol:22 +143: [21:37:37] Rep: 100 Mol:26 +143: [21:37:37] Rep: 100 Mol:30 +143: [21:37:37] Rep: 100 Mol:1 +143: [21:37:37] Rep: 100 Mol:5 +143: [21:37:37] Rep: 100 Mol:9 +143: [21:37:37] Rep: 100 Mol:13 +143: [21:37:37] Rep: 100 Mol:17 +143: [21:37:37] Rep: 100 Mol:21 +143: [21:37:37] Rep: 100 Mol:25 +143: [21:37:37] Rep: 100 Mol:29 +141: [21:37:37] Rep: 80 Mol:2 +141: [21:37:37] Rep: 80 Mol:6 +141: [21:37:37] Rep: 80 Mol:10 +141: [21:37:37] Rep: 80 Mol:14 +141: [21:37:37] Rep: 80 Mol:18 +141: [21:37:37] Rep: 80 Mol:22 +141: [21:37:37] Rep: 80 Mol:26 +141: [21:37:37] Rep: 80 Mol:30 +148: .[21:37:37] Molecule does not have explicit Hs. Consider calling AddHs() +141: [21:37:37] done +141: [21:37:37] ------------------------------------- +141: [21:37:37] Test MMFF multithreading2 +148: [21:37:37] Molecule does not have explicit Hs. Consider calling AddHs() +148: [21:37:37] Molecule does not have explicit Hs. Consider calling AddHs() +148: [21:37:37] Molecule does not have explicit Hs. Consider calling AddHs() +148: ..[21:37:37] Molecule does not have explicit Hs. Consider calling AddHs() +148: [21:37:37] Molecule does not have explicit Hs. Consider calling AddHs() +148: [21:37:37] Molecule does not have explicit Hs. Consider calling AddHs() +148: [21:37:37] Molecule does not have explicit Hs. Consider calling AddHs() +148: [21:37:37] Molecule does not have explicit Hs. Consider calling AddHs() +148: [21:37:37] Molecule does not have explicit Hs. Consider calling AddHs() +148: [21:37:37] Molecule does not have explicit Hs. Consider calling AddHs() +148: [21:37:37] Molecule does not have explicit Hs. Consider calling AddHs() +148: [21:37:37] Molecule does not have explicit Hs. Consider calling AddHs() +148: [21:37:37] Molecule does not have explicit Hs. Consider calling AddHs() +148: [21:37:37] Molecule does not have explicit Hs. Consider calling AddHs() +148: ..[21:37:37] Molecule does not have explicit Hs. Consider calling AddHs() +147: [21:37:37] UFFTYPER: Warning: hybridization set to SP3 for atom 6 +148: .[21:37:37] Molecule does not have explicit Hs. Consider calling AddHs() +128: [21:37:37] done +128: [21:37:37] ------------------------------------- +128: [21:37:37] Test GitHub Issue 258: Bad pattern fingerprint for query molecule +128: [21:37:37] done +128: [21:37:37] ------------------------------------- +128: [21:37:37] Test GitHub Issue 334: explicit Hs in SMILES modifies atom pair (and topological torsion) FP. +128: [21:37:37] DEPRECATION WARNING: please use AtomPairGenerator +128: [21:37:37] DEPRECATION WARNING: please use AtomPairGenerator +128: [21:37:37] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [21:37:37] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [21:37:37] done +128: [21:37:37] ------------------------------------- +128: [21:37:37] Test GitHub Issue 695: Include cis/trans stereochemistry when useChirality=true with the morgan fingerprints +128: [21:37:37] done +128: [21:37:37] ------------------------------------- +128: [21:37:37] Test GitHub Issue 811: rooted atom fingerprint non identical for the same molecules #811 +128: [21:37:37] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [21:37:37] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [21:37:37] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [21:37:37] done +128: [21:37:37] ------------------------------------- +128: [21:37:37] Test unfolded version of RDKFP +128: [21:37:37] ------------------------------------- +128: [21:37:37] Test bitinfo of RDKFP 128: 562: [ 2 ], 128: 709: [ 0 1 ], 128: 1118: [ 0 1 2 ], @@ -26809,338 +27195,106 @@ 128: 1772: [ 0 ], [ 1 ], 128: 1813: [ 0 1 ], 128: ------------ -128: [12:42:41] ------------------------------------- -128: [12:42:41] Single atoms setting radius 1 bits in Morgan fingerprints -128: [12:42:41] done -128: [12:42:41] ------------------------------------- -128: [12:42:41] Github #879: Pattern fingerprint should set bits for single-atom fragments. -128: [12:42:41] done -128: [12:42:41] ------------------------------------- -128: [12:42:41] Github #1496: Pattern fingerprint setting bad bits for degree zero atoms -128: [12:42:41] done -128: [12:42:41] ------------------------------------- -128: [12:42:41] Github #1793: Fingerprint segfaults with branchedPaths=False and useHs=False -128: [12:42:41] done -128: [12:42:41] ------------------------------------- -128: [12:42:41] Github #1993: fingerprinters that use R/S labels should force a call to assignStereochemistry() if it hasn't already been called -128: [12:42:41] DEPRECATION WARNING: please use AtomPairGenerator -128: [12:42:41] DEPRECATION WARNING: please use AtomPairGenerator -128: [12:42:41] DEPRECATION WARNING: please use AtomPairGenerator -128: [12:42:41] DEPRECATION WARNING: please use AtomPairGenerator -128: [12:42:41] DEPRECATION WARNING: please use AtomPairGenerator -128: [12:42:41] DEPRECATION WARNING: please use AtomPairGenerator -128: [12:42:41] DEPRECATION WARNING: please use AtomPairGenerator -128: [12:42:41] DEPRECATION WARNING: please use AtomPairGenerator -128: [12:42:41] DEPRECATION WARNING: please use AtomPairGenerator -128: [12:42:41] DEPRECATION WARNING: please use AtomPairGenerator -128: [12:42:41] DEPRECATION WARNING: please use AtomPairGenerator -128: [12:42:41] DEPRECATION WARNING: please use AtomPairGenerator -128: [12:42:41] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [12:42:41] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [12:42:41] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [12:42:41] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [12:42:41] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [12:42:41] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [12:42:41] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [12:42:41] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [12:42:41] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [12:42:41] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [12:42:41] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [12:42:41] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [12:42:41] done -128: [12:42:41] ------------------------------------- -128: [12:42:41] Github #2115: BitInfo not complete for RDKFingerprint -128: [12:42:41] done -128: [12:42:41] ------------------------------------- -128: [12:42:41] Github #3723: Fingerprint crash for mols with Zero order bonds -128: [12:42:41] done -143: [12:42:41] Rep: 0 Mol:20 -143: [12:42:41] Rep: 0 Mol:25 -143: [12:42:41] Rep: 0 Mol:29 -143: [12:42:41] Rep: 0 Mol:24 -143: [12:42:41] Rep: 0 Mol:14 -143: [12:42:41] Rep: 0 Mol:28 -135/236 Test #128: testFingerprints ....................... Passed 2.00 sec -test 147 - Start 147: distGeomHelpersCatch - -147: Test command: /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/GraphMol/DistGeomHelpers/distGeomHelpersCatch -147: Working Directory: /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/GraphMol/DistGeomHelpers -147: Test timeout computed to be: 1500 -143: [12:42:41] Rep: 0 Mol:18 -143: [12:42:41] Rep: 0 Mol:22 -143: [12:42:41] Rep: 0 Mol:26 -95: 0,0 0 -95: 0,1 0 -95: 1,0 0 -95: 1,1 0 -95: 2,0 0 -95: 2,1 0 -141: [12:42:41] Rep: 20 Mol:3 -141: [12:42:41] Rep: 20 Mol:7 -141: [12:42:41] Rep: 20 Mol:11 -141: [12:42:41] Rep: 20 Mol:15 -141: [12:42:41] Rep: 20 Mol:19 -141: [12:42:41] Rep: 20 Mol:23 -141: [12:42:41] Rep: 20 Mol:27 -141: [12:42:41] Rep: 20 Mol:31 -136/236 Test #95: testEnumeration ........................ Passed 4.71 sec -test 148 - Start 148: pyDistGeomHelpers - -148: Test command: /usr/bin/python3 "/build/reproducible-path/rdkit-202409.4/Code/GraphMol/DistGeomHelpers/Wrap/testDistGeom.py" -148: Working Directory: /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/GraphMol/DistGeomHelpers/Wrap -148: Test timeout computed to be: 1500 -147: Randomness seeded to: 2533936403 -143: [12:42:41] Rep: 0 Mol:30 -141: [12:42:41] Rep: 40 Mol:1 -141: [12:42:41] Rep: 40 Mol:5 -141: [12:42:41] Rep: 40 Mol:9 -141: [12:42:41] Rep: 40 Mol:13 -141: [12:42:41] Rep: 40 Mol:17 -141: [12:42:41] Rep: 40 Mol:21 -141: [12:42:41] Rep: 40 Mol:25 -141: [12:42:41] Rep: 40 Mol:29 -147: [12:42:41] [C:1][NH:2]!@;-[C:3](=[NH2:4])[NH2]: 100 101 102 104, [(1 0), (-1 100), (1 0), (1 0), (1 0), (1 0)] -147: [12:42:41] [NH2][C:1](=[NH2])[NH:2]!@;-[CH2:3][C:4]: 102 101 100 99, [(1 0), (1 0), (1 2.5), (1 0), (1 0), (1 0)] -147: [12:42:42] [OX2:1][CX4:2]!@;-[CX4:3][N:4]: 32 31 30 33, [(1 0), (1 0), (1 4), (1 0), (1 0), (1 0)] -147: [12:42:42] [OX2:1][CX4:2]!@;-[CX4:3][N:4]: 48 46 45 49, [(1 0), (1 0), (1 4), (1 0), (1 0), (1 0)] -147: [12:42:42] [!#1:1][CX4H2:2]!@;-[CX4H2:3][!#1:4]: 36 37 38 39, [(1 0), (1 0), (1 4), (1 0), (1 0), (1 0)] -147: [12:42:42] [!#1:1][CX4H2:2]!@;-[CX4H2:3][!#1:4]: 37 38 39 40, [(1 0), (1 0), (1 4), (1 0), (1 0), (1 0)] -147: [12:42:42] [!#1:1][CX4H2:2]!@;-[CX4H2:3][!#1:4]: 38 39 40 41, [(1 0), (1 0), (1 4), (1 0), (1 0), (1 0)] -147: [12:42:42] [!#1:1][CX4H2:2]!@;-[CX4H2:3][!#1:4]: 97 98 99 100, [(1 0), (1 0), (1 4), (1 0), (1 0), (1 0)] -147: [12:42:42] [!#1:1][CX4H2:2]!@;-[CX4H2:3][!#1:4]: 98 99 100 101, [(1 0), (1 0), (1 4), (1 0), (1 0), (1 0)] -147: [12:42:42] [!#1:1][CX4:2]!@;-[CX4:3][!#1:4]: 0 1 2 3, [(1 0), (1 0), (1 7), (1 0), (1 0), (1 0)] -147: [12:42:42] [!#1:1][CX4:2]!@;-[CX4:3][!#1:4]: 1 2 4 5, [(1 0), (1 0), (1 7), (1 0), (1 0), (1 0)] -147: [12:42:42] [!#1:1][CX4:2]!@;-[CX4:3][!#1:4]: 20 22 23 24, [(1 0), (1 0), (1 7), (1 0), (1 0), (1 0)] -147: [12:42:42] [!#1:1][CX4:2]!@;-[CX4:3][!#1:4]: 22 23 25 26, [(1 0), (1 0), (1 7), (1 0), (1 0), (1 0)] -147: [12:42:42] [!#1:1][CX4:2]!@;-[CX4:3][!#1:4]: 34 36 37 38, [(1 0), (1 0), (1 7), (1 0), (1 0), (1 0)] -147: [12:42:42] [!#1:1][CX4:2]!@;-[CX4:3][!#1:4]: 66 67 68 69, [(1 0), (1 0), (1 7), (1 0), (1 0), (1 0)] -147: [12:42:42] [!#1:1][CX4:2]!@;-[CX4:3][!#1:4]: 84 85 86 87, [(1 0), (1 0), (1 7), (1 0), (1 0), (1 0)] -147: [12:42:42] [!#1:1][CX4:2]!@;-[CX4:3][!#1:4]: 96 97 98 99, [(1 0), (1 0), (1 7), (1 0), (1 0), (1 0)] -147: [12:42:42] [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: [12:42:42] [cH1:1][c:2]([cH1])!@;-[CX4H2:3][CX4:4]: 70 69 68 67, [(1 0), (1 3.6), (1 0), (1 0), (1 0), (1 0)] -147: [12:42:42] [*:1][X3,X2:2]=[X3,X2:3][*:4]: 101 102 104 220, [(1 0), (-1 100), (1 0), (1 0), (1 0), (1 0)] -147: [12:42:42] [C:1][C;r{9-}:2](=O)@;-[NX3H0;r:3][CX4H1:4]: 15 13 12 8, [(1 0), (-1 8), (1 0), (1 0), (1 0), (1 0)] -147: [12:42:42] [C:1][C;r{9-}:2](=O)@;-[NX3H0;r:3][CX4H1:4]: 22 20 19 15, [(1 0), (-1 8), (1 0), (1 0), (1 0), (1 0)] -147: [12:42:42] [C:1][C;r{9-}:2](=O)@;-[NX3H0;r:3][CX4H1:4]: 67 75 77 81, [(1 0), (-1 8), (1 0), (1 0), (1 0), (1 0)] -147: [12:42:42] [C:1][C;r{9-}:2](=O)@;-[NX3H1;r:3][CX4H1:4]: 4 62 61 60, [(1 0), (-1 8), (1 0), (1 0), (1 0), (1 0)] -147: [12:42:42] [C:1][C;r{9-}:2](=O)@;-[NX3H1;r:3][CX4H1:4]: 8 6 5 4, [(1 0), (-1 8), (1 0), (1 0), (1 0), (1 0)] -147: [12:42:42] [C:1][C;r{9-}:2](=O)@;-[NX3H1;r:3][CX4H1:4]: 30 28 27 22, [(1 0), (-1 8), (1 0), (1 0), (1 0), (1 0)] -147: [12:42:42] [C:1][C;r{9-}:2](=O)@;-[NX3H1;r:3][CX4H1:4]: 36 34 33 30, [(1 0), (-1 8), (1 0), (1 0), (1 0), (1 0)] -147: [12:42:42] [C:1][C;r{9-}:2](=O)@;-[NX3H1;r:3][CX4H1:4]: 45 43 42 36, [(1 0), (-1 8), (1 0), (1 0), (1 0), (1 0)] -147: [12:42:42] [C:1][C;r{9-}:2](=O)@;-[NX3H1;r:3][CX4H1:4]: 81 82 84 85, [(1 0), (-1 8), (1 0), (1 0), (1 0), (1 0)] -147: [12:42:42] [C:1][C;r{9-}:2](=O)@;-[NX3H1;r:3][CX4H1:4]: 93 94 96 97, [(1 0), (-1 8), (1 0), (1 0), (1 0), (1 0)] -147: [12:42:42] [C:1][C;r{9-}:2](=O)@;-[NX3H1;r:3][CX4H1:4]: 97 105 107 52, [(1 0), (-1 8), (1 0), (1 0), (1 0), (1 0)] -147: [12:42:42] [$([CX3]=O):1][NX3H1;r{9-}:2]@;-[CX4H2;r{9-}:3][C:4]: 90 92 93 94, [(1 0), (1 0), (1 4), (1 0), (1 0), (1 0)] -147: [12:42:42] [$(C=O):1][NX3H1;r{9-}:2]@;-[CX4H1;r{9-}:3][H:4]: 6 5 4 117, [(-1 5), (1 0), (1 0), (1 0), (1 0), (1 0)] -147: [12:42:42] [$(C=O):1][NX3H1;r{9-}:2]@;-[CX4H1;r{9-}:3][H:4]: 28 27 22 133, [(-1 5), (1 0), (1 0), (1 0), (1 0), (1 0)] -147: [12:42:42] [$(C=O):1][NX3H1;r{9-}:2]@;-[CX4H1;r{9-}:3][H:4]: 34 33 30 144, [(-1 5), (1 0), (1 0), (1 0), (1 0), (1 0)] -147: [12:42:42] [$(C=O):1][NX3H1;r{9-}:2]@;-[CX4H1;r{9-}:3][H:4]: 43 42 36 149, [(-1 5), (1 0), (1 0), (1 0), (1 0), (1 0)] -147: [12:42:42] [$(C=O):1][NX3H1;r{9-}:2]@;-[CX4H1;r{9-}:3][H:4]: 62 61 60 181, [(-1 5), (1 0), (1 0), (1 0), (1 0), (1 0)] -147: [12:42:42] [$(C=O):1][NX3H1;r{9-}:2]@;-[CX4H1;r{9-}:3][H:4]: 82 84 85 202, [(-1 5), (1 0), (1 0), (1 0), (1 0), (1 0)] -147: [12:42:42] [$(C=O):1][NX3H1;r{9-}:2]@;-[CX4H1;r{9-}:3][H:4]: 94 96 97 210, [(-1 5), (1 0), (1 0), (1 0), (1 0), (1 0)] -147: [12:42:42] [$(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: [12:42:42] [O:1]=[CX3;r{9-}:2]@;-[NX3H1;r{9-}:3][!#1:4]: 91 90 92 93, [(-1 100), (1 0), (1 0), (1 0), (1 0), (1 0)] -147: [12:42:42] [C:1][CX4;r{9-}:2]@;-[NX3;r{9-}:3][C:4]: 43 45 49 50, [(1 0), (1 0), (1 1), (1 0), (1 0), (1 0)] -147: [12:42:42] [C:1][CX4;r{9-}:2]@;-[NX3;r{9-}:3][C:4]: 52 50 49 45, [(1 0), (1 0), (1 1), (1 0), (1 0), (1 0)] -147: [12:42:42] [C:1][CX4;r{9-}:2]@;-[NX3;r{9-}:3][C:4]: 60 64 66 67, [(1 0), (1 0), (1 1), (1 0), (1 0), (1 0)] -147: [12:42:42] [C:1][CX4;r{9-}:2]@;-[NX3;r{9-}:3][C:4]: 68 67 66 64, [(1 0), (1 0), (1 1), (1 0), (1 0), (1 0)] -147: [12:42:42] N[C;r{9-}:2](=[O:1])@;-[CH2;r{9-}:3][N:4]: 95 94 93 92, [(1 0), (-1 10), (1 0), (1 0), (1 0), (1 0)] -147: [12:42:42] [OX2:1][CX4;r{9-}:2]@;-[CX4;r{9-}:3][N:4]: 51 50 52 107, [(1 0), (1 0), (1 4), (1 0), (1 0), (1 0)] -147: [12:42:42] [OX2:1][CX4;r{9-}:2]@;-[CX4;r{9-}:3][N:4]: 65 64 60 61, [(1 0), (1 0), (1 4), (1 0), (1 0), (1 0)] -147: [12:42:42] [!#1:1][CX4&r;r{9-}:2]@;-[CX4&r;r{9-}:3][!#1:4]: 50 52 53 54, [(1 0), (1 0), (1 2), (1 0), (1 0), (1 0)] -147: [12:42:42] [!#1:1][CX4&r;r{9-}:2]@;-[CX4&r;r{9-}:3][!#1:4]: 58 59 60 61, [(1 0), (1 0), (1 2), (1 0), (1 0), (1 0)] -147: [12:42:42] [NH1:1][CX4;r{9-}:2]@;-[CX3;r{9-}:3]=[O:4]: 5 4 62 63, [(1 0), (-1 3), (1 0), (1 0), (1 0), (1 0)] -147: [12:42:42] [NH1:1][CX4;r{9-}:2]@;-[CX3;r{9-}:3]=[O:4]: 27 22 20 21, [(1 0), (-1 3), (1 0), (1 0), (1 0), (1 0)] -147: [12:42:42] [NH1:1][CX4;r{9-}:2]@;-[CX3;r{9-}:3]=[O:4]: 33 30 28 29, [(1 0), (-1 3), (1 0), (1 0), (1 0), (1 0)] -147: [12:42:42] [NH1:1][CX4;r{9-}:2]@;-[CX3;r{9-}:3]=[O:4]: 42 36 34 35, [(1 0), (-1 3), (1 0), (1 0), (1 0), (1 0)] -147: [12:42:42] [NH1:1][CX4;r{9-}:2]@;-[CX3;r{9-}:3]=[O:4]: 49 45 43 44, [(1 0), (-1 3), (1 0), (1 0), (1 0), (1 0)] -147: [12:42:42] [NH1:1][CX4;r{9-}:2]@;-[CX3;r{9-}:3]=[O:4]: 66 67 75 76, [(1 0), (-1 3), (1 0), (1 0), (1 0), (1 0)] -147: [12:42:42] [NH1:1][CX4;r{9-}:2]@;-[CX3;r{9-}:3]=[O:4]: 84 85 90 91, [(1 0), (-1 3), (1 0), (1 0), (1 0), (1 0)] -147: [12:42:42] [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: [12:42:42] [C:1][C;r{9-}:2](=O)@;-[NX3H1;r:3][CX4H1:4]: 2 1 10 9, [(1 0), (-1 8), (1 0), (1 0), (1 0), (1 0)] -147: [12:42:42] [C:1][C;r{9-}:2](=O)@;-[NX3H1;r:3][CX4H1:4]: 14 12 11 9, [(1 0), (-1 8), (1 0), (1 0), (1 0), (1 0)] -147: [12:42:42] [$([CX3]=O):1][NX3H1;r{9-}:2]@;-[CX4H2;r{9-}:3][C:4]: 4 3 2 1, [(1 0), (1 0), (1 4), (1 0), (1 0), (1 0)] -147: [12:42:42] [$([CX3]=O):1][NX3H1;r{9-}:2]@;-[CX4H2;r{9-}:3][C:4]: 16 15 14 12, [(1 0), (1 0), (1 4), (1 0), (1 0), (1 0)] -147: [12:42:42] [$(C=O):1][NX3H1;r{9-}:2]@;-[CX4H1;r{9-}:3][H:4]: 1 10 9 26, [(-1 5), (1 0), (1 0), (1 0), (1 0), (1 0)] -147: [12:42:42] [$(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)] -145: [12:42:42] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -147: [12:42:42] [O:1]=[CX3;r{9-}:2]@;-[NX3H1;r{9-}:3][!#1:4]: 5 4 3 2, [(-1 100), (1 0), (1 0), (1 0), (1 0), (1 0)] -147: [12:42:42] [O:1]=[CX3;r{9-}:2]@;-[NX3H1;r{9-}:3][!#1:4]: 17 16 15 14, [(-1 100), (1 0), (1 0), (1 0), (1 0), (1 0)] -147: [12:42:42] N[C;r{9-}:2](=[O:1])@;-[CH2;r{9-}:3][N:4]: 0 1 2 3, [(1 0), (-1 10), (1 0), (1 0), (1 0), (1 0)] -147: [12:42:42] 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)] -145: [12:42:42] Molecule does not have explicit Hs. Consider calling AddHs() -145: [12:42:42] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -147: [12:42:42] [!#1:1][CX4&r;r{9-}:2]@;-[CX4&r;r{9-}:3][!#1:4]: 4 6 7 8, [(1 0), (1 0), (1 2), (1 0), (1 0), (1 0)] -147: [12:42:42] [!#1:1][CX4&r;r{9-}:2]@;-[CX4&r;r{9-}:3][!#1:4]: 6 7 8 9, [(1 0), (1 0), (1 2), (1 0), (1 0), (1 0)] -147: [12:42:42] [!#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)] -145: [12:42:42] Molecule does not have explicit Hs. Consider calling AddHs() -145: [12:42:42] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -145: [12:42:42] Molecule does not have explicit Hs. Consider calling AddHs() -145: [12:42:42] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -145: [12:42:42] Molecule does not have explicit Hs. Consider calling AddHs() -145: [12:42:42] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -145: [12:42:42] Molecule does not have explicit Hs. Consider calling AddHs() -145: ..[12:42:42] Molecule does not have explicit Hs. Consider calling AddHs() -147: [12:42:42] [C:1][CX4;r{9-}:2]@;-[CX3;r{9-}:3]=[O:4]: 4 6 16 17, [(1 0), (1 0), (-1 1), (1 0), (1 0), (1 0)] -147: [12:42:42] [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: [12:42:42] [C:1][C;r{9-}:2](=O)@;-[NX3H1;r:3][CX4H1:4]: 13 14 16 3, [(1 0), (-1 8), (1 0), (1 0), (1 0), (1 0)] -147: [12:42:42] [$([CX3]=O):1][NX3H1;r{9-}:2]@;-[CX4H2;r{9-}:3][C:4]: 10 12 13 14, [(1 0), (1 0), (1 4), (1 0), (1 0), (1 0)] -147: [12:42:42] [O:1]=[CX3;r{9-}:2]@;-[NX3H1;r{9-}:3][!#1:4]: 11 10 12 13, [(-1 100), (1 0), (1 0), (1 0), (1 0), (1 0)] -147: [12:42:42] 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: ----------- -145: [12:42:42] Molecule does not have explicit Hs. Consider calling AddHs() -145: .[12:42:42] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -145: [12:42:42] Molecule does not have explicit Hs. Consider calling AddHs() -147: ----------- -145: .[12:42:42] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -145: [12:42:42] Molecule does not have explicit Hs. Consider calling AddHs() -147: [12:42:42] [C:1][C;r{9-}:2](=O)@;-[NX3H1;r:3][CX4H1:4]: 2 1 15 14, [(1 0), (-1 8), (1 0), (1 0), (1 0), (1 0)] -147: [12:42:42] [C:1][C;r{9-}:2](=O)@;-[NX3H1;r:3][CX4H1:4]: 2 3 5 6, [(1 0), (-1 8), (1 0), (1 0), (1 0), (1 0)] -147: [12:42:42] [C:1][C;r{9-}:2](=O)@;-[NX3H1;r:3][CX4H1:4]: 10 8 7 6, [(1 0), (-1 8), (1 0), (1 0), (1 0), (1 0)] -147: [12:42:42] [C:1][C;r{9-}:2](=O)@;-[NX3H1;r:3][CX4H1:4]: 10 11 13 14, [(1 0), (-1 8), (1 0), (1 0), (1 0), (1 0)] -147: [12:42:42] [C:1][C;r{9-}:2](=O)@;-[NX3H1;r:3][CX4H1:4]: 19 17 16 14, [(1 0), (-1 8), (1 0), (1 0), (1 0), (1 0)] -147: [12:42:42] [C:1][C;r{9-}:2](=O)@;-[NX3H1;r:3][CX4H1:4]: 19 20 22 6, [(1 0), (-1 8), (1 0), (1 0), (1 0), (1 0)] -147: [12:42:42] [$(C=O):1][NX3H1;r{9-}:2]@;-[CX4H1;r{9-}:3][H:4]: 1 15 14 31, [(-1 5), (1 0), (1 0), (1 0), (1 0), (1 0)] -147: [12:42:42] [$(C=O):1][NX3H1;r{9-}:2]@;-[CX4H1;r{9-}:3][H:4]: 3 5 6 26, [(-1 5), (1 0), (1 0), (1 0), (1 0), (1 0)] -147: [12:42:42] [$(C=O):1][NX3H1;r{9-}:2]@;-[CX4H1;r{9-}:3][H:4]: 8 7 6 26, [(-1 5), (1 0), (1 0), (1 0), (1 0), (1 0)] -147: [12:42:42] [$(C=O):1][NX3H1;r{9-}:2]@;-[CX4H1;r{9-}:3][H:4]: 11 13 14 31, [(-1 5), (1 0), (1 0), (1 0), (1 0), (1 0)] -147: [12:42:42] [$(C=O):1][NX3H1;r{9-}:2]@;-[CX4H1;r{9-}:3][H:4]: 17 16 14 31, [(-1 5), (1 0), (1 0), (1 0), (1 0), (1 0)] -147: [12:42:42] [$(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: [12:42:42] [O:1]=[CX3;r{9-}:2]([NH1])@;-[CH2;r{9-}:3][CX3:4]=O: 0 1 2 3, [(1 0), (1 0), (1 2), (1 0), (1 0), (1 0)] -147: [12:42:42] [O:1]=[CX3;r{9-}:2]([NH1])@;-[CH2;r{9-}:3][CX3:4]=O: 4 3 2 1, [(1 0), (1 0), (1 2), (1 0), (1 0), (1 0)] -147: [12:42:42] [O:1]=[CX3;r{9-}:2]([NH1])@;-[CH2;r{9-}:3][CX3:4]=O: 9 8 10 11, [(1 0), (1 0), (1 2), (1 0), (1 0), (1 0)] -147: [12:42:42] [O:1]=[CX3;r{9-}:2]([NH1])@;-[CH2;r{9-}:3][CX3:4]=O: 12 11 10 8, [(1 0), (1 0), (1 2), (1 0), (1 0), (1 0)] -147: [12:42:42] [O:1]=[CX3;r{9-}:2]([NH1])@;-[CH2;r{9-}:3][CX3:4]=O: 18 17 19 20, [(1 0), (1 0), (1 2), (1 0), (1 0), (1 0)] -147: [12:42:42] [O:1]=[CX3;r{9-}:2]([NH1])@;-[CH2;r{9-}:3][CX3:4]=O: 21 20 19 17, [(1 0), (1 0), (1 2), (1 0), (1 0), (1 0)] -141: [12:42:42] Rep: 40 Mol:0 -141: [12:42:42] Rep: 40 Mol:4 -141: [12:42:42] Rep: 40 Mol:8 -141: [12:42:42] Rep: 40 Mol:12 -141: [12:42:42] Rep: 40 Mol:16 -141: [12:42:42] Rep: 40 Mol:20 -141: [12:42:42] Rep: 40 Mol:24 -141: [12:42:42] Rep: 40 Mol:28 -145: .[12:42:42] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -145: [12:42:42] Molecule does not have explicit Hs. Consider calling AddHs() -145: .[12:42:42] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -145: [12:42:42] Molecule does not have explicit Hs. Consider calling AddHs() -141: [12:42:42] Rep: 40 Mol:3 -141: [12:42:42] Rep: 40 Mol:7 -141: [12:42:42] Rep: 40 Mol:11 -141: [12:42:42] Rep: 40 Mol:15 -141: [12:42:42] Rep: 40 Mol:19 -141: [12:42:42] Rep: 40 Mol:23 -141: [12:42:42] Rep: 40 Mol:27 -141: [12:42:42] Rep: 40 Mol:31 -145: .[12:42:42] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -145: [12:42:42] Molecule does not have explicit Hs. Consider calling AddHs() -145: .[12:42:42] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -145: [12:42:42] Molecule does not have explicit Hs. Consider calling AddHs() -145: .[12:42:42] UFFTYPER: Unrecognized hybridization for atom: 0 -145: [12:42:42] UFFTYPER: Unrecognized atom type: Cu+1 (0) -145: .[12:42:42] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -145: [12:42:42] Molecule does not have explicit Hs. Consider calling AddHs() -145: [12:42:42] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -145: [12:42:42] Molecule does not have explicit Hs. Consider calling AddHs() -145: [12:42:42] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -145: [12:42:42] Molecule does not have explicit Hs. Consider calling AddHs() -145: [12:42:42] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -145: [12:42:42] Molecule does not have explicit Hs. Consider calling AddHs() -145: [12:42:42] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -145: [12:42:42] Molecule does not have explicit Hs. Consider calling AddHs() -145: .[12:42:42] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -145: [12:42:42] Molecule does not have explicit Hs. Consider calling AddHs() -145: .[12:42:42] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -145: [12:42:42] Molecule does not have explicit Hs. Consider calling AddHs() -145: .[12:42:42] Molecule does not have explicit Hs. Consider calling AddHs() -145: [12:42:42] Molecule does not have explicit Hs. Consider calling AddHs() -141: [12:42:42] Rep: 20 Mol:2 -141: [12:42:42] Rep: 20 Mol:6 -141: [12:42:42] Rep: 20 Mol:10 -141: [12:42:42] Rep: 20 Mol:14 -147: [12:42:42] UFFTYPER: Unrecognized atom type: Pt5+2 (1) -145: ...[12:42:42] Molecule does not have explicit Hs. Consider calling AddHs() -145: [12:42:42] Molecule does not have explicit Hs. Consider calling AddHs() -141: [12:42:42] Rep: 20 Mol:18 -141: [12:42:42] Rep: 20 Mol:22 -141: [12:42:42] Rep: 20 Mol:26 -147: [12:42:42] UFFTYPER: Unrecognized charge state for atom: 1 -141: [12:42:42] Rep: 20 Mol:30 -147: [12:42:42] UFFTYPER: Unrecognized charge state for atom: 1 -147: [12:42:42] UFFTYPER: Unrecognized charge state for atom: 1 -145: [12:42:42] Molecule does not have explicit Hs. Consider calling AddHs() -145: ... -145: ---------------------------------------------------------------------- -145: Ran 19 tests in 0.099s -145: -145: OK -147: [12:42:42] UFFTYPER: Unrecognized charge state for atom: 5 -141: [12:42:42] Rep: 60 Mol:1 -141: [12:42:42] Rep: 60 Mol:5 -141: [12:42:42] Rep: 60 Mol:9 -141: [12:42:42] Rep: 60 Mol:13 -141: [12:42:42] Rep: 60 Mol:17 -141: [12:42:42] Rep: 60 Mol:21 -141: [12:42:42] Rep: 60 Mol:25 -141: [12:42:42] Rep: 60 Mol:29 -147: [12:42:42] UFFTYPER: Unrecognized charge state for atom: 5 -147: [12:42:42] UFFTYPER: Unrecognized charge state for atom: 5 -141: [12:42:42] Rep: 60 Mol:3 -141: [12:42:42] Rep: 60 Mol:7 -141: [12:42:42] Rep: 60 Mol:11 -141: [12:42:42] Rep: 60 Mol:15 -141: [12:42:42] Rep: 60 Mol:19 -141: [12:42:42] Rep: 60 Mol:23 -141: [12:42:42] Rep: 60 Mol:27 -141: [12:42:42] Rep: 60 Mol:31 -143: [12:42:42] Rep: 100 Mol:3 -143: [12:42:42] Rep: 100 Mol:7 -143: [12:42:42] Rep: 100 Mol:11 -143: [12:42:42] Rep: 100 Mol:15 -143: [12:42:42] Rep: 100 Mol:19 -143: [12:42:42] Rep: 100 Mol:23 -143: [12:42:42] Rep: 100 Mol:27 -143: [12:42:42] Rep: 100 Mol:31 -137/236 Test #145: pyForceFieldHelpers .................... Passed 0.37 sec +128: [21:37:37] ------------------------------------- +128: [21:37:37] Single atoms setting radius 1 bits in Morgan fingerprints +128: [21:37:37] done +128: [21:37:37] ------------------------------------- +128: [21:37:37] Github #879: Pattern fingerprint should set bits for single-atom fragments. +128: [21:37:37] done +128: [21:37:37] ------------------------------------- +128: [21:37:37] Github #1496: Pattern fingerprint setting bad bits for degree zero atoms +128: [21:37:37] done +128: [21:37:37] ------------------------------------- +128: [21:37:37] Github #1793: Fingerprint segfaults with branchedPaths=False and useHs=False +128: [21:37:37] done +128: [21:37:37] ------------------------------------- +128: [21:37:37] Github #1993: fingerprinters that use R/S labels should force a call to assignStereochemistry() if it hasn't already been called +128: [21:37:37] DEPRECATION WARNING: please use AtomPairGenerator +128: [21:37:37] DEPRECATION WARNING: please use AtomPairGenerator +128: [21:37:37] DEPRECATION WARNING: please use AtomPairGenerator +128: [21:37:37] DEPRECATION WARNING: please use AtomPairGenerator +128: [21:37:37] DEPRECATION WARNING: please use AtomPairGenerator +128: [21:37:37] DEPRECATION WARNING: please use AtomPairGenerator +128: [21:37:37] DEPRECATION WARNING: please use AtomPairGenerator +128: [21:37:37] DEPRECATION WARNING: please use AtomPairGenerator +128: [21:37:37] DEPRECATION WARNING: please use AtomPairGenerator +128: [21:37:37] DEPRECATION WARNING: please use AtomPairGenerator +128: [21:37:37] DEPRECATION WARNING: please use AtomPairGenerator +128: [21:37:37] DEPRECATION WARNING: please use AtomPairGenerator +128: [21:37:37] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [21:37:37] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [21:37:37] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [21:37:37] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [21:37:37] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [21:37:37] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [21:37:37] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [21:37:37] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [21:37:37] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [21:37:37] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [21:37:37] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [21:37:37] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [21:37:37] done +128: [21:37:37] ------------------------------------- +128: [21:37:37] Github #2115: BitInfo not complete for RDKFingerprint +128: [21:37:37] done +128: [21:37:37] ------------------------------------- +128: [21:37:37] Github #3723: Fingerprint crash for mols with Zero order bonds +148: [21:37:37] Molecule does not have explicit Hs. Consider calling AddHs() +148: [21:37:37] Molecule does not have explicit Hs. Consider calling AddHs() +148: [21:37:37] Molecule does not have explicit Hs. Consider calling AddHs() +148: [21:37:37] Molecule does not have explicit Hs. Consider calling AddHs() +148: [21:37:37] Molecule does not have explicit Hs. Consider calling AddHs() +128: [21:37:37] done +137/236 Test #128: testFingerprints ....................... Passed 3.16 sec test 149 Start 149: testMolAlign 149: Test command: /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/GraphMol/MolAlign/testMolAlign 149: Working Directory: /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/GraphMol/MolAlign 149: Test timeout computed to be: 1500 -141: [12:42:42] Rep: 60 Mol:0 -141: [12:42:42] Rep: 60 Mol:4 -147: [12:42:42] UFFTYPER: Unrecognized charge state for atom: 6 -141: [12:42:42] Rep: 60 Mol:8 -141: [12:42:42] Rep: 60 Mol:12 -141: [12:42:42] Rep: 60 Mol:16 -141: [12:42:42] Rep: 60 Mol:20 -141: [12:42:42] Rep: 60 Mol:24 -141: [12:42:42] Rep: 60 Mol:28 -147: [12:42:42] UFFTYPER: Unrecognized charge state for atom: 6 -147: [12:42:42] UFFTYPER: Unrecognized charge state for atom: 6 -141: [12:42:42] Rep: 40 Mol:2 -141: [12:42:42] Rep: 40 Mol:6 -141: [12:42:42] Rep: 40 Mol:10 -141: [12:42:42] Rep: 40 Mol:14 -141: [12:42:42] Rep: 40 Mol:18 -141: [12:42:42] Rep: 40 Mol:22 -141: [12:42:42] Rep: 40 Mol:26 -141: [12:42:42] Rep: 40 Mol:30 -141: [12:42:42] Rep: 80 Mol:1 -141: [12:42:42] Rep: 80 Mol:5 -141: [12:42:42] Rep: 80 Mol:9 -141: [12:42:42] Rep: 80 Mol:13 -141: [12:42:42] Rep: 80 Mol:17 -141: [12:42:42] Rep: 80 Mol:21 -141: [12:42:42] Rep: 80 Mol:25 -141: [12:42:42] Rep: 80 Mol:29 -29: Checking against /build/reproducible-path/rdkit-202409.4/Code/ForceField/MMFF/test_data/MMFF94_reference.log... -148: .[12:42:42] Molecule does not have explicit Hs. Consider calling AddHs() +147: [21:37:37] UFFTYPER: Warning: hybridization set to SP3 for atom 6 +148: [21:37:37] Molecule does not have explicit Hs. Consider calling AddHs() +148: [21:37:37] Molecule does not have explicit Hs. Consider calling AddHs() +148: [21:37:37] Molecule does not have explicit Hs. Consider calling AddHs() +148: [21:37:37] Molecule does not have explicit Hs. Consider calling AddHs() +148: [21:37:37] Molecule does not have explicit Hs. Consider calling AddHs() +148: [21:37:37] Molecule does not have explicit Hs. Consider calling AddHs() +147: [21:37:38] UFFTYPER: Warning: hybridization set to SP3 for atom 6 +148: [21:37:37] Molecule does not have explicit Hs. Consider calling AddHs() +148: [21:37:38] Molecule does not have explicit Hs. Consider calling AddHs() +148: [21:37:38] Molecule does not have explicit Hs. Consider calling AddHs() +148: [21:37:38] Molecule does not have explicit Hs. Consider calling AddHs() +148: [21:37:38] Molecule does not have explicit Hs. Consider calling AddHs() +148: [21:37:38] Molecule does not have explicit Hs. Consider calling AddHs() +148: [21:37:38] Molecule does not have explicit Hs. Consider calling AddHs() +148: [21:37:38] Molecule does not have explicit Hs. Consider calling AddHs() +148: [21:37:38] Molecule does not have explicit Hs. Consider calling AddHs() +148: [21:37:38] Molecule does not have explicit Hs. Consider calling AddHs() +148: [21:37:38] Molecule does not have explicit Hs. Consider calling AddHs() +147: [21:37:38] UFFTYPER: Warning: hybridization set to SP3 for atom 11 +147: [21:37:38] UFFTYPER: Warning: hybridization set to SP3 for atom 11 +148: [21:37:38] Molecule does not have explicit Hs. Consider calling AddHs() +148: [21:37:38] Molecule does not have explicit Hs. Consider calling AddHs() +148: [21:37:38] Molecule does not have explicit Hs. Consider calling AddHs() +148: [21:37:38] Molecule does not have explicit Hs. Consider calling AddHs() +148: [21:37:38] Molecule does not have explicit Hs. Consider calling AddHs() +147: [21:37:38] UFFTYPER: Warning: hybridization set to SP3 for atom 11 +148: [21:37:38] Molecule does not have explicit Hs. Consider calling AddHs() +148: [21:37:38] Molecule does not have explicit Hs. Consider calling AddHs() +148: [21:37:38] Molecule does not have explicit Hs. Consider calling AddHs() +148: [21:37:38] Molecule does not have explicit Hs. Consider calling AddHs() +148: [21:37:38] Molecule does not have explicit Hs. Consider calling AddHs() +148: [21:37:38] Molecule does not have explicit Hs. Consider calling AddHs() +148: [21:37:38] Molecule does not have explicit Hs. Consider calling AddHs() +148: [21:37:38] Molecule does not have explicit Hs. Consider calling AddHs() +148: [21:37:38] Molecule does not have explicit Hs. Consider calling AddHs() +148: [21:37:38] Molecule does not have explicit Hs. Consider calling AddHs() +148: [21:37:38] Molecule does not have explicit Hs. Consider calling AddHs() +148: [21:37:38] Molecule does not have explicit Hs. Consider calling AddHs() +148: [21:37:38] Molecule does not have explicit Hs. Consider calling AddHs() +148: [21:37:38] Molecule does not have explicit Hs. Consider calling AddHs() +148: [21:37:38] Molecule does not have explicit Hs. Consider calling AddHs() +148: [21:37:38] Molecule does not have explicit Hs. Consider calling AddHs() 149: *********************************************************** 149: Testing MolAlign 149: --------------------------------- @@ -27162,167 +27316,343 @@ 149: testIssue241 149: 149: *********************************************************** -148: [12:42:42] Molecule does not have explicit Hs. Consider calling AddHs() -148: [12:42:42] Molecule does not have explicit Hs. Consider calling AddHs() -141: [12:42:42] Rep: 80 Mol:0 -141: [12:42:42] Rep: 80 Mol:4 -141: [12:42:42] Rep: 80 Mol:8 -138/236 Test #149: testMolAlign ........................... Passed 0.11 sec -141: [12:42:42] Rep: 80 Mol:12 +138/236 Test #149: testMolAlign ........................... Passed 0.22 sec test 150 Start 150: testO3AAlign 150: Test command: /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/GraphMol/MolAlign/testO3AAlign 150: Working Directory: /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/GraphMol/MolAlign 150: Test timeout computed to be: 1500 -141: [12:42:42] Rep: 80 Mol:16 -141: [12:42:42] Rep: 80 Mol:20 -141: [12:42:42] Rep: 80 Mol:24 -141: [12:42:42] Rep: 80 Mol:28 -148: [12:42:42] Molecule does not have explicit Hs. Consider calling AddHs() -148: ..[12:42:42] Molecule does not have explicit Hs. Consider calling AddHs() -148: [12:42:42] Molecule does not have explicit Hs. Consider calling AddHs() -148: [12:42:42] Molecule does not have explicit Hs. Consider calling AddHs() -148: [12:42:42] Molecule does not have explicit Hs. Consider calling AddHs() -148: [12:42:42] Molecule does not have explicit Hs. Consider calling AddHs() -148: [12:42:42] Molecule does not have explicit Hs. Consider calling AddHs() -148: [12:42:42] Molecule does not have explicit Hs. Consider calling AddHs() -141: [12:42:42] Rep: 80 Mol:3 -141: [12:42:42] Rep: 80 Mol:7 -141: [12:42:42] Rep: 80 Mol:11 -141: [12:42:42] Rep: 80 Mol:15 -141: [12:42:42] Rep: 80 Mol:19 -141: [12:42:42] Rep: 80 Mol:23 -141: [12:42:42] Rep: 80 Mol:27 -141: [12:42:42] Rep: 80 Mol:31 -148: [12:42:42] Molecule does not have explicit Hs. Consider calling AddHs() -148: [12:42:42] Molecule does not have explicit Hs. Consider calling AddHs() -148: [12:42:42] Molecule does not have explicit Hs. Consider calling AddHs() -148: [12:42:42] Molecule does not have explicit Hs. Consider calling AddHs() -148: ..[12:42:42] Molecule does not have explicit Hs. Consider calling AddHs() -148: .[12:42:42] Molecule does not have explicit Hs. Consider calling AddHs() -148: [12:42:42] Molecule does not have explicit Hs. Consider calling AddHs() -29: All 191 tests passed -29: done -29: ------------------------------------- -29: Unit tests for all MMFF constraint terms. -148: [12:42:42] Molecule does not have explicit Hs. Consider calling AddHs() -148: [12:42:42] Molecule does not have explicit Hs. Consider calling AddHs() -148: [12:42:42] Molecule does not have explicit Hs. Consider calling AddHs() -148: [12:42:42] Molecule does not have explicit Hs. Consider calling AddHs() -148: [12:42:42] Molecule does not have explicit Hs. Consider calling AddHs() -148: [12:42:42] Molecule does not have explicit Hs. Consider calling AddHs() -148: [12:42:42] Molecule does not have explicit Hs. Consider calling AddHs() -148: [12:42:42] Molecule does not have explicit Hs. Consider calling AddHs() -148: [12:42:42] Molecule does not have explicit Hs. Consider calling AddHs() -148: [12:42:42] Molecule does not have explicit Hs. Consider calling AddHs() -148: [12:42:42] Molecule does not have explicit Hs. Consider calling AddHs() -148: [12:42:42] Molecule does not have explicit Hs. Consider calling AddHs() -148: [12:42:42] Molecule does not have explicit Hs. Consider calling AddHs() -29: 10.0003 -148: [12:42:42] Molecule does not have explicit Hs. Consider calling AddHs() -148: [12:42:42] Molecule does not have explicit Hs. Consider calling AddHs() -148: [12:42:42] Molecule does not have explicit Hs. Consider calling AddHs() +148: [21:37:38] Molecule does not have explicit Hs. Consider calling AddHs() +148: [21:37:38] Molecule does not have explicit Hs. Consider calling AddHs() +148: [21:37:38] Molecule does not have explicit Hs. Consider calling AddHs() +148: [21:37:38] Molecule does not have explicit Hs. Consider calling AddHs() +148: [21:37:38] Molecule does not have explicit Hs. Consider calling AddHs() +148: [21:37:38] Molecule does not have explicit Hs. Consider calling AddHs() +148: [21:37:38] Molecule does not have explicit Hs. Consider calling AddHs() +143: [21:37:38] done +143: [21:37:38] ------------------------------------- +143: [21:37:38] Test UFF multithreading2 +148: [21:37:38] Molecule does not have explicit Hs. Consider calling AddHs() +148: [21:37:38] Molecule does not have explicit Hs. Consider calling AddHs() +148: [21:37:38] Molecule does not have explicit Hs. Consider calling AddHs() +141: [21:37:38] done +141: [21:37:38] ------------------------------------- +141: [21:37:38] Test MMFF multithreading3 +148: [21:37:38] Molecule does not have explicit Hs. Consider calling AddHs() +148: [21:37:38] Molecule does not have explicit Hs. Consider calling AddHs() +148: [21:37:38] Molecule does not have explicit Hs. Consider calling AddHs() +148: [21:37:38] Molecule does not have explicit Hs. Consider calling AddHs() +148: [21:37:38] Molecule does not have explicit Hs. Consider calling AddHs() +148: [21:37:38] Molecule does not have explicit Hs. Consider calling AddHs() +148: [21:37:38] Molecule does not have explicit Hs. Consider calling AddHs() +148: [21:37:38] Molecule does not have explicit Hs. Consider calling AddHs() +148: .[21:37:38] 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 +148: [21:37:39] Molecule does not have explicit Hs. Consider calling AddHs() +125: =============================================================================== +125: All tests passed (515 assertions in 10 test cases) +125: +139/236 Test #125: descriptorsTestCatch ................... Passed 4.94 sec +test 151 + Start 151: molAlignCatchTest + +151: Test command: /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/GraphMol/MolAlign/molAlignCatchTest +151: Working Directory: /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/GraphMol/MolAlign +151: Test timeout computed to be: 1500 +143: [21:37:39] done +143: [21:37:39] ------------------------------------- +143: [21:37:39] Test UFF multithreading3 +151: Randomness seeded to: 103065911 +151: 42260920 +141: [21:37:39] done +141: [21:37:39] ------------------------------------- +141: [21:37:39] Testing github 162: Incorrect SMILES after MMFF parameterization . +141: [21:37:39] done +141: [21:37:39] ------------------------------------- +141: [21:37:39] Testing github 224: crash during MMFF parameterization . +141: [21:37:39] done +141: [21:37:39] ------------------------------------- +141: [21:37:39] Testing github6728: crash due to missing stretch-bend params. +140/236 Test #141: testMMFFForceFieldHelpers .............. Passed 3.23 sec +test 152 + Start 152: pyMolAlign + +152: Test command: /usr/bin/python3 "/build/reproducible-path/rdkit-202409.4/Code/GraphMol/MolAlign/Wrap/testMolAlign.py" +152: Working Directory: /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/GraphMol/MolAlign/Wrap +152: Test timeout computed to be: 1500 +146: [21:37:36] --------------------------------- +146: [21:37:36] test3 +146: +146: [21:37:36] --------------------------------- +146: [21:37:36] test4 +146: +146: [21:37:36] --------------------------------- +146: [21:37:36] test5 +146: +146: [21:37:39] --------------------------------- +146: [21:37:39] test6 +146: +146: [21:37:39] --------------------------------- +146: [21:37:39] test15Dists +146: +146: [21:37:39] --------------------------------- +146: [21:37:39] test Issue 215 +146: +146: [21:37:39] --------------------------------- +146: [21:37:39] testMultipleConfs +146: +146: [21:37:39] --------------------------------- +146: [21:37:39] testMultipleConfsExpTors +146: +146: [21:37:39] --------------------------------- +146: [21:37:39] testIssue227 +146: +146: [21:37:39] --------------------------------- +146: [21:37:39] testIssue236 +146: +146: [21:37:39] --------------------------------- +146: [21:37:39] testOrdering +146: +146: [21:37:39] --------------------------------- +146: [21:37:39] testIssue244 +146: +146: [21:37:39] --------------------------------- +146: [21:37:39] testIssue251 +146: +146: [21:37:39] --------------------------------- +146: [21:37:39] testIssue276 +146: [21:37:39] --------------------------------- +146: [21:37:39] testIssue284 +146: +146: [21:37:39] --------------------------------- +146: [21:37:39] testIssue285 +146: +146: [21:37:39] --------------------------------- +146: [21:37:39] testIssue355 +146: +146: [21:37:39] --------------------------------- +146: [21:37:39] testRandomCoords +146: +146: [21:37:39] --------------------------------- +146: [21:37:39] test sf.net issue 1989539 +146: +146: [21:37:39] --------------------------------- +146: [21:37:39] test sf.net issue 2091864 +146: +146: [21:37:39] --------------------------------- +146: [21:37:39] test constrained embedding +146: +146: [21:37:39] ssd: 0.0752641 +146: [21:37:39] ssd: 0.0659363 +151: 55422640 +148: [21:37:39] Molecule does not have explicit Hs. Consider calling AddHs() +146: [21:37:39] --------------------------------- +146: [21:37:39] test sf.net issue 2091974 +146: +146: [21:37:39] --------------------------------- +146: [21:37:39] test sf.net issue 2835784 +146: +146: [21:37:39] --------------------------------- +146: [21:37:39] test sf.net issue 3019283 +146: +146: [21:37:39] --------------------------------- +146: [21:37:39] test sf.net issue 3238580 +146: +146: [21:37:39] --------------------------------- +146: [21:37:39] test sf.net issue 3483968 +146: +146: [21:37:39] --------------------------------- +146: [21:37:39] test github issue 55 +146: +146: [21:37:39] --------------------------------- +146: [21:37:39] test1 +146: +146: [21:37:39] --------------------------------- +146: [21:37:39] test multi-threading +146: +146: building molecules +146: generating reference data +148: [21:37:39] Molecule does not have explicit Hs. Consider calling AddHs() +148: [21:37:39] Molecule does not have explicit Hs. Consider calling AddHs() +143: [21:37:39] done +143: [21:37:39] ------------------------------------- +143: [21:37:39] Testing GitHubIssue62. +143: [21:37:39] beta-lactam 39.6387 +143: [21:37:39] cyclopropanone 174.698 +143: [21:37:39] aziridine 337.986 +143: [21:37:39] aziridinone 115.248 +143: [21:37:39] isobutene 2.48217 +143: [21:37:39] acetone 1.91788 +143: [21:37:39] cyclopentanone 10.1648 +143: [21:37:39] cyclopropene 99.4921 +143: [21:37:39] cyclobutene 41.0156 +143: [21:37:39] cyclopropane 267.236 +143: [21:37:39] gamma-lactam 15.7471 +143: [21:37:39] trans-2,3-diphenylcyclopropan-1-one 203.398 +143: [21:37:40] cis-2,3-diphenylcyclopropan-1-one 206.852 +143: [21:37:40] 2,3-diphenylcyclopropa-2-en-1-one 20.0443 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 +143: [21:37:40] cyclopropylidencyclobutane 218.879 126: Warning: Atom Count for residue ARG64A does not match expected count -148: [12:42:42] Molecule does not have explicit Hs. Consider calling AddHs() -148: [12:42:42] Molecule does not have explicit Hs. Consider calling AddHs() -29: done -29: ------------------------------------- -29: Unit test for MMFF TorsionConstraint close to 0 degrees. -29: done -29: ------------------------------------- -29: Unit tests for copying MMFF ForceFields. -148: [12:42:42] Molecule does not have explicit Hs. Consider calling AddHs() -148: [12:42:42] Molecule does not have explicit Hs. Consider calling AddHs() 126: Warning: Atom Count for residue LYS80A does not match expected count -148: [12:42:42] Molecule does not have explicit Hs. Consider calling AddHs() -148: [12:42:42] Molecule does not have explicit Hs. Consider calling AddHs() -148: [12:42:42] Molecule does not have explicit Hs. Consider calling AddHs() 126: Warning: Atom Count for residue GLU150A does not match expected count 126: Warning: Atom Count for residue ASN157A does not match expected count -29: done -29: ------------------------------------- -29: Unit test for MMFF butane scan. -148: [12:42:42] Molecule does not have explicit Hs. Consider calling AddHs() -148: [12:42:42] Molecule does not have explicit Hs. Consider calling AddHs() -148: [12:42:42] Molecule does not have explicit Hs. Consider calling AddHs() -148: [12:42:42] Molecule does not have explicit Hs. Consider calling AddHs() -141: [12:42:42] Rep: 60 Mol:2 -141: [12:42:42] Rep: 60 Mol:6 -141: [12:42:42] Rep: 60 Mol:10 -141: [12:42:42] Rep: 60 Mol:14 -141: [12:42:42] Rep: 60 Mol:18 -141: [12:42:42] Rep: 60 Mol:22 -141: [12:42:42] Rep: 60 Mol:26 -141: [12:42:42] Rep: 60 Mol:30 -148: [12:42:42] Molecule does not have explicit Hs. Consider calling AddHs() -148: [12:42:42] Molecule does not have explicit Hs. Consider calling AddHs() -148: [12:42:42] Molecule does not have explicit Hs. Consider calling AddHs() -148: [12:42:42] Molecule does not have explicit Hs. Consider calling AddHs() -148: [12:42:42] Molecule does not have explicit Hs. Consider calling AddHs() -126: .[12:42:42] DEPRECATION WARNING: please use MorganGenerator -126: .[12:42:42] DEPRECATION WARNING: please use MorganGenerator -126: ..[12:42:42] DEPRECATION WARNING: please use AtomPairGenerator -126: [12:42:42] DEPRECATION WARNING: please use AtomPairGenerator -126: [12:42:42] DEPRECATION WARNING: please use AtomPairGenerator -126: [12:42:42] DEPRECATION WARNING: please use AtomPairGenerator -126: [12:42:42] DEPRECATION WARNING: please use AtomPairGenerator -126: [12:42:42] DEPRECATION WARNING: please use AtomPairGenerator -126: .[12:42:42] DEPRECATION WARNING: please use TopologicalTorsionGenerator -126: [12:42:42] DEPRECATION WARNING: please use TopologicalTorsionGenerator -126: ...[12:42:42] DEPRECATION WARNING: please use MorganGenerator -126: [12:42:42] DEPRECATION WARNING: please use MorganGenerator -126: [12:42:42] DEPRECATION WARNING: please use MorganGenerator -126: [12:42:42] DEPRECATION WARNING: please use MorganGenerator -126: [12:42:42] DEPRECATION WARNING: please use MorganGenerator -126: [12:42:42] DEPRECATION WARNING: please use MorganGenerator -126: [12:42:42] DEPRECATION WARNING: please use MorganGenerator -126: [12:42:42] DEPRECATION WARNING: please use MorganGenerator -126: [12:42:42] DEPRECATION WARNING: please use MorganGenerator -126: [12:42:42] DEPRECATION WARNING: please use MorganGenerator -126: [12:42:42] DEPRECATION WARNING: please use MorganGenerator -126: [12:42:42] DEPRECATION WARNING: please use MorganGenerator -126: [12:42:42] DEPRECATION WARNING: please use MorganGenerator -126: [12:42:42] DEPRECATION WARNING: please use MorganGenerator -126: [12:42:42] DEPRECATION WARNING: please use MorganGenerator -126: [12:42:42] DEPRECATION WARNING: please use MorganGenerator -126: [12:42:42] DEPRECATION WARNING: please use MorganGenerator -148: [12:42:42] Molecule does not have explicit Hs. Consider calling AddHs() -148: [12:42:42] Molecule does not have explicit Hs. Consider calling AddHs() -126: [12:42:42] DEPRECATION WARNING: please use MorganGenerator -126: [12:42:42] DEPRECATION WARNING: please use MorganGenerator -126: [12:42:42] DEPRECATION WARNING: please use MorganGenerator -126: [12:42:42] DEPRECATION WARNING: please use MorganGenerator -126: [12:42:42] DEPRECATION WARNING: please use MorganGenerator -148: [12:42:42] Molecule does not have explicit Hs. Consider calling AddHs() -148: [12:42:42] Molecule does not have explicit Hs. Consider calling AddHs() -148: [12:42:42] Molecule does not have explicit Hs. Consider calling AddHs() -126: ....[12:42:42] DEPRECATION WARNING: please use AtomPairGenerator -126: [12:42:42] DEPRECATION WARNING: please use AtomPairGenerator -148: [12:42:42] Molecule does not have explicit Hs. Consider calling AddHs() -148: [12:42:42] Molecule does not have explicit Hs. Consider calling AddHs() -148: [12:42:42] Molecule does not have explicit Hs. Consider calling AddHs() -126: ....[12:42:42] DEPRECATION WARNING: please use AtomPairGenerator -126: [12:42:42] DEPRECATION WARNING: please use AtomPairGenerator -126: .[12:42:42] DEPRECATION WARNING: please use TopologicalTorsionGenerator -126: [12:42:42] DEPRECATION WARNING: please use TopologicalTorsionGenerator -126: [12:42:42] DEPRECATION WARNING: please use TopologicalTorsionGenerator -126: [12:42:42] DEPRECATION WARNING: please use TopologicalTorsionGenerator -126: [12:42:42] DEPRECATION WARNING: please use TopologicalTorsionGenerator -126: ..[12:42:42] DEPRECATION WARNING: please use TopologicalTorsionGenerator -126: [12:42:42] DEPRECATION WARNING: please use TopologicalTorsionGenerator -126: [12:42:42] DEPRECATION WARNING: please use TopologicalTorsionGenerator -126: [12:42:42] DEPRECATION WARNING: please use TopologicalTorsionGenerator -126: [12:42:42] DEPRECATION WARNING: please use TopologicalTorsionGenerator -126: [12:42:42] DEPRECATION WARNING: please use TopologicalTorsionGenerator -126: .[12:42:42] DEPRECATION WARNING: please use TopologicalTorsionGenerator -126: [12:42:42] DEPRECATION WARNING: please use TopologicalTorsionGenerator +148: [21:37:40] Molecule does not have explicit Hs. Consider calling AddHs() +143: [21:37:40] diphenylmethylidencyclobutane 79.6139 +143: [21:37:40] done +143: [21:37:40] ------------------------------------- +143: [21:37:40] Test Github Issue 613: UFF Atom type not properly assigned to lanthanides. +143: [21:37:40] done +143: [21:37:40] ------------------------------------- +143: [21:37:40] Test square planar complexes +143: [21:37:40] done +143: [21:37:40] ------------------------------------- +143: [21:37:40] Test octahedral complexes +143: [21:37:40] done +141/236 Test #143: testUFFForceFieldHelpers ............... Passed 3.83 sec +test 153 + Start 153: testFeatures + +153: Test command: /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/GraphMol/MolChemicalFeatures/testFeatures +153: Working Directory: /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/GraphMol/MolChemicalFeatures +153: Test timeout computed to be: 1500 +126: .[21:37:40] DEPRECATION WARNING: please use MorganGenerator +126: .[21:37:40] DEPRECATION WARNING: please use MorganGenerator +126: ..[21:37:40] DEPRECATION WARNING: please use AtomPairGenerator +126: [21:37:40] DEPRECATION WARNING: please use AtomPairGenerator +126: [21:37:40] DEPRECATION WARNING: please use AtomPairGenerator +126: [21:37:40] DEPRECATION WARNING: please use AtomPairGenerator +126: [21:37:40] DEPRECATION WARNING: please use AtomPairGenerator +126: [21:37:40] DEPRECATION WARNING: please use AtomPairGenerator +126: .[21:37:40] DEPRECATION WARNING: please use TopologicalTorsionGenerator +126: [21:37:40] DEPRECATION WARNING: please use TopologicalTorsionGenerator +126: ...[21:37:40] DEPRECATION WARNING: please use MorganGenerator +126: [21:37:40] DEPRECATION WARNING: please use MorganGenerator +126: [21:37:40] DEPRECATION WARNING: please use MorganGenerator +126: [21:37:40] DEPRECATION WARNING: please use MorganGenerator +126: [21:37:40] DEPRECATION WARNING: please use MorganGenerator +126: [21:37:40] DEPRECATION WARNING: please use MorganGenerator +126: [21:37:40] DEPRECATION WARNING: please use MorganGenerator +126: [21:37:40] DEPRECATION WARNING: please use MorganGenerator +126: [21:37:40] DEPRECATION WARNING: please use MorganGenerator +126: [21:37:40] DEPRECATION WARNING: please use MorganGenerator +126: [21:37:40] DEPRECATION WARNING: please use MorganGenerator +126: [21:37:40] DEPRECATION WARNING: please use MorganGenerator +126: [21:37:40] DEPRECATION WARNING: please use MorganGenerator +126: [21:37:40] DEPRECATION WARNING: please use MorganGenerator +126: [21:37:40] DEPRECATION WARNING: please use MorganGenerator +126: [21:37:40] DEPRECATION WARNING: please use MorganGenerator +126: [21:37:40] DEPRECATION WARNING: please use MorganGenerator +126: [21:37:40] DEPRECATION WARNING: please use MorganGenerator +126: [21:37:40] DEPRECATION WARNING: please use MorganGenerator +126: [21:37:40] DEPRECATION WARNING: please use MorganGenerator +126: [21:37:40] DEPRECATION WARNING: please use MorganGenerator +126: [21:37:40] DEPRECATION WARNING: please use MorganGenerator +153: [21:37:40] ------------------------------------- +153: [21:37:40] AtomType parser testing. +153: [21:37:40] SMARTS Parse Error: syntax error while parsing: [$([!$([NH0])_100;N,O,$([S])_101,$([N,O)_102])_103] +153: [21:37:40] SMARTS Parse Error: Failed parsing SMARTS '[$([!$([NH0])_100;N,O,$([S])_101,$([N,O)_102])_103]' for input: '[$([!$([NH0]);N,O,$([S]),$([N,O)])]' +153: [21:37:40] done +153: [21:37:40] ------------------------------------- +153: [21:37:40] FeatureDefinition parser testing. +153: [21:37:40] done +153: [21:37:40] ------------------------------------- +153: [21:37:40] Test pulling feat defs from a string. +153: [21:37:40] done +153: [21:37:40] ------------------------------------- +153: [21:37:40] FeatureDef functionality testing. +126: ....[21:37:40] DEPRECATION WARNING: please use AtomPairGenerator +126: [21:37:40] DEPRECATION WARNING: please use AtomPairGenerator +126: ....[21:37:40] DEPRECATION WARNING: please use AtomPairGenerator +126: [21:37:40] DEPRECATION WARNING: please use AtomPairGenerator +126: .[21:37:40] DEPRECATION WARNING: please use TopologicalTorsionGenerator +126: [21:37:40] DEPRECATION WARNING: please use TopologicalTorsionGenerator +126: [21:37:40] DEPRECATION WARNING: please use TopologicalTorsionGenerator +126: [21:37:40] DEPRECATION WARNING: please use TopologicalTorsionGenerator +126: [21:37:40] DEPRECATION WARNING: please use TopologicalTorsionGenerator +126: ..[21:37:40] DEPRECATION WARNING: please use TopologicalTorsionGenerator +126: [21:37:40] DEPRECATION WARNING: please use TopologicalTorsionGenerator +126: [21:37:40] DEPRECATION WARNING: please use TopologicalTorsionGenerator +126: [21:37:40] DEPRECATION WARNING: please use TopologicalTorsionGenerator +126: [21:37:40] DEPRECATION WARNING: please use TopologicalTorsionGenerator +126: [21:37:40] DEPRECATION WARNING: please use TopologicalTorsionGenerator +126: .[21:37:40] DEPRECATION WARNING: please use TopologicalTorsionGenerator +126: [21:37:40] DEPRECATION WARNING: please use TopologicalTorsionGenerator +153: [21:37:40] done +153: [21:37:40] ------------------------------------- +153: [21:37:40] FeatureFactory testing. +153: [21:37:40] 1 +153: [21:37:40] 2 +153: [21:37:40] 3 +153: [21:37:40] 4 +153: [21:37:40] 5 +153: [21:37:40] 6 +153: [21:37:40] done +153: [21:37:40] ------------------------------------- +153: [21:37:40] Feature Location testing. +153: [21:37:40] done +153: [21:37:40] ------------------------------------- +153: [21:37:40] Test building a FeatureFactory from a file +153: [21:37:40] done +153: [21:37:40] ------------------------------------- +153: [21:37:40] Testing Issue 224. +153: [21:37:40] done +153: [21:37:40] ------------------------------------- +153: [21:37:40] Testing Issue 225. +153: [21:37:40] done +153: [21:37:40] ------------------------------------- +153: [21:37:40] Test Issue346 +153: [21:37:40] done +153: [21:37:40] ------------------------------------- +153: [21:37:40] Test Issue347 +153: [21:37:40] done +153: [21:37:40] ------------------------------------- +153: [21:37:40] Testing Issue 348. +153: [21:37:40] SMARTS Parse Error: syntax error while parsing: [C[C] +153: [21:37:40] SMARTS Parse Error: Failed parsing SMARTS '[C[C]' for input: '[C[C]' +153: [21:37:40] ------------------------------------- +153: [21:37:40] Testing Nested AtomType definitions. +153: [$([$([$([C;!$(C=[O,N,P,S]);!$(C#N)]),c]);R])] +153: [21:37:40] ------------------------------------- +153: [21:37:40] Testing Github Issue #252: crash when calling getPos() with no conformer. +153: [21:37:40] expect a precondition failure message below +153: [21:37:40] +153: +153: **** +153: Pre-condition Violation +153: molecule has no conformers +153: Violation occurred on line 37 in file ./Code/GraphMol/MolChemicalFeatures/MolChemicalFeature.cpp +153: Failed Expression: dp_mol->getNumConformers() +153: ---------- +153: Stacktrace: +153: 0# Invar::Invariant::toString[abi:cxx11]() const in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu//lib/libRDKitRDGeneral.so.1 +153: 1# Invar::operator<<(std::ostream&, Invar::Invariant const&) in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu//lib/libRDKitRDGeneral.so.1 +153: 2# RDKit::MolChemicalFeature::getPos(int) const in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu//lib/libRDKitMolChemicalFeatures.so.1 +153: 3# RDKit::MolChemicalFeature::getPos() const in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu//lib/libRDKitMolChemicalFeatures.so.1 +153: 4# 0x0000AAAABA801850 in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/GraphMol/MolChemicalFeatures/testFeatures +153: 5# 0x0000AAAABA7F42C8 in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/GraphMol/MolChemicalFeatures/testFeatures +153: 6# 0x0000FFFF9B65229C in /lib/aarch64-linux-gnu/libc.so.6 +153: 7# __libc_start_main in /lib/aarch64-linux-gnu/libc.so.6 +153: 8# 0x0000AAAABA7F4470 in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/GraphMol/MolChemicalFeatures/testFeatures +153: ---------- +153: **** +153: +153: [21:37:40] Done +153: [21:37:40] ------------------------------------- +153: [21:37:40] Testing github 2077: add confId argument to MolChemicalFeatureFactor::getFeaturesForMol() +153: [21:37:40] done 126: ... 126: ---------------------------------------------------------------------- -126: Ran 31 tests in 2.854s +126: Ran 31 tests in 5.381s 126: 126: OK 126: exactmw 78.046950192 @@ -27371,184 +27701,32 @@ 126: CustomNumAtoms 6.0 126: exactmw 78.046950192 126: lipinskiHBA 0.0 -148: [12:42:42] Molecule does not have explicit Hs. Consider calling AddHs() -148: [12:42:42] Molecule does not have explicit Hs. Consider calling AddHs() -143: [12:42:42] Rep: 100 Mol:0 -143: [12:42:42] Rep: 100 Mol:4 -143: [12:42:42] Rep: 100 Mol:8 -143: [12:42:42] Rep: 100 Mol:12 -143: [12:42:42] Rep: 100 Mol:16 -143: [12:42:42] Rep: 100 Mol:20 -143: [12:42:42] Rep: 100 Mol:24 -143: [12:42:42] Rep: 100 Mol:28 -125: Warning: Atom Count for residue GLU5A does not match expected count -125: Warning: Atom Count for residue ASN39A does not match expected count -148: [12:42:42] Molecule does not have explicit Hs. Consider calling AddHs() -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 -148: [12:42:42] Molecule does not have explicit Hs. Consider calling AddHs() -148: [12:42:42] Molecule does not have explicit Hs. Consider calling AddHs() -139/236 Test #126: pyMolDescriptors ....................... Passed 3.19 sec -125: =============================================================================== -125: All tests passed (515 assertions in 10 test cases) -125: -test 151 - Start 151: molAlignCatchTest - -151: Test command: /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/GraphMol/MolAlign/molAlignCatchTest -151: Working Directory: /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/GraphMol/MolAlign -151: Test timeout computed to be: 1500 -148: [12:42:42] Molecule does not have explicit Hs. Consider calling AddHs() -141: [12:42:42] Rep: 80 Mol:2 -140/236 Test #125: descriptorsTestCatch ................... Passed 3.26 sec -test 152 - Start 152: pyMolAlign - -152: Test command: /usr/bin/python3 "/build/reproducible-path/rdkit-202409.4/Code/GraphMol/MolAlign/Wrap/testMolAlign.py" -152: Working Directory: /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/GraphMol/MolAlign/Wrap -152: Test timeout computed to be: 1500 -141: [12:42:42] Rep: 80 Mol:6 -141: [12:42:42] Rep: 80 Mol:10 -141: [12:42:42] Rep: 80 Mol:14 -141: [12:42:42] Rep: 80 Mol:18 -141: [12:42:42] Rep: 80 Mol:22 -141: [12:42:42] Rep: 80 Mol:26 -141: [12:42:42] Rep: 80 Mol:30 -148: [12:42:42] Molecule does not have explicit Hs. Consider calling AddHs() -148: [12:42:42] Molecule does not have explicit Hs. Consider calling AddHs() -143: [12:42:42] Rep: 100 Mol:1 -143: [12:42:42] Rep: 100 Mol:5 -143: [12:42:42] Rep: 100 Mol:9 -143: [12:42:42] Rep: 100 Mol:13 -143: [12:42:42] Rep: 100 Mol:17 -143: [12:42:42] Rep: 100 Mol:21 -143: [12:42:42] Rep: 100 Mol:25 -143: [12:42:42] Rep: 100 Mol:29 -29: done -141/236 Test #29: testMMFFForceField ..................... Passed 7.23 sec -test 153 - Start 153: testFeatures - -153: Test command: /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/GraphMol/MolChemicalFeatures/testFeatures -153: Working Directory: /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/GraphMol/MolChemicalFeatures -153: Test timeout computed to be: 1500 -148: [12:42:42] Molecule does not have explicit Hs. Consider calling AddHs() -151: Randomness seeded to: 3439341491 -151: 25763029 -153: [12:42:42] ------------------------------------- -153: [12:42:42] AtomType parser testing. -153: [12:42:42] SMARTS Parse Error: syntax error while parsing: [$([!$([NH0])_100;N,O,$([S])_101,$([N,O)_102])_103] -153: [12:42:42] SMARTS Parse Error: Failed parsing SMARTS '[$([!$([NH0])_100;N,O,$([S])_101,$([N,O)_102])_103]' for input: '[$([!$([NH0]);N,O,$([S]),$([N,O)])]' -153: [12:42:42] done -153: [12:42:42] ------------------------------------- -153: [12:42:42] FeatureDefinition parser testing. -153: [12:42:42] done -153: [12:42:42] ------------------------------------- -153: [12:42:42] Test pulling feat defs from a string. -153: [12:42:42] done -153: [12:42:42] ------------------------------------- -153: [12:42:42] FeatureDef functionality testing. -148: [12:42:42] Molecule does not have explicit Hs. Consider calling AddHs() -153: [12:42:42] done -153: [12:42:42] ------------------------------------- -153: [12:42:42] FeatureFactory testing. -153: [12:42:42] 1 -153: [12:42:42] 2 -153: [12:42:42] 3 -153: [12:42:42] 4 -153: [12:42:42] 5 -153: [12:42:42] 6 -153: [12:42:42] done -153: [12:42:42] ------------------------------------- -153: [12:42:42] Feature Location testing. -153: [12:42:42] done -153: [12:42:42] ------------------------------------- -153: [12:42:42] Test building a FeatureFactory from a file -153: [12:42:42] done -153: [12:42:42] ------------------------------------- -153: [12:42:42] Testing Issue 224. -153: [12:42:42] done -153: [12:42:42] ------------------------------------- -153: [12:42:42] Testing Issue 225. -153: [12:42:42] done -153: [12:42:42] ------------------------------------- -153: [12:42:42] Test Issue346 -153: [12:42:42] done -153: [12:42:42] ------------------------------------- -153: [12:42:42] Test Issue347 -153: [12:42:42] done -153: [12:42:42] ------------------------------------- -153: [12:42:42] Testing Issue 348. -153: [12:42:42] SMARTS Parse Error: syntax error while parsing: [C[C] -153: [12:42:42] SMARTS Parse Error: Failed parsing SMARTS '[C[C]' for input: '[C[C]' -153: [12:42:42] ------------------------------------- -153: [12:42:42] Testing Nested AtomType definitions. -153: [$([$([$([C;!$(C=[O,N,P,S]);!$(C#N)]),c]);R])] -153: [12:42:42] ------------------------------------- -153: [12:42:42] Testing Github Issue #252: crash when calling getPos() with no conformer. -153: [12:42:42] expect a precondition failure message below -153: [12:42:42] -153: -153: **** -153: Pre-condition Violation -153: molecule has no conformers -153: Violation occurred on line 37 in file ./Code/GraphMol/MolChemicalFeatures/MolChemicalFeature.cpp -153: Failed Expression: dp_mol->getNumConformers() -153: ---------- -153: Stacktrace: -153: 0# Invar::Invariant::toString[abi:cxx11]() const in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu//lib/libRDKitRDGeneral.so.1 -153: 1# Invar::operator<<(std::ostream&, Invar::Invariant const&) in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu//lib/libRDKitRDGeneral.so.1 -153: 2# RDKit::MolChemicalFeature::getPos(int) const in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu//lib/libRDKitMolChemicalFeatures.so.1 -153: 3# RDKit::MolChemicalFeature::getPos() const in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu//lib/libRDKitMolChemicalFeatures.so.1 -153: 4# 0x0000AAAADE981850 in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/GraphMol/MolChemicalFeatures/testFeatures -153: 5# 0x0000AAAADE9742C8 in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/GraphMol/MolChemicalFeatures/testFeatures -153: 6# 0x0000FFFF899E229C in /lib/aarch64-linux-gnu/libc.so.6 -153: 7# __libc_start_main in /lib/aarch64-linux-gnu/libc.so.6 -153: 8# 0x0000AAAADE974470 in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/GraphMol/MolChemicalFeatures/testFeatures -153: ---------- -153: **** -153: -153: [12:42:42] Done -153: [12:42:42] ------------------------------------- -153: [12:42:42] Testing github 2077: add confId argument to MolChemicalFeatureFactor::getFeaturesForMol() -153: [12:42:42] done -142/236 Test #153: testFeatures ........................... Passed 0.02 sec +142/236 Test #153: testFeatures ........................... Passed 0.04 sec test 154 Start 154: pyChemicalFeatures 154: Test command: /usr/bin/python3 "/build/reproducible-path/rdkit-202409.4/Code/GraphMol/MolChemicalFeatures/Wrap/testChemicalFeatures.py" 154: Working Directory: /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/GraphMol/MolChemicalFeatures/Wrap 154: Test timeout computed to be: 1500 -148: [12:42:42] Molecule does not have explicit Hs. Consider calling AddHs() -52: Randomness seeded to: 2218871961 -52: =============================================================================== -52: All tests passed (14835 assertions in 14 test cases) -52: -143/236 Test #52: canonTestsCatch ........................ Passed 6.92 sec +29: Checking against /build/reproducible-path/rdkit-202409.4/Code/ForceField/MMFF/test_data/MMFF94_reference.log... +143/236 Test #126: pyMolDescriptors ....................... Passed 5.92 sec test 155 Start 155: testShapeHelpers 155: Test command: /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/GraphMol/ShapeHelpers/testShapeHelpers 155: Working Directory: /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/GraphMol/ShapeHelpers 155: Test timeout computed to be: 1500 -148: [12:42:42] Molecule does not have explicit Hs. Consider calling AddHs() -151: 22877573 -148: [12:42:42] Molecule does not have explicit Hs. Consider calling AddHs() -141: [12:42:42] done -141: [12:42:42] ------------------------------------- -141: [12:42:42] Test MMFF multithreading2 -143: [12:42:42] Rep: 100 Mol:2 -143: [12:42:42] Rep: 100 Mol:6 -143: [12:42:42] Rep: 100 Mol:10 -143: [12:42:42] Rep: 100 Mol:14 -143: [12:42:42] Rep: 100 Mol:18 -143: [12:42:42] Rep: 100 Mol:22 -143: [12:42:42] Rep: 100 Mol:26 -143: [12:42:42] Rep: 100 Mol:30 -148: [12:42:42] Molecule does not have explicit Hs. Consider calling AddHs() +52: Randomness seeded to: 674652360 +52: =============================================================================== +52: All tests passed (14835 assertions in 14 test cases) +52: +144/236 Test #52: canonTestsCatch ........................ Passed 12.50 sec +test 156 + Start 156: pyShapeHelpers + +156: Test command: /usr/bin/python3 "/build/reproducible-path/rdkit-202409.4/Code/GraphMol/ShapeHelpers/Wrap/testShapeHelpers.py" +156: Working Directory: /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/GraphMol/ShapeHelpers/Wrap +156: Test timeout computed to be: 1500 155: *********************************************************** 155: Testing ShapeHelpers 155: --------------------------------- @@ -27561,167 +27739,71 @@ 155: testGithub4364 155: 155: *********************************************************** -144/236 Test #155: testShapeHelpers ....................... Passed 0.02 sec -148: [12:42:42] Molecule does not have explicit Hs. Consider calling AddHs() -test 156 - Start 156: pyShapeHelpers - -156: Test command: /usr/bin/python3 "/build/reproducible-path/rdkit-202409.4/Code/GraphMol/ShapeHelpers/Wrap/testShapeHelpers.py" -156: Working Directory: /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/GraphMol/ShapeHelpers/Wrap -156: Test timeout computed to be: 1500 -148: [12:42:42] Molecule does not have explicit Hs. Consider calling AddHs() -148: [12:42:42] Molecule does not have explicit Hs. Consider calling AddHs() -148: [12:42:42] Molecule does not have explicit Hs. Consider calling AddHs() -148: [12:42:42] Molecule does not have explicit Hs. Consider calling AddHs() -148: [12:42:42] Molecule does not have explicit Hs. Consider calling AddHs() -148: .[12:42:42] Molecule does not have explicit Hs. Consider calling AddHs() -146: [12:42:41] --------------------------------- -146: [12:42:41] test3 -146: -146: [12:42:41] --------------------------------- -146: [12:42:41] test4 -146: -146: [12:42:41] --------------------------------- -146: [12:42:41] test5 -146: -146: [12:42:42] --------------------------------- -146: [12:42:42] test6 -146: -146: [12:42:42] --------------------------------- -146: [12:42:42] test15Dists -146: -146: [12:42:42] --------------------------------- -146: [12:42:42] test Issue 215 -146: -146: [12:42:42] --------------------------------- -146: [12:42:42] testMultipleConfs -146: -146: [12:42:42] --------------------------------- -146: [12:42:42] testMultipleConfsExpTors -146: -146: [12:42:42] --------------------------------- -146: [12:42:42] testIssue227 -146: -146: [12:42:42] --------------------------------- -146: [12:42:42] testIssue236 -146: -146: [12:42:42] --------------------------------- -146: [12:42:42] testOrdering -146: -146: [12:42:42] --------------------------------- -146: [12:42:42] testIssue244 -146: -146: [12:42:42] --------------------------------- -146: [12:42:42] testIssue251 -146: -146: [12:42:42] --------------------------------- -146: [12:42:42] testIssue276 -146: [12:42:42] --------------------------------- -146: [12:42:42] testIssue284 -146: -146: [12:42:42] --------------------------------- -146: [12:42:42] testIssue285 -146: -146: [12:42:42] --------------------------------- -146: [12:42:42] testIssue355 -146: -146: [12:42:42] --------------------------------- -146: [12:42:42] testRandomCoords -146: -146: [12:42:42] --------------------------------- -146: [12:42:42] test sf.net issue 1989539 -146: -146: [12:42:42] --------------------------------- -146: [12:42:42] test sf.net issue 2091864 -146: -146: [12:42:42] --------------------------------- -146: [12:42:42] test constrained embedding -146: -146: [12:42:42] ssd: 0.0752641 -146: [12:42:42] ssd: 0.0659363 -147: [12:42:42] UFFTYPER: Warning: hybridization set to SP3 for atom 6 -146: [12:42:42] --------------------------------- -146: [12:42:42] test sf.net issue 2091974 -146: -146: [12:42:42] --------------------------------- -146: [12:42:42] test sf.net issue 2835784 -146: -146: [12:42:42] --------------------------------- -146: [12:42:42] test sf.net issue 3019283 -146: -146: [12:42:42] --------------------------------- -146: [12:42:42] test sf.net issue 3238580 -146: -146: [12:42:42] --------------------------------- -146: [12:42:42] test sf.net issue 3483968 -146: -146: [12:42:42] --------------------------------- -146: [12:42:42] test github issue 55 -146: -146: [12:42:42] --------------------------------- -146: [12:42:42] test1 -146: -146: [12:42:42] --------------------------------- -146: [12:42:42] test multi-threading -146: -146: building molecules -146: generating reference data -147: [12:42:42] UFFTYPER: Warning: hybridization set to SP3 for atom 6 -148: [12:42:42] Molecule does not have explicit Hs. Consider calling AddHs() -147: [12:42:42] UFFTYPER: Warning: hybridization set to SP3 for atom 6 -147: [12:42:42] UFFTYPER: Warning: hybridization set to SP3 for atom 11 -147: [12:42:42] UFFTYPER: Warning: hybridization set to SP3 for atom 11 -147: [12:42:42] UFFTYPER: Warning: hybridization set to SP3 for atom 11 -154: .[12:42:42] Molecule does not have explicit Hs. Consider calling AddHs() -156: . -156: ---------------------------------------------------------------------- -156: Ran 1 test in 0.026s -156: -156: OK -156: Testing Shape Helpers wrapper -154: .[12:42:42] Molecule does not have explicit Hs. Consider calling AddHs() -141: [12:42:42] done -141: [12:42:42] ------------------------------------- -141: [12:42:42] Test MMFF multithreading3 -154: ..[12:42:42] Molecule does not have explicit Hs. Consider calling AddHs() -154: .[12:42:42] Molecule does not have explicit Hs. Consider calling AddHs() -154: .[12:42:42] SMARTS Parse Error: syntax error while parsing: [N,O;!HQ] -154: [12:42:42] SMARTS Parse Error: Failed parsing SMARTS '[N,O;!HQ]' for input: '[N,O;!HQ]' -154: ... -154: ---------------------------------------------------------------------- -154: Ran 9 tests in 0.084s -154: -154: OK -148: [12:42:42] Molecule does not have explicit Hs. Consider calling AddHs() -145/236 Test #156: pyShapeHelpers ......................... Passed 0.42 sec +145/236 Test #155: testShapeHelpers ....................... Passed 0.05 sec test 157 Start 157: testMolCatalog 157: Test command: /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/GraphMol/MolCatalog/testMolCatalog 157: Working Directory: /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/GraphMol/MolCatalog 157: Test timeout computed to be: 1500 -146/236 Test #157: testMolCatalog ......................... Passed 0.03 sec +29: All 191 tests passed +29: done +29: ------------------------------------- +29: Unit tests for all MMFF constraint terms. +146/236 Test #157: testMolCatalog ......................... Passed 0.04 sec test 158 Start 158: pyMolCatalog 158: Test command: /usr/bin/python3 "/build/reproducible-path/rdkit-202409.4/Code/GraphMol/MolCatalog/Wrap/rough_test.py" 158: Working Directory: /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/GraphMol/MolCatalog/Wrap 158: Test timeout computed to be: 1500 -143: [12:42:43] done -143: [12:42:43] ------------------------------------- -143: [12:42:43] Test UFF multithreading2 -147/236 Test #154: pyChemicalFeatures ..................... Passed 0.58 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. +151: 1334369280 +146: validating reference data +154: .[21:37:40] Molecule does not have explicit Hs. Consider calling AddHs() +154: .[21:37:40] Molecule does not have explicit Hs. Consider calling AddHs() +156: . +156: ---------------------------------------------------------------------- +156: Ran 1 test in 0.053s +156: +156: OK +156: Testing Shape Helpers wrapper +29: done +147/236 Test #29: testMMFFForceField ..................... Passed 13.60 sec test 159 Start 159: moldraw2DTest1 159: Test command: /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/GraphMol/MolDraw2D/moldraw2DTest1 159: Working Directory: /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/GraphMol/MolDraw2D 159: Test timeout computed to be: 1500 +158: . +158: ---------------------------------------------------------------------- +158: Ran 1 test in 0.010s +158: +158: OK +154: ..[21:37:40] Molecule does not have explicit Hs. Consider calling AddHs() +154: .[21:37:40] Molecule does not have explicit Hs. Consider calling AddHs() +154: .[21:37:40] SMARTS Parse Error: syntax error while parsing: [N,O;!HQ] +154: [21:37:40] SMARTS Parse Error: Failed parsing SMARTS '[N,O;!HQ]' for input: '[N,O;!HQ]' +154: ... +154: ---------------------------------------------------------------------- +154: Ran 9 tests in 0.122s +154: +154: OK +148: [21:37:40] Molecule does not have explicit Hs. Consider calling AddHs() 159: ----------------- Test 1 159: file test1_6.svg gave hash 1109656969U not the expected 2635907956U 159: Done 159: ----------------- Test 2 -148: [12:42:43] Molecule does not have explicit Hs. Consider calling AddHs() 159: file test2_1.png gave hash 2432381627U not the expected 307437906U 159: file test2_2.png gave hash 4038208473U not the expected 610424244U 159: file test2_3.png gave hash 2294574389U not the expected 2179746375U @@ -27730,11 +27812,33 @@ 159: file test4_1.png gave hash 3853762228U not the expected 1403972924U 159: Done 159: ----------------- Test 5 +148/236 Test #156: pyShapeHelpers ......................... Passed 0.65 sec +test 160 + Start 160: moldraw2DTestCatch + +160: Test command: /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/GraphMol/MolDraw2D/moldraw2DTestCatch +160: Working Directory: /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/GraphMol/MolDraw2D +160: Test timeout computed to be: 1500 159: file test5_1.png gave hash 2657697431U not the expected 1269428339U +149/236 Test #158: pyMolCatalog ........................... Passed 0.60 sec +test 161 + Start 161: moldraw2DRxnTest1 + +161: Test command: /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/GraphMol/MolDraw2D/moldraw2DRxnTest1 +161: Working Directory: /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/GraphMol/MolDraw2D +161: Test timeout computed to be: 1500 159: file test5_2.png gave hash 3478552006U not the expected 3073694291U 159: file test5_3.png gave hash 998470489U not the expected 1865192682U 159: Done 159: ----------------- Test 6 (atom labels) +148: [21:37:40] Molecule does not have explicit Hs. Consider calling AddHs() +150/236 Test #154: pyChemicalFeatures ..................... Passed 0.86 sec +test 162 + Start 162: pyMolDraw2D + +162: Test command: /usr/bin/python3 "/build/reproducible-path/rdkit-202409.4/Code/GraphMol/MolDraw2D/Wrap/testMolDraw2D.py" +162: Working Directory: /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/GraphMol/MolDraw2D/Wrap +162: Test timeout computed to be: 1500 159: Done 159: ----------------- Test 7 (backgrounds) 159: file test7_1.png gave hash 3620297203U not the expected 3033050306U @@ -27744,95 +27848,73 @@ 159: Done 159: ----------------- Test multi-threaded drawing 159: reading molecules +161: ----------------- Test 1 159: generating reference drawings -141: [12:42:43] done -141: [12:42:43] ------------------------------------- -141: [12:42:43] Testing github 162: Incorrect SMILES after MMFF parameterization . -141: [12:42:43] done -141: [12:42:43] ------------------------------------- -141: [12:42:43] Testing github 224: crash during MMFF parameterization . -141: [12:42:43] done -141: [12:42:43] ------------------------------------- -141: [12:42:43] Testing github6728: crash due to missing stretch-bend params. -148/236 Test #141: testMMFFForceFieldHelpers .............. Passed 2.03 sec -test 160 - Start 160: moldraw2DTestCatch - -160: Test command: /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/GraphMol/MolDraw2D/moldraw2DTestCatch -160: Working Directory: /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/GraphMol/MolDraw2D -160: Test timeout computed to be: 1500 -159: processing -159: launch :0 -159: launch :1 -159: launch :2 -159: launch :3 -160: Randomness seeded to: 2591034191 +161: file rxn_test1_1.png gave hash 247850884U not the expected 1556334749U +160: Randomness seeded to: 2628338110 160: file contourMol_1.svg gave hash 4125787245U not the expected 2604538953U 160: file contourMol_2.svg gave hash 2761342533U not the expected 572669511U +161: file rxn_test1_2.png gave hash 1462400260U not the expected 1924084263U 160: file contourMol_3.svg gave hash 1333854566U not the expected 936771429U 160: file contourMol_4.svg gave hash 4249475618U not the expected 3302971362U 160: file contourMol_5.svg gave hash 3376179346U not the expected 2230414999U -158: . -158: ---------------------------------------------------------------------- -158: Ran 1 test in 0.006s -158: -158: OK +161: file rxn_test1_3.png gave hash 1729781197U not the expected 1644921059U 160: file testGithub3226_1.png gave hash 2923995808U not the expected 2350054896U 160: file testGithub3226_2.png gave hash 2054669313U not the expected 606206725U -148: [12:42:43] Molecule does not have explicit Hs. Consider calling AddHs() +161: file rxn_test1_4.png gave hash 123018244U not the expected 2471435686U 160: file testGithub3226_3.png gave hash 3808523831U not the expected 2282880418U 160: file testPNGMetadata_1.png gave hash 3885682853U not the expected 2423299691U -143: [12:42:43] done -143: [12:42:43] ------------------------------------- -143: [12:42:43] Test UFF multithreading3 +161: file rxn_test1_5.png gave hash 3759567997U not the expected 1428782307U +148: [21:37:41] Molecule does not have explicit Hs. Consider calling AddHs() 160: file testPNGMetadata_2.png gave hash 1579824122U not the expected 2803353117U -149/236 Test #158: pyMolCatalog ........................... Passed 0.50 sec -test 161 - Start 161: moldraw2DRxnTest1 +159: processing +159: launch :0 +159: launch :1 +159: launch :2 +159: launch :3 +161: file rxn_test1_6.png gave hash 3836874965U not the expected 483353696U +151: 551491480 +151: =============================================================================== +151: All tests passed (73 assertions in 3 test cases) +151: +151/236 Test #151: molAlignCatchTest ...................... Passed 2.11 sec +test 163 + Start 163: testFMCS -161: Test command: /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/GraphMol/MolDraw2D/moldraw2DRxnTest1 -161: Working Directory: /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/GraphMol/MolDraw2D -161: Test timeout computed to be: 1500 -161: ----------------- Test 1 -160: [12:42:43] Font file /build/reproducible-path/rdkit-202409.4/Data/Fonts/ComicNeue-Regular.ttf not found. -160: [12:42:43] Falling back to original font file /build/reproducible-path/rdkit-202409.4/Data/Fonts/Telex-Regular.ttf. -148: [12:42:43] Molecule does not have explicit Hs. Consider calling AddHs() -161: file rxn_test1_1.png gave hash 247850884U not the expected 1556334749U +163: Test command: /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/GraphMol/FMCS/testFMCS +163: Working Directory: /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/GraphMol/FMCS +163: Test timeout computed to be: 1500 +160: [21:37:41] Font file /build/reproducible-path/rdkit-202409.4/Data/Fonts/ComicNeue-Regular.ttf not found. +160: [21:37:41] Falling back to original font file /build/reproducible-path/rdkit-202409.4/Data/Fonts/Telex-Regular.ttf. 160: file testHandDrawn-1.svg gave hash 1143910631U not the expected 2253418236U -160: [12:42:43] Font file /build/reproducible-path/rdkit-202409.4/Data/Fonts/ComicNeue-Regular.ttf not found. -160: [12:42:43] Falling back to original font file /build/reproducible-path/rdkit-202409.4/Data/Fonts/Telex-Regular.ttf. -160: file testHandDrawn-1.png gave hash 1841922610U not the expected 698316547U -161: file rxn_test1_2.png gave hash 1462400260U not the expected 1924084263U -161: file rxn_test1_3.png gave hash 1729781197U not the expected 1644921059U -161: file rxn_test1_4.png gave hash 123018244U not the expected 2471435686U -160: [12:42:43] Font file /build/reproducible-path/rdkit-202409.4/Data/Fonts/ComicNeue-Regular.ttf not found. -160: [12:42:43] Falling back to original font file /build/reproducible-path/rdkit-202409.4/Data/Fonts/Telex-Regular.ttf. -161: file rxn_test1_5.png gave hash 3759567997U not the expected 1428782307U -160: file testHandDrawn-2.svg gave hash 700659102U not the expected 4132716144U -160: [12:42:43] Font file /build/reproducible-path/rdkit-202409.4/Data/Fonts/ComicNeue-Regular.ttf not found. -160: [12:42:43] Falling back to original font file /build/reproducible-path/rdkit-202409.4/Data/Fonts/Telex-Regular.ttf. -161: file rxn_test1_6.png gave hash 3836874965U not the expected 483353696U -160: file testHandDrawn-2.png gave hash 2680117957U not the expected 1605553248U -160: [12:42:43] Font file /build/reproducible-path/rdkit-202409.4/Data/Fonts/ComicNeue-Regular.ttf not found. -160: [12:42:43] Falling back to original font file /build/reproducible-path/rdkit-202409.4/Data/Fonts/Telex-Regular.ttf. -160: file testHandDrawn-3.svg gave hash 2359787964U not the expected 4199337510U -160: [12:42:43] Font file /build/reproducible-path/rdkit-202409.4/Data/Fonts/ComicNeue-Regular.ttf not found. -160: [12:42:43] Falling back to original font file /build/reproducible-path/rdkit-202409.4/Data/Fonts/Telex-Regular.ttf. -160: file testHandDrawn-3.png gave hash 3170392294U not the expected 2881952238U -160: [12:42:43] Font file /build/reproducible-path/rdkit-202409.4/Data/Fonts/ComicNeue-Regular.ttf not found. -160: [12:42:43] Falling back to original font file /build/reproducible-path/rdkit-202409.4/Data/Fonts/Telex-Regular.ttf. +160: [21:37:41] Font file /build/reproducible-path/rdkit-202409.4/Data/Fonts/ComicNeue-Regular.ttf not found. +160: [21:37:41] Falling back to original font file /build/reproducible-path/rdkit-202409.4/Data/Fonts/Telex-Regular.ttf. 161: file rxn_test1_7.png gave hash 1681482819U not the expected 528963379U 161: Done 161: ----------------- Test 2: some examples that caused problems in testing -160: file testHandDrawn-4.svg gave hash 1880974760U not the expected 4197407865U -160: [12:42:43] Font file /build/reproducible-path/rdkit-202409.4/Data/Fonts/ComicNeue-Regular.ttf not found. -160: [12:42:43] Falling back to original font file /build/reproducible-path/rdkit-202409.4/Data/Fonts/Telex-Regular.ttf. -160: file testHandDrawn-4.png gave hash 956318745U not the expected 3431655453U +160: file testHandDrawn-1.png gave hash 1841922610U not the expected 698316547U 161: file rxn_test2_1.png gave hash 2768289447U not the expected 399415052U +160: [21:37:41] Font file /build/reproducible-path/rdkit-202409.4/Data/Fonts/ComicNeue-Regular.ttf not found. +160: [21:37:41] Falling back to original font file /build/reproducible-path/rdkit-202409.4/Data/Fonts/Telex-Regular.ttf. +160: file testHandDrawn-2.svg gave hash 700659102U not the expected 4132716144U +160: [21:37:41] Font file /build/reproducible-path/rdkit-202409.4/Data/Fonts/ComicNeue-Regular.ttf not found. +160: [21:37:41] Falling back to original font file /build/reproducible-path/rdkit-202409.4/Data/Fonts/Telex-Regular.ttf. 161: 3 [cH:1]1[cH:2][cH:3][c:4][cH:5][cH:6]1>>CC(C)[c:1]1[cH:2][cH:3][c:4][cH:5][cH:6]1 CN1CCC(CC1)N(C)S(=O)(=O)c2ccccc2 CC(C)c1ccc(cc1)S(=O)(=O)N(C)C2CCN(CC2)C +160: file testHandDrawn-2.png gave hash 2680117957U not the expected 1605553248U 161: file rxn_test2_2_1.png gave hash 501093229U not the expected 1215378243U -151: 1234499875 +160: [21:37:41] Font file /build/reproducible-path/rdkit-202409.4/Data/Fonts/ComicNeue-Regular.ttf not found. +160: [21:37:41] Falling back to original font file /build/reproducible-path/rdkit-202409.4/Data/Fonts/Telex-Regular.ttf. +160: file testHandDrawn-3.svg gave hash 2359787964U not the expected 4199337510U +160: [21:37:41] Font file /build/reproducible-path/rdkit-202409.4/Data/Fonts/ComicNeue-Regular.ttf not found. +160: [21:37:41] Falling back to original font file /build/reproducible-path/rdkit-202409.4/Data/Fonts/Telex-Regular.ttf. +160: file testHandDrawn-3.png gave hash 3170392294U not the expected 2881952238U 161: 3 [cH:1]1[cH:2][cH:3][c:4][cH:5][cH:6]1>>[cH:3]1[cH:2][c:1]([cH:6][cH:5][c:4]1)Cl Cc1cccc(c1C)N2CCN(CC2)CCCNC(=O)c3cc([nH]c3C)c4ccccc4 Cc1cccc(c1C)N2CCN(CC2)CCCNC(=O)c3cc([nH]c3C)c4ccc(cc4)Cl +160: [21:37:41] Font file /build/reproducible-path/rdkit-202409.4/Data/Fonts/ComicNeue-Regular.ttf not found. +160: [21:37:41] Falling back to original font file /build/reproducible-path/rdkit-202409.4/Data/Fonts/Telex-Regular.ttf. +160: file testHandDrawn-4.svg gave hash 1880974760U not the expected 4197407865U +160: [21:37:41] Font file /build/reproducible-path/rdkit-202409.4/Data/Fonts/ComicNeue-Regular.ttf not found. +160: [21:37:41] Falling back to original font file /build/reproducible-path/rdkit-202409.4/Data/Fonts/Telex-Regular.ttf. +160: file testHandDrawn-4.png gave hash 956318745U not the expected 3431655453U 161: file rxn_test2_2_2.png gave hash 2982833713U not the expected 3645141778U 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 @@ -27842,6 +27924,7 @@ 161: file rxn_test2_2_4.png gave hash 973659076U not the expected 4234617566U 161: Done 161: ----------------- Test 3: test reactant highlighting +148: [21:37:41] Molecule does not have explicit Hs. Consider calling AddHs() 161: file rxn_test3_1.png gave hash 3930938785U not the expected 4176857511U 161: Done 161: ----------------- Test 4: some examples from SMARTS in testing @@ -27849,70 +27932,17 @@ 161: file rxn_test4_1.png gave hash 881241024U not the expected 4187207676U 161: done 161: file rxn_test4_2.png gave hash 2931217441U not the expected 3490081297U +162: ...[21:37:41] Font file /build/reproducible-path/rdkit-202409.4/Code/GraphMol/MolDraw2D/Amadeus.ttf not found. +162: [21:37:41] Falling back to original font file /build/reproducible-path/rdkit-202409.4/Data/Fonts/Telex-Regular.ttf. 161: Done -150/236 Test #161: moldraw2DRxnTest1 ...................... Passed 0.47 sec -test 162 - Start 162: pyMolDraw2D - -162: Test command: /usr/bin/python3 "/build/reproducible-path/rdkit-202409.4/Code/GraphMol/MolDraw2D/Wrap/testMolDraw2D.py" -162: Working Directory: /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/GraphMol/MolDraw2D/Wrap -162: Test timeout computed to be: 1500 -143: [12:42:43] done -143: [12:42:43] ------------------------------------- -143: [12:42:43] Testing GitHubIssue62. -143: [12:42:43] beta-lactam 39.6387 -143: [12:42:43] cyclopropanone 174.698 -143: [12:42:43] aziridine 337.986 -143: [12:42:43] aziridinone 115.248 -143: [12:42:43] isobutene 2.48217 -143: [12:42:43] acetone 1.91788 -143: [12:42:44] cyclopentanone 10.1648 -143: [12:42:44] cyclopropene 99.4921 -143: [12:42:44] cyclobutene 41.0156 -143: [12:42:44] cyclopropane 267.236 -143: [12:42:44] gamma-lactam 15.7471 -146: validating reference data -143: [12:42:44] trans-2,3-diphenylcyclopropan-1-one 203.398 -143: [12:42:44] cis-2,3-diphenylcyclopropan-1-one 206.852 -143: [12:42:44] 2,3-diphenylcyclopropa-2-en-1-one 20.0443 -143: [12:42:44] cyclopropylidencyclobutane 218.879 -143: [12:42:44] diphenylmethylidencyclobutane 79.6139 -143: [12:42:44] done -143: [12:42:44] ------------------------------------- -143: [12:42:44] Test Github Issue 613: UFF Atom type not properly assigned to lanthanides. -143: [12:42:44] done -143: [12:42:44] ------------------------------------- -143: [12:42:44] Test square planar complexes -143: [12:42:44] done -143: [12:42:44] ------------------------------------- -143: [12:42:44] Test octahedral complexes -143: [12:42:44] done -151/236 Test #143: testUFFForceFieldHelpers ............... Passed 2.56 sec -test 163 - Start 163: testFMCS - -163: Test command: /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/GraphMol/FMCS/testFMCS -163: Working Directory: /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/GraphMol/FMCS -163: Test timeout computed to be: 1500 -148: [12:42:44] Molecule does not have explicit Hs. Consider calling AddHs() -151: 375071934 -151: =============================================================================== -151: All tests passed (73 assertions in 3 test cases) -151: -152/236 Test #151: molAlignCatchTest ...................... Passed 1.74 sec +152/236 Test #161: moldraw2DRxnTest1 ...................... Passed 0.56 sec test 164 Start 164: pyFMCS 164: Test command: /usr/bin/python3 "/build/reproducible-path/rdkit-202409.4/Code/GraphMol/FMCS/Wrap/testFMCS.py" 164: Working Directory: /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/GraphMol/FMCS/Wrap 164: Test timeout computed to be: 1500 -148: [12:42:44] Molecule does not have explicit Hs. Consider calling AddHs() -162: ...[12:42:44] Font file /build/reproducible-path/rdkit-202409.4/Code/GraphMol/MolDraw2D/Amadeus.ttf not found. -162: [12:42:44] Falling back to original font file /build/reproducible-path/rdkit-202409.4/Data/Fonts/Telex-Regular.ttf. -160: file testHandDrawn-5a.svg gave hash 2796249138U not the expected 3628607349U -160: [12:42:44] Font file /build/reproducible-path/rdkit-202409.4/Data/Fonts/ComicNeue-Regular.ttf not found. -160: [12:42:44] Falling back to original font file /build/reproducible-path/rdkit-202409.4/Data/Fonts/Telex-Regular.ttf. -162: ..........[12:42:44] +162: ..........[21:37:41] 162: 162: **** 162: Pre-condition Violation @@ -27926,7 +27956,7 @@ 162: 2# RDKit::prepMolForDrawing(RDKit::ROMol const*, bool, bool, bool, bool, bool) in /build/reproducible-path/rdkit-202409.4/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-202409.4/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# 0x0000FFFFBC0B2680 in /lib/aarch64-linux-gnu/libboost_python313.so.1.83.0 +162: 5# 0x0000FFFF7E2A2680 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-202409.4/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-202409.4/obj-aarch64-linux-gnu/rdkit/Chem/rdDepictor.so @@ -27937,17 +27967,17 @@ 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-202409.4/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-202409.4/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-202409.4/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so -162: 16# 0x0000FFFFBB6C9FA0 in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so -162: 17# 0x0000FFFFBB6C9F38 in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so -162: 18# 0x0000FFFFBB6C9EC8 in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so -162: 19# 0x0000FFFFBB6C9E60 in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so -162: 20# 0x0000FFFFBB6C9DF8 in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so +162: 16# 0x0000FFFF7D8B9FA0 in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so +162: 17# 0x0000FFFF7D8B9F38 in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so +162: 18# 0x0000FFFF7D8B9EC8 in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so +162: 19# 0x0000FFFF7D8B9E60 in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so +162: 20# 0x0000FFFF7D8B9DF8 in /build/reproducible-path/rdkit-202409.4/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-202409.4/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-202409.4/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-202409.4/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-202409.4/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# 0x0000FFFFBC0AF25C in /lib/aarch64-linux-gnu/libboost_python313.so.1.83.0 +162: 26# 0x0000FFFF7E29F25C 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# 0x000000000052F1D8 in /usr/bin/python3 @@ -27979,38 +28009,33 @@ 162: 55# 0x0000000000621C6C in /usr/bin/python3 162: 56# Py_RunMain in /usr/bin/python3 162: 57# Py_BytesMain in /usr/bin/python3 -162: 58# 0x0000FFFFBE53229C in /lib/aarch64-linux-gnu/libc.so.6 +162: 58# 0x0000FFFF8072229C 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: -160: file testHandDrawn-5b.svg gave hash 4043231252U not the expected 2522138089U -160: [12:42:44] Font file /build/reproducible-path/rdkit-202409.4/Data/Fonts/ComicNeue-Regular.ttf not found. -160: [12:42:44] Falling back to original font file /build/reproducible-path/rdkit-202409.4/Data/Fonts/Telex-Regular.ttf. -160: file testHandDrawn-5.png gave hash 3931760583U not the expected 3439548169U -148: [12:42:44] Molecule does not have explicit Hs. Consider calling AddHs() -160: file testBrackets-5a.svg gave hash 279553678U not the expected 2676997151U -160: file testSGroupData-3a.svg gave hash 62481132U not the expected 2405789536U -160: file testSGroupData-3a.svg gave hash 62481132U not the expected 2405789536U -160: file testPositionVariation-1b.svg gave hash 3055422087U not the expected 174339626U +148: [21:37:41] Molecule does not have explicit Hs. Consider calling AddHs() 162: ...................... 162: ---------------------------------------------------------------------- -162: Ran 35 tests in 0.132s +162: Ran 35 tests in 0.278s 162: 162: OK 162: json lasso -148: [12:42:44] Molecule does not have explicit Hs. Consider calling AddHs() -160: [12:42:44] unrecognized bond typefile testGithub2976.svg gave hash 2858811732U not the expected 2669316911U -160: file testGithub4238_1.png gave hash 3148130411U not the expected 3410617836U -160: file testGithub4323_1.png gave hash 2843631142U not the expected 3723958844U -153/236 Test #162: pyMolDraw2D ............................ Passed 0.45 sec +160: file testHandDrawn-5a.svg gave hash 2796249138U not the expected 3628607349U +160: [21:37:41] Font file /build/reproducible-path/rdkit-202409.4/Data/Fonts/ComicNeue-Regular.ttf not found. +160: [21:37:41] Falling back to original font file /build/reproducible-path/rdkit-202409.4/Data/Fonts/Telex-Regular.ttf. +153/236 Test #162: pyMolDraw2D ............................ Passed 0.90 sec test 165 Start 165: FMCStest 165: Test command: /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/GraphMol/FMCS/Test/FMCStest 165: Working Directory: /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/GraphMol/FMCS/Test 165: Test timeout computed to be: 1500 +160: file testHandDrawn-5b.svg gave hash 4043231252U not the expected 2522138089U +160: [21:37:41] Font file /build/reproducible-path/rdkit-202409.4/Data/Fonts/ComicNeue-Regular.ttf not found. +160: [21:37:41] Falling back to original font file /build/reproducible-path/rdkit-202409.4/Data/Fonts/Telex-Regular.ttf. +148: [21:37:41] Molecule does not have explicit Hs. Consider calling AddHs() 165: fopen testChEMBL_Txt(): No such file or directory 165: fopen testChEMBL_Txt(): No such file or directory 165: fopen testChEMBL_Txt(): No such file or directory @@ -29976,17 +30001,53 @@ 165: 165: testFileSDF_RandomSet(): benchmark/chembl13_threshold_90.smi 165: ERROR: RDKit could not load input file -148: [12:42:44] Molecule does not have explicit Hs. Consider calling AddHs() -148: [12:42:44] Molecule does not have explicit Hs. Consider calling AddHs() -154/236 Test #165: FMCStest ............................... Passed 0.14 sec +160: file testHandDrawn-5.png gave hash 3931760583U not the expected 3439548169U +154/236 Test #165: FMCStest ............................... Passed 0.06 sec test 166 Start 166: molHashCatchTest 166: Test command: /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/GraphMol/MolHash/molHashCatchTest 166: Working Directory: /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/GraphMol/MolHash 166: Test timeout computed to be: 1500 +160: file testBrackets-5a.svg gave hash 279553678U not the expected 2676997151U +160: file testSGroupData-3a.svg gave hash 62481132U not the expected 2405789536U +160: file testSGroupData-3a.svg gave hash 62481132U not the expected 2405789536U +160: file testPositionVariation-1b.svg gave hash 3055422087U not the expected 174339626U +166: Randomness seeded to: 3371588316 +166: =============================================================================== +166: All tests passed (332 assertions in 13 test cases) +166: +155/236 Test #166: molHashCatchTest ....................... Passed 0.09 sec +test 167 + Start 167: pyMolHash + +167: Test command: /usr/bin/python3 "/build/reproducible-path/rdkit-202409.4/Code/GraphMol/MolHash/Wrap/testMolHash.py" +167: Working Directory: /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/GraphMol/MolHash/Wrap +167: Test timeout computed to be: 1500 +160: [21:37:42] unrecognized bond typefile testGithub2976.svg gave hash 2858811732U not the expected 2669316911U +160: file testGithub4238_1.png gave hash 3148130411U not the expected 3410617836U +160: file testGithub4323_1.png gave hash 2843631142U not the expected 3723958844U 160: file testGithub4323_3.png gave hash 2020541711U not the expected 2185913679U -160: [12:42:44] FIELDDISP info not found for DAT SGroup which isn't associated with an atom. SGroup will not be rendered. +160: [21:37:42] 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 +160: file testFlexiCanvas.2a.png gave hash 2084781451U not the expected 3217758043U +160: file testFlexiCanvas.2b.png gave hash 1617297844U not the expected 4070063910U +160: file testFlexiCanvas.3.svg gave hash 3867616289U not the expected 2819587550U +160: file testGithub4764.sz1.svg gave hash 2364628953U not the expected 3611125861U +160: file testGithub4764.sz2.svg gave hash 1490175526U not the expected 1936114454U +160: file testGithub4764.sz3.svg gave hash 1662881340U not the expected 2712214121U +160: file testGithub4764.sz1.png gave hash 2798567004U not the expected 98827714U +160: file testGithub4764.sz2.png gave hash 2534857731U not the expected 89252465U +167: .... +167: ---------------------------------------------------------------------- +167: Ran 4 tests in 0.020s +167: +167: OK +160: file testGithub4764.sz3.png gave hash 1531035136U not the expected 148503574U 150: *********************************************************** 150: Testing O3AAlign 150: --------------------------------- @@ -30017,31 +30078,6 @@ 150: testMMFFO3A multithreading 150: 150: generating reference data -166: Randomness seeded to: 1133425047 -166: =============================================================================== -166: All tests passed (332 assertions in 13 test cases) -166: -155/236 Test #166: molHashCatchTest ....................... Passed 0.08 sec -test 167 - Start 167: pyMolHash - -167: Test command: /usr/bin/python3 "/build/reproducible-path/rdkit-202409.4/Code/GraphMol/MolHash/Wrap/testMolHash.py" -167: Working Directory: /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/GraphMol/MolHash/Wrap -167: Test timeout computed to be: 1500 -160: file testFlexiCanvas.2a.png gave hash 2084781451U not the expected 3217758043U -160: file testFlexiCanvas.2b.png gave hash 1617297844U not the expected 4070063910U -160: file testFlexiCanvas.3.svg gave hash 3867616289U not the expected 2819587550U -160: file testGithub4764.sz1.svg gave hash 2364628953U not the expected 3611125861U -160: file testGithub4764.sz2.svg gave hash 1490175526U not the expected 1936114454U -160: file testGithub4764.sz3.svg gave hash 1662881340U not the expected 2712214121U -160: file testGithub4764.sz1.png gave hash 2798567004U not the expected 98827714U -146: processing -146: launch :0 -146: launch :1 -146: launch :2 -146: launch :3 -160: file testGithub4764.sz2.png gave hash 2534857731U not the expected 89252465U -160: file testGithub4764.sz3.png gave hash 1531035136U not the expected 148503574U 160: file testGithub_5061.svg gave hash 4026821599U not the expected 83338095U 160: file github5383_1.svg gave hash 2761342533U not the expected 3666750661U 160: file github5383_2.svg gave hash 2560846108U not the expected 0U @@ -30054,39 +30090,20 @@ 160: file acs1996_8.svg gave hash 3359655656U not the expected 2477908768U 160: file acs1996_9.svg gave hash 231896677U not the expected 3747924004U 160: file acs1996_10.svg gave hash 1008047306U not the expected 2229333301U -160: [12:42:45] 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: [21:37:42] 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 1272407071U not the expected 2956924065U -160: file test_github5947.svg gave hash 737562322U not the expected 3122633523U -148: .[12:42:45] Molecule does not have explicit Hs. Consider calling AddHs() -167: .... -167: ---------------------------------------------------------------------- -167: Ran 4 tests in 0.011s -167: -167: OK -160: file test_github6112.svg gave hash 3291975047U not the expected 3278777629U -160: file test_github6200_1.svg gave hash 1975293465U not the expected 1044179149U -160: file github6336_1.png gave hash 1930712448U not the expected 2958833204U -160: file test_github6397_2.svg gave hash 2405824082U not the expected 3422233570U -160: file test_github6397_3.svg gave hash 759740391U not the expected 3320683230U -160: file test_github6397_4.svg gave hash 2454933776U not the expected 2960192928U -160: file test_github6397_5.svg gave hash 1843492326U not the expected 1245534660U -160: file github6504_1.svg gave hash 3649936662U not the expected 1429448598U -160: file github6504_2.svg gave hash 106020287U not the expected 2871662880U -160: file github6569_1.svg gave hash 1698514747U not the expected 116573839U -160: file github6569_2.svg gave hash 2778768241U not the expected 2367779037U -156/236 Test #167: pyMolHash .............................. Passed 0.52 sec +156/236 Test #167: pyMolHash .............................. Passed 0.85 sec test 168 Start 168: testMMPA 168: Test command: /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/GraphMol/MMPA/testMMPA 168: Working Directory: /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/GraphMol/MMPA 168: Test timeout computed to be: 1500 -160: file AtropCanon1.svg gave hash 818325437U not the expected 526339583U -160: file AtropManyChiralsEnhanced.svg gave hash 292902747U not the expected 348414093U -160: file testGithub6968.svg gave hash 940962291U not the expected 1554428830U +160: file test_github5947.svg gave hash 737562322U not the expected 3122633523U +148: .[21:37:42] Molecule does not have explicit Hs. Consider calling AddHs() 168: 168: TEST mol: Case1 Cc1ccccc1NC(=O)[C:7](C)[NH+]1CCCC1 Case1 -168: Time elapsed 0.002325 seconds +168: Time elapsed 0.002306 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 @@ -30115,11 +30132,6 @@ 168: 13: NOREF. Reference data NOT LISTED in test case. 168: 14: res= [C:0]([*:1])([*:2])[*:3],C1CC[NH+]([*:3])C1.C[*:1].Cc1ccccc1NC(=O)[*:2] 168: 14: NOREF. Reference data NOT LISTED in test case. -150: processing -150: launch :0 -150: launch :1 -150: launch :2 -150: launch :3 168: 15: res= C[C:0]([*:1])[*:2],C1CC[NH+]([*:2])C1.Cc1ccccc1NC(=O)[*:1] 168: 15: NOREF. Reference data NOT LISTED in test case. 168: 16: res= NULL,C[*:1].Cc1ccccc1NC(=O)[C:2]([NH+]1CCCC1)[*:1] @@ -30132,7 +30144,7 @@ 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 0.001976 seconds +168: Time elapsed 0.010243 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 @@ -30174,9 +30186,10 @@ 168: ----------------------------------- 168: 168: TEST mol: ZINC21984717 Cc1c(C(=O)NCCO)[n+](=O)c2ccccc2n1[O-] ZINC21984717 -168: Time elapsed 0.001979 seconds +168: Time elapsed 0.002003 seconds 168: 1: res= NULL,C[*:1].O=C(NCCO)c1c([*:1])n([O-])c2ccccc2[n+]1=O 168: 1: PASSED. matchedRefRes = 4 +160: file test_github6112.svg gave hash 3291975047U not the expected 3278777629U 168: 2: res= O=[n+]1c([*:2])c([*:1])n([O-])c2ccccc21,C[*:1].O=C(NCCO)[*:2] 168: 2: PASSED. matchedRefRes = 1 168: 3: res= O=C(N[*:2])c1c([*:1])n([O-])c2ccccc2[n+]1=O,C[*:1].OCC[*:2] @@ -30214,7 +30227,7 @@ 168: ----------------------------------- 168: 168: TEST mol: Case1-SIMPLE CC(N1CC1)C(=O) Case1-SIMPLE -168: Time elapsed 0.000596 seconds +168: Time elapsed 0.000573 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] @@ -30236,7 +30249,7 @@ 168: ----------------------------------- 168: 168: TEST mol: Case1 Cc1ccccc1NC(=O)[C:7](C)[NH+]1CCCC1 Case1 -168: Time elapsed 0.002771 seconds +168: Time elapsed 0.002196 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 @@ -30245,6 +30258,7 @@ 168: 3: NOREF. Reference data NOT LISTED in test case. 168: 4: res= O=C(Nc1ccccc1[*:1])[C:0]([NH+]1CCCC1)[*:2],C[*:1].C[*:2] 168: 4: NOREF. Reference data NOT LISTED in test case. +160: file test_github6200_1.svg gave hash 1975293465U not the expected 1044179149U 168: 5: res= O=C(Nc1ccccc1[*:1])[C:0]([*:2])[*:3],C1CC[NH+]([*:3])C1.C[*:1].C[*:2] 168: 5: NOREF. Reference data NOT LISTED in test case. 168: 6: res= C[C:0](C(=O)Nc1ccccc1[*:1])[*:2],C1CC[NH+]([*:2])C1.C[*:1] @@ -30267,26 +30281,22 @@ 168: 14: NOREF. Reference data NOT LISTED in test case. 168: 15: res= C[C:0]([*:1])[*:2],C1CC[NH+]([*:2])C1.Cc1ccccc1NC(=O)[*:1] 168: 15: NOREF. Reference data NOT LISTED in test case. +160: file github6336_1.png gave hash 1930712448U not the expected 2958833204U 168: 16: res= NULL,C[*:1].Cc1ccccc1NC(=O)[C:2]([NH+]1CCCC1)[*:1] 168: 16: NOREF. Reference data NOT LISTED in test case. -160: file testWedgeNonSingleBonds-1.svg gave hash 2116685919U not the expected 865601717U 168: 17: res= Cc1ccccc1NC(=O)[C:0]([*:1])[*:2],C1CC[NH+]([*:2])C1.C[*:1] 168: 17: NOREF. Reference data NOT LISTED in test case. 168: 18: res= NULL,C1CC[NH+]([*:1])C1.Cc1ccccc1NC(=O)[C:2](C)[*:1] 168: 18: NOREF. Reference data NOT LISTED in test case. -160: file testWedgeNonSingleBonds-2.svg gave hash 1174395532U not the expected 2960559495U -160: file testWedgeNonSingleBonds-3.svg gave hash 2542970771U not the expected 1428196589U -160: file testWedgeNonSingleBonds-4.svg gave hash 700876833U not the expected 3897680387U -160: file testWedgeNonSingleBonds-5.svg gave hash 2012191155U not the expected 2183530217U -160: file testWedgeNonSingleBonds-6.svg gave hash 2517061935U not the expected 238313010U -160: file testWedgeNonSingleBonds-7.svg gave hash 157069219U not the expected 3641456570U +160: file test_github6397_2.svg gave hash 2405824082U not the expected 3422233570U +160: file test_github6397_3.svg gave hash 759740391U not the expected 3320683230U 168: 168: --- UNMATCHED Reference RESULTS: --- 168: 1: Cc1ccccc1NC(=O)[C:7](C)[NH+]1CCCC1,Case1,[*:1][C:7]([*:2])[*:3],C1CC[NH+]([*:3])C1.C[*:2].Cc1ccccc1NC(=O)[*:1] 168: ----------------------------------- 168: 168: TEST mol: Case2 O=C(OCc1ccccc1)C(O)c1ccccc1 Case2 -168: Time elapsed 0.002330 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 @@ -30309,8 +30319,6 @@ 168: 10: NOREF. Reference data NOT LISTED in test case. 168: 11: res= O=C(OC[*:1])C(O)[*:2],c1ccc([*:1])cc1.c1ccc([*:2])cc1 168: 11: NOREF. Reference data NOT LISTED in test case. -160: file testWedgeNonSingleBonds-8.svg gave hash 3431784338U not the expected 3209701539U -160: file testWedgingShouldBeOnSingleBond.svg gave hash 2637422009U not the expected 1002741488U 168: 12: res= NULL,O=C(OCc1ccccc1)[*:1].OC(c1ccccc1)[*:1] 168: 12: NOREF. Reference data NOT LISTED in test case. 168: 13: res= c1ccc(C([*:1])[*:2])cc1,O=C(OCc1ccccc1)[*:1].O[*:2] @@ -30329,152 +30337,56 @@ 168: --- ALL PASSED --- 168: ----------------------------------- 168: 5 TEST CASES FAILED -157/236 Test #168: testMMPA ............................... Passed 0.14 sec +160: file test_github6397_4.svg gave hash 2454933776U not the expected 2960192928U +160: file test_github6397_5.svg gave hash 1843492326U not the expected 1245534660U +157/236 Test #168: testMMPA ............................... Passed 0.19 sec test 169 Start 169: pyMMPA 169: Test command: /usr/bin/python3 "/build/reproducible-path/rdkit-202409.4/Code/GraphMol/MMPA/Wrap/testMMPA.py" 169: Working Directory: /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/GraphMol/MMPA/Wrap 169: Test timeout computed to be: 1500 -160: file testHighlightHeteroAtoms_1.svg gave hash 4006401146U not the expected 1769258632U -160: file testHighlightHeteroAtoms_2.svg gave hash 1248188292U not the expected 893937335U -160: file testGithub_7739_1.svg gave hash 233164329U not the expected 52079325U -160: file testGithub_7739_3.svg gave hash 1653424667U not the expected 1126644226U -160: file testGithub_7739_4.svg gave hash 3214282623U not the expected 9844878U -160: [12:42:45] -160: -160: **** -160: Pre-condition Violation -160: -160: Violation occurred on line 206 in file ./Code/GraphMol/MolDraw2D/DrawMolMCHCircleAndLine.cpp -160: Failed Expression: atomIdx < atCds_.size() && atomIdx < atomLabels_.size() -160: ---------- -160: Stacktrace: -160: 0# Invar::Invariant::toString[abi:cxx11]() const in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu//lib/libRDKitRDGeneral.so.1 -160: 1# Invar::operator<<(std::ostream&, Invar::Invariant const&) in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu//lib/libRDKitRDGeneral.so.1 -160: 2# RDKit::MolDraw2D_detail::DrawMolMCHCircleAndLine::calcSymbolEllipse(unsigned int, RDGeom::Point2D&, double&, double&) const in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu//lib/libRDKitMolDraw2D.so.1 -160: 3# RDKit::MolDraw2D_detail::DrawMolMCHCircleAndLine::makeAtomHighlights(std::vector >, std::allocator > > >&) in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu//lib/libRDKitMolDraw2D.so.1 -160: 4# RDKit::MolDraw2D_detail::DrawMolMCHCircleAndLine::extractMCHighlights() in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu//lib/libRDKitMolDraw2D.so.1 -160: 5# RDKit::MolDraw2D_detail::DrawMol::extractAll(double) in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu//lib/libRDKitMolDraw2D.so.1 -160: 6# RDKit::MolDraw2D_detail::DrawMol::createDrawObjects() in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu//lib/libRDKitMolDraw2D.so.1 -160: 7# RDKit::MolDraw2D::drawMoleculeWithHighlights(RDKit::ROMol const&, std::__cxx11::basic_string, std::allocator > const&, std::map >, std::less, std::allocator > > > > const&, std::map >, std::less, std::allocator > > > > const&, std::map, std::allocator > > const&, std::map, std::allocator > > const&, int) in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu//lib/libRDKitMolDraw2D.so.1 -160: 8# 0x0000AAAAC43345A8 in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/GraphMol/MolDraw2D/moldraw2DTestCatch -160: 9# 0x0000AAAAC43FD74C in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/GraphMol/MolDraw2D/moldraw2DTestCatch -160: 10# 0x0000AAAAC43FE100 in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/GraphMol/MolDraw2D/moldraw2DTestCatch -160: 11# 0x0000AAAAC43FE534 in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/GraphMol/MolDraw2D/moldraw2DTestCatch -160: 12# 0x0000AAAAC43D1F38 in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/GraphMol/MolDraw2D/moldraw2DTestCatch -160: 13# 0x0000AAAAC43D2484 in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/GraphMol/MolDraw2D/moldraw2DTestCatch -160: 14# 0x0000AAAAC432DC70 in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/GraphMol/MolDraw2D/moldraw2DTestCatch -160: 15# 0x0000FFFF85AE229C in /lib/aarch64-linux-gnu/libc.so.6 -160: 16# __libc_start_main in /lib/aarch64-linux-gnu/libc.so.6 -160: 17# 0x0000AAAAC432DD30 in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/GraphMol/MolDraw2D/moldraw2DTestCatch -160: ---------- -160: **** -160: -160: [12:42:45] -160: -160: **** -160: Range Error -160: idx -160: Violation occurred on line 329 in file ./Code/GraphMol/ROMol.cpp -160: Failed Expression: 2 < 0 -160: ---------- -160: Stacktrace: -160: 0# Invar::Invariant::toString[abi:cxx11]() const in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu//lib/libRDKitRDGeneral.so.1 -160: 1# Invar::operator<<(std::ostream&, Invar::Invariant const&) in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu//lib/libRDKitRDGeneral.so.1 -160: 2# RDKit::ROMol::getBondWithIdx(unsigned int) const in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu//lib/libRDKitGraphMol.so.1 -160: 3# RDKit::MolDraw2D_detail::DrawMolMCHCircleAndLine::makeBondHighlights(std::vector >, std::allocator > > >&) in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu//lib/libRDKitMolDraw2D.so.1 -160: 4# RDKit::MolDraw2D_detail::DrawMolMCHCircleAndLine::extractMCHighlights() in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu//lib/libRDKitMolDraw2D.so.1 -160: 5# RDKit::MolDraw2D_detail::DrawMol::extractAll(double) in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu//lib/libRDKitMolDraw2D.so.1 -160: 6# RDKit::MolDraw2D_detail::DrawMol::createDrawObjects() in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu//lib/libRDKitMolDraw2D.so.1 -160: 7# RDKit::MolDraw2D::drawMoleculeWithHighlights(RDKit::ROMol const&, std::__cxx11::basic_string, std::allocator > const&, std::map >, std::less, std::allocator > > > > const&, std::map >, std::less, std::allocator > > > > const&, std::map, std::allocator > > const&, std::map, std::allocator > > const&, int) in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu//lib/libRDKitMolDraw2D.so.1 -160: 8# 0x0000AAAAC4333FEC in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/GraphMol/MolDraw2D/moldraw2DTestCatch -160: 9# 0x0000AAAAC43FD74C in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/GraphMol/MolDraw2D/moldraw2DTestCatch -160: 10# 0x0000AAAAC43FE100 in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/GraphMol/MolDraw2D/moldraw2DTestCatch -160: 11# 0x0000AAAAC43FE534 in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/GraphMol/MolDraw2D/moldraw2DTestCatch -160: 12# 0x0000AAAAC43D1F38 in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/GraphMol/MolDraw2D/moldraw2DTestCatch -160: 13# 0x0000AAAAC43D2484 in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/GraphMol/MolDraw2D/moldraw2DTestCatch -160: 14# 0x0000AAAAC432DC70 in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/GraphMol/MolDraw2D/moldraw2DTestCatch -160: 15# 0x0000FFFF85AE229C in /lib/aarch64-linux-gnu/libc.so.6 -160: 16# __libc_start_main in /lib/aarch64-linux-gnu/libc.so.6 -160: 17# 0x0000AAAAC432DD30 in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/GraphMol/MolDraw2D/moldraw2DTestCatch -160: ---------- -160: **** -160: -160: [12:42:45] -160: -160: **** -160: Range Error -160: idx -160: Violation occurred on line 329 in file ./Code/GraphMol/ROMol.cpp -160: Failed Expression: 0 < 0 -160: ---------- -160: Stacktrace: -160: 0# Invar::Invariant::toString[abi:cxx11]() const in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu//lib/libRDKitRDGeneral.so.1 -160: 1# Invar::operator<<(std::ostream&, Invar::Invariant const&) in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu//lib/libRDKitRDGeneral.so.1 -160: 2# RDKit::ROMol::getBondWithIdx(unsigned int) const in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu//lib/libRDKitGraphMol.so.1 -160: 3# RDKit::MolDraw2D_detail::DrawMolMCHCircleAndLine::makeBondHighlights(std::vector >, std::allocator > > >&) in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu//lib/libRDKitMolDraw2D.so.1 -160: 4# RDKit::MolDraw2D_detail::DrawMolMCHCircleAndLine::extractMCHighlights() in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu//lib/libRDKitMolDraw2D.so.1 -160: 5# RDKit::MolDraw2D_detail::DrawMol::extractAll(double) in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu//lib/libRDKitMolDraw2D.so.1 -160: 6# RDKit::MolDraw2D_detail::DrawMol::createDrawObjects() in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu//lib/libRDKitMolDraw2D.so.1 -160: 7# RDKit::MolDraw2D::drawMoleculeWithHighlights(RDKit::ROMol const&, std::__cxx11::basic_string, std::allocator > const&, std::map >, std::less, std::allocator > > > > const&, std::map >, std::less, std::allocator > > > > const&, std::map, std::allocator > > const&, std::map, std::allocator > > const&, int) in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu//lib/libRDKitMolDraw2D.so.1 -160: 8# 0x0000AAAAC4334654 in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/GraphMol/MolDraw2D/moldraw2DTestCatch -160: 9# 0x0000AAAAC43FD74C in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/GraphMol/MolDraw2D/moldraw2DTestCatch -160: 10# 0x0000AAAAC43FE100 in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/GraphMol/MolDraw2D/moldraw2DTestCatch -160: 11# 0x0000AAAAC43FE534 in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/GraphMol/MolDraw2D/moldraw2DTestCatch -160: 12# 0x0000AAAAC43D1F38 in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/GraphMol/MolDraw2D/moldraw2DTestCatch -160: 13# 0x0000AAAAC43D2484 in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/GraphMol/MolDraw2D/moldraw2DTestCatch -160: 14# 0x0000AAAAC432DC70 in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/GraphMol/MolDraw2D/moldraw2DTestCatch -160: 15# 0x0000FFFF85AE229C in /lib/aarch64-linux-gnu/libc.so.6 -160: 16# __libc_start_main in /lib/aarch64-linux-gnu/libc.so.6 -160: 17# 0x0000AAAAC432DD30 in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/GraphMol/MolDraw2D/moldraw2DTestCatch -160: ---------- -160: **** -160: -160: =============================================================================== -160: All tests passed (6814 assertions in 107 test cases) -160: -158/236 Test #160: moldraw2DTestCatch ..................... Passed 2.07 sec -test 170 - Start 170: testRascalMCES - -170: Test command: /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/GraphMol/RascalMCES/testRascalMCES -170: Working Directory: /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/GraphMol/RascalMCES -170: Test timeout computed to be: 1500 +160: file github6504_1.svg gave hash 3649936662U not the expected 1429448598U +160: file github6504_2.svg gave hash 106020287U not the expected 2871662880U +160: file github6569_1.svg gave hash 1698514747U not the expected 116573839U +160: file github6569_2.svg gave hash 2778768241U not the expected 2367779037U +160: file AtropCanon1.svg gave hash 818325437U not the expected 526339583U +160: file AtropManyChiralsEnhanced.svg gave hash 292902747U not the expected 348414093U +160: file testGithub6968.svg gave hash 940962291U not the expected 1554428830U 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 0.072 seconds +163: Time elapsed 0.080 seconds 163: 163: test190() 163: MCS: [#6]1:[#6]:[#6]2:[#8]:[#6](:[#7]:[#6]:2:[#6]:[#6]:1)-[#6]1:[#6]:[#6](-[#7]-[#6](=[#8])-[#6]):[#6]:[#6]:[#6]:1 19 atoms, 21 bonds -163: Time elapsed 0.009 seconds +163: Time elapsed 0.005 seconds 163: 163: test3() 163: MCS: [#6]1:[#6]:[#6]:[#6]:[#6]:[#6]:1-[#6]-[#6](=[#8])-[#7]-[#6]-[#6]-[#6]-[#6] 14 atoms, 14 bonds -163: Time elapsed 0.012 seconds +163: Time elapsed 0.016 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 0.114 seconds +163: Time elapsed 0.137 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 0.060 seconds +163: Time elapsed 0.127 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 0.095 seconds +163: Time elapsed 0.143 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 0.063 seconds +163: Time elapsed 0.149 seconds 163: 163: testSegFault() 163: MCS: [#6]1:&@[#6]:&@[#6]:&@[#6]:&@[#6]:&@[#6]:&@1 6 atoms, 6 bonds -163: Time elapsed 0.005 seconds +163: Time elapsed 0.013 seconds 163: MCS MatchFusedRings: [#6]1:&@[#6]:&@[#6]:&@[#6]:&@[#6]:&@[#6]:&@1 6 atoms, 6 bonds -163: Time elapsed 0.007 seconds +163: Time elapsed 0.015 seconds 163: MCS MatchFusedRingsStrict: [#6;r6,!R1]1:&@[#6;r6,!R1]:&@[#6;r6,!R1]:&@[#6;r6,!R1]:&@[#6;r6,!R1]:&@[#6;r6,!R1]:&@1 6 atoms, 6 bonds -163: Time elapsed 0.007 seconds +163: Time elapsed 0.019 seconds 163: 163: testThreshold() 163: MCS: [#6]-[#6]-[#6] 3 atoms, 2 bonds @@ -30482,11 +30394,11 @@ 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 0.175 seconds +163: Time elapsed 0.408 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 0.317 seconds +163: Time elapsed 0.416 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 0.407 seconds +163: Time elapsed 0.475 seconds 163: 163: testAtomCompareIsotopes() 163: MCS: [0*]-[0*]-[13*] 3 atoms, 2 bonds @@ -30510,27 +30422,39 @@ 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 0.017 seconds 163: MCS: [#6]-[#6]-[#8]-[#6]1:[#6](:[#6](:[#6]:[#6](:[#7]:1)-[#7]-[#6](=[#8])-[#6]-[#6]1:[#6]:[#6]:[#6]:[#6](:[#6]:1)-[#6,#8])-[#7])-[#6]#[#7] *c1cccc(CC(=O)Nc2cc(N)c(C#N)c(OCC)n2)c1 23 atoms, 24 bonds +160: file testWedgeNonSingleBonds-1.svg gave hash 2116685919U not the expected 865601717U +160: file testWedgeNonSingleBonds-2.svg gave hash 1174395532U not the expected 2960559495U +160: file testWedgeNonSingleBonds-3.svg gave hash 2542970771U not the expected 1428196589U +160: file testWedgeNonSingleBonds-4.svg gave hash 700876833U not the expected 3897680387U +160: file testWedgeNonSingleBonds-5.svg gave hash 2012191155U not the expected 2183530217U +160: file testWedgeNonSingleBonds-6.svg gave hash 2517061935U not the expected 238313010U +160: file testWedgeNonSingleBonds-7.svg gave hash 157069219U not the expected 3641456570U +160: file testWedgeNonSingleBonds-8.svg gave hash 3431784338U not the expected 3209701539U +160: file testWedgingShouldBeOnSingleBond.svg gave hash 2637422009U not the expected 1002741488U +160: file testHighlightHeteroAtoms_1.svg gave hash 4006401146U not the expected 1769258632U +160: file testHighlightHeteroAtoms_2.svg gave hash 1248188292U not the expected 893937335U +160: file testGithub_7739_1.svg gave hash 233164329U not the expected 52079325U 163: Time elapsed 0.001 seconds 163: 163: test18() 163: Query +MAP [CH3:0][c:1]1[n:2][c:3]([CH2:4][N:5]([CH:6]([CH3:7])[c:8]2[n:9][cH:10][cH:11][cH:12][cH:13]2)[CH2:14][CH2:15][CH2:16][CH2:17][NH2:18])[cH:19][cH:20][cH:21]1 163: MCS: [#6](:[#7]:[#6]-[#6]-[#7](-[#6](-[#6])-[#6]1:[#7]:[#6]:[#6]:[#6]:[#6]:1)-[#6]-[#6]-[#6]-[#6]-[#7]):[#6]:[#6]:[#6] 21 atoms, 21 bonds -163: Time elapsed 0.004 seconds +163: Time elapsed 0.008 seconds 163: 163: test504() 163: Query +MAP [CH2:0]([CH2:1][CH2:2][NH:3][C:4]([CH:5]1[CH2:6][CH:7]1[c:8]1[c:9][c:10]([Cl:11])[c:12]([Cl:13])[cH:14][c:15]1)=[O:16])[CH2:17][CH2:18][N:19]1[CH2:20][CH2:21][CH:22]([NH:23][C:24]([NH:25][c:26]2[cH:27][cH:28][c:29]([Cl:30])[cH:31][cH:32]2)=[O:33])[CH2:34]1 163: MCS: [#6](-[#6]-[#6]-[#7]-[#6](-[#6]1-[#6]-[#6]-1-[#6]1:[#6]:[#6](-[#17]):[#6](:[#6]:[#6]:1)-[#17])=[#8])-[#6]-[#6]-[#7](-[#6]-[#6]-[#6]-[#7]-[#6](-[#7]-[#6]1:[#6]:[#6]:[#6]:[#6]:[#6]:1)=[#8])-[#6] 34 atoms, 36 bonds -163: Time elapsed 0.092 seconds +163: Time elapsed 0.091 seconds 163: MCS: [#6]-[#6]1-[#6]-[#6]-[#6]-[#6]-[#6]-1 7 atoms, 7 bonds -163: Time elapsed 0.009 seconds +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 0.022 seconds +163: Time elapsed 0.023 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 0.0090 seconds. bond[0]=6 +163: 1 Seeds:1 MCS 25 atoms, 28 bonds for 0.0009 seconds. bond[0]=6 163: STATISTICS: -163: Total Growing Steps = 1, MCS found on 1 step, for 0.0090 seconds +163: Total Growing Steps = 1, MCS found on 1 step, for 0.0009 seconds 163: Initial Seeds = 1, Mismatched 0 163: Inspected Seeds = 2 163: Rejected by BestSize = 0 @@ -30549,7 +30473,7 @@ 163: HashFoundInCache= 0 163: ExactMatchCalls = 0 163: ExactMatchFound = 0 -163: Time elapsed 0.009 seconds +163: Time elapsed 0.001 seconds 163: query=OCCl SubstructMatch(useChirality=false) res =1 size=3 163: query=OCCl SubstructMatch(useChirality=true ) res =1 size=3 163: test target = O[C@H](F)CCl query = C(F)C useChirality = 0 @@ -30645,31 +30569,166 @@ 163: res sub = 1 size=3 163: MCS: [#6]-[#6]-[#6] 3 atoms, 2 bonds 163: done -164: ........................................[12:42:46] The provided InitialSeed is not an MCS and will be ignored -164: [12:42:46] The provided InitialSeed is not an MCS and will be ignored -164: [12:42:46] The provided InitialSeed is not an MCS and will be ignored -164: .[12:42:46] The provided InitialSeed is not an MCS and will be ignored -164: [12:42:46] The provided InitialSeed is not an MCS and will be ignored -164: [12:42:46] The provided InitialSeed is not an MCS and will be ignored -164: .[12:42:46] The provided InitialSeed is not an MCS and will be ignored -164: [12:42:46] The provided InitialSeed is not an MCS and will be ignored -164: [12:42:46] The provided InitialSeed is not an MCS and will be ignored -164: .[12:42:46] The provided InitialSeed is not an MCS and will be ignored -164: [12:42:46] The provided InitialSeed is not an MCS and will be ignored -164: [12:42:46] The provided InitialSeed is not an MCS and will be ignored +160: file testGithub_7739_3.svg gave hash 1653424667U not the expected 1126644226U +160: file testGithub_7739_4.svg gave hash 3214282623U not the expected 9844878U +160: [21:37:43] +160: +160: **** +160: Pre-condition Violation +160: +160: Violation occurred on line 206 in file ./Code/GraphMol/MolDraw2D/DrawMolMCHCircleAndLine.cpp +160: Failed Expression: atomIdx < atCds_.size() && atomIdx < atomLabels_.size() +160: ---------- +160: Stacktrace: +160: 0# Invar::Invariant::toString[abi:cxx11]() const in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu//lib/libRDKitRDGeneral.so.1 +160: 1# Invar::operator<<(std::ostream&, Invar::Invariant const&) in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu//lib/libRDKitRDGeneral.so.1 +160: 2# RDKit::MolDraw2D_detail::DrawMolMCHCircleAndLine::calcSymbolEllipse(unsigned int, RDGeom::Point2D&, double&, double&) const in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu//lib/libRDKitMolDraw2D.so.1 +160: 3# RDKit::MolDraw2D_detail::DrawMolMCHCircleAndLine::makeAtomHighlights(std::vector >, std::allocator > > >&) in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu//lib/libRDKitMolDraw2D.so.1 +160: 4# RDKit::MolDraw2D_detail::DrawMolMCHCircleAndLine::extractMCHighlights() in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu//lib/libRDKitMolDraw2D.so.1 +160: 5# RDKit::MolDraw2D_detail::DrawMol::extractAll(double) in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu//lib/libRDKitMolDraw2D.so.1 +160: 6# RDKit::MolDraw2D_detail::DrawMol::createDrawObjects() in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu//lib/libRDKitMolDraw2D.so.1 +160: 7# RDKit::MolDraw2D::drawMoleculeWithHighlights(RDKit::ROMol const&, std::__cxx11::basic_string, std::allocator > const&, std::map >, std::less, std::allocator > > > > const&, std::map >, std::less, std::allocator > > > > const&, std::map, std::allocator > > const&, std::map, std::allocator > > const&, int) in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu//lib/libRDKitMolDraw2D.so.1 +160: 8# 0x0000AAAAE55645A8 in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/GraphMol/MolDraw2D/moldraw2DTestCatch +160: 9# 0x0000AAAAE562D74C in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/GraphMol/MolDraw2D/moldraw2DTestCatch +160: 10# 0x0000AAAAE562E100 in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/GraphMol/MolDraw2D/moldraw2DTestCatch +160: 11# 0x0000AAAAE562E534 in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/GraphMol/MolDraw2D/moldraw2DTestCatch +160: 12# 0x0000AAAAE5601F38 in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/GraphMol/MolDraw2D/moldraw2DTestCatch +160: 13# 0x0000AAAAE5602484 in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/GraphMol/MolDraw2D/moldraw2DTestCatch +160: 14# 0x0000AAAAE555DC70 in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/GraphMol/MolDraw2D/moldraw2DTestCatch +160: 15# 0x0000FFFFB54D229C in /lib/aarch64-linux-gnu/libc.so.6 +160: 16# __libc_start_main in /lib/aarch64-linux-gnu/libc.so.6 +160: 17# 0x0000AAAAE555DD30 in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/GraphMol/MolDraw2D/moldraw2DTestCatch +160: ---------- +160: **** +160: +160: [21:37:43] +160: +160: **** +160: Range Error +160: idx +160: Violation occurred on line 329 in file ./Code/GraphMol/ROMol.cpp +160: Failed Expression: 2 < 0 +160: ---------- +160: Stacktrace: +160: 0# Invar::Invariant::toString[abi:cxx11]() const in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu//lib/libRDKitRDGeneral.so.1 +160: 1# Invar::operator<<(std::ostream&, Invar::Invariant const&) in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu//lib/libRDKitRDGeneral.so.1 +160: 2# RDKit::ROMol::getBondWithIdx(unsigned int) const in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu//lib/libRDKitGraphMol.so.1 +160: 3# RDKit::MolDraw2D_detail::DrawMolMCHCircleAndLine::makeBondHighlights(std::vector >, std::allocator > > >&) in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu//lib/libRDKitMolDraw2D.so.1 +160: 4# RDKit::MolDraw2D_detail::DrawMolMCHCircleAndLine::extractMCHighlights() in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu//lib/libRDKitMolDraw2D.so.1 +160: 5# RDKit::MolDraw2D_detail::DrawMol::extractAll(double) in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu//lib/libRDKitMolDraw2D.so.1 +160: 6# RDKit::MolDraw2D_detail::DrawMol::createDrawObjects() in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu//lib/libRDKitMolDraw2D.so.1 +160: 7# RDKit::MolDraw2D::drawMoleculeWithHighlights(RDKit::ROMol const&, std::__cxx11::basic_string, std::allocator > const&, std::map >, std::less, std::allocator > > > > const&, std::map >, std::less, std::allocator > > > > const&, std::map, std::allocator > > const&, std::map, std::allocator > > const&, int) in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu//lib/libRDKitMolDraw2D.so.1 +160: 8# 0x0000AAAAE5563FEC in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/GraphMol/MolDraw2D/moldraw2DTestCatch +160: 9# 0x0000AAAAE562D74C in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/GraphMol/MolDraw2D/moldraw2DTestCatch +160: 10# 0x0000AAAAE562E100 in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/GraphMol/MolDraw2D/moldraw2DTestCatch +160: 11# 0x0000AAAAE562E534 in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/GraphMol/MolDraw2D/moldraw2DTestCatch +160: 12# 0x0000AAAAE5601F38 in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/GraphMol/MolDraw2D/moldraw2DTestCatch +160: 13# 0x0000AAAAE5602484 in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/GraphMol/MolDraw2D/moldraw2DTestCatch +160: 14# 0x0000AAAAE555DC70 in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/GraphMol/MolDraw2D/moldraw2DTestCatch +160: 15# 0x0000FFFFB54D229C in /lib/aarch64-linux-gnu/libc.so.6 +160: 16# __libc_start_main in /lib/aarch64-linux-gnu/libc.so.6 +160: 17# 0x0000AAAAE555DD30 in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/GraphMol/MolDraw2D/moldraw2DTestCatch +160: ---------- +160: **** +160: +160: [21:37:43] +160: +160: **** +160: Range Error +160: idx +160: Violation occurred on line 329 in file ./Code/GraphMol/ROMol.cpp +160: Failed Expression: 0 < 0 +160: ---------- +160: Stacktrace: +160: 0# Invar::Invariant::toString[abi:cxx11]() const in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu//lib/libRDKitRDGeneral.so.1 +160: 1# Invar::operator<<(std::ostream&, Invar::Invariant const&) in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu//lib/libRDKitRDGeneral.so.1 +160: 2# RDKit::ROMol::getBondWithIdx(unsigned int) const in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu//lib/libRDKitGraphMol.so.1 +160: 3# RDKit::MolDraw2D_detail::DrawMolMCHCircleAndLine::makeBondHighlights(std::vector >, std::allocator > > >&) in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu//lib/libRDKitMolDraw2D.so.1 +160: 4# RDKit::MolDraw2D_detail::DrawMolMCHCircleAndLine::extractMCHighlights() in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu//lib/libRDKitMolDraw2D.so.1 +160: 5# RDKit::MolDraw2D_detail::DrawMol::extractAll(double) in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu//lib/libRDKitMolDraw2D.so.1 +160: 6# RDKit::MolDraw2D_detail::DrawMol::createDrawObjects() in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu//lib/libRDKitMolDraw2D.so.1 +160: 7# RDKit::MolDraw2D::drawMoleculeWithHighlights(RDKit::ROMol const&, std::__cxx11::basic_string, std::allocator > const&, std::map >, std::less, std::allocator > > > > const&, std::map >, std::less, std::allocator > > > > const&, std::map, std::allocator > > const&, std::map, std::allocator > > const&, int) in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu//lib/libRDKitMolDraw2D.so.1 +160: 8# 0x0000AAAAE5564654 in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/GraphMol/MolDraw2D/moldraw2DTestCatch +160: 9# 0x0000AAAAE562D74C in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/GraphMol/MolDraw2D/moldraw2DTestCatch +160: 10# 0x0000AAAAE562E100 in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/GraphMol/MolDraw2D/moldraw2DTestCatch +160: 11# 0x0000AAAAE562E534 in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/GraphMol/MolDraw2D/moldraw2DTestCatch +160: 12# 0x0000AAAAE5601F38 in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/GraphMol/MolDraw2D/moldraw2DTestCatch +160: 13# 0x0000AAAAE5602484 in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/GraphMol/MolDraw2D/moldraw2DTestCatch +160: 14# 0x0000AAAAE555DC70 in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/GraphMol/MolDraw2D/moldraw2DTestCatch +160: 15# 0x0000FFFFB54D229C in /lib/aarch64-linux-gnu/libc.so.6 +160: 16# __libc_start_main in /lib/aarch64-linux-gnu/libc.so.6 +160: 17# 0x0000AAAAE555DD30 in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/GraphMol/MolDraw2D/moldraw2DTestCatch +160: ---------- +160: **** +160: +160: =============================================================================== +160: All tests passed (6814 assertions in 107 test cases) +160: +158/236 Test #160: moldraw2DTestCatch ..................... Passed 2.59 sec +test 170 + Start 170: testRascalMCES + +170: Test command: /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/GraphMol/RascalMCES/testRascalMCES +170: Working Directory: /build/reproducible-path/rdkit-202409.4/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 +163: [21:37:45] The provided InitialSeed is not an MCS and will be ignored +164: ........................................[21:37:45] The provided InitialSeed is not an MCS and will be ignored +164: [21:37:45] The provided InitialSeed is not an MCS and will be ignored +164: [21:37:45] The provided InitialSeed is not an MCS and will be ignored +164: .[21:37:45] The provided InitialSeed is not an MCS and will be ignored +164: [21:37:45] The provided InitialSeed is not an MCS and will be ignored +164: [21:37:45] The provided InitialSeed is not an MCS and will be ignored +164: .[21:37:45] The provided InitialSeed is not an MCS and will be ignored +164: [21:37:45] The provided InitialSeed is not an MCS and will be ignored +164: [21:37:45] The provided InitialSeed is not an MCS and will be ignored +164: .[21:37:45] The provided InitialSeed is not an MCS and will be ignored +164: [21:37:45] The provided InitialSeed is not an MCS and will be ignored +164: [21:37:45] The provided InitialSeed is not an MCS and will be ignored 164: ................. 164: ---------------------------------------------------------------------- -164: Ran 60 tests in 2.107s +164: Ran 60 tests in 3.845s 164: 164: OK -159/236 Test #164: pyFMCS ................................. Passed 2.64 sec +159/236 Test #164: pyFMCS ................................. Passed 4.41 sec test 171 Start 171: testRascalCluster 171: Test command: /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/GraphMol/RascalMCES/testRascalCluster 171: Working Directory: /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/GraphMol/RascalMCES 171: Test timeout computed to be: 1500 -163: [12:42:47] The provided InitialSeed is not an MCS and will be ignored +169: ......... +169: ---------------------------------------------------------------------- +169: Ran 9 tests in 2.716s +169: +169: OK +160/236 Test #169: pyMMPA ................................. Passed 3.47 sec +test 172 + Start 172: pyRascalMCES + +172: Test command: /usr/bin/python3 "/build/reproducible-path/rdkit-202409.4/Code/GraphMol/RascalMCES/Wrap/testRascalMCES.py" +172: Working Directory: /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/GraphMol/RascalMCES/Wrap +172: Test timeout computed to be: 1500 +172: ..........Too many matching bond pairs (1032) so can't continue. +172: ... +172: ---------------------------------------------------------------------- +172: Ran 13 tests in 2.214s +172: +172: OK +161/236 Test #172: pyRascalMCES ........................... Passed 2.84 sec +test 173 + Start 173: testSynthonSpaceSubstructureSearch + +173: Test command: /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/GraphMol/SynthonSpaceSearch/testSynthonSpaceSubstructureSearch +173: Working Directory: /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/GraphMol/SynthonSpaceSearch +173: Test timeout computed to be: 1500 +173: Randomness seeded to: 2019357667 +173: enumerating to /tmp/fileLhOqP9 +173: [21:37:50] Writing the enumerated file may take quite some time and result in a large file. 159: Done 159: ----------------- Test Github #781: Rendering single-atom molecules 159: Done @@ -30686,11 +30745,6 @@ 159: file test3_7.png gave hash 2590220702U not the expected 248355372U 159: Done 159: ----------------- Test Github774: upside-down drawings -169: ......... -169: ---------------------------------------------------------------------- -169: Ran 9 tests in 1.571s -169: -169: OK 159: file test774_1.png gave hash 387763501U not the expected 927423591U 159: file test774_2.png gave hash 2270183485U not the expected 1171827286U 159: Done @@ -30736,13 +30790,6 @@ 159: ----------------- Testing github 1035: overflow bug in SVG color generation 159: Done 159: ----------------- Testing github 1271: MolDraw2D not drawing anything for molecules aligned with the X or Y axes -160/236 Test #169: pyMMPA ................................. Passed 2.15 sec -test 172 - Start 172: pyRascalMCES - -172: Test command: /usr/bin/python3 "/build/reproducible-path/rdkit-202409.4/Code/GraphMol/RascalMCES/Wrap/testRascalMCES.py" -172: Working Directory: /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/GraphMol/RascalMCES/Wrap -172: Test timeout computed to be: 1500 159: Done 159: ----------------- Testing github 1322: add custom atom labels 159: Done @@ -30805,114 +30852,101 @@ 159: Done 159: ----------------- Test AND queries 159: Done -161/236 Test #159: moldraw2DTest1 ......................... Passed 4.70 sec -test 173 - Start 173: testSynthonSpaceSubstructureSearch - -173: Test command: /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/GraphMol/SynthonSpaceSearch/testSynthonSpaceSubstructureSearch -173: Working Directory: /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/GraphMol/SynthonSpaceSearch -173: Test timeout computed to be: 1500 -172: ..........Too many matching bond pairs (1032) so can't continue. -173: Randomness seeded to: 2424829534 -173: enumerating to /tmp/filebCMuIx -173: [12:42:48] Writing the enumerated file may take quite some time and result in a large file. -172: ... -172: ---------------------------------------------------------------------- -172: Ran 13 tests in 1.238s -172: -172: OK -162/236 Test #172: pyRascalMCES ........................... Passed 1.70 sec +162/236 Test #159: moldraw2DTest1 ......................... Passed 11.26 sec test 174 Start 174: testSynthonSpaceFingerprintSearch 174: Test command: /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/GraphMol/SynthonSpaceSearch/testSynthonSpaceFingerprintSearch 174: Working Directory: /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/GraphMol/SynthonSpaceSearch 174: Test timeout computed to be: 1500 -174: Randomness seeded to: 1938178416 -174: [12:42:49] Building the fingerprints may take some time. -174: [12:42:49] Building the fingerprints may take some time. -174: [12:42:49] Building the fingerprints may take some time. -173: [12:42:49] Building the fingerprints may take some time. -152: .............[12:42:50] Molecule does not have explicit Hs. Consider calling AddHs() -152: [12:42:50] Molecule does not have explicit Hs. Consider calling AddHs() -152: [12:42:50] Molecule does not have explicit Hs. Consider calling AddHs() -152: [12:42:50] Molecule does not have explicit Hs. Consider calling AddHs() -152: [12:42:50] Molecule does not have explicit Hs. Consider calling AddHs() -152: [12:42:50] Molecule does not have explicit Hs. Consider calling AddHs() -152: [12:42:50] Molecule does not have explicit Hs. Consider calling AddHs() -152: [12:42:50] Molecule does not have explicit Hs. Consider calling AddHs() -152: [12:42:50] Molecule does not have explicit Hs. Consider calling AddHs() -152: [12:42:50] Molecule does not have explicit Hs. Consider calling AddHs() -152: [12:42:50] Molecule does not have explicit Hs. Consider calling AddHs() -171: Randomness seeded to: 3722467287 +171: Randomness seeded to: 1033689955 171: /build/reproducible-path/rdkit-202409.4/Code/GraphMol/RascalMCES/data/chembl_1907596.smi -152: ...[12:42:51] Molecule does not have explicit Hs. Consider calling AddHs() -152: [12:42:51] Molecule does not have explicit Hs. Consider calling AddHs() -152: [12:42:51] Molecule does not have explicit Hs. Consider calling AddHs() -152: [12:42:51] Molecule does not have explicit Hs. Consider calling AddHs() -152: [12:42:51] Molecule does not have explicit Hs. Consider calling AddHs() +174: Randomness seeded to: 1216889717 +174: [21:37:52] Building the fingerprints may take some time. +174: [21:37:52] Building the fingerprints may take some time. +174: [21:37:52] Building the fingerprints may take some time. +173: [21:37:53] Building the fingerprints may take some time. +170: Randomness seeded to: 2596722569 +170: Timed out after 11 seconds. +152: .............[21:37:54] Molecule does not have explicit Hs. Consider calling AddHs() +152: [21:37:54] Molecule does not have explicit Hs. Consider calling AddHs() +152: [21:37:54] Molecule does not have explicit Hs. Consider calling AddHs() +152: [21:37:54] Molecule does not have explicit Hs. Consider calling AddHs() +152: [21:37:54] Molecule does not have explicit Hs. Consider calling AddHs() +152: [21:37:54] Molecule does not have explicit Hs. Consider calling AddHs() +152: [21:37:54] Molecule does not have explicit Hs. Consider calling AddHs() +152: [21:37:55] Molecule does not have explicit Hs. Consider calling AddHs() +152: [21:37:55] Molecule does not have explicit Hs. Consider calling AddHs() +152: [21:37:55] Molecule does not have explicit Hs. Consider calling AddHs() +152: [21:37:55] Molecule does not have explicit Hs. Consider calling AddHs() +152: ...[21:37:58] Molecule does not have explicit Hs. Consider calling AddHs() +152: [21:37:58] Molecule does not have explicit Hs. Consider calling AddHs() +152: [21:37:58] Molecule does not have explicit Hs. Consider calling AddHs() +152: [21:37:58] Molecule does not have explicit Hs. Consider calling AddHs() +152: [21:37:58] Molecule does not have explicit Hs. Consider calling AddHs() 152: ... 152: ---------------------------------------------------------------------- -152: Ran 19 tests in 8.997s +152: Ran 19 tests in 19.074s 152: 152: OK 152: Testing MolAlign Wrappers -163/236 Test #152: pyMolAlign ............................. Passed 9.36 sec +163/236 Test #152: pyMolAlign ............................. Passed 19.57 sec test 175 Start 175: pySynthonSpaceSearch 175: Test command: /usr/bin/python3 "/build/reproducible-path/rdkit-202409.4/Code/GraphMol/SynthonSpaceSearch/Wrap/testSynthonSpaceSearch.py" 175: Working Directory: /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/GraphMol/SynthonSpaceSearch/Wrap 175: Test timeout computed to be: 1500 -175: [12:42:52] Writing the enumerated file may take quite some time and result in a large file. -148: .........[12:42:54] Molecule does not have explicit Hs. Consider calling AddHs() -148: .[12:42:54] Molecule does not have explicit Hs. Consider calling AddHs() -148: [12:42:54] Molecule does not have explicit Hs. Consider calling AddHs() -148: [12:42:54] Molecule does not have explicit Hs. Consider calling AddHs() -148: [12:42:54] Molecule does not have explicit Hs. Consider calling AddHs() -148: [12:42:54] Molecule does not have explicit Hs. Consider calling AddHs() -148: [12:42:54] Molecule does not have explicit Hs. Consider calling AddHs() -148: [12:42:54] Molecule does not have explicit Hs. Consider calling AddHs() -148: [12:42:54] Molecule does not have explicit Hs. Consider calling AddHs() -148: [12:42:54] Molecule does not have explicit Hs. Consider calling AddHs() -148: [12:42:54] Molecule does not have explicit Hs. Consider calling AddHs() -148: .[12:42:54] Molecule does not have explicit Hs. Consider calling AddHs() -148: [12:42:54] Molecule does not have explicit Hs. Consider calling AddHs() -148: [12:42:54] Molecule does not have explicit Hs. Consider calling AddHs() -148: [12:42:54] Molecule does not have explicit Hs. Consider calling AddHs() -148: [12:42:54] Molecule does not have explicit Hs. Consider calling AddHs() -148: [12:42:54] Molecule does not have explicit Hs. Consider calling AddHs() -148: [12:42:54] Molecule does not have explicit Hs. Consider calling AddHs() -148: [12:42:54] Molecule does not have explicit Hs. Consider calling AddHs() -148: [12:42:54] Molecule does not have explicit Hs. Consider calling AddHs() -148: [12:42:54] Molecule does not have explicit Hs. Consider calling AddHs() +175: [21:37:59] Writing the enumerated file may take quite some time and result in a large file. +174: [21:38:00] Building the fingerprints may take some time. +148: .........[21:38:02] Molecule does not have explicit Hs. Consider calling AddHs() +148: .[21:38:02] Molecule does not have explicit Hs. Consider calling AddHs() +148: [21:38:02] Molecule does not have explicit Hs. Consider calling AddHs() +148: [21:38:02] Molecule does not have explicit Hs. Consider calling AddHs() +148: [21:38:02] Molecule does not have explicit Hs. Consider calling AddHs() +148: [21:38:02] Molecule does not have explicit Hs. Consider calling AddHs() +148: [21:38:02] Molecule does not have explicit Hs. Consider calling AddHs() +148: [21:38:02] Molecule does not have explicit Hs. Consider calling AddHs() +148: [21:38:02] Molecule does not have explicit Hs. Consider calling AddHs() +148: [21:38:02] Molecule does not have explicit Hs. Consider calling AddHs() +148: [21:38:02] Molecule does not have explicit Hs. Consider calling AddHs() +148: .[21:38:02] Molecule does not have explicit Hs. Consider calling AddHs() +148: [21:38:02] Molecule does not have explicit Hs. Consider calling AddHs() +148: [21:38:02] Molecule does not have explicit Hs. Consider calling AddHs() +148: [21:38:02] Molecule does not have explicit Hs. Consider calling AddHs() +148: [21:38:02] Molecule does not have explicit Hs. Consider calling AddHs() +148: [21:38:02] Molecule does not have explicit Hs. Consider calling AddHs() +148: [21:38:02] Molecule does not have explicit Hs. Consider calling AddHs() +148: [21:38:02] Molecule does not have explicit Hs. Consider calling AddHs() +148: [21:38:02] Molecule does not have explicit Hs. Consider calling AddHs() +148: [21:38:02] Molecule does not have explicit Hs. Consider calling AddHs() 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 10.92 seconds -164/236 Test #163: testFMCS ............................... Passed 10.97 sec +163: TOTAL Time elapsed 21.62 seconds +164/236 Test #163: testFMCS ............................... Passed 21.70 sec test 176 Start 176: testCIPLabeler 176: Test command: /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/GraphMol/CIPLabeler/testCIPLabeler 176: Working Directory: /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/GraphMol/CIPLabeler 176: Test timeout computed to be: 1500 -176: Randomness seeded to: 37451458 -176: [12:42:55] non kekulizable aromatic bond being treated as bond order 1 -176: [12:42:55] non kekulizable aromatic bond being treated as bond order 1 -176: [12:42:55] non kekulizable aromatic bond being treated as bond order 1 -176: [12:42:55] non kekulizable aromatic bond being treated as bond order 1 -176: [12:42:55] non kekulizable aromatic bond being treated as bond order 1 -176: [12:42:55] non kekulizable aromatic bond being treated as bond order 1 -176: [12:42:55] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored -176: [12:42:55] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored +176: Randomness seeded to: 2750573659 +176: [21:38:02] non kekulizable aromatic bond being treated as bond order 1 +176: [21:38:02] non kekulizable aromatic bond being treated as bond order 1 +176: [21:38:02] non kekulizable aromatic bond being treated as bond order 1 +176: [21:38:02] non kekulizable aromatic bond being treated as bond order 1 +176: [21:38:02] non kekulizable aromatic bond being treated as bond order 1 +176: [21:38:02] non kekulizable aromatic bond being treated as bond order 1 +176: [21:38:03] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored +176: [21:38:03] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored 176: =============================================================================== 176: All tests passed (6577 assertions in 19 test cases) 176: -165/236 Test #176: testCIPLabeler ......................... Passed 0.11 sec +165/236 Test #176: testCIPLabeler ......................... Passed 0.30 sec test 177 Start 177: pyCIPLabelsWrapTest @@ -30921,18 +30955,16 @@ 177: Test timeout computed to be: 1500 177: .... 177: ---------------------------------------------------------------------- -177: Ran 4 tests in 0.009s +177: Ran 4 tests in 0.022s 177: 177: OK -174: [12:42:55] Building the fingerprints may take some time. -166/236 Test #177: pyCIPLabelsWrapTest .................... Passed 0.30 sec +166/236 Test #177: pyCIPLabelsWrapTest .................... Passed 0.86 sec test 178 Start 178: pyCIPLabelsValidation 178: Test command: /usr/bin/python3 "/build/reproducible-path/rdkit-202409.4/Code/GraphMol/CIPLabeler/Wrap/pyCIPLabelsValidation.py" 178: Working Directory: /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/GraphMol/CIPLabeler/Wrap 178: Test timeout computed to be: 1500 -175: .[12:42:55] Building the fingerprints may take some time. 150: --------------------------------- 150: test O3A multithreading bug 150: @@ -30940,8 +30972,6 @@ 150: testCrippenO3A multithreading 150: 150: generating reference data -170: Randomness seeded to: 3138504786 -170: Timed out after 11 seconds. 150: processing 150: launch :0 150: launch :1 @@ -30949,21 +30979,21 @@ 150: launch :3 148: ... 148: ---------------------------------------------------------------------- -148: Ran 22 tests in 15.586s +148: Ran 22 tests in 29.361s 148: 148: OK -167/236 Test #148: pyDistGeomHelpers ...................... Passed 16.03 sec +167/236 Test #148: pyDistGeomHelpers ...................... Passed 30.00 sec test 179 Start 179: deprotectTest 179: Test command: /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/GraphMol/Deprotect/deprotectTest 179: Working Directory: /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/GraphMol/Deprotect 179: Test timeout computed to be: 1500 -179: Randomness seeded to: 1244218269 +179: Randomness seeded to: 984724425 179: =============================================================================== 179: All tests passed (111 assertions in 3 test cases) 179: -168/236 Test #179: deprotectTest .......................... Passed 0.10 sec +168/236 Test #179: deprotectTest .......................... Passed 0.09 sec test 180 Start 180: pyDeprotect @@ -30972,7 +31002,7 @@ 180: Test timeout computed to be: 1500 180: ..... 180: ---------------------------------------------------------------------- -180: Ran 5 tests in 0.050s +180: Ran 5 tests in 0.025s 180: 180: OK 180: Testing tert-butyldimethylsilyl @@ -31025,7 +31055,7 @@ 180: Testing acetamide 180: Testing carbobenzyloxy 180: Testing Acetal/Ketal -169/236 Test #180: pyDeprotect ............................ Passed 0.51 sec +169/236 Test #180: pyDeprotect ............................ Passed 0.33 sec test 181 Start 181: testReducedGraphs @@ -31050,7 +31080,7 @@ 181: 181: Size: 315 [ 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0.3, 1, 0.3, 0, 0, 0, 0, 0, 0, 0, 0, 0.3, 1, 0.3, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0.3, 1, 0.3, 0, 0, 0, 0, 0, 0, 0, 0, 0.3, 1, 0.3, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0.3, 1, 0.3, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, ] 181: -170/236 Test #181: testReducedGraphs ...................... Passed 0.02 sec +170/236 Test #181: testReducedGraphs ...................... Passed 0.04 sec test 182 Start 182: pyReducedGraphs @@ -31059,46 +31089,47 @@ 182: Test timeout computed to be: 1500 182: ..... 182: ---------------------------------------------------------------------- -182: Ran 5 tests in 0.009s +182: Ran 5 tests in 0.021s 182: 182: OK -171/236 Test #182: pyReducedGraphs ........................ Passed 0.25 sec +171/236 Test #182: pyReducedGraphs ........................ Passed 0.51 sec test 183 Start 183: trajectoryTest 183: Test command: /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/GraphMol/Trajectory/trajectoryTest 183: Working Directory: /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/GraphMol/Trajectory 183: Test timeout computed to be: 1500 -172/236 Test #183: trajectoryTest ......................... Passed 0.19 sec +172/236 Test #183: trajectoryTest ......................... Passed 0.38 sec test 184 Start 184: substructLibraryTest 184: Test command: /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/GraphMol/SubstructLibrary/substructLibraryTest 184: Working Directory: /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/GraphMol/SubstructLibrary 184: Test timeout computed to be: 1500 -184: [12:42:59] ------------------------------------- -184: [12:42:59] Test1 -184: [12:42:59] done -184: [12:42:59] ------------------------------------- -184: [12:42:59] Test2 -184: [12:42:59] done -184: [12:42:59] ------------------------------------- -184: [12:42:59] Test3 (stereo options) -184: [12:42:59] Done (stereo options) -184: [12:42:59] ------------------------------------- -184: [12:42:59] Test4 (trusted smiles) -184: [12:42:59] Done (trusted smiles) -184: [12:42:59] ------------------------------------- -184: [12:42:59] Testing C++ docs -184: [12:42:59] Done (C++ doc tests) -184: [12:42:59] ------------------------------------- -184: [12:42:59] Testing C++ ring query: PatternHolder -184: [12:42:59] Done (C++ ring query tests) -184: [12:42:59] ------------------------------------- -184: [12:42:59] Testing C++ ring query: TautomerPatternHolder -184: [12:42:59] Done (C++ ring query tests) -184: [12:42:59] ------------------------------------- -184: [12:42:59] Add Patterns +184: [21:38:08] ------------------------------------- +184: [21:38:08] Test1 +184: [21:38:09] done +184: [21:38:09] ------------------------------------- +184: [21:38:09] Test2 +184: [21:38:09] done +184: [21:38:09] ------------------------------------- +184: [21:38:09] Test3 (stereo options) +184: [21:38:09] Done (stereo options) +184: [21:38:09] ------------------------------------- +184: [21:38:09] Test4 (trusted smiles) +184: [21:38:09] Done (trusted smiles) +184: [21:38:09] ------------------------------------- +184: [21:38:09] Testing C++ docs +184: [21:38:09] Done (C++ doc tests) +184: [21:38:09] ------------------------------------- +184: [21:38:09] Testing C++ ring query: PatternHolder +184: [21:38:09] Done (C++ ring query tests) +184: [21:38:09] ------------------------------------- +184: [21:38:09] Testing C++ ring query: TautomerPatternHolder +184: [21:38:09] Done (C++ ring query tests) +184: [21:38:09] ------------------------------------- +184: [21:38:09] Add Patterns +175: .[21:38:10] Building the fingerprints may take some time. 178: VS001: PASSED 178: VS002: PASSED 178: VS003: PASSED @@ -31401,1082 +31432,1081 @@ 178: VS300: PASSED 178: Check finished: 0 molecules failed. 178: Failed: -173/236 Test #178: pyCIPLabelsValidation .................. Passed 5.12 sec +173/236 Test #178: pyCIPLabelsValidation .................. Passed 7.32 sec test 185 Start 185: substructLibraryCatchTest 185: Test command: /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/GraphMol/SubstructLibrary/substructLibraryCatchTest 185: Working Directory: /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/GraphMol/SubstructLibrary 185: Test timeout computed to be: 1500 -185: Randomness seeded to: 1363835258 +185: Randomness seeded to: 2522352257 185: =============================================================================== 185: All tests passed (171 assertions in 5 test cases) 185: -174/236 Test #185: substructLibraryCatchTest .............. Passed 1.44 sec +174/236 Test #185: substructLibraryCatchTest .............. Passed 1.62 sec test 186 Start 186: pySubstructLibrary 186: Test command: /usr/bin/python3 "/build/reproducible-path/rdkit-202409.4/Code/GraphMol/SubstructLibrary/Wrap/rough_test.py" 186: Working Directory: /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/GraphMol/SubstructLibrary/Wrap 186: Test timeout computed to be: 1500 -174: [12:43:02] Building the fingerprints may take some time. -33: [12:43:03] Finished -33: [12:43:03] ------------------------------------- -33: [12:43:03] Test github1843: RWMol.clear() should not destroy ring pointer. -33: [12:43:03] Finished -33: [12:43:03] ------------------------------------- -33: [12:43:03] Test Github 6370: non-physical radical counts being preserved -33: [12:43:03] Finished -175/236 Test #33: graphmolTest1 .......................... Passed 28.31 sec -test 187 - Start 187: testRGroupDecomp - -187: Test command: /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/GraphMol/RGroupDecomposition/testRGroupDecomp -187: Working Directory: /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/GraphMol/RGroupDecomposition -187: Test timeout computed to be: 1500 -187: [12:43:04] Non terminal R group defined. To allow set allowNonTerminalRGroups in RGroupDecompositionParameters -187: [12:43:04] WARNING: not removing hydrogen atom with dummy atom neighbors -184: [12:43:04] ------------------------------------- -184: [12:43:04] testing PatternHolder -184: [12:43:04] ------------------------------------- -184: [12:43:04] testing TautomerPatternHolder -184: [12:43:04] ------------------------------------- -184: [12:43:04] testSegFaultInHolder -184: [12:43:04] SMILES Parse Error: syntax error while parsing: dsafsdf[12:43:04] SMILES Parse Error: syntax error while parsing: dsafsdf -184: [12:43:04] SMILES Parse Error: check for mistakes around position 1: -184: [12:43:04] [12:43:04] SMILES Parse Error: syntax error while parsing: dsafsdf -184: [12:43:04] SMILES Parse Error: check for mistakes around position 1: -184: [12:43:04] dsafsdf -184: [12:43:04] ^ -184: [12:43:04] [12:43:04] SMILES Parse Error: syntax error while parsing: dsafsdf -184: [12:43:04] SMILES Parse Error: check for mistakes around position 1: -184: [12:43:04] dsafsdf -184: [12:43:04] ^ -184: [12:43:04] SMILES Parse Error: syntax error while parsing: dsafsdf -184: [12:43:04] SMILES Parse Error: check for mistakes around position 1: -184: [12:43:04] -184: [12:43:04] SMILES Parse Error: check for mistakes around position 1: -184: [12:43:04] dsafsdf -184: [12:43:04] ^ -184: [12:43:04] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -184: [12:43:04] SMILES Parse Error: syntax error while parsing: dsafsdf -184: [12:43:04] SMILES Parse Error: check for mistakes around position 1: -184: [12:43:04] dsafsdf -184: [12:43:04] ^ -184: [12:43:04] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -184: [12:43:04] SMILES Parse Error: syntax error while parsing: dsafsdf -184: [12:43:04] SMILES Parse Error: check for mistakes around position 1: -184: [12:43:04] dsafsdf -184: [12:43:04] ^ -184: [12:43:04] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -184: [12:43:04] SMILES Parse Error: syntax error while parsing: dsafsdf -184: [12:43:04] SMILES Parse Error: check for mistakes around position 1: -184: [12:43:04] dsafsdf -184: [12:43:04] ^ -184: [12:43:04] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -184: [12:43:04] SMILES Parse Error: syntax error while parsing: dsafsdf -184: [12:43:04] SMILES Parse Error: check for mistakes around position 1: -184: [12:43:04] dsafsdf -184: [12:43:04] ^ -184: [12:43:04] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -184: [12:43:04] SMILES Parse Error: syntax error while parsing: dsafsdf -184: [12:43:04] SMILES Parse Error: check for mistakes around position 1: -184: [12:43:04] dsafsdf -184: [12:43:04] ^ -184: [12:43:04] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -184: [12:43:04] SMILES Parse Error: syntax error while parsing: dsafsdf -184: [12:43:04] SMILES Parse Error: check for mistakes around position 1: -184: [12:43:04] dsafsdf -184: [12:43:04] ^ -184: [12:43:04] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -184: [12:43:04] SMILES Parse Error: syntax error while parsing: dsafsdf -184: [12:43:04] SMILES Parse Error: check for mistakes around position 1: -184: [12:43:04] dsafsdf -184: [12:43:04] ^ -184: [12:43:04] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -184: [12:43:04] SMILES Parse Error: syntax error while parsing: dsafsdf -184: [12:43:04] SMILES Parse Error: check for mistakes around position 1: -184: [12:43:04] dsafsdf -184: [12:43:04] ^ -184: [12:43:04] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -184: dsafsdf -184: [12:43:04] ^ -184: [12:43:04] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -184: [12:43:04] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -184: [12:43:04] SMILES Parse Error: syntax error while parsing: dsafsdf -184: [12:43:04] SMILES Parse Error: check for mistakes around position 1: -184: [12:43:04] dsafsdf -184: [12:43:04] ^ -184: [12:43:04] SMILES Parse Error: syntax error while parsing: dsafsdf -184: [12:43:04] SMILES Parse Error: check for mistakes around position 1: -184: [12:43:04] dsafsdf -184: [12:43:04] ^ -184: [12:43:04] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -184: [12:43:04] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -184: [12:43:04] SMILES Parse Error: syntax error while parsing: dsafsdf -184: [12:43:04] SMILES Parse Error: check for mistakes around position 1: -184: [12:43:04] dsafsdf -184: [12:43:04] ^ -184: [12:43:04] SMILES Parse Error: syntax error while parsing: dsafsdf -184: [12:43:04] SMILES Parse Error: check for mistakes around position 1: -184: [12:43:04] SMILES[12:43:04] Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -184: [12:43:04] SMILES Parse Error: syntax error while parsing: dsafsdf -184: [12:43:04] SMILES Parse Error: check for mistakes around position 1: -184: [12:43:04] dsafsdf -184: [12:43:04] ^ -184: [12:43:04] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -184: [12:43:04] dsafsdf -184: [12:43:04] ^ -184: dsafsdf -184: [12:43:04] ^ -184: [12:43:04] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -184: [12:43:04] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -184: [12:43:04] SMILES Parse Error: syntax error while parsing: dsafsdf -184: [12:43:04] SMILES Parse Error: check for mistakes around position 1: -184: [12:43:04] dsafsdf -184: [12:43:04] ^ -184: [12:43:04] SMILES Parse Error: syntax error while parsing: [12:43:04] SMILESdsafsdf -184: [12:43:04] SMILES Parse Error: check for mistakes around position 1: -184: [12:43:04] dsafsdf -184: [12:43:04] ^ -184: [12:43:04] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -184: [12:43:04] SMILES Parse Error: syntax error while parsing: dsafsdf -184: [12:43:04] SMILES Parse Error: check for mistakes around position 1: -184: [12:43:04] dsafsdf -184: [12:43:04] ^ -184: [12:43:04] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -184: [12:43:04] SMILES Parse Error: syntax error while parsing: dsafsdf -184: [12:43:04] SMILES Parse Error: check for mistakes around position 1: -184: [12:43:04] dsafsdf -184: [12:43:04] ^ -184: [12:43:04] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -184: [12:43:04] SMILES Parse Error: syntax error while parsing: dsafsdf -184: [12:43:04] SMILES Parse Error: check for mistakes around position 1: -184: [12:43:04] dsafsdf -184: [12:43:04] ^ -184: [12:43:04] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -184: SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf'SMILES Parse Error: [12:43:04] SMILES Parse Error: syntax error while parsing: dsafsdf -184: syntax error -184: while parsing: dsafsdf -184: [12:43:04] SMILES Parse Error: check for mistakes around position 1: -184: [12:43:04] dsafsdf -184: [12:43:04] ^ -184: [12:43:04] SMILES Parse Error: syntax error while parsing: dsafsdf -184: [12:43:04] SMILES Parse Error: check for mistakes around position 1: -184: [12:43:04] dsafsdf -184: [12:43:04] ^ -184: [12:43:04] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -184: Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -184: [12:43:04] SMILES Parse Error: [12:43:04] [12:43:04] SMILES Parse Error: check for mistakes around position SMILESsyntax error while parsing: dsafsdf -184: Parse Error: 1: -184: [12:43:04] dsafsdf -184: [12:43:04] ^ -184: [12:43:04] SMILES Parse Error: syntax error while parsing: dsafsdf -184: [12:43:04] SMILES Parse Error: check for mistakes around position 1: -184: [12:43:04] dsafsdf -184: [12:43:04] ^ -184: [12:43:04] SMILES Parse Error: syntax error while parsing: dsafsdf -184: [12:43:04] SMILES Parse Error: check for mistakes around position 1: -184: [12:43:04] [12:43:04] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdfSMILES Parse Error: [12:43:04] SMILES Parse Error: check for mistakes around position [12:43:04] SMILES Parse Error: ' -184: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -184: [12:43:04] SMILES Parse Error: syntax error while parsing: dsafsdf -184: [12:43:04] SMILES Parse Error: check for mistakes around position 1: -184: [12:43:04] dsafsdf1: -184: syntax error while parsing: dsafsdf[12:43:04] SMILES Parse Error: -184: [12:43:04] dsafsdf -184: [12:43:04] syntax error while parsing: dsafsdf[12:43:04] SMILES Parse Error: check for mistakes around position -184: [12:43:04] 1 -184: [12:43:04] ^ -184: ^ -184: [12:43:04] SMILES[12:43:04] : -184: SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'SMILES Parse Error: check for mistakes around position 1dsafsdf Parse Error: Failed parsing SMILES 'dsafsdf' for input: '[12:43:04] dsafsdf +174: [21:38:13] Building the fingerprints may take some time. +184: [21:38:15] ------------------------------------- +184: [21:38:15] testing PatternHolder +184: [21:38:15] ------------------------------------- +184: [21:38:15] testing TautomerPatternHolder +184: [21:38:15] ------------------------------------- +184: [21:38:15] testSegFaultInHolder +184: [21:38:15] SMILES Parse Error: syntax error while parsing: dsafsdf +184: [21:38:15] SMILES Parse Error: check for mistakes around position 1: +184: [21:38:15] dsafsdf +184: [21:38:15] ^ +184: [21:38:15] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +184: [21:38:15] SMILES Parse Error: syntax error while parsing: dsafsdf +184: [21:38:15] SMILES Parse Error: check for mistakes around position 1: +184: [21:38:15] dsafsdf +184: [21:38:15] ^ +184: [21:38:15] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +184: [21:38:15] SMILES Parse Error: syntax error while parsing: dsafsdf +184: [21:38:15] SMILES Parse Error: check for mistakes around position 1: +184: [21:38:15] dsafsdf +184: [21:38:15] ^ +184: [21:38:15] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +184: [21:38:15] SMILES Parse Error: syntax error while parsing: dsafsdf +184: [21:38:15] SMILES Parse Error: check for mistakes around position 1: +184: [21:38:15] dsafsdf +184: [21:38:15] ^ +184: [21:38:15] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +184: [21:38:15] SMILES Parse Error: syntax error while parsing: dsafsdf +184: [21:38:15] SMILES Parse Error: check for mistakes around position 1: +184: [21:38:15] dsafsdf +184: [21:38:15] ^ +184: [21:38:15] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +184: [21:38:15] SMILES Parse Error: syntax error while parsing: dsafsdf +184: [21:38:15] SMILES Parse Error: check for mistakes around position 1: +184: [21:38:15] dsafsdf +184: [21:38:15] ^ +184: [21:38:15] SMILES Parse Error: syntax error while parsing: dsafsdf +184: [21:38:15] SMILES Parse Error: check for mistakes around position 1: +184: [21:38:15] dsafsdf +184: [21:38:15] ^ +184: [21:38:15] [21:38:15] SMILES Parse Error: syntax error while parsing: dsafsdf +184: [21:38:15] [21:38:15] [21:38:15] SMILES Parse Error: [21:38:15] SMILES Parse Error: syntax errorSMILES Parse Error: while parsing: dsafsdf +184: SMILES Parse Error: syntax error while parsing: dsafsdf +184: [21:38:15] SMILES Parse Error: check for mistakes around position 1: +184: [21:38:15] SMILES Parse Error: syntax error while parsing: dsafsdf +184: syntax error while parsing: [21:38:15] dsafsdfdsafsdf[21:38:15] SMILES Parse Error: check for mistakes around position syntax error while parsing: dsafsdf1 +184: :[21:38:15] SMILES Parse Error: check for mistakes around position +184: [21:38:15] 1 +184: [21:38:15] +184: [21:38:15] ^ 184: : -184: [12:43:04] [12:43:04] dsafsdf' -184: ^ -184: [12:43:04] SMILES Parse Error: Failed parsing SMILES 'dsafsdf'[12:43:04] [12:43:04] SMILES Parse Error: syntax error while parsing: dsafsdf for input: 'dsafsdf -184: dsafsdfdsafsdf' +184: [21:38:15] dsafsdf +184: [21:38:15] ^ +184: [21:38:15] [21:38:15] [21:38:15] SMILES Parse Error: check for mistakes around position 1SMILESSMILES Parse Error: : +184: Failed parsing SMILES 'dsafsdf' Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf +184: dsafsdf[21:38:15] [21:38:15] dsafsdf +184: ^' +184: +184: [21:38:15] ^ +184: [21:38:15] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +184: [21:38:15] SMILES Parse Error: Failed parsing SMILES 'dsafsdf'[21:38:15] SMILES Parse Error: syntax error while parsing: dsafsdf +184: [21:38:15] SMILES Parse Error: check for mistakes around position 1: +184: [21:38:15] dsafsdf +184: [21:38:15] ^ +184: [21:38:15] SMILES Parse Error: syntax error while parsing: dsafsdf +184: [21:38:15] SMILES Parse Error: check for mistakes around position 1: +184: [21:38:15] dsafsdf +184: [21:38:15] ^ +184: [21:38:15] SMILES Parse Error: [21:38:15] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +184: [21:38:15] SMILES Parse Error: syntax error while parsing: dsafsdf +184: [21:38:15] SMILES Parse Error: check for mistakes around position 1: +184: [21:38:15] dsafsdf +184: [21:38:15] ^ +184: [21:38:15] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +184: [21:38:15] SMILES Parse Error: syntax error while parsing: dsafsdf +184: [21:38:15] SMILES Parse Error: check for mistakes around position 1: +184: [21:38:15] dsafsdf +184: [21:38:15] ^ +184: [21:38:15] [21:38:15] for input: 'dsafsdf'Failed parsing SMILES 'dsafsdf' for input: 'dsafsdfSMILES Parse Error: syntax error while parsing: SMILES Parse Error: dsafsdf' for input: 'Failed parsing SMILES 'dsafsdf'dsafsdf' 184: -184: [12:43:04] ^ -184: [12:43:04] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -184: [12:43:04] SMILES Parse Error: syntax error while parsing: dsafsdf -184: [12:43:04] SMILES Parse Error: check for mistakes around position [12:43:04] ' -184: SMILES Parse Error: 1:syntax error while parsing: dsafsdf -184: [12:43:04] SMILES Parse Error: check for mistakes around position 1: -184: [12:43:04] [12:43:04] -184: [12:43:04] SMILES Parse Error: check for mistakes around position 1: -184: ^[12:43:04] SMILES Parse Error: -184: [12:43:04] dsafsdfsyntax errordsafsdf -184: while parsing: -184: [12:43:04] [12:43:04] -184: ^ -184: [12:43:04] dsafsdf -184: [12:43:04] ^ -184: [12:43:04] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -184: [12:43:04] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -184: [12:43:04] SMILES Parse Error: syntax error while parsing: dsafsdf -184: [12:43:04] SMILES Parse Error: check for mistakes around position 1: -184: [12:43:04] [12:43:04] [12:43:04] ^ +184: [21:38:15] SMILES Parse Error: syntax error while parsing: dsafsdf +184: [21:38:15] SMILES Parse Error: check for mistakes around position 1: +184: [21:38:15] dsafsdf +184: [21:38:15] [21:38:15] for input: 'dsafsdf'SMILES Parse Error: ^ +184: syntax error while parsing: dsafsdf +184: [21:38:15] SMILES Parse Error: check for mistakes around position 1: +184: [21:38:15] dsafsdf +184: [21:38:15] [21:38:15] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +184: [21:38:15] SMILES Parse Error: syntax error while parsing: dsafsdf +184: [21:38:15] SMILES Parse Error: check for mistakes around position 1: +184: [21:38:15] dsafsdf +184: [21:38:15] ^ +184: [21:38:15] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +184: +184: +184: [21:38:15] SMILES Parse Error: check for mistakes around position 1: +184: [21:38:15] dsafsdf +184: [21:38:15] ^ +184: [21:38:15] [21:38:15] 184: SMILES Parse Error: syntax error while parsing: dsafsdf -184: [12:43:04] SMILES Parse Error: check for mistakes around position 1: -184: [12:43:04] dsafsdf -184: [12:43:04] ^[12:43:04] dsafsdf -184: [12:43:04] dsafsdf -184: SMILES Parse Error: check for mistakes around position SMILES Parse Error: Failed parsing SMILES 'dsafsdf' -184: for input: 'dsafsdf' -184: [12:43:04] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -184: SMILES[12:43:04] SMILES Parse Error: syntax error while parsing: dsafsdf -184: [12:43:04] [12:43:04] [12:43:04] ^ -184: SMILES Parse Error: SMILES Parse Error: check for mistakes around position 1:syntax error Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf1: -184: '[12:43:04] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' -184: [12:43:04] dsafsdf -184: for input: ' while parsing: dsafsdf -184: dsafsdf[12:43:04] ^ +184: [21:38:15] SMILES Parse Error: check for mistakes around position 1: +184: [21:38:15] dsafsdf +184: [21:38:15] ^ +184: [21:38:15] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +184: [21:38:15] SMILES Parse Error: syntax error while parsing: dsafsdf +184: [21:38:15] SMILES Parse Error: check for mistakes around position 1: +184: [21:38:15] dsafsdf +184: [21:38:15] ^ +184: [21:38:15] SMILES Parse Error: syntax error while parsing: dsafsdf +184: [21:38:15] SMILES Parse Error: check for mistakes around position 1: +184: [21:38:15] [21:38:15] SMILES Parse Error: syntax error while parsing: SMILES Parse Error: Failed parsing SMILES 'dsafsdf'[21:38:15] dsafsdfSMILES Parse Error: Failed parsing SMILES 'dsafsdf'dsafsdf +184: for input: ' +184: [21:38:15] for input: 'dsafsdf' +184: ^dsafsdf' +184: [21:38:15] SMILES Parse Error: check for mistakes around position 1: +184: [21:38:15] dsafsdf +184: [21:38:15] ^ +184: [21:38:15] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +184: [21:38:15] SMILES Parse Error: syntax error while parsing: dsafsdf +184: [21:38:15] SMILES Parse Error: check for mistakes around position 1: +184: [21:38:15] dsafsdf +184: [21:38:15] ^ +184: [21:38:15] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' 184: -184: [12:43:04] [12:43:04] SMILES Parse Error: check for mistakes around position 1' -184: : -184: [12:43:04] dsafsdf -184: [12:43:04] ^ -184: [12:43:04] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -184: [12:43:04] SMILES Parse Error: syntax error while parsing: dsafsdf -184: [12:43:04] SMILES Parse Error: check for mistakes around position 1: -184: [12:43:04] dsafsdf -184: [12:43:04] ^ -184: [12:43:04] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -184: [12:43:04] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -184: dsafsdf -184: [12:43:04] ^ -184: [12:43:04] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +184: [21:38:15] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +184: [21:38:15] SMILES Parse Error: syntax error while parsing: dsafsdf +184: [21:38:15] SMILES Parse Error: check for mistakes around position 1: +184: [21:38:15] dsafsdf +184: [21:38:15] SMILES Parse Error: syntax error while parsing: dsafsdf +184: [21:38:15] SMILES Parse Error: check for mistakes around position 1: +184: [21:38:15] dsafsdf +184: [21:38:15] ^ +184: [21:38:15] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +184: [21:38:15] ^ +184: [21:38:15] [21:38:15] SMILES Parse Error: syntax error while parsing: dsafsdf +184: [21:38:15] SMILES Parse Error: check for mistakes around position 1: +184: [21:38:15] dsafsdf +184: [21:38:15] ^ +184: [21:38:15] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +184: SMILES Parse Error: SMILES[21:38:15] [21:38:15] syntax error while parsing: dsafsdf +184: SMILES Parse Error: Parse Error: ^Failed parsing SMILES 'dsafsdf' +184: for input: 'dsafsdf' +184: [21:38:15] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +184: [21:38:15] SMILES Parse Error: syntax error while parsing: dsafsdf +184: [21:38:15] SMILES Parse Error: check for mistakes around position [21:38:15] SMILES Parse Error: syntax error while parsing: dsafsdf +184: [21:38:15] SMILES Parse Error: check for mistakes around position 1: +184: [21:38:15] dsafsdf +184: [21:38:15] ^ +184: [21:38:15] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +184: [21:38:15] SMILES Parse Error: syntax error while parsing: dsafsdf +184: [21:38:15] SMILES Parse Error: check for mistakes around position 1: +184: [21:38:15] dsafsdf +184: [21:38:15] ^ +184: [21:38:15] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +184: [21:38:15] SMILES Parse Error: check for mistakes around position 1: +184: [21:38:15] dsafsdf +184: [21:38:15] ^ +184: [21:38:15] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +184: [21:38:15] SMILES Parse Error: syntax error while parsing: dsafsdf +184: [21:38:15] SMILES Parse Error: check for mistakes around position 1: +184: [21:38:15] dsafsdf +184: [21:38:15] ^ +184: [21:38:15] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +184: [21:38:15] SMILES Parse Error: syntax error while parsing: dsafsdf +184: [21:38:15] SMILES Parse Error: check for mistakes around position 1: +184: [21:38:15] dsafsdf +184: [21:38:15] ^ +184: [21:38:15] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +184: [21:38:15] SMILES Parse Error: syntax error while parsing: dsafsdf +184: [21:38:15] SMILES Parse Error: check for mistakes around position 1: +184: [21:38:15] dsafsdf +184: [21:38:15] ^ +184: [21:38:15] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +184: 1: +184: [21:38:15] dsafsdf +184: [21:38:15] ^ +184: [21:38:15] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +184: [21:38:15] SMILES Parse Error: syntax error while parsing: dsafsdf +184: [21:38:15] SMILES Parse Error: check for mistakes around position 1: +184: [21:38:15] dsafsdf +184: [21:38:15] ^ +184: [21:38:15] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +184: [21:38:15] SMILES Parse Error: syntax error while parsing: dsafsdf +184: [21:38:15] SMILES Parse Error: check for mistakes around position 1: +184: [21:38:15] dsafsdf +184: [21:38:15] ^ +184: [21:38:15] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +184: [21:38:15] SMILES Parse Error: syntax error while parsing: dsafsdf +184: [21:38:15] SMILES Parse Error: check for mistakes around position 1: +184: [21:38:15] dsafsdf +184: [21:38:15] ^ +184: [21:38:15] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +184: SMILES Parse Error: check for mistakes around position [21:38:15] SMILES Parse Error: check for mistakes around position 1: +184: [21:38:15] dsafsdf +184: [21:38:15] ^ +184: [21:38:15] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +184: [21:38:15] SMILES Parse Error: syntax error while parsing: dsafsdf +184: [21:38:15] SMILES Parse Error: check for mistakes around position 1: +184: [21:38:15] dsafsdf +184: [21:38:15] ^ +184: [21:38:15] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +184: [21:38:15] SMILES Parse Error: syntax error while parsing: dsafsdf +184: [21:38:15] SMILES Parse Error: check for mistakes around position 1: +184: [21:38:15] dsafsdf +184: [21:38:15] ^ +184: [21:38:15] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +184: [21:38:15] SMILES Parse Error: syntax error while parsing: dsafsdf +184: [21:38:15] SMILES Parse Error: check for mistakes around position 1: +184: [21:38:15] dsafsdf +184: [21:38:15] ^ +184: [21:38:15] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +184: [21:38:15] SMILES Parse Error: syntax error while parsing: dsafsdf +184: [21:38:15] SMILES Parse Error: check for mistakes around position 1: +184: [21:38:15] dsafsdf +184: [21:38:15] ^ +184: [21:38:15] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' 184: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -184: [12:43:04] SMILES Parse Error: syntax error while parsing: dsafsdf -184: [12:43:04] SMILES Parse Error: check for mistakes around position 1: -184: [12:43:04] dsafsdf -184: [12:43:04] ^ -184: [12:43:04] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -184: [12:43:04] SMILES Parse Error: syntax error while parsing: dsafsdf -184: [12:43:04] SMILES Parse Error: check for mistakes around position 1: -184: [12:43:04] dsafsdf -184: [12:43:04] ^ -184: [12:43:04] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -184: [12:43:04] SMILES Parse Error: syntax error while parsing: dsafsdf -184: [12:43:04] SMILES Parse Error: check for mistakes around position 1: -184: [12:43:04] dsafsdf -184: [12:43:04] ^ -184: [12:43:04] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -184: [12:43:04] SMILES Parse Error: syntax error while parsing: dsafsdf -184: [12:43:04] SMILES Parse Error: check for mistakes around position 1: -184: [12:43:04] dsafsdf -184: [12:43:04] ^ -184: [12:43:04] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -184: [12:43:04] SMILES Parse Error: syntax error while parsing: dsafsdf -184: [12:43:04] SMILES Parse Error: check for mistakes around position 1: -184: [12:43:04] dsafsdf -184: [12:43:04] ^ -184: [12:43:04] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -184: [12:43:04] SMILES Parse Error: syntax error while parsing: dsafsdf -184: [12:43:04] SMILES Parse Error: check for mistakes around position 1: -184: [12:43:04] dsafsdf -184: [12:43:04] ^ -184: [12:43:04] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -184: [12:43:04] SMILES Parse Error: syntax error while parsing: dsafsdf -184: [12:43:04] SMILES Parse Error: check for mistakes around position 1: -184: [12:43:04] dsafsdf -184: [12:43:04] ^ -184: [12:43:04] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -184: [12:43:04] SMILES Parse Error: syntax error while parsing: dsafsdf -184: [12:43:04] SMILES Parse Error: check for mistakes around position 1: -184: [12:43:04] dsafsdf -184: [12:43:04] ^ -184: [12:43:04] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -184: [12:43:04] SMILES Parse Error: syntax error while parsing: dsafsdf -184: [12:43:04] SMILES Parse Error: check for mistakes around position 1: -184: [12:43:04] dsafsdf -184: [12:43:04] ^ -184: [12:43:04] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -184: [12:43:04] SMILES Parse Error: syntax error while parsing: dsafsdf -184: [12:43:04] SMILES Parse Error: check for mistakes around position 1: -184: [12:43:04] dsafsdf -184: [12:43:04] ^ -184: [12:43:04] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -184: [12:43:04] SMILES Parse Error: syntax error while parsing: dsafsdf -184: [12:43:04] SMILES Parse Error: check for mistakes around position 1: -184: [12:43:04] dsafsdf -184: [12:43:04] ^ -184: [12:43:04] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -184: [12:43:04] SMILES Parse Error: syntax error while parsing: dsafsdf -184: [12:43:04] SMILES Parse Error: check for mistakes around position 1: -184: [12:43:04] dsafsdf -184: [12:43:04] ^ -184: [12:43:04] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -184: [12:43:04] SMILES Parse Error: syntax error while parsing: dsafsdf -184: [12:43:04] SMILES Parse Error: check for mistakes around position 1: -184: [12:43:04] dsafsdf -184: [12:43:04] ^ -184: [12:43:04] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -184: [12:43:04] SMILES Parse Error: syntax error while parsing: dsafsdf -184: [12:43:04] SMILES Parse Error: check for mistakes around position 1: -184: [12:43:04] dsafsdf -184: [12:43:04] ^ -184: [12:43:04] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -184: [12:43:04] SMILES Parse Error: syntax error while parsing: dsafsdf -184: [12:43:04] SMILES Parse Error: check for mistakes around position 1: -184: [12:43:04] dsafsdf -184: [12:43:04] ^ -184: [12:43:04] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -184: [12:43:04] SMILES Parse Error: syntax error while parsing: dsafsdf -184: [12:43:04] SMILES Parse Error: check for mistakes around position 1: -184: [12:43:04] dsafsdf -184: [12:43:04] ^ -184: [12:43:04] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -184: [12:43:04] SMILES Parse Error: syntax error while parsing: dsafsdf -184: [12:43:04] SMILES Parse Error: check for mistakes around position 1: -184: [12:43:04] dsafsdf -184: [12:43:04] ^ -184: [12:43:04] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -184: [12:43:04] SMILES Parse Error: syntax error while parsing: dsafsdf -184: [12:43:04] SMILES Parse Error: check for mistakes around position 1: -184: [12:43:04] dsafsdf -184: [12:43:04] ^ -184: [12:43:04] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -184: [12:43:04] SMILES Parse Error: syntax error while parsing: dsafsdf -184: [12:43:04] SMILES Parse Error: check for mistakes around position 1: -184: [12:43:04] dsafsdf -184: [12:43:04] ^ -184: [12:43:04] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -184: [12:43:04] SMILES Parse Error: syntax error while parsing: dsafsdf -184: [12:43:04] SMILES Parse Error: check for mistakes around position 1: -184: [12:43:04] dsafsdf -184: [12:43:04] ^ -184: [12:43:04] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -184: [12:43:04] SMILES Parse Error: syntax error while parsing: dsafsdf -184: [12:43:04] SMILES Parse Error: check for mistakes around position 1: -184: [12:43:04] dsafsdf -184: [12:43:04] ^ -184: [12:43:04] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -184: [12:43:04] SMILES Parse Error: syntax error while parsing: dsafsdf -184: [12:43:04] SMILES Parse Error: check for mistakes around position 1: -184: [12:43:04] dsafsdf -184: [12:43:04] ^ -184: [12:43:04] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -184: [12:43:04] SMILES Parse Error: syntax error while parsing: dsafsdf -184: [12:43:04] SMILES Parse Error: check for mistakes around position 1: -184: [12:43:04] dsafsdf -184: [12:43:04] ^ -184: [12:43:04] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -184: [12:43:04] SMILES Parse Error: syntax error while parsing: dsafsdf -184: [12:43:04] SMILES Parse Error: check for mistakes around position 1: -184: [12:43:04] dsafsdf -184: [12:43:04] ^ -184: [12:43:04] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -184: [12:43:04] SMILES Parse Error: syntax error while parsing: dsafsdf -184: [12:43:04] SMILES Parse Error: check for mistakes around position 1: -184: [12:43:04] dsafsdf -184: [12:43:04] ^ -184: [12:43:04] SMILES Parse Error: syntax error while parsing: dsafsdf -184: [12:43:04] SMILES Parse Error: check for mistakes around position [12:43:04] 1[12:43:04] SMILES Parse Error: syntax error while parsing: dsafsdf -184: [12:43:04] SMILES Parse Error: check for mistakes around position 1: -184: [12:43:04] dsafsdf -184: [12:43:04] ^ -184: [12:43:04] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -184: [12:43:04] SMILES Parse Error: syntax error while parsing: dsafsdf -184: [12:43:04] SMILES Parse Error: check for mistakes around position 1: -184: [12:43:04] dsafsdf -184: [12:43:04] ^ -184: [12:43:04] SMILES Parse Error: syntax error while parsing: dsafsdf -184: [12:43:04] SMILES Parse Error: check for mistakes around position 1:[12:43:04] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +184: [21:38:15] SMILES Parse Error: syntax error while parsing: dsafsdf +184: [21:38:15] SMILES Parse Error: check for mistakes around position 1: +184: [21:38:15] dsafsdf +184: [21:38:15] ^ +184: [21:38:15] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +184: [21:38:15] SMILES Parse Error: syntax error while parsing: dsafsdf +184: [21:38:15] SMILES Parse Error: check for mistakes around position 1: +184: [21:38:15] dsafsdf +184: [21:38:15] ^ +184: [21:38:15] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +184: [21:38:15] SMILES Parse Error: syntax error while parsing: dsafsdf +184: [21:38:15] SMILES Parse Error: check for mistakes around position 1: +184: [21:38:15] dsafsdf +184: [21:38:15] ^ +184: [21:38:15] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +184: [21:38:15] SMILES Parse Error: syntax error while parsing: dsafsdf +184: [21:38:15] SMILES Parse Error: check for mistakes around position 1: +184: [21:38:15] dsafsdf +184: [21:38:15] ^ +184: [21:38:15] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +184: SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +184: 1: +184: [21:38:15] dsafsdf +184: [21:38:15] ^ +184: [21:38:15] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +184: [21:38:15] SMILES Parse Error: syntax error while parsing: dsafsdf +184: [21:38:15] SMILES Parse Error: check for mistakes around position 1: +184: [21:38:15] dsafsdf +184: [21:38:15] ^ +184: [21:38:15] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +184: [21:38:15] SMILES Parse Error: syntax error while parsing: dsafsdf +184: [21:38:15] SMILES Parse Error: check for mistakes around position 1: +184: [21:38:15] dsafsdf +184: [21:38:15] ^ +184: [21:38:15] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +184: [21:38:15] SMILES Parse Error: syntax error while parsing: dsafsdf +184: [21:38:15] SMILES Parse Error: check for mistakes around position 1: +184: [21:38:15] dsafsdf +184: [21:38:15] ^ +184: [21:38:15] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +184: [21:38:15] SMILES Parse Error: syntax error while parsing: dsafsdf +184: [21:38:15] SMILES Parse Error: check for mistakes around position 1: +184: [21:38:15] dsafsdf +184: [21:38:15] ^ +184: [21:38:15] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +184: [21:38:15] SMILES Parse Error: syntax error while parsing: dsafsdf +184: [21:38:15] SMILES Parse Error: check for mistakes around position 1: +184: [21:38:15] dsafsdf +184: [21:38:15] ^ +184: [21:38:15] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +184: [21:38:15] SMILES Parse Error: syntax error while parsing: dsafsdf +184: [21:38:15] SMILES Parse Error: check for mistakes around position 1: +184: [21:38:15] dsafsdf +184: [21:38:15] ^ +184: [21:38:15] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +184: [21:38:15] SMILES Parse Error: syntax error while parsing: dsafsdf +184: [21:38:15] SMILES Parse Error: check for mistakes around position 1: +184: [21:38:15] dsafsdf +184: [21:38:15] ^ +184: [21:38:15] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +184: [21:38:15] SMILES Parse Error: syntax error while parsing: dsafsdf +184: [21:38:15] SMILES Parse Error: check for mistakes around position 1: +184: [21:38:15] dsafsdf +184: [21:38:15] ^ +184: [21:38:15] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +184: [21:38:15] SMILES Parse Error: syntax error while parsing: dsafsdf +184: [21:38:15] SMILES Parse Error: check for mistakes around position 1: +184: [21:38:15] dsafsdf +184: [21:38:15] ^ +184: [21:38:15] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +184: [21:38:15] SMILES Parse Error: syntax error while parsing: dsafsdf +184: [21:38:15] SMILES Parse Error: check for mistakes around position 1: +184: [21:38:15] dsafsdf +184: [21:38:15] ^ +184: [21:38:15] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +184: [21:38:15] SMILES Parse Error: syntax error while parsing: dsafsdf +184: [21:38:15] SMILES Parse Error: check for mistakes around position 1: +184: [21:38:15] dsafsdf +184: [21:38:15] ^ +184: [21:38:15] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +184: [21:38:15] SMILES Parse Error: syntax error while parsing: dsafsdf +184: [21:38:15] SMILES Parse Error: check for mistakes around position 1: +184: [21:38:15] dsafsdf +184: [21:38:15] ^ +184: [21:38:15] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +184: [21:38:15] SMILES Parse Error: syntax error while parsing: dsafsdf +184: [21:38:15] SMILES Parse Error: check for mistakes around position 1: +184: [21:38:15] dsafsdf +184: [21:38:15] ^ +184: [21:38:15] SMILES Parse Error: syntax error while parsing: dsafsdf +184: [21:38:15] SMILES Parse Error: check for mistakes around position 1: +184: [21:38:15] dsafsdf +184: [21:38:15] ^ +184: [21:38:15] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +184: [21:38:15] SMILES Parse Error: syntax error while parsing: dsafsdf +184: [21:38:15] SMILES Parse Error: check for mistakes around position 1: +184: [21:38:15] dsafsdf +184: [21:38:15] ^ +184: [21:38:15] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +184: [21:38:15] SMILES Parse Error: syntax error while parsing: dsafsdf +184: [21:38:15] SMILES Parse Error: check for mistakes around position 1: +184: [21:38:15] dsafsdf +184: [21:38:15] ^ +184: [21:38:15] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +184: [21:38:15] SMILES Parse Error: syntax error while parsing: dsafsdf +184: [21:38:15] SMILES Parse Error: check for mistakes around position 1: +184: [21:38:15] dsafsdf +184: [21:38:15] ^ +184: [21:38:15] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +184: [21:38:15] SMILES Parse Error: syntax error while parsing: dsafsdf +184: [21:38:15] SMILES Parse Error: check for mistakes around position 1: +184: [21:38:15] dsafsdf +184: [21:38:15] ^ +184: [21:38:15] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +184: [21:38:15] SMILES Parse Error: syntax error while parsing: dsafsdf +184: [21:38:15] SMILES Parse Error: check for mistakes around position 1: +184: [21:38:15] dsafsdf +184: [21:38:15] ^ +184: [21:38:15] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +184: [21:38:15] SMILES Parse Error: syntax error while parsing: dsafsdf +184: [21:38:15] SMILES Parse Error: check for mistakes around position 1: +184: [21:38:15] dsafsdf +184: [21:38:15] ^ +184: [21:38:15] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +184: [21:38:15] SMILES Parse Error: syntax error while parsing: dsafsdf +184: [21:38:15] SMILES Parse Error: check for mistakes around position 1: +184: [21:38:15] dsafsdf +184: [21:38:15] ^ +184: [21:38:15] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +184: [21:38:15] SMILES Parse Error: syntax error while parsing: dsafsdf +184: [21:38:15] SMILES Parse Error: check for mistakes around position 1: +184: [21:38:15] dsafsdf +184: [21:38:15] ^ +184: [21:38:15] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +184: [21:38:15] [21:38:15] [21:38:15] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +184: [21:38:15] SMILES Parse Error: syntax error while parsing: dsafsdf +184: [21:38:15] SMILES Parse Error: check for mistakes around position 1: +184: [21:38:15] dsafsdf +184: [21:38:15] ^ +184: [21:38:15] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +184: [21:38:15] SMILES Parse Error: [21:38:15] SMILES Parse Error: syntax error while parsing: dsafsdf +184: [21:38:15] SMILES Parse Error: check for mistakes around position [21:38:15] SMILES Parse Error: syntax error while parsing: syntax error while parsing: dsafsdf +184: [21:38:15] SMILES Parse Error: check for mistakes around position 1dsafsdf1: 184: -184: [12:43:04] dsafsdf -184: [12:43:04] ^ -184: [12:43:04] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -184: [12:43:04] SMILES Parse Error: syntax error while parsing: dsafsdf -184: [12:43:04] SMILES Parse Error: check for mistakes around position 1: -184: [12:43:04] dsafsdf -184: [12:43:04] ^ -184: [12:43:04] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -184: [12:43:04] SMILES Parse Error: syntax error while parsing: dsafsdf -184: [12:43:04] SMILES Parse Error: check for mistakes around position 1: -184: [12:43:04] dsafsdf -184: [12:43:04] ^ -184: [12:43:04] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -184: [12:43:04] SMILES Parse Error: syntax error while parsing: dsafsdf -184: [12:43:04] SMILES Parse Error: check for mistakes around position 1: -184: [12:43:04] dsafsdf -184: [12:43:04] ^ -184: [12:43:04] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -184: [12:43:04] SMILES Parse Error: syntax error while parsing: dsafsdf -184: [12:43:04] SMILES Parse Error: check for mistakes around position 1: -184: [12:43:04] dsafsdf -184: [12:43:04] ^ -184: [12:43:04] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -184: [12:43:04] SMILES Parse Error: syntax error while parsing: dsafsdf -184: [12:43:04] SMILES Parse Error: check for mistakes around position 1: -184: [12:43:04] dsafsdf -184: [12:43:04] ^ -184: [12:43:04] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -184: [12:43:04] SMILES Parse Error: syntax error while parsing: dsafsdf -184: [12:43:04] SMILES Parse Error: check for mistakes around position 1: -184: [12:43:04] dsafsdf -184: [12:43:04] ^ -184: [12:43:04] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -184: [12:43:04] SMILES Parse Error: syntax error while parsing: dsafsdf -184: [12:43:04] SMILES Parse Error: check for mistakes around position 1: -184: [12:43:04] dsafsdf -184: [12:43:04] ^ -184: [12:43:04] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -184: [12:43:04] SMILES Parse Error: syntax error while parsing: dsafsdf -184: [12:43:04] SMILES Parse Error: check for mistakes around position 1: -184: [12:43:04] dsafsdf -184: [12:43:04] ^ -184: [12:43:04] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -184: [12:43:04] SMILES Parse Error: syntax error while parsing: dsafsdf -184: [12:43:04] SMILES Parse Error: check for mistakes around position 1: -184: [12:43:04] dsafsdf -184: [12:43:04] ^ -184: [12:43:04] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -184: [12:43:04] SMILES Parse Error: syntax error while parsing: dsafsdf -184: [12:43:04] SMILES Parse Error: check for mistakes around position 1: -184: [12:43:04] dsafsdf -184: [12:43:04] ^ -184: [12:43:04] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -184: [12:43:04] [12:43:04] SMILES Parse Error: syntax error while parsing: dsafsdf -184: [12:43:04] SMILES Parse Error: check for mistakes around position 1: -184: [12:43:04] dsafsdf -184: [12:43:04] ^ -184: [12:43:04] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +184: : +184: [21:38:15] dsafsdf +184: [21:38:15] ^ +184: [21:38:15] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +184: [21:38:15] SMILES Parse Error: syntax error while parsing: dsafsdf +184: [21:38:15] SMILES Parse Error: check for mistakes around position 1: +184: [21:38:15] dsafsdf +184: [21:38:15] ^ +184: [21:38:15] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +184: [21:38:15] SMILES Parse Error: syntax error while parsing: dsafsdf +184: [21:38:15] SMILES Parse Error: check for mistakes around position 1: +184: [21:38:15] dsafsdf +184: [21:38:15] ^ +184: [21:38:15] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +184: [21:38:15] dsafsdf +184: [21:38:15] ^ +184: [21:38:15] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +184: [21:38:15] SMILES Parse Error: syntax error while parsing: dsafsdf +184: [21:38:15] SMILES Parse Error: check for mistakes around position 1: +184: [21:38:15] dsafsdf +184: [21:38:15] ^ +184: [21:38:15] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +184: [21:38:15] SMILES Parse Error: syntax error while parsing: dsafsdf +184: [21:38:15] SMILES Parse Error: check for mistakes around position 1: +184: [21:38:15] dsafsdf +184: [21:38:15] ^ +184: [21:38:15] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +184: [21:38:15] SMILES Parse Error: syntax error while parsing: dsafsdf +184: [21:38:15] SMILES Parse Error: check for mistakes around position 1: +184: [21:38:15] dsafsdf +184: [21:38:15] ^ +184: [21:38:15] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +184: [21:38:15] SMILES Parse Error: syntax error while parsing: dsafsdf +184: [21:38:15] SMILES Parse Error: check for mistakes around position 1: +184: [21:38:15] dsafsdf +184: [21:38:15] ^ +184: [21:38:15] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +184: [21:38:15] SMILES Parse Error: check for mistakes around position 1: +184: [21:38:15] dsafsdf +184: [21:38:15] ^ +184: [21:38:15] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +184: [21:38:15] SMILES Parse Error: syntax error while parsing: dsafsdf +184: [21:38:15] SMILES Parse Error: check for mistakes around position 1: +184: [21:38:15] dsafsdf +184: [21:38:15] ^ +184: [21:38:15] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +184: [21:38:15] SMILES Parse Error: syntax error while parsing: dsafsdf +184: [21:38:15] SMILES Parse Error: check for mistakes around position 1: +184: [21:38:15] dsafsdf +184: [21:38:15] ^ +184: [21:38:15] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +184: [21:38:15] SMILES Parse Error: syntax error while parsing: dsafsdf +184: [21:38:15] SMILES Parse Error: check for mistakes around position 1: +184: [21:38:15] dsafsdf +184: [21:38:15] ^ +184: [21:38:15] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' 184: SMILES Parse Error: syntax error while parsing: dsafsdf -184: [12:43:04] SMILES Parse Error: check for mistakes around position 1: -184: [12:43:04] dsafsdf -184: [12:43:04] ^ -184: [12:43:04] SMILES Parse Error: syntax error[12:43:04] : -184: [12:43:04] dsafsdf -184: [12:43:04] ^ -184: [12:43:04] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -184: [12:43:04] SMILES Parse Error: syntax error while parsing: dsafsdf -184: [12:43:04] SMILES Parse Error: check for mistakes around position 1: -184: [12:43:04] dsafsdf -184: [12:43:04] ^ -184: [12:43:04] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -184: [12:43:04] SMILES Parse Error: syntax error while parsing: dsafsdf -184: [12:43:04] SMILES Parse Error: check for mistakes around position 1: -184: [12:43:04] dsafsdf -184: [12:43:04] ^ -184: [12:43:04] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -184: [12:43:04] SMILES Parse Error: syntax error while parsing: dsafsdf -184: [12:43:04] SMILES Parse Error: check for mistakes around position 1: -184: [12:43:04] dsafsdf -184: [12:43:04] ^ -184: [12:43:04] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -184: while parsing: dsafsdf -184: [12:43:04] SMILES Parse Error: check for mistakes around position 1: -184: [12:43:04] dsafsdf -184: [12:43:04] ^ -184: [12:43:04] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -184: [12:43:04] SMILES Parse Error: syntax error while parsing: dsafsdf -184: [12:43:04] SMILES Parse Error: check for mistakes around position 1: -184: [12:43:04] dsafsdf -184: [12:43:04] ^ -184: [12:43:04] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -184: SMILES[12:43:04] SMILES Parse Error: syntax error while parsing: dsafsdf -184: [12:43:04] SMILES Parse Error: check for mistakes around position 1: -184: [12:43:04] dsafsdf -184: [12:43:04] ^ -184: [12:43:04] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -184: [12:43:04] SMILES Parse Error: syntax error while parsing: dsafsdf -184: [12:43:04] SMILES Parse Error: check for mistakes around position 1: -184: [12:43:04] dsafsdf -184: [12:43:04] ^ -184: [12:43:04] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -184: [12:43:04] SMILES Parse Error: syntax error while parsing: dsafsdf -184: [12:43:04] SMILES Parse Error: check for mistakes around position 1: -184: [12:43:04] dsafsdf -184: [12:43:04] ^ -184: [12:43:04] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -184: [12:43:04] SMILES Parse Error: syntax error while parsing: dsafsdf -184: [12:43:04] SMILES Parse Error: check for mistakes around position 1: -184: [12:43:04] dsafsdf -184: [12:43:04] ^ -184: [12:43:04] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -184: [12:43:04] SMILES Parse Error: syntax error while parsing: dsafsdf -184: [12:43:04] SMILES Parse Error: check for mistakes around position 1: -184: [12:43:04] dsafsdf -184: [12:43:04] ^ -184: [12:43:04] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -184: [12:43:04] SMILES Parse Error: syntax error while parsing: dsafsdf -184: [12:43:04] SMILES Parse Error: check for mistakes around position 1: -184: [12:43:04] dsafsdf -184: [12:43:04] ^ -184: [12:43:04] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -184: [12:43:04] SMILES Parse Error: syntax error while parsing: dsafsdf -184: [12:43:04] SMILES Parse Error: check for mistakes around position 1: -184: [12:43:04] dsafsdf -184: [12:43:04] ^ -184: [12:43:04] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -184: [12:43:04] SMILES Parse Error: syntax error while parsing: dsafsdf -184: [12:43:04] SMILES Parse Error: check for mistakes around position 1: -184: [12:43:04] dsafsdf -184: [12:43:04] ^ -184: [12:43:04] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -184: [12:43:04] SMILES Parse Error: syntax error while parsing: dsafsdf -184: [12:43:04] SMILES Parse Error: check for mistakes around position 1: -184: [12:43:04] dsafsdf -184: [12:43:04] ^ -184: [12:43:04] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -184: SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -184: [12:43:04] SMILES Parse Error: syntax error while parsing: dsafsdf -184: [12:43:04] SMILES Parse Error: check for mistakes around position 1: -184: [12:43:04] dsafsdf -184: [12:43:04] ^ -184: [12:43:04] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -184: Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -184: [12:43:04] SMILES Parse Error: syntax error while parsing: dsafsdf -184: [12:43:04] SMILES Parse Error: check for mistakes around position 1: -184: [12:43:04] dsafsdf -184: [12:43:04] ^ -184: [12:43:04] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -184: [12:43:04] SMILES Parse Error: syntax error while parsing: dsafsdf -184: [12:43:04] SMILES Parse Error: check for mistakes around position 1: -184: [12:43:04] dsafsdf -184: [12:43:04] ^ -184: [12:43:04] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -184: [12:43:04] SMILES Parse Error: syntax error while parsing: dsafsdf -184: [12:43:04] SMILES Parse Error: check for mistakes around position 1: -184: [12:43:04] dsafsdf -184: [12:43:04] ^ -184: [12:43:04] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -184: [12:43:04] SMILES Parse Error: syntax error while parsing: dsafsdf -184: [12:43:04] SMILES Parse Error: check for mistakes around position 1: -184: [12:43:04] dsafsdf -184: [12:43:04] ^ -184: [12:43:04] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -184: [12:43:04] SMILES Parse Error: syntax error while parsing: dsafsdf -184: [12:43:04] SMILES Parse Error: check for mistakes around position 1: -184: [12:43:04] dsafsdf -184: [12:43:04] ^ -184: [12:43:04] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -184: [12:43:04] SMILES Parse Error: syntax error while parsing: dsafsdf -184: [12:43:04] SMILES Parse Error: check for mistakes around position 1: -184: [12:43:04] dsafsdf -184: [12:43:04] ^ -184: [12:43:04] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -184: [12:43:04] SMILES Parse Error: syntax error while parsing: dsafsdf -184: [12:43:04] SMILES Parse Error: check for mistakes around position 1: -184: [12:43:04] dsafsdf -184: [12:43:04] ^ -184: [12:43:04] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -184: [12:43:04] SMILES Parse Error: syntax error while parsing: dsafsdf -184: [12:43:04] SMILES Parse Error: check for mistakes around position 1: -184: [12:43:04] dsafsdf -184: [12:43:04] ^ -184: [12:43:04] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -184: [12:43:04] SMILES Parse Error: syntax error while parsing: dsafsdf -184: [12:43:04] SMILES Parse Error: check for mistakes around position 1: -184: [12:43:04] dsafsdf -184: [12:43:04] ^ -184: [12:43:04] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -184: [12:43:04] SMILES Parse Error: syntax error while parsing: dsafsdf -184: [12:43:04] SMILES Parse Error: check for mistakes around position 1: -184: [12:43:04] dsafsdf -184: [12:43:04] ^ -184: [12:43:04] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -184: [12:43:04] SMILES Parse Error: syntax error while parsing: dsafsdf -184: [12:43:04] SMILES Parse Error: check for mistakes around position 1: -184: [12:43:04] dsafsdf -184: [12:43:04] ^ -184: [12:43:04] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -184: [12:43:04] SMILES Parse Error: syntax error while parsing: dsafsdf -184: [12:43:04] SMILES Parse Error: check for mistakes around position 1: -184: [12:43:04] dsafsdf -184: [12:43:04] ^ -184: [12:43:04] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -184: [12:43:04] SMILES Parse Error: syntax error while parsing: dsafsdf -184: [12:43:04] SMILES Parse Error: check for mistakes around position 1: -184: [12:43:04] dsafsdf -184: [12:43:04] ^ -184: [12:43:04] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -184: [12:43:04] SMILES Parse Error: syntax error while parsing: dsafsdf -184: [12:43:04] SMILES Parse Error: check for mistakes around position 1: -184: [12:43:04] dsafsdf -184: [12:43:04] ^ -184: [12:43:04] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -184: [12:43:04] SMILES Parse Error: syntax error while parsing: dsafsdf -184: [12:43:04] SMILES Parse Error: check for mistakes around position 1: -184: [12:43:04] dsafsdf -184: [12:43:04] ^ -184: [12:43:04] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -184: [12:43:04] SMILES Parse Error: syntax error while parsing: dsafsdf -184: [12:43:04] SMILES Parse Error: check for mistakes around position 1: -184: [12:43:04] dsafsdf -184: [12:43:04] ^ -184: [12:43:04] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -184: [12:43:04] SMILES Parse Error: syntax error while parsing: dsafsdf -184: [12:43:04] SMILES Parse Error: check for mistakes around position 1: -184: [12:43:04] dsafsdf -184: [12:43:04] ^ -184: [12:43:04] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -184: [12:43:04] SMILES Parse Error: syntax error while parsing: dsafsdf -184: [12:43:04] SMILES Parse Error: check for mistakes around position 1: -184: [12:43:04] dsafsdf -184: [12:43:04] ^ -184: [12:43:04] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -184: [12:43:04] SMILES Parse Error: syntax error while parsing: dsafsdf -184: [12:43:04] SMILES Parse Error: check for mistakes around position 1: -184: [12:43:04] dsafsdf -184: [12:43:04] ^ -184: [12:43:04] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -184: [12:43:04] SMILES Parse Error: syntax error while parsing: dsafsdf -184: [12:43:04] SMILES Parse Error: check for mistakes around position 1: -184: [12:43:04] dsafsdf -184: [12:43:04] ^ -184: [12:43:04] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -184: [12:43:04] SMILES Parse Error: syntax error while parsing: dsafsdf -184: [12:43:04] SMILES Parse Error: check for mistakes around position 1: -184: [12:43:04] dsafsdf -184: [12:43:04] ^ -184: [12:43:04] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -184: [12:43:04] SMILES Parse Error: syntax error while parsing: dsafsdf -184: [12:43:04] SMILES Parse Error: check for mistakes around position 1: -184: [12:43:04] dsafsdf -184: [12:43:04] ^ -184: [12:43:04] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -184: [12:43:04] SMILES Parse Error: syntax error while parsing: dsafsdf -184: [12:43:04] SMILES Parse Error: check for mistakes around position 1: -184: [12:43:04] dsafsdf -184: [12:43:04] ^ -184: [12:43:04] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -184: [12:43:04] SMILES Parse Error: syntax error while parsing: dsafsdf -184: [12:43:04] SMILES Parse Error: check for mistakes around position 1: -184: [12:43:04] dsafsdf -184: [12:43:04] ^ -184: [12:43:04] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -184: [12:43:04] SMILES Parse Error: syntax error while parsing: dsafsdf -184: [12:43:04] SMILES Parse Error: check for mistakes around position 1: -184: [12:43:04] dsafsdf -184: [12:43:04] ^ -184: [12:43:04] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -184: [12:43:04] SMILES Parse Error: syntax error while parsing: dsafsdf -184: [12:43:04] SMILES Parse Error: check for mistakes around position 1: -184: [12:43:04] dsafsdf -184: [12:43:04] ^ -184: [12:43:04] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -184: [12:43:04] SMILES Parse Error: syntax error while parsing: dsafsdf -184: [12:43:04] SMILES Parse Error: check for mistakes around position 1: -184: [12:43:04] dsafsdf -184: [12:43:04] ^ -184: [12:43:04] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -184: [12:43:04] SMILES Parse Error: syntax error while parsing: dsafsdf -184: [12:43:04] SMILES Parse Error: check for mistakes around position 1: -184: [12:43:04] dsafsdf -184: [12:43:04] ^ -184: [12:43:04] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -184: [12:43:04] SMILES Parse Error: syntax error while parsing: dsafsdf -184: [12:43:04] SMILES Parse Error: check for mistakes around position 1: -184: [12:43:04] dsafsdf -184: [12:43:04] ^ -184: [12:43:04] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -184: [12:43:04] SMILES Parse Error: syntax error while parsing: dsafsdf -184: [12:43:04] SMILES Parse Error: check for mistakes around position 1: -184: [12:43:04] dsafsdf -184: [12:43:04] ^ -184: [12:43:04] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -184: [12:43:04] SMILES Parse Error: syntax error while parsing: dsafsdf -184: [12:43:04] SMILES Parse Error: check for mistakes around position 1: -184: [12:43:04] dsafsdf -184: [12:43:04] ^ -184: [12:43:04] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -184: [12:43:04] SMILES Parse Error: syntax error while parsing: dsafsdf -184: [12:43:04] SMILES Parse Error: check for mistakes around position 1: -184: [12:43:04] dsafsdf -184: [12:43:04] ^ -184: [12:43:04] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -184: [12:43:04] SMILES Parse Error: syntax error while parsing: dsafsdf -184: [12:43:04] SMILES Parse Error: check for mistakes around position 1: -184: [12:43:04] dsafsdf -184: [12:43:04] ^ -184: [12:43:04] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -184: [12:43:04] SMILES Parse Error: syntax error while parsing: dsafsdf -184: [12:43:04] SMILES Parse Error: check for mistakes around position 1: -184: [12:43:04] dsafsdf -184: [12:43:04] ^ -184: [12:43:04] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -184: [12:43:04] SMILES Parse Error: syntax error while parsing: dsafsdf -184: [12:43:04] SMILES Parse Error: check for mistakes around position 1: -184: [12:43:04] dsafsdf -184: [12:43:04] ^ -184: [12:43:04] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -184: [12:43:04] SMILES Parse Error: syntax error while parsing: dsafsdf -184: [12:43:04] SMILES Parse Error: check for mistakes around position 1: -184: [12:43:04] dsafsdf -184: [12:43:04] ^ -184: [12:43:04] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -184: [12:43:04] SMILES Parse Error: syntax error while parsing: dsafsdf -184: [12:43:04] SMILES Parse Error: check for mistakes around position 1: -184: [12:43:04] dsafsdf -184: [12:43:04] ^ -184: [12:43:04] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -184: [12:43:04] SMILES Parse Error: syntax error while parsing: dsafsdf -184: [12:43:04] SMILES Parse Error: check for mistakes around position 1: -184: [12:43:04] dsafsdf -184: [12:43:04] ^ -184: [12:43:04] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -184: [12:43:04] SMILES Parse Error: syntax error while parsing: dsafsdf -184: [12:43:04] SMILES Parse Error: check for mistakes around position 1: -184: [12:43:04] dsafsdf -184: [12:43:04] ^ -184: [12:43:04] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -184: [12:43:04] SMILES Parse Error: syntax error while parsing: dsafsdf -184: [12:43:04] SMILES Parse Error: check for mistakes around position 1: -184: [12:43:04] dsafsdf -184: [12:43:04] ^ -184: [12:43:04] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -184: [12:43:04] SMILES Parse Error: syntax error while parsing: dsafsdf -184: [12:43:04] SMILES Parse Error: check for mistakes around position 1: -184: [12:43:04] dsafsdf -184: [12:43:04] ^ -184: [12:43:04] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -184: [12:43:04] SMILES Parse Error: syntax error while parsing: dsafsdf -184: [12:43:04] SMILES Parse Error: check for mistakes around position 1: -184: [12:43:04] dsafsdf -184: [12:43:04] ^ -184: [12:43:04] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -184: [12:43:04] SMILES Parse Error: syntax error while parsing: dsafsdf -184: [12:43:04] SMILES Parse Error: check for mistakes around position 1: -184: [12:43:04] dsafsdf -184: [12:43:04] ^ -184: [12:43:04] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -184: [12:43:04] SMILES Parse Error: syntax error while parsing: dsafsdf -184: [12:43:04] SMILES Parse Error: check for mistakes around position 1: -184: [12:43:04] dsafsdf -184: [12:43:04] ^ -184: [12:43:04] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -184: [12:43:04] SMILES Parse Error: syntax error while parsing: dsafsdf -184: [12:43:04] SMILES Parse Error: check for mistakes around position 1: -184: [12:43:04] dsafsdf -184: [12:43:04] ^ -184: [12:43:04] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -184: [12:43:04] SMILES Parse Error: syntax error while parsing: dsafsdf -184: [12:43:04] SMILES Parse Error: check for mistakes around position 1: -184: [12:43:04] dsafsdf -184: [12:43:04] ^ -184: [12:43:04] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -184: [12:43:04] SMILES Parse Error: syntax error while parsing: dsafsdf -184: [12:43:04] SMILES Parse Error: check for mistakes around position 1: -184: [12:43:04] dsafsdf -184: [12:43:04] ^ -184: [12:43:04] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -184: [12:43:04] SMILES Parse Error: syntax error while parsing: dsafsdf -184: [12:43:04] SMILES Parse Error: check for mistakes around position 1: -184: [12:43:04] dsafsdf -184: [12:43:04] ^ -184: [12:43:04] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -184: [12:43:04] SMILES Parse Error: syntax error while parsing: dsafsdf -184: [12:43:04] SMILES Parse Error: check for mistakes around position 1: -184: [12:43:04] dsafsdf -184: [12:43:04] ^ -184: [12:43:04] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -184: [12:43:04] SMILES Parse Error: syntax error while parsing: dsafsdf -184: [12:43:04] SMILES Parse Error: check for mistakes around position 1: -184: [12:43:04] dsafsdf -184: [12:43:04] ^ -184: [12:43:04] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -184: [12:43:04] SMILES Parse Error: syntax error while parsing: dsafsdf -184: [12:43:04] SMILES Parse Error: check for mistakes around position 1: -184: [12:43:04] dsafsdf -184: [12:43:04] ^ -184: [12:43:04] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -184: [12:43:04] SMILES Parse Error: syntax error while parsing: dsafsdf -184: [12:43:04] SMILES Parse Error: check for mistakes around position 1: -184: [12:43:04] dsafsdf -184: [12:43:04] ^ -184: [12:43:04] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -184: [12:43:04] SMILES Parse Error: syntax error while parsing: dsafsdf -184: [12:43:04] SMILES Parse Error: check for mistakes around position 1: -184: [12:43:04] dsafsdf -184: [12:43:04] ^ -184: [12:43:04] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -184: [12:43:04] SMILES Parse Error: syntax error while parsing: dsafsdf -184: [12:43:04] SMILES Parse Error: check for mistakes around position 1: -184: [12:43:04] dsafsdf -184: [12:43:04] ^ -184: [12:43:04] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -184: [12:43:04] SMILES Parse Error: syntax error while parsing: dsafsdf -184: [12:43:04] SMILES Parse Error: check for mistakes around position 1: -184: [12:43:04] dsafsdf -184: [12:43:04] ^ -184: [12:43:04] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -184: [12:43:04] SMILES Parse Error: syntax error while parsing: dsafsdf -184: [12:43:04] SMILES Parse Error: check for mistakes around position 1: -184: [12:43:04] dsafsdf -184: [12:43:04] ^ -184: [12:43:04] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -184: [12:43:04] SMILES Parse Error: syntax error while parsing: dsafsdf -184: [12:43:04] SMILES Parse Error: check for mistakes around position 1: -184: [12:43:04] dsafsdf -184: [12:43:04] ^ -184: [12:43:04] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -184: [12:43:04] SMILES Parse Error: syntax error while parsing: dsafsdf -184: [12:43:04] SMILES Parse Error: check for mistakes around position 1: -184: [12:43:04] dsafsdf -184: [12:43:04] ^ -184: [12:43:04] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -184: [12:43:04] SMILES Parse Error: syntax error while parsing: dsafsdf -184: [12:43:04] SMILES Parse Error: check for mistakes around position 1: -184: [12:43:04] dsafsdf -184: [12:43:04] ^ -184: [12:43:04] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -184: [12:43:04] SMILES Parse Error: syntax error while parsing: dsafsdf -184: [12:43:04] SMILES Parse Error: check for mistakes around position 1: -184: [12:43:04] dsafsdf -184: [12:43:04] ^ -184: [12:43:04] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -184: [12:43:04] SMILES Parse Error: syntax error while parsing: dsafsdf -184: [12:43:04] SMILES Parse Error: check for mistakes around position 1: -184: [12:43:04] dsafsdf -184: [12:43:04] ^ -184: [12:43:04] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -184: [12:43:04] SMILES Parse Error: syntax error while parsing: dsafsdf -184: [12:43:04] SMILES Parse Error: check for mistakes around position 1: -184: [12:43:04] dsafsdf -184: [12:43:04] ^ -184: [12:43:04] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -184: [12:43:04] SMILES Parse Error: syntax error while parsing: dsafsdf -184: [12:43:04] SMILES Parse Error: check for mistakes around position 1: -184: [12:43:04] dsafsdf -184: [12:43:04] ^ -184: [12:43:04] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -184: [12:43:04] SMILES Parse Error: syntax error while parsing: dsafsdf -184: [12:43:04] SMILES Parse Error: check for mistakes around position 1: -184: [12:43:04] dsafsdf -184: [12:43:04] ^ -184: [12:43:04] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -184: [12:43:04] SMILES Parse Error: syntax error while parsing: dsafsdf -184: [12:43:04] SMILES Parse Error: check for mistakes around position 1: -184: [12:43:04] dsafsdf -184: [12:43:04] ^ -184: [12:43:04] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -184: [12:43:04] SMILES Parse Error: syntax error while parsing: dsafsdf -184: [12:43:04] SMILES Parse Error: check for mistakes around position 1: -184: [12:43:04] dsafsdf -184: [12:43:04] ^ -184: [12:43:04] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -184: [12:43:04] SMILES Parse Error: syntax error while parsing: dsafsdf -184: [12:43:04] SMILES Parse Error: check for mistakes around position 1: -184: [12:43:04] dsafsdf -184: [12:43:04] ^ -184: [12:43:04] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -184: [12:43:04] SMILES Parse Error: syntax error while parsing: dsafsdf -184: [12:43:04] SMILES Parse Error: check for mistakes around position 1: -184: [12:43:04] dsafsdf -184: [12:43:04] ^ -184: [12:43:04] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -184: [12:43:04] SMILES Parse Error: syntax error while parsing: dsafsdf -184: [12:43:04] SMILES Parse Error: check for mistakes around position 1: -184: [12:43:04] dsafsdf -184: [12:43:04] ^ -184: [12:43:04] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -184: [12:43:04] SMILES Parse Error: syntax error while parsing: dsafsdf -184: [12:43:04] SMILES Parse Error: check for mistakes around position 1: -184: [12:43:04] dsafsdf -184: [12:43:04] ^ -184: [12:43:04] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -184: [12:43:04] SMILES Parse Error: syntax error while parsing: dsafsdf -184: [12:43:04] SMILES Parse Error: check for mistakes around position 1: -184: [12:43:04] dsafsdf -184: [12:43:04] ^ -184: [12:43:04] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -184: [12:43:04] SMILES Parse Error: syntax error while parsing: dsafsdf -184: [12:43:04] SMILES Parse Error: check for mistakes around position 1: -184: [12:43:04] dsafsdf -184: [12:43:04] ^ -184: [12:43:04] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -184: [12:43:04] SMILES Parse Error: syntax error while parsing: dsafsdf -184: [12:43:04] SMILES Parse Error: check for mistakes around position 1: -184: [12:43:04] dsafsdf -184: [12:43:04] ^ -184: [12:43:04] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -184: [12:43:04] SMILES Parse Error: syntax error while parsing: dsafsdf -184: [12:43:04] SMILES Parse Error: check for mistakes around position 1: -184: [12:43:04] dsafsdf -184: [12:43:04] ^ -184: [12:43:04] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -184: [12:43:04] SMILES Parse Error: syntax error while parsing: dsafsdf -184: [12:43:04] SMILES Parse Error: check for mistakes around position 1: -184: [12:43:04] dsafsdf -184: [12:43:04] ^ -184: [12:43:04] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -184: [12:43:04] SMILES Parse Error: syntax error while parsing: dsafsdf -184: [12:43:04] SMILES Parse Error: check for mistakes around position 1: -184: [12:43:04] dsafsdf -184: [12:43:04] ^ -184: [12:43:04] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -184: [12:43:04] SMILES Parse Error: syntax error while parsing: dsafsdf -184: [12:43:04] SMILES Parse Error: check for mistakes around position 1: -184: [12:43:04] dsafsdf -184: [12:43:04] ^ -184: [12:43:04] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -184: [12:43:04] SMILES Parse Error: syntax error while parsing: dsafsdf -184: [12:43:04] SMILES Parse Error: check for mistakes around position 1: -184: [12:43:04] dsafsdf -184: [12:43:04] ^ -184: [12:43:04] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -184: [12:43:04] SMILES Parse Error: syntax error while parsing: dsafsdf -184: [12:43:04] SMILES Parse Error: check for mistakes around position 1: -184: [12:43:04] dsafsdf -184: [12:43:04] ^ -184: [12:43:04] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -184: [12:43:04] SMILES Parse Error: syntax error while parsing: dsafsdf -184: [12:43:04] SMILES Parse Error: check for mistakes around position 1: -184: [12:43:04] dsafsdf -184: [12:43:04] ^ -184: [12:43:04] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -184: [12:43:04] SMILES Parse Error: syntax error while parsing: dsafsdf -184: [12:43:04] SMILES Parse Error: check for mistakes around position 1: -184: [12:43:04] dsafsdf -184: [12:43:04] ^ -184: [12:43:04] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -184: [12:43:04] SMILES Parse Error: syntax error while parsing: dsafsdf -184: [12:43:04] SMILES Parse Error: check for mistakes around position 1: -184: [12:43:04] dsafsdf -184: [12:43:04] ^ -184: [12:43:04] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -184: [12:43:04] SMILES Parse Error: syntax error while parsing: dsafsdf -184: [12:43:04] SMILES Parse Error: check for mistakes around position 1: -184: [12:43:04] dsafsdf -184: [12:43:04] ^ -184: [12:43:04] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -184: [12:43:04] SMILES Parse Error: syntax error while parsing: dsafsdf -184: [12:43:04] SMILES Parse Error: check for mistakes around position 1: -184: [12:43:04] dsafsdf -184: [12:43:04] ^ -184: [12:43:04] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -184: [12:43:04] SMILES Parse Error: syntax error while parsing: dsafsdf -184: [12:43:04] SMILES Parse Error: check for mistakes around position 1: -184: [12:43:04] dsafsdf -184: [12:43:04] ^ -184: [12:43:04] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -184: [12:43:04] SMILES Parse Error: syntax error while parsing: dsafsdf -184: [12:43:04] SMILES Parse Error: check for mistakes around position 1: -184: [12:43:04] dsafsdf -184: [12:43:04] ^ -184: [12:43:04] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -184: [12:43:04] SMILES Parse Error: syntax error while parsing: dsafsdf -184: [12:43:04] SMILES Parse Error: check for mistakes around position 1: -184: [12:43:04] dsafsdf -184: [12:43:04] ^ -184: [12:43:04] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -184: [12:43:04] SMILES Parse Error: syntax error while parsing: dsafsdf -184: [12:43:04] SMILES Parse Error: check for mistakes around position 1: -184: [12:43:04] dsafsdf -184: [12:43:04] ^ -184: [12:43:04] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -184: [12:43:04] SMILES Parse Error: syntax error while parsing: dsafsdf -184: [12:43:04] SMILES Parse Error: check for mistakes around position 1: -184: [12:43:04] dsafsdf -184: [12:43:04] ^ -184: [12:43:04] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -184: [12:43:04] SMILES Parse Error: syntax error while parsing: dsafsdf -184: [12:43:04] SMILES Parse Error: check for mistakes around position 1: -184: [12:43:04] dsafsdf -184: [12:43:04] ^ -184: [12:43:04] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -184: [12:43:04] SMILES Parse Error: syntax error while parsing: dsafsdf -184: [12:43:04] SMILES Parse Error: check for mistakes around position 1: -184: [12:43:04] dsafsdf -184: [12:43:04] ^ -184: [12:43:04] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -184: [12:43:04] SMILES Parse Error: syntax error while parsing: dsafsdf -184: [12:43:04] SMILES Parse Error: check for mistakes around position 1: -184: [12:43:04] dsafsdf -184: [12:43:04] ^ -184: [12:43:04] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -184: [12:43:04] SMILES Parse Error: syntax error while parsing: dsafsdf -184: [12:43:04] SMILES Parse Error: check for mistakes around position 1: -184: [12:43:04] dsafsdf -184: [12:43:04] ^ -184: [12:43:04] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -184: [12:43:04] SMILES Parse Error: syntax error while parsing: dsafsdf -184: [12:43:04] SMILES Parse Error: check for mistakes around position 1: -184: [12:43:04] dsafsdf -184: [12:43:04] ^ -184: [12:43:04] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -184: [12:43:04] SMILES Parse Error: syntax error while parsing: dsafsdf -184: [12:43:04] SMILES Parse Error: check for mistakes around position 1: -184: [12:43:04] dsafsdf -184: [12:43:04] ^ -184: [12:43:04] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -184: [12:43:04] SMILES Parse Error: syntax error while parsing: dsafsdf -184: [12:43:04] SMILES Parse Error: check for mistakes around position 1: -184: [12:43:04] dsafsdf -184: [12:43:04] ^ -184: [12:43:04] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -184: [12:43:04] SMILES Parse Error: syntax error while parsing: dsafsdf -184: [12:43:04] SMILES Parse Error: check for mistakes around position 1: -184: [12:43:04] dsafsdf -184: [12:43:04] ^ -184: [12:43:04] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -184: [12:43:04] SMILES Parse Error: syntax error while parsing: dsafsdf -184: [12:43:04] SMILES Parse Error: check for mistakes around position 1: -184: [12:43:04] dsafsdf -184: [12:43:04] ^ -184: [12:43:04] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -184: [12:43:04] SMILES Parse Error: syntax error while parsing: dsafsdf -184: [12:43:04] SMILES Parse Error: check for mistakes around position 1: -184: [12:43:04] dsafsdf -184: [12:43:04] ^ -184: [12:43:04] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -184: [12:43:04] SMILES Parse Error: syntax error while parsing: dsafsdf -184: [12:43:04] SMILES Parse Error: check for mistakes around position 1: -184: [12:43:04] dsafsdf -184: [12:43:04] ^ -184: [12:43:04] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -184: [12:43:04] SMILES Parse Error: syntax error while parsing: dsafsdf -184: [12:43:04] SMILES Parse Error: check for mistakes around position 1: -184: [12:43:04] dsafsdf -184: [12:43:04] ^ -184: [12:43:04] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -184: [12:43:04] SMILES Parse Error: syntax error while parsing: dsafsdf -184: [12:43:04] SMILES Parse Error: check for mistakes around position 1: -184: [12:43:04] dsafsdf -184: [12:43:04] ^ -184: [12:43:04] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -184: [12:43:04] SMILES Parse Error: syntax error while parsing: dsafsdf -184: [12:43:04] SMILES Parse Error: check for mistakes around position 1: -184: [12:43:04] dsafsdf -184: [12:43:04] ^ -184: [12:43:04] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -184: [12:43:04] ------------------------------------- -184: [12:43:04] Results do not depend on numThreads -187: iterative +184: SMILES Parse Error: syntax error while parsing: dsafsdf +184: [21:38:15] SMILES Parse Error: syntax error while parsing: dsafsdf +184: [21:38:15] SMILES Parse Error: check for mistakes around position 1: +184: [21:38:15] dsafsdf +184: [21:38:15] ^ +184: [21:38:15] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +184: [21:38:15] SMILES Parse Error: syntax error while parsing: dsafsdf +184: [21:38:15] SMILES Parse Error: check for mistakes around position 1: +184: [21:38:15] dsafsdf +184: [21:38:15] ^ +184: [21:38:15] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +184: [21:38:15] SMILES Parse Error: syntax error while parsing: dsafsdf +184: [21:38:15] SMILES Parse Error: check for mistakes around position 1: +184: [21:38:15] dsafsdf +184: [21:38:15] ^ +184: [21:38:15] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +184: [21:38:15] SMILES Parse Error: syntax error while parsing: dsafsdf +184: [21:38:15] SMILES Parse Error: check for mistakes around position 1: +184: [21:38:15] dsafsdf +184: [21:38:15] ^ +184: [21:38:15] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +184: [21:38:15] SMILES Parse Error: syntax error while parsing: dsafsdf +184: [21:38:15] SMILES Parse Error: check for mistakes around position 1: +184: [21:38:15] dsafsdf +184: [21:38:15] ^ +184: [21:38:15] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +184: [21:38:15] SMILES Parse Error: syntax error while parsing: dsafsdf +184: [21:38:15] SMILES Parse Error: check for mistakes around position 1: +184: [21:38:15] dsafsdf +184: [21:38:15] ^ +184: [21:38:15] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +184: [21:38:15] SMILES Parse Error: syntax error while parsing: dsafsdf +184: [21:38:15] SMILES Parse Error: check for mistakes around position 1: +184: [21:38:15] dsafsdf +184: [21:38:15] ^ +184: [21:38:15] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +184: [21:38:15] SMILES Parse Error: syntax error while parsing: dsafsdf +184: [21:38:15] SMILES Parse Error: check for mistakes around position 1: +184: [21:38:15] dsafsdf +184: [21:38:15] ^ +184: [21:38:15] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +184: [21:38:15] SMILES Parse Error: syntax error while parsing: dsafsdf +184: [21:38:15] SMILES Parse Error: check for mistakes around position 1: +184: [21:38:15] dsafsdf +184: [21:38:15] ^ +184: [21:38:15] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +184: [21:38:15] SMILES Parse Error: check for mistakes around position 1: +184: [21:38:15] dsafsdf +184: [21:38:15] ^ +184: [21:38:15] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +184: [21:38:15] SMILES Parse Error: syntax error while parsing: dsafsdf +184: [21:38:15] SMILES Parse Error: check for mistakes around position 1: +184: [21:38:15] dsafsdf +184: [21:38:15] ^ +184: [21:38:15] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +184: [21:38:15] SMILES Parse Error: syntax error while parsing: dsafsdf +184: [21:38:15] SMILES Parse Error: check for mistakes around position 1: +184: [21:38:15] dsafsdf +184: [21:38:15] ^ +184: [21:38:15] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +184: [21:38:15] SMILES Parse Error: syntax error while parsing: dsafsdf +184: [21:38:15] SMILES Parse Error: check for mistakes around position 1: +184: [21:38:15] dsafsdf +184: [21:38:15] ^ +184: [21:38:15] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +184: [21:38:15] SMILES Parse Error: syntax error while parsing: dsafsdf +184: [21:38:15] SMILES Parse Error: check for mistakes around position 1: +184: [21:38:15] dsafsdf +184: [21:38:15] ^ +184: [21:38:15] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +184: [21:38:15] SMILES Parse Error: check for mistakes around position 1: +184: [21:38:15] dsafsdf +184: [21:38:15] ^ +184: [21:38:15] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +184: [21:38:15] SMILES Parse Error: syntax error while parsing: dsafsdf +184: [21:38:15] SMILES Parse Error: check for mistakes around position 1: +184: [21:38:15] dsafsdf +184: [21:38:15] ^ +184: [21:38:15] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +184: [21:38:15] SMILES Parse Error: syntax error while parsing: dsafsdf +184: [21:38:15] SMILES Parse Error: check for mistakes around position 1: +184: [21:38:15] dsafsdf +184: [21:38:15] ^ +184: [21:38:15] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +184: [21:38:15] SMILES Parse Error: syntax error while parsing: dsafsdf +184: [21:38:15] SMILES Parse Error: check for mistakes around position 1: +184: [21:38:15] dsafsdf +184: [21:38:15] ^ +184: [21:38:15] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +184: [21:38:15] SMILES Parse Error: syntax error while parsing: dsafsdf +184: [21:38:15] SMILES Parse Error: check for mistakes around position 1: +184: [21:38:15] dsafsdf +184: [21:38:15] ^ +184: [21:38:15] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +184: [21:38:15] SMILES Parse Error: syntax error while parsing: dsafsdf +184: [21:38:15] SMILES Parse Error: check for mistakes around position 1: +184: [21:38:15] dsafsdf +184: [21:38:15] ^ +184: [21:38:15] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +184: [21:38:15] SMILES Parse Error: syntax error while parsing: dsafsdf +184: [21:38:15] SMILES Parse Error: check for mistakes around position 1: +184: [21:38:15] dsafsdf +184: [21:38:15] ^ +184: [21:38:15] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +184: [21:38:15] SMILES Parse Error: syntax error while parsing: dsafsdf +184: [21:38:15] SMILES Parse Error: check for mistakes around position 1: +184: [21:38:15] dsafsdf +184: [21:38:15] ^ +184: [21:38:15] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +184: [21:38:15] SMILES Parse Error: syntax error while parsing: dsafsdf +184: [21:38:15] SMILES Parse Error: check for mistakes around position 1: +184: [21:38:15] dsafsdf +184: [21:38:15] ^ +184: [21:38:15] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +184: [21:38:15] SMILES Parse Error: syntax error while parsing: dsafsdf +184: [21:38:15] SMILES Parse Error: check for mistakes around position 1: +184: [21:38:15] dsafsdf +184: [21:38:15] ^ +184: [21:38:15] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +184: [21:38:15] SMILES Parse Error: syntax error while parsing: dsafsdf +184: [21:38:15] SMILES Parse Error: check for mistakes around position 1: +184: [21:38:15] dsafsdf +184: [21:38:15] ^ +184: [21:38:15] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +184: [21:38:15] SMILES Parse Error: syntax error while parsing: dsafsdf +184: [21:38:15] SMILES Parse Error: check for mistakes around position 1: +184: [21:38:15] dsafsdf +184: [21:38:15] ^ +184: [21:38:15] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +184: [21:38:15] SMILES Parse Error: syntax error while parsing: dsafsdf +184: [21:38:15] SMILES Parse Error: check for mistakes around position 1: +184: [21:38:15] dsafsdf +184: [21:38:15] ^ +184: [21:38:15] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +184: [21:38:15] SMILES Parse Error: syntax error while parsing: dsafsdf +184: [21:38:15] SMILES Parse Error: check for mistakes around position 1: +184: [21:38:15] dsafsdf +184: [21:38:15] ^ +184: [21:38:15] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +184: [21:38:15] SMILES Parse Error: syntax error while parsing: dsafsdf +184: [21:38:15] SMILES Parse Error: check for mistakes around position 1: +184: [21:38:15] dsafsdf +184: [21:38:15] ^ +184: [21:38:15] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +184: [21:38:15] SMILES Parse Error: syntax error while parsing: dsafsdf +184: [21:38:15] SMILES Parse Error: check for mistakes around position 1: +184: [21:38:15] dsafsdf +184: [21:38:15] ^ +184: [21:38:15] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +184: [21:38:15] SMILES Parse Error: syntax error while parsing: dsafsdf +184: [21:38:15] SMILES Parse Error: check for mistakes around position 1: +184: [21:38:15] dsafsdf +184: [21:38:15] ^ +184: [21:38:15] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +184: [21:38:15] SMILES Parse Error: syntax error while parsing: dsafsdf +184: [21:38:15] SMILES Parse Error: check for mistakes around position 1: +184: [21:38:15] dsafsdf +184: [21:38:15] ^ +184: [21:38:15] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +184: [21:38:15] SMILES Parse Error: syntax error while parsing: dsafsdf +184: [21:38:15] SMILES Parse Error: check for mistakes around position 1: +184: [21:38:15] dsafsdf +184: [21:38:15] ^ +184: [21:38:15] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +184: [21:38:15] SMILES Parse Error: syntax error while parsing: dsafsdf +184: [21:38:15] SMILES Parse Error: check for mistakes around position 1: +184: [21:38:15] dsafsdf +184: [21:38:15] ^ +184: [21:38:15] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +184: [21:38:15] SMILES Parse Error: syntax error while parsing: dsafsdf +184: [21:38:15] SMILES Parse Error: check for mistakes around position 1: +184: [21:38:15] dsafsdf +184: [21:38:15] ^ +184: [21:38:15] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +184: [21:38:15] SMILES Parse Error: syntax error while parsing: dsafsdf +184: [21:38:15] SMILES Parse Error: check for mistakes around position 1: +184: [21:38:15] dsafsdf +184: [21:38:15] ^ +184: [21:38:15] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +184: [21:38:15] SMILES Parse Error: syntax error while parsing: dsafsdf +184: [21:38:15] SMILES Parse Error: check for mistakes around position 1: +184: [21:38:15] dsafsdf +184: [21:38:15] ^ +184: [21:38:15] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +184: [21:38:15] SMILES Parse Error: syntax error while parsing: dsafsdf +184: [21:38:15] SMILES Parse Error: check for mistakes around position 1: +184: [21:38:15] dsafsdf +184: [21:38:15] ^ +184: [21:38:15] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +184: [21:38:15] SMILES Parse Error: syntax error while parsing: dsafsdf +184: [21:38:15] SMILES Parse Error: check for mistakes around position 1: +184: [21:38:15] dsafsdf +184: [21:38:15] ^ +184: [21:38:15] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +184: [21:38:15] SMILES Parse Error: syntax error while parsing: dsafsdf +184: [21:38:15] SMILES Parse Error: check for mistakes around position 1: +184: [21:38:15] dsafsdf +184: [21:38:15] ^ +184: [21:38:15] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +184: [21:38:15] SMILES Parse Error: syntax error while parsing: dsafsdf +184: [21:38:15] SMILES Parse Error: check for mistakes around position 1: +184: [21:38:15] dsafsdf +184: [21:38:15] ^ +184: [21:38:15] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +184: [21:38:15] SMILES Parse Error: syntax error while parsing: dsafsdf +184: [21:38:15] SMILES Parse Error: check for mistakes around position 1: +184: [21:38:15] dsafsdf +184: [21:38:15] ^ +184: [21:38:15] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +184: [21:38:15] SMILES Parse Error: syntax error while parsing: dsafsdf +184: [21:38:15] SMILES Parse Error: check for mistakes around position 1: +184: [21:38:15] dsafsdf +184: [21:38:15] ^ +184: [21:38:15] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +184: [21:38:15] SMILES Parse Error: syntax error while parsing: dsafsdf +184: [21:38:15] SMILES Parse Error: check for mistakes around position 1: +184: [21:38:15] dsafsdf +184: [21:38:15] ^ +184: [21:38:15] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +184: [21:38:15] SMILES Parse Error: syntax error while parsing: dsafsdf +184: [21:38:15] SMILES Parse Error: check for mistakes around position 1: +184: [21:38:15] dsafsdf +184: [21:38:15] ^ +184: [21:38:15] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +184: [21:38:15] SMILES Parse Error: syntax error while parsing: dsafsdf +184: [21:38:15] SMILES Parse Error: check for mistakes around position 1: +184: [21:38:15] dsafsdf +184: [21:38:15] ^ +184: [21:38:15] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +184: [21:38:15] SMILES Parse Error: syntax error while parsing: dsafsdf +184: [21:38:15] SMILES Parse Error: check for mistakes around position 1: +184: [21:38:15] dsafsdf +184: [21:38:15] ^ +184: [21:38:15] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +184: [21:38:15] SMILES Parse Error: syntax error while parsing: dsafsdf +184: [21:38:15] SMILES Parse Error: check for mistakes around position 1: +184: [21:38:15] dsafsdf +184: [21:38:15] ^ +184: [21:38:15] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +184: [21:38:15] SMILES Parse Error: syntax error while parsing: dsafsdf +184: [21:38:15] SMILES Parse Error: check for mistakes around position 1: +184: [21:38:15] dsafsdf +184: [21:38:15] ^ +184: [21:38:15] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +184: [21:38:15] SMILES Parse Error: syntax error while parsing: dsafsdf +184: [21:38:15] SMILES Parse Error: check for mistakes around position 1: +184: [21:38:15] dsafsdf +184: [21:38:15] ^ +184: [21:38:15] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +184: [21:38:15] SMILES Parse Error: syntax error while parsing: dsafsdf +184: [21:38:15] SMILES Parse Error: check for mistakes around position 1: +184: [21:38:15] dsafsdf +184: [21:38:15] ^ +184: [21:38:15] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +184: [21:38:15] SMILES Parse Error: syntax error while parsing: dsafsdf +184: [21:38:15] SMILES Parse Error: check for mistakes around position 1: +184: [21:38:15] dsafsdf +184: [21:38:15] ^ +184: [21:38:15] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +184: [21:38:15] SMILES Parse Error: syntax error while parsing: dsafsdf +184: [21:38:15] SMILES Parse Error: check for mistakes around position 1: +184: [21:38:15] dsafsdf +184: [21:38:15] ^ +184: [21:38:15] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +184: [21:38:15] SMILES Parse Error: syntax error while parsing: dsafsdf +184: [21:38:15] SMILES Parse Error: check for mistakes around position 1: +184: [21:38:15] dsafsdf +184: [21:38:15] ^ +184: [21:38:15] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +184: [21:38:15] SMILES Parse Error: syntax error while parsing: dsafsdf +184: [21:38:15] SMILES Parse Error: check for mistakes around position 1: +184: [21:38:15] dsafsdf +184: [21:38:15] ^ +184: [21:38:15] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +184: [21:38:15] SMILES Parse Error: syntax error while parsing: dsafsdf +184: [21:38:15] SMILES Parse Error: check for mistakes around position 1: +184: [21:38:15] dsafsdf +184: [21:38:15] ^ +184: [21:38:15] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +184: [21:38:15] SMILES Parse Error: syntax error while parsing: dsafsdf +184: [21:38:15] SMILES Parse Error: check for mistakes around position 1: +184: [21:38:15] dsafsdf +184: [21:38:15] ^ +184: [21:38:15] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +184: [21:38:15] SMILES Parse Error: syntax error while parsing: dsafsdf +184: [21:38:15] SMILES Parse Error: check for mistakes around position 1: +184: [21:38:15] dsafsdf +184: [21:38:15] ^ +184: [21:38:15] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +184: [21:38:15] SMILES Parse Error: syntax error while parsing: dsafsdf +184: [21:38:15] SMILES Parse Error: check for mistakes around position 1: +184: [21:38:15] dsafsdf +184: [21:38:15] ^ +184: [21:38:15] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +184: [21:38:15] SMILES Parse Error: syntax error while parsing: dsafsdf +184: [21:38:15] SMILES Parse Error: check for mistakes around position 1: +184: [21:38:15] dsafsdf +184: [21:38:15] ^ +184: [21:38:15] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +184: [21:38:15] SMILES Parse Error: syntax error while parsing: dsafsdf +184: [21:38:15] SMILES Parse Error: check for mistakes around position 1: +184: [21:38:15] dsafsdf +184: [21:38:15] ^ +184: [21:38:15] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +184: [21:38:15] SMILES Parse Error: syntax error while parsing: dsafsdf +184: [21:38:15] SMILES Parse Error: check for mistakes around position 1: +184: [21:38:15] dsafsdf +184: [21:38:15] ^ +184: [21:38:15] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +184: [21:38:15] SMILES Parse Error: syntax error while parsing: dsafsdf +184: [21:38:15] SMILES Parse Error: check for mistakes around position 1: +184: [21:38:15] dsafsdf +184: [21:38:15] ^ +184: [21:38:15] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +184: [21:38:15] SMILES Parse Error: syntax error while parsing: dsafsdf +184: [21:38:15] SMILES Parse Error: check for mistakes around position 1: +184: [21:38:15] dsafsdf +184: [21:38:15] ^ +184: [21:38:15] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +184: [21:38:15] SMILES Parse Error: syntax error while parsing: dsafsdf +184: [21:38:15] SMILES Parse Error: check for mistakes around position 1: +184: [21:38:15] dsafsdf +184: [21:38:15] ^ +184: [21:38:15] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +184: [21:38:15] SMILES Parse Error: syntax error while parsing: dsafsdf +184: [21:38:15] SMILES Parse Error: check for mistakes around position 1: +184: [21:38:15] dsafsdf +184: [21:38:15] ^ +184: [21:38:15] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +184: [21:38:15] SMILES Parse Error: syntax error while parsing: dsafsdf +184: [21:38:15] SMILES Parse Error: check for mistakes around position 1: +184: [21:38:15] dsafsdf +184: [21:38:15] ^ +184: [21:38:15] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +184: [21:38:15] SMILES Parse Error: syntax error while parsing: dsafsdf +184: [21:38:15] SMILES Parse Error: check for mistakes around position 1: +184: [21:38:15] dsafsdf +184: [21:38:15] ^ +184: [21:38:15] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +184: [21:38:15] SMILES Parse Error: syntax error while parsing: dsafsdf +184: [21:38:15] SMILES Parse Error: check for mistakes around position 1: +184: [21:38:15] dsafsdf +184: [21:38:15] ^ +184: [21:38:15] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +184: [21:38:15] SMILES Parse Error: syntax error while parsing: dsafsdf +184: [21:38:15] SMILES Parse Error: check for mistakes around position 1: +184: [21:38:15] dsafsdf +184: [21:38:15] ^ +184: [21:38:15] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +184: [21:38:15] SMILES Parse Error: syntax error while parsing: dsafsdf +184: [21:38:15] SMILES Parse Error: check for mistakes around position 1: +184: [21:38:15] dsafsdf +184: [21:38:15] ^ +184: [21:38:15] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +184: [21:38:15] SMILES Parse Error: syntax error while parsing: dsafsdf +184: [21:38:15] SMILES Parse Error: check for mistakes around position 1: +184: [21:38:15] dsafsdf +184: [21:38:15] ^ +184: [21:38:15] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +184: [21:38:15] SMILES Parse Error: syntax error while parsing: dsafsdf +184: [21:38:15] SMILES Parse Error: check for mistakes around position 1: +184: [21:38:15] dsafsdf +184: [21:38:15] ^ +184: [21:38:15] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +184: [21:38:15] SMILES Parse Error: syntax error while parsing: dsafsdf +184: [21:38:15] SMILES Parse Error: check for mistakes around position 1: +184: [21:38:15] dsafsdf +184: [21:38:15] ^ +184: [21:38:15] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +184: [21:38:15] SMILES Parse Error: syntax error while parsing: dsafsdf +184: [21:38:15] SMILES Parse Error: check for mistakes around position 1: +184: [21:38:15] dsafsdf +184: [21:38:15] ^ +184: [21:38:15] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +184: [21:38:15] SMILES Parse Error: syntax error while parsing: dsafsdf +184: [21:38:15] SMILES Parse Error: check for mistakes around position 1: +184: [21:38:15] dsafsdf +184: [21:38:15] ^ +184: [21:38:15] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +184: [21:38:15] SMILES Parse Error: syntax error while parsing: dsafsdf +184: [21:38:15] SMILES Parse Error: check for mistakes around position 1: +184: [21:38:15] dsafsdf +184: [21:38:15] ^ +184: [21:38:15] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +184: [21:38:15] SMILES Parse Error: syntax error while parsing: dsafsdf +184: [21:38:15] SMILES Parse Error: check for mistakes around position 1: +184: [21:38:15] dsafsdf +184: [21:38:15] ^ +184: [21:38:15] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +184: [21:38:15] SMILES Parse Error: syntax error while parsing: dsafsdf +184: [21:38:15] SMILES Parse Error: check for mistakes around position 1: +184: [21:38:15] dsafsdf +184: [21:38:15] ^ +184: [21:38:15] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +184: [21:38:15] SMILES Parse Error: syntax error while parsing: dsafsdf +184: [21:38:15] SMILES Parse Error: check for mistakes around position 1: +184: [21:38:15] dsafsdf +184: [21:38:15] ^ +184: [21:38:15] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +184: [21:38:15] SMILES Parse Error: syntax error while parsing: dsafsdf +184: [21:38:15] SMILES Parse Error: check for mistakes around position 1: +184: [21:38:15] dsafsdf +184: [21:38:15] ^ +184: [21:38:15] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +184: [21:38:15] SMILES Parse Error: syntax error while parsing: dsafsdf +184: [21:38:15] SMILES Parse Error: check for mistakes around position 1: +184: [21:38:15] dsafsdf +184: [21:38:15] ^ +184: [21:38:15] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +184: [21:38:15] SMILES Parse Error: syntax error while parsing: dsafsdf +184: [21:38:15] SMILES Parse Error: check for mistakes around position 1: +184: [21:38:15] dsafsdf +184: [21:38:15] ^ +184: [21:38:15] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +184: [21:38:15] SMILES Parse Error: syntax error while parsing: dsafsdf +184: [21:38:15] SMILES Parse Error: check for mistakes around position 1: +184: [21:38:15] dsafsdf +184: [21:38:15] ^ +184: [21:38:15] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +184: [21:38:15] SMILES Parse Error: syntax error while parsing: dsafsdf +184: [21:38:15] SMILES Parse Error: check for mistakes around position 1: +184: [21:38:15] dsafsdf +184: [21:38:15] ^ +184: [21:38:15] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +184: [21:38:15] SMILES Parse Error: syntax error while parsing: dsafsdf +184: [21:38:15] SMILES Parse Error: check for mistakes around position 1: +184: [21:38:15] dsafsdf +184: [21:38:15] ^ +184: [21:38:15] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +184: [21:38:15] SMILES Parse Error: syntax error while parsing: dsafsdf +184: [21:38:15] SMILES Parse Error: check for mistakes around position 1: +184: [21:38:15] dsafsdf +184: [21:38:15] ^ +184: [21:38:15] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +184: [21:38:15] SMILES Parse Error: syntax error while parsing: dsafsdf +184: [21:38:15] SMILES Parse Error: check for mistakes around position 1: +184: [21:38:15] dsafsdf +184: [21:38:15] ^ +184: [21:38:15] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +184: [21:38:15] SMILES Parse Error: syntax error while parsing: dsafsdf +184: [21:38:15] SMILES Parse Error: check for mistakes around position 1: +184: [21:38:15] dsafsdf +184: [21:38:15] ^ +184: [21:38:15] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +184: [21:38:15] SMILES Parse Error: syntax error while parsing: dsafsdf +184: [21:38:15] SMILES Parse Error: check for mistakes around position 1: +184: [21:38:15] dsafsdf +184: [21:38:15] ^ +184: [21:38:15] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +184: [21:38:15] SMILES Parse Error: syntax error while parsing: dsafsdf +184: [21:38:15] SMILES Parse Error: check for mistakes around position 1: +184: [21:38:15] dsafsdf +184: [21:38:15] ^ +184: [21:38:15] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +184: [21:38:15] SMILES Parse Error: syntax error while parsing: dsafsdf +184: [21:38:15] SMILES Parse Error: check for mistakes around position 1: +184: [21:38:15] dsafsdf +184: [21:38:15] ^ +184: [21:38:15] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +184: [21:38:15] SMILES Parse Error: syntax error while parsing: dsafsdf +184: [21:38:15] SMILES Parse Error: check for mistakes around position 1: +184: [21:38:15] dsafsdf +184: [21:38:15] ^ +184: [21:38:15] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +184: [21:38:15] SMILES Parse Error: syntax error while parsing: dsafsdf +184: [21:38:15] SMILES Parse Error: check for mistakes around position 1: +184: [21:38:15] dsafsdf +184: [21:38:15] ^ +184: [21:38:15] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +184: [21:38:15] SMILES Parse Error: syntax error while parsing: dsafsdf +184: [21:38:15] SMILES Parse Error: check for mistakes around position 1: +184: [21:38:15] dsafsdf +184: [21:38:15] ^ +184: [21:38:15] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +184: [21:38:15] SMILES Parse Error: syntax error while parsing: dsafsdf +184: [21:38:15] SMILES Parse Error: check for mistakes around position 1: +184: [21:38:15] dsafsdf +184: [21:38:15] ^ +184: [21:38:15] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +184: [21:38:15] SMILES Parse Error: syntax error while parsing: dsafsdf +184: [21:38:15] SMILES Parse Error: check for mistakes around position 1: +184: [21:38:15] dsafsdf +184: [21:38:15] ^ +184: [21:38:15] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +184: [21:38:15] SMILES Parse Error: syntax error while parsing: dsafsdf +184: [21:38:15] SMILES Parse Error: check for mistakes around position 1: +184: [21:38:15] dsafsdf +184: [21:38:15] ^ +184: [21:38:15] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +184: [21:38:15] SMILES Parse Error: syntax error while parsing: dsafsdf +184: [21:38:15] SMILES Parse Error: check for mistakes around position 1: +184: [21:38:15] dsafsdf +184: [21:38:15] ^ +184: [21:38:15] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +184: [21:38:15] SMILES Parse Error: syntax error while parsing: dsafsdf +184: [21:38:15] SMILES Parse Error: check for mistakes around position 1: +184: [21:38:15] dsafsdf +184: [21:38:15] ^ +184: [21:38:15] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +184: [21:38:15] SMILES Parse Error: syntax error while parsing: dsafsdf +184: [21:38:15] SMILES Parse Error: check for mistakes around position 1: +184: [21:38:15] dsafsdf +184: [21:38:15] ^ +184: [21:38:15] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +184: [21:38:15] SMILES Parse Error: syntax error while parsing: dsafsdf +184: [21:38:15] SMILES Parse Error: check for mistakes around position 1: +184: [21:38:15] dsafsdf +184: [21:38:15] ^ +184: [21:38:15] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +184: [21:38:15] SMILES Parse Error: syntax error while parsing: dsafsdf +184: [21:38:15] SMILES Parse Error: check for mistakes around position 1: +184: [21:38:15] dsafsdf +184: [21:38:15] ^ +184: [21:38:15] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +184: [21:38:15] SMILES Parse Error: syntax error while parsing: dsafsdf +184: [21:38:15] SMILES Parse Error: check for mistakes around position 1: +184: [21:38:15] dsafsdf +184: [21:38:15] ^ +184: [21:38:15] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +184: [21:38:15] SMILES Parse Error: syntax error while parsing: dsafsdf +184: [21:38:15] SMILES Parse Error: check for mistakes around position 1: +184: [21:38:15] dsafsdf +184: [21:38:15] ^ +184: [21:38:15] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +184: [21:38:15] SMILES Parse Error: syntax error while parsing: dsafsdf +184: [21:38:15] SMILES Parse Error: check for mistakes around position 1: +184: [21:38:15] dsafsdf +184: [21:38:15] ^ +184: [21:38:15] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +184: [21:38:15] SMILES Parse Error: syntax error while parsing: dsafsdf +184: [21:38:15] SMILES Parse Error: check for mistakes around position 1: +184: [21:38:15] dsafsdf +184: [21:38:15] ^ +184: [21:38:15] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +184: [21:38:15] SMILES Parse Error: syntax error while parsing: dsafsdf +184: [21:38:15] SMILES Parse Error: check for mistakes around position 1: +184: [21:38:15] dsafsdf +184: [21:38:15] ^ +184: [21:38:15] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +184: [21:38:15] SMILES Parse Error: syntax error while parsing: dsafsdf +184: [21:38:15] SMILES Parse Error: check for mistakes around position 1: +184: [21:38:15] dsafsdf +184: [21:38:15] ^ +184: [21:38:15] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +184: [21:38:15] SMILES Parse Error: syntax error while parsing: dsafsdf +184: [21:38:15] SMILES Parse Error: check for mistakes around position 1: +184: [21:38:15] dsafsdf +184: [21:38:15] ^ +184: [21:38:15] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +184: [21:38:15] SMILES Parse Error: syntax error while parsing: dsafsdf +184: [21:38:15] SMILES Parse Error: check for mistakes around position 1: +184: [21:38:15] dsafsdf +184: [21:38:15] ^ +184: [21:38:15] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +184: [21:38:15] SMILES Parse Error: syntax error while parsing: dsafsdf +184: [21:38:15] SMILES Parse Error: check for mistakes around position 1: +184: [21:38:15] dsafsdf +184: [21:38:15] ^ +184: [21:38:15] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +184: [21:38:15] SMILES Parse Error: syntax error while parsing: dsafsdf +184: [21:38:15] SMILES Parse Error: check for mistakes around position 1: +184: [21:38:15] dsafsdf +184: [21:38:15] ^ +184: [21:38:15] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +184: [21:38:15] SMILES Parse Error: syntax error while parsing: dsafsdf +184: [21:38:15] SMILES Parse Error: check for mistakes around position 1: +184: [21:38:15] dsafsdf +184: [21:38:15] ^ +184: [21:38:15] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +184: [21:38:15] SMILES Parse Error: syntax error while parsing: dsafsdf +184: [21:38:15] SMILES Parse Error: check for mistakes around position 1: +184: [21:38:15] dsafsdf +184: [21:38:15] ^ +184: [21:38:15] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +184: [21:38:15] SMILES Parse Error: syntax error while parsing: dsafsdf +184: [21:38:15] SMILES Parse Error: check for mistakes around position 1: +184: [21:38:15] dsafsdf +184: [21:38:15] ^ +184: [21:38:15] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +184: [21:38:15] SMILES Parse Error: syntax error while parsing: dsafsdf +184: [21:38:15] SMILES Parse Error: check for mistakes around position 1: +184: [21:38:15] dsafsdf +184: [21:38:15] ^ +184: [21:38:15] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +184: [21:38:15] SMILES Parse Error: syntax error while parsing: dsafsdf +184: [21:38:15] SMILES Parse Error: check for mistakes around position 1: +184: [21:38:15] dsafsdf +184: [21:38:15] ^ +184: [21:38:15] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +184: [21:38:15] ------------------------------------- +184: [21:38:15] Results do not depend on numThreads 150: --------------------------------- 150: test getO3AForProbeConfs 150: 150: *********************************************************** -176/236 Test #150: testO3AAlign ........................... Passed 23.51 sec +175/236 Test #150: testO3AAlign ........................... Passed 41.06 sec +test 187 + Start 187: testRGroupDecomp + +187: Test command: /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/GraphMol/RGroupDecomposition/testRGroupDecomp +187: Working Directory: /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/GraphMol/RGroupDecomposition +187: Test timeout computed to be: 1500 +184: [21:38:19] ------------------------------------- +184: [21:38:19] Results do not depend on numThreads (all same) +187: [21:38:19] Non terminal R group defined. To allow set allowNonTerminalRGroups in RGroupDecompositionParameters +187: [21:38:19] WARNING: not removing hydrogen atom with dummy atom neighbors +184: [21:38:19] ------------------------------------- +184: [21:38:19] testTautomerQueries +184: [21:38:20] Pattern fingerprints for tautomersearch aren't tautomer fingerprints, ignoring... +184: [21:38:20] ------------------------------------- +184: [21:38:20] github3881 recursive smarts with rings +176/236 Test #184: substructLibraryTest ................... Passed 11.34 sec test 188 Start 188: testRGroupDecompInternals 188: Test command: /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/GraphMol/RGroupDecomposition/testRGroupDecompInternals 188: Working Directory: /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/GraphMol/RGroupDecomposition 188: Test timeout computed to be: 1500 -188: [12:43:05] WARNING: not removing hydrogen atom with dummy atom neighbors -188: [12:43:05] WARNING: not removing hydrogen atom with dummy atom neighbors -188: [12:43:05] WARNING: not removing hydrogen atom with dummy atom neighbors -188: [12:43:05] WARNING: not removing hydrogen atom with dummy atom neighbors -188: [12:43:05] WARNING: not removing hydrogen atom with dummy atom neighbors -188: [12:43:05] WARNING: not removing hydrogen atom with dummy atom neighbors -188: [12:43:05] WARNING: not removing hydrogen atom with dummy atom neighbors -188: [12:43:05] WARNING: not removing hydrogen atom with dummy atom neighbors -188: [12:43:05] WARNING: not removing hydrogen atom with dummy atom neighbors -188: [12:43:05] WARNING: not removing hydrogen atom with dummy atom neighbors -188: [12:43:05] WARNING: not removing hydrogen atom with dummy atom neighbors -188: [12:43:05] WARNING: not removing hydrogen atom with dummy atom neighbors -188: [12:43:05] WARNING: not removing hydrogen atom with dummy atom neighbors -188: [12:43:05] WARNING: not removing hydrogen atom with dummy atom neighbors -188: [12:43:05] WARNING: not removing hydrogen atom with dummy atom neighbors -188: [12:43:05] WARNING: not removing hydrogen atom with dummy atom neighbors -188: [12:43:05] WARNING: not removing hydrogen atom with dummy atom neighbors -188: [12:43:05] WARNING: not removing hydrogen atom with dummy atom neighbors -188: [12:43:05] WARNING: not removing hydrogen atom with dummy atom neighbors -188: [12:43:05] WARNING: not removing hydrogen atom with dummy atom neighbors -188: [12:43:05] WARNING: not removing hydrogen atom with dummy atom neighbors +188: [21:38:20] WARNING: not removing hydrogen atom with dummy atom neighbors +188: [21:38:20] WARNING: not removing hydrogen atom with dummy atom neighbors +188: [21:38:20] WARNING: not removing hydrogen atom with dummy atom neighbors +188: [21:38:20] WARNING: not removing hydrogen atom with dummy atom neighbors +188: [21:38:20] WARNING: not removing hydrogen atom with dummy atom neighbors +188: [21:38:20] WARNING: not removing hydrogen atom with dummy atom neighbors +188: [21:38:20] WARNING: not removing hydrogen atom with dummy atom neighbors +188: [21:38:20] WARNING: not removing hydrogen atom with dummy atom neighbors +188: [21:38:20] WARNING: not removing hydrogen atom with dummy atom neighbors +188: [21:38:20] WARNING: not removing hydrogen atom with dummy atom neighbors +188: [21:38:20] WARNING: not removing hydrogen atom with dummy atom neighbors +188: [21:38:20] WARNING: not removing hydrogen atom with dummy atom neighbors +188: [21:38:20] WARNING: not removing hydrogen atom with dummy atom neighbors +188: [21:38:20] WARNING: not removing hydrogen atom with dummy atom neighbors +188: [21:38:20] WARNING: not removing hydrogen atom with dummy atom neighbors +188: [21:38:20] WARNING: not removing hydrogen atom with dummy atom neighbors +188: [21:38:20] WARNING: not removing hydrogen atom with dummy atom neighbors +188: [21:38:20] WARNING: not removing hydrogen atom with dummy atom neighbors +188: [21:38:20] WARNING: not removing hydrogen atom with dummy atom neighbors +188: [21:38:20] WARNING: not removing hydrogen atom with dummy atom neighbors +188: [21:38:20] WARNING: not removing hydrogen atom with dummy atom neighbors 177/236 Test #188: testRGroupDecompInternals .............. Passed 0.06 sec test 189 Start 189: rgroupCatchTests @@ -32484,85 +32514,81 @@ 189: Test command: /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/GraphMol/RGroupDecomposition/rgroupCatchTests 189: Working Directory: /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/GraphMol/RGroupDecomposition 189: Test timeout computed to be: 1500 -187: bulk -189: Randomness seeded to: 4196935879 +189: Randomness seeded to: 1559517221 189: =============================================================================== 189: All tests passed (1475 assertions in 14 test cases) 189: -178/236 Test #189: rgroupCatchTests ....................... Passed 0.35 sec +178/236 Test #189: rgroupCatchTests ....................... Passed 0.34 sec test 190 Start 190: pyRGroupDecomposition 190: Test command: /usr/bin/python3 "/build/reproducible-path/rdkit-202409.4/Code/GraphMol/RGroupDecomposition/Wrap/test_rgroups.py" 190: Working Directory: /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/GraphMol/RGroupDecomposition/Wrap 190: Test timeout computed to be: 1500 -147: [12:43:06] UFFTYPER: Unrecognized atom type: S_6+6 (0) -147: [12:43:06] UFFTYPER: Warning: hybridization set to SP3 for atom 0 -147: [12:43:06] UFFTYPER: Unrecognized charge state for atom: 0 -174: [12:43:07] Building the fingerprints may take some time. -184: [12:43:07] ------------------------------------- -184: [12:43:07] Results do not depend on numThreads (all same) +187: iterative 190: .................... 190: ---------------------------------------------------------------------- -190: Ran 20 tests in 1.180s +190: Ran 20 tests in 1.511s 190: 190: OK -179/236 Test #190: pyRGroupDecomposition .................. Passed 1.62 sec +174: [21:38:22] Building the fingerprints may take some time. +187: bulk +179/236 Test #190: pyRGroupDecomposition .................. Passed 1.96 sec test 191 Start 191: molInterchangeTest1 191: Test command: /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/GraphMol/MolInterchange/molInterchangeTest1 191: Working Directory: /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/GraphMol/MolInterchange 191: Test timeout computed to be: 1500 -191: [12:43:07] test1: basics -191: [12:43:07] done -191: [12:43:07] test2: basic writing +191: [21:38:22] test1: basics +191: [21:38:22] done +191: [21:38:22] test2: basic writing 191: {"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":"2024.09.4","cipRanks":[0,0]}]}]} 191: {"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":"2024.09.4","cipRanks":[3,1,4,2,0],"cipCodes":[[1,"S"]]}]}]} 191: {"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":"2024.09.4","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]]}]}]} 191: {"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":"2024.09.4","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]]}]}]} -191: [12:43:07] done -191: [12:43:07] test3: writing conformers +191: [21:38:22] done +191: [21:38:22] test3: writing conformers 191: {"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":"2024.09.4","cipCodes":[[1,"S"]]},{"name":"partialCharges","generator":"RDKit","formatVersion":10,"generatorVersion":"2024.09.4","values":[-0.352,0.273,-0.055,-0.198,0.215,0.117]}]}]} -191: [12:43:07] done -191: [12:43:07] test4: writing properties +191: [21:38:22] done +191: [21:38:22] test4: writing properties 191: {"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":"2024.09.4","cipRanks":[0,0]}]}]} -191: [12:43:07] done -191: [12:43:07] test5: writing partial charges +191: [21:38:22] done +191: [21:38:22] test5: writing partial charges 191: {"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":"2024.09.4","cipRanks":[0,1]},{"name":"partialCharges","generator":"RDKit","formatVersion":10,"generatorVersion":"2024.09.4","values":[0.5,-0.5]}]}]} -191: [12:43:07] testing parse options -191: [12:43:07] done -191: [12:43:07] testing github #2046: CIPRank values from JSONDataToMols are not unsigned +191: [21:38:22] testing parse options +191: [21:38:22] done +191: [21:38:22] testing github #2046: CIPRank values from JSONDataToMols are not unsigned 191: {"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":"2024.09.4","cipRanks":[1,0,2,4,3,5],"cipCodes":[[4,"S"]],"atomRings":[[0,1,2,3,4]]}]}]} -191: [12:43:07] done -191: [12:43:07] testing 'either' stereochemistry -191: [12:43:07] done -180/236 Test #191: molInterchangeTest1 .................... Passed 0.02 sec +191: [21:38:22] done +191: [21:38:22] testing 'either' stereochemistry +191: [21:38:22] done +180/236 Test #191: molInterchangeTest1 .................... Passed 0.04 sec test 192 Start 192: molInterchangeCatchTest 192: Test command: /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/GraphMol/MolInterchange/molInterchangeCatchTest 192: Working Directory: /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/GraphMol/MolInterchange 192: Test timeout computed to be: 1500 -192: Randomness seeded to: 3501657170 -192: [12:43:07] unrecognized bond type 12 set to zero while writing -192: [12:43:07] unrecognized bond type 0 set to zero while writing +192: Randomness seeded to: 390736968 +192: [21:38:22] unrecognized bond type 12 set to zero while writing +192: [21:38:22] unrecognized bond type 0 set to zero while writing 192: =============================================================================== 192: All tests passed (125 assertions in 7 test cases) 192: -181/236 Test #192: molInterchangeCatchTest ................ Passed 0.02 sec +181/236 Test #192: molInterchangeCatchTest ................ Passed 0.08 sec test 193 Start 193: pyMolInterchange 193: Test command: /usr/bin/python3 "/build/reproducible-path/rdkit-202409.4/Code/GraphMol/MolInterchange/Wrap/testMolInterchange.py" 193: Working Directory: /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/GraphMol/MolInterchange/Wrap 193: Test timeout computed to be: 1500 -184: [12:43:07] ------------------------------------- -184: [12:43:07] testTautomerQueries -184: [12:43:07] Pattern fingerprints for tautomersearch aren't tautomer fingerprints, ignoring... -184: [12:43:07] ------------------------------------- -184: [12:43:07] github3881 recursive smarts with rings -182/236 Test #184: substructLibraryTest ................... Passed 8.87 sec +193: .. +193: ---------------------------------------------------------------------- +193: Ran 2 tests in 0.015s +193: +193: OK +182/236 Test #193: pyMolInterchange ....................... Passed 0.50 sec test 194 Start 194: testSLNParse @@ -32582,34 +32608,35 @@ 194: 2 0->3 order: 1 194: 3 0->4 order: 1 194: 4 0->5 order: 1 -194: [12:43:07] SLN Parse Error: syntax error while parsing: CH4[I=13] -194: [12:43:07] Failed parsing SLN 'CH4[I=13]' -194: [12:43:07] SLN Parser error: Atom ID 1 appears *after* its ring closure. -194: [12:43:07] SLN Parser error: Ring closure 1 does not have a corresponding opener. -194: [12:43:07] SLN Parse Error: syntax error while parsing: CH2(C@1H2)CH2(CH2CH2C[1]H2) -194: [12:43:07] Failed parsing SLN 'CH2(C@1H2)CH2(CH2CH2C[1]H2)' -194: [12:43:07] SLN Parse Error: syntax error while parsing: CH2(CH2[1])CH2(CH2CH2CH2@1) -194: [12:43:07] Failed parsing SLN 'CH2(CH2[1])CH2(CH2CH2CH2@1)' -194: [12:43:07] SLN Parse Error: syntax error while parsing: CH4 fff -194: [12:43:07] Failed parsing SLN 'CH4 fff' -194: [12:43:07] SLN Parse Error: syntax error while parsing: C[charge=+1] foo -194: [12:43:07] Failed parsing SLN 'C[charge=+1] foo' -194: [12:43:07] Query property 'is' ignored on non-query atom -194: [12:43:07] Query property 'is' ignored on non-query atom +194: [21:38:23] SLN Parse Error: syntax error while parsing: CH4[I=13] +194: [21:38:23] Failed parsing SLN 'CH4[I=13]' +194: [21:38:23] SLN Parser error: Atom ID 1 appears *after* its ring closure. +194: [21:38:23] SLN Parser error: Ring closure 1 does not have a corresponding opener. +194: [21:38:23] SLN Parse Error: syntax error while parsing: CH2(C@1H2)CH2(CH2CH2C[1]H2) +194: [21:38:23] Failed parsing SLN 'CH2(C@1H2)CH2(CH2CH2C[1]H2)' +194: [21:38:23] SLN Parse Error: syntax error while parsing: CH2(CH2[1])CH2(CH2CH2CH2@1) +194: [21:38:23] Failed parsing SLN 'CH2(CH2[1])CH2(CH2CH2CH2@1)' +33: [21:38:23] Finished +194: [21:38:23] SLN Parse Error: syntax error while parsing: CH4 fff +194: [21:38:23] Failed parsing SLN 'CH4 fff' +194: [21:38:23] SLN Parse Error: syntax error while parsing: C[charge=+1] foo +194: [21:38:23] Failed parsing SLN 'C[charge=+1] foo' +194: [21:38:23] Query property 'is' ignored on non-query atom +194: [21:38:23] Query property 'is' ignored on non-query atom +33: [21:38:23] ------------------------------------- 183/236 Test #194: testSLNParse ........................... Passed 0.05 sec +33: [21:38:23] Test github1843: RWMol.clear() should not destroy ring pointer. +33: [21:38:23] Finished +33: [21:38:23] ------------------------------------- +33: [21:38:23] Test Github 6370: non-physical radical counts being preserved test 195 Start 195: pySLNParse 195: Test command: /usr/bin/python3 "/build/reproducible-path/rdkit-202409.4/Code/GraphMol/SLNParse/Wrap/testSLN.py" 195: Working Directory: /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/GraphMol/SLNParse/Wrap 195: Test timeout computed to be: 1500 -193: .. -193: ---------------------------------------------------------------------- -193: Ran 2 tests in 0.007s -193: -193: OK -187: bulk, no symmetry -184/236 Test #193: pyMolInterchange ....................... Passed 0.23 sec +33: [21:38:23] Finished +184/236 Test #33: graphmolTest1 .......................... Passed 55.79 sec test 196 Start 196: pyGraphMolWrap @@ -32621,49 +32648,55 @@ 195: Ran 2 tests in 0.014s 195: 195: OK -187: [12:43:08] Relabelling existing label -196: ..............[12:43:08] SMARTS Parse Error: syntax error while parsing: fiib -196: [12:43:08] SMARTS Parse Error: Failed parsing SMARTS 'fiib' for input: 'fiib' -196: ....[12:43:08] ERROR: Problems encountered parsing data fields -196: [12:43:08] ERROR: moving to the beginning of the next molecule -196: [12:43:08] ERROR: Problems encountered parsing data fields -196: [12:43:08] ERROR: moving to the beginning of the next molecule -196: [12:43:08] Spurious data before the first property will be ignored -196: [12:43:08] Property will be truncated after the first blank line -196: [12:43:08] Property will be truncated after the first blank line -196: [12:43:08] Property will be truncated after the first blank line -196: [12:43:08] ERROR: Problems encountered parsing data fields -196: [12:43:08] ERROR: moving to the beginning of the next molecule -196: [12:43:08] ERROR: Problems encountered parsing data fields -196: [12:43:08] ERROR: moving to the beginning of the next molecule -196: [12:43:08] Spurious data before the first property will be ignored -196: [12:43:08] Property will be truncated after the first blank line -196: [12:43:08] Property will be truncated after the first blank line -196: [12:43:08] Property will be truncated after the first blank line -196: [12:43:08] ERROR: Problems encountered parsing data fields -196: [12:43:08] ERROR: moving to the beginning of the next molecule -196: [12:43:08] Property will be truncated after the first blank line -196: [12:43:08] ERROR: Problems encountered parsing data fields -196: [12:43:08] ERROR: moving to the beginning of the next molecule -196: [12:43:08] Property will be truncated after the first blank line -196: .[12:43:08] SMILES Parse Error: syntax error while parsing: fail -196: [12:43:08] SMILES Parse Error: check for mistakes around position 1: -196: [12:43:08] fail -196: [12:43:08] ^ -196: [12:43:08] SMILES Parse Error: Failed parsing SMILES 'fail' for input: 'fail' -196: [12:43:08] ERROR: Smiles parse error on line 2 -196: [12:43:08] ERROR: Cannot create molecule from : 'fail' +185/236 Test #195: pySLNParse ............................. Passed 0.50 sec +test 197 + Start 197: pyTestConformerWrap + +197: Test command: /usr/bin/python3 "/build/reproducible-path/rdkit-202409.4/Code/GraphMol/Wrap/testConformer.py" +197: Working Directory: /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/GraphMol/Wrap +197: Test timeout computed to be: 1500 +196: ..............[21:38:23] SMARTS Parse Error: syntax error while parsing: fiib +196: [21:38:23] SMARTS Parse Error: Failed parsing SMARTS 'fiib' for input: 'fiib' +196: ....[21:38:23] ERROR: Problems encountered parsing data fields +196: [21:38:23] ERROR: moving to the beginning of the next molecule +196: [21:38:23] ERROR: Problems encountered parsing data fields +196: [21:38:23] ERROR: moving to the beginning of the next molecule +196: [21:38:23] Spurious data before the first property will be ignored +196: [21:38:23] Property will be truncated after the first blank line +196: [21:38:23] Property will be truncated after the first blank line +196: [21:38:23] Property will be truncated after the first blank line +196: [21:38:23] ERROR: Problems encountered parsing data fields +196: [21:38:23] ERROR: moving to the beginning of the next molecule +196: [21:38:23] ERROR: Problems encountered parsing data fields +196: [21:38:23] ERROR: moving to the beginning of the next molecule +196: [21:38:23] Spurious data before the first property will be ignored +196: [21:38:23] Property will be truncated after the first blank line +196: [21:38:23] Property will be truncated after the first blank line +196: [21:38:23] Property will be truncated after the first blank line +196: [21:38:23] ERROR: Problems encountered parsing data fields +196: [21:38:23] ERROR: moving to the beginning of the next molecule +196: [21:38:23] Property will be truncated after the first blank line +196: [21:38:23] ERROR: Problems encountered parsing data fields +196: [21:38:23] ERROR: moving to the beginning of the next molecule +196: [21:38:23] Property will be truncated after the first blank line +196: .[21:38:23] SMILES Parse Error: syntax error while parsing: fail +196: [21:38:23] SMILES Parse Error: check for mistakes around position 1: +196: [21:38:23] fail +196: [21:38:23] ^ +196: [21:38:23] SMILES Parse Error: Failed parsing SMILES 'fail' for input: 'fail' +196: [21:38:23] ERROR: Smiles parse error on line 2 +196: [21:38:23] ERROR: Cannot create molecule from : 'fail' 196: >>> This may result in an infinite loop. It should finish almost instantly 196: <<< OK, it finished. -196: ............[12:43:08] Explicit valence for atom # 1 C, 5, is greater than permitted -196: ......[12:43:08] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -196: [12:43:08] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -196: [12:43:08] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -196: [12:43:08] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +196: ............[21:38:23] Explicit valence for atom # 1 C, 5, is greater than permitted +196: ......[21:38:23] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +196: [21:38:23] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +196: [21:38:23] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +196: [21:38:23] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 196: .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)| -196: ........[12:43:08] non-ring atom 0 marked aromatic -196: [12:43:08] non-ring atom 0 marked aromatic -196: [12:43:08] +196: ........[21:38:23] non-ring atom 0 marked aromatic +196: [21:38:23] non-ring atom 0 marked aromatic +196: [21:38:23] 196: 196: **** 196: Range Error @@ -32676,9 +32709,9 @@ 196: 1# Invar::operator<<(std::ostream&, Invar::Invariant const&) in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu//lib/libRDKitRDGeneral.so.1 196: 2# RDKit::ROMol::getAtomWithIdx(unsigned int) in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu//lib/libRDKitGraphMol.so.1 196: 3# RDKit::RWMol::removeAtom(unsigned int) in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu//lib/libRDKitGraphMol.so.1 -196: 4# 0x0000FFFFBA6C6970 in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so +196: 4# 0x0000FFFFA5616970 in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so 196: 5# boost::python::objects::function::call(_object*, _object*) const in /lib/aarch64-linux-gnu/libboost_python313.so.1.83.0 -196: 6# 0x0000FFFFBCB72680 in /lib/aarch64-linux-gnu/libboost_python313.so.1.83.0 +196: 6# 0x0000FFFFA7AC2680 in /lib/aarch64-linux-gnu/libboost_python313.so.1.83.0 196: 7# boost::python::detail::exception_handler::operator()(boost::function0 const&) const in /lib/aarch64-linux-gnu/libboost_python313.so.1.83.0 196: 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-202409.4/obj-aarch64-linux-gnu/rdkit/Chem/rdSLNParse.so 196: 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-202409.4/obj-aarch64-linux-gnu/rdkit/Chem/rdChemReactions.so @@ -32689,17 +32722,17 @@ 196: 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-202409.4/obj-aarch64-linux-gnu/rdkit/Chem/rdmolfiles.so 196: 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-202409.4/obj-aarch64-linux-gnu/rdkit/Chem/rdCIPLabeler.so 196: 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-202409.4/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so -196: 17# 0x0000FFFFBA5F9FA0 in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so -196: 18# 0x0000FFFFBA5F9F38 in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so -196: 19# 0x0000FFFFBA5F9EC8 in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so -196: 20# 0x0000FFFFBA5F9E60 in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so -196: 21# 0x0000FFFFBA5F9DF8 in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so +196: 17# 0x0000FFFFA5549FA0 in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so +196: 18# 0x0000FFFFA5549F38 in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so +196: 19# 0x0000FFFFA5549EC8 in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so +196: 20# 0x0000FFFFA5549E60 in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so +196: 21# 0x0000FFFFA5549DF8 in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so 196: 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-202409.4/obj-aarch64-linux-gnu/rdkit/rdBase.so 196: 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-202409.4/obj-aarch64-linux-gnu/rdkit/rdBase.so 196: 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-202409.4/obj-aarch64-linux-gnu/rdkit/rdBase.so 196: 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-202409.4/obj-aarch64-linux-gnu/rdkit/rdBase.so 196: 26# boost::python::handle_exception_impl(boost::function0) in /lib/aarch64-linux-gnu/libboost_python313.so.1.83.0 -196: 27# 0x0000FFFFBCB6F25C in /lib/aarch64-linux-gnu/libboost_python313.so.1.83.0 +196: 27# 0x0000FFFFA7ABF25C in /lib/aarch64-linux-gnu/libboost_python313.so.1.83.0 196: 28# _PyObject_MakeTpCall in /usr/bin/python3 196: 29# _PyEval_EvalFrameDefault in /usr/bin/python3 196: 30# 0x000000000052F1D8 in /usr/bin/python3 @@ -32731,15 +32764,15 @@ 196: 56# 0x0000000000621C6C in /usr/bin/python3 196: 57# Py_RunMain in /usr/bin/python3 196: 58# Py_BytesMain in /usr/bin/python3 -196: 59# 0x0000FFFFBD98229C in /lib/aarch64-linux-gnu/libc.so.6 +196: 59# 0x0000FFFFA88D229C in /lib/aarch64-linux-gnu/libc.so.6 196: 60# __libc_start_main in /lib/aarch64-linux-gnu/libc.so.6 196: 61# _start in /usr/bin/python3 196: ---------- 196: **** 196: -196: [12:43:08] non-ring atom 0 marked aromatic -196: [12:43:08] non-ring atom 0 marked aromatic -196: [12:43:08] +196: [21:38:23] non-ring atom 0 marked aromatic +196: [21:38:23] non-ring atom 0 marked aromatic +196: [21:38:23] 196: 196: **** 196: Range Error @@ -32752,9 +32785,9 @@ 196: 1# Invar::operator<<(std::ostream&, Invar::Invariant const&) in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu//lib/libRDKitRDGeneral.so.1 196: 2# RDKit::ROMol::getAtomWithIdx(unsigned int) in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu//lib/libRDKitGraphMol.so.1 196: 3# RDKit::RWMol::removeAtom(unsigned int) in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu//lib/libRDKitGraphMol.so.1 -196: 4# 0x0000FFFFBA6C6970 in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so +196: 4# 0x0000FFFFA5616970 in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so 196: 5# boost::python::objects::function::call(_object*, _object*) const in /lib/aarch64-linux-gnu/libboost_python313.so.1.83.0 -196: 6# 0x0000FFFFBCB72680 in /lib/aarch64-linux-gnu/libboost_python313.so.1.83.0 +196: 6# 0x0000FFFFA7AC2680 in /lib/aarch64-linux-gnu/libboost_python313.so.1.83.0 196: 7# boost::python::detail::exception_handler::operator()(boost::function0 const&) const in /lib/aarch64-linux-gnu/libboost_python313.so.1.83.0 196: 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-202409.4/obj-aarch64-linux-gnu/rdkit/Chem/rdSLNParse.so 196: 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-202409.4/obj-aarch64-linux-gnu/rdkit/Chem/rdChemReactions.so @@ -32765,17 +32798,17 @@ 196: 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-202409.4/obj-aarch64-linux-gnu/rdkit/Chem/rdmolfiles.so 196: 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-202409.4/obj-aarch64-linux-gnu/rdkit/Chem/rdCIPLabeler.so 196: 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-202409.4/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so -196: 17# 0x0000FFFFBA5F9FA0 in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so -196: 18# 0x0000FFFFBA5F9F38 in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so -196: 19# 0x0000FFFFBA5F9EC8 in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so -196: 20# 0x0000FFFFBA5F9E60 in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so -196: 21# 0x0000FFFFBA5F9DF8 in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so +196: 17# 0x0000FFFFA5549FA0 in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so +196: 18# 0x0000FFFFA5549F38 in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so +196: 19# 0x0000FFFFA5549EC8 in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so +196: 20# 0x0000FFFFA5549E60 in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so +196: 21# 0x0000FFFFA5549DF8 in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so 196: 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-202409.4/obj-aarch64-linux-gnu/rdkit/rdBase.so 196: 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-202409.4/obj-aarch64-linux-gnu/rdkit/rdBase.so 196: 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-202409.4/obj-aarch64-linux-gnu/rdkit/rdBase.so 196: 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-202409.4/obj-aarch64-linux-gnu/rdkit/rdBase.so 196: 26# boost::python::handle_exception_impl(boost::function0) in /lib/aarch64-linux-gnu/libboost_python313.so.1.83.0 -196: 27# 0x0000FFFFBCB6F25C in /lib/aarch64-linux-gnu/libboost_python313.so.1.83.0 +196: 27# 0x0000FFFFA7ABF25C in /lib/aarch64-linux-gnu/libboost_python313.so.1.83.0 196: 28# _PyObject_MakeTpCall in /usr/bin/python3 196: 29# _PyEval_EvalFrameDefault in /usr/bin/python3 196: 30# 0x000000000052F1D8 in /usr/bin/python3 @@ -32807,45 +32840,33 @@ 196: 56# 0x0000000000621C6C in /usr/bin/python3 196: 57# Py_RunMain in /usr/bin/python3 196: 58# Py_BytesMain in /usr/bin/python3 -196: 59# 0x0000FFFFBD98229C in /lib/aarch64-linux-gnu/libc.so.6 +196: 59# 0x0000FFFFA88D229C in /lib/aarch64-linux-gnu/libc.so.6 196: 60# __libc_start_main in /lib/aarch64-linux-gnu/libc.so.6 196: 61# _start in /usr/bin/python3 196: ---------- 196: **** 196: -185/236 Test #195: pySLNParse ............................. Passed 0.49 sec -test 197 - Start 197: pyTestConformerWrap - -197: Test command: /usr/bin/python3 "/build/reproducible-path/rdkit-202409.4/Code/GraphMol/Wrap/testConformer.py" -197: Working Directory: /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/GraphMol/Wrap -197: Test timeout computed to be: 1500 -196: ...............[12:43:08] WARNING: the onlyHeavy argument to mol.GetNumAtoms() has been deprecated. Please use the onlyExplicit argument instead or mol.GetNumHeavyAtoms() if you want the heavy atom count. -196: [12:43:08] WARNING: the onlyHeavy argument to mol.GetNumAtoms() has been deprecated. Please use the onlyExplicit argument instead or mol.GetNumHeavyAtoms() if you want the heavy atom count. -196: ..............[12:43:08] Can't kekulize mol. Unkekulized atoms: 0 1 2 3 4 -196: [12:43:08] Explicit valence for atom # 1 C, 5, is greater than permitted -187: Best mapping -186/236 Test #187: testRGroupDecomp ....................... Passed 4.88 sec +196: ...............[21:38:23] WARNING: the onlyHeavy argument to mol.GetNumAtoms() has been deprecated. Please use the onlyExplicit argument instead or mol.GetNumHeavyAtoms() if you want the heavy atom count. +196: [21:38:23] WARNING: the onlyHeavy argument to mol.GetNumAtoms() has been deprecated. Please use the onlyExplicit argument instead or mol.GetNumHeavyAtoms() if you want the heavy atom count. +147: [21:38:23] UFFTYPER: Unrecognized atom type: S_6+6 (0) +147: [21:38:23] UFFTYPER: Warning: hybridization set to SP3 for atom 0 +147: [21:38:23] UFFTYPER: Unrecognized charge state for atom: 0 +196: ..............[21:38:23] Can't kekulize mol. Unkekulized atoms: 0 1 2 3 4 +196: [21:38:23] Explicit valence for atom # 1 C, 5, is greater than permitted +197: ...... +197: ---------------------------------------------------------------------- +197: Ran 6 tests in 0.017s +197: +197: OK +186/236 Test #197: pyTestConformerWrap .................... Passed 0.52 sec test 198 Start 198: pyTestTrajectory 198: Test command: /usr/bin/python3 "/build/reproducible-path/rdkit-202409.4/Code/GraphMol/Wrap/testTrajectory.py" 198: Working Directory: /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/GraphMol/Wrap 198: Test timeout computed to be: 1500 -197: ...... -197: ---------------------------------------------------------------------- -197: Ran 6 tests in 0.008s -197: -197: OK -187/236 Test #197: pyTestConformerWrap .................... Passed 0.28 sec -test 199 - Start 199: pyTestSGroups - -199: Test command: /usr/bin/python3 "/build/reproducible-path/rdkit-202409.4/Code/GraphMol/Wrap/testSGroups.py" -199: Working Directory: /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/GraphMol/Wrap -199: Test timeout computed to be: 1500 -196: ............................[12:43:08] unable to set wavy bonds for double bonds: 3 -196: .............[12:43:08] +196: ............................[21:38:24] unable to set wavy bonds for double bonds: 3 +196: .............[21:38:24] 196: 196: **** 196: Range Error @@ -32860,7 +32881,7 @@ 196: 3# RDKit::RWMol::removeAtom(unsigned int) in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu//lib/libRDKitGraphMol.so.1 196: 4# boost::python::objects::caller_py_function_impl > >::operator()(_object*, _object*) in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so 196: 5# boost::python::objects::function::call(_object*, _object*) const in /lib/aarch64-linux-gnu/libboost_python313.so.1.83.0 -196: 6# 0x0000FFFFBCB72680 in /lib/aarch64-linux-gnu/libboost_python313.so.1.83.0 +196: 6# 0x0000FFFFA7AC2680 in /lib/aarch64-linux-gnu/libboost_python313.so.1.83.0 196: 7# boost::python::detail::exception_handler::operator()(boost::function0 const&) const in /lib/aarch64-linux-gnu/libboost_python313.so.1.83.0 196: 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-202409.4/obj-aarch64-linux-gnu/rdkit/Chem/rdSLNParse.so 196: 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-202409.4/obj-aarch64-linux-gnu/rdkit/Chem/rdChemReactions.so @@ -32871,17 +32892,17 @@ 196: 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-202409.4/obj-aarch64-linux-gnu/rdkit/Chem/rdmolfiles.so 196: 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-202409.4/obj-aarch64-linux-gnu/rdkit/Chem/rdCIPLabeler.so 196: 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-202409.4/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so -196: 17# 0x0000FFFFBA5F9FA0 in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so -196: 18# 0x0000FFFFBA5F9F38 in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so -196: 19# 0x0000FFFFBA5F9EC8 in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so -196: 20# 0x0000FFFFBA5F9E60 in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so -196: 21# 0x0000FFFFBA5F9DF8 in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so +196: 17# 0x0000FFFFA5549FA0 in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so +196: 18# 0x0000FFFFA5549F38 in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so +196: 19# 0x0000FFFFA5549EC8 in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so +196: 20# 0x0000FFFFA5549E60 in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so +196: 21# 0x0000FFFFA5549DF8 in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so 196: 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-202409.4/obj-aarch64-linux-gnu/rdkit/rdBase.so 196: 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-202409.4/obj-aarch64-linux-gnu/rdkit/rdBase.so 196: 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-202409.4/obj-aarch64-linux-gnu/rdkit/rdBase.so 196: 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-202409.4/obj-aarch64-linux-gnu/rdkit/rdBase.so 196: 26# boost::python::handle_exception_impl(boost::function0) in /lib/aarch64-linux-gnu/libboost_python313.so.1.83.0 -196: 27# 0x0000FFFFBCB6F25C in /lib/aarch64-linux-gnu/libboost_python313.so.1.83.0 +196: 27# 0x0000FFFFA7ABF25C in /lib/aarch64-linux-gnu/libboost_python313.so.1.83.0 196: 28# _PyObject_MakeTpCall in /usr/bin/python3 196: 29# _PyEval_EvalFrameDefault in /usr/bin/python3 196: 30# 0x000000000052F1D8 in /usr/bin/python3 @@ -32913,13 +32934,13 @@ 196: 56# 0x0000000000621C6C in /usr/bin/python3 196: 57# Py_RunMain in /usr/bin/python3 196: 58# Py_BytesMain in /usr/bin/python3 -196: 59# 0x0000FFFFBD98229C in /lib/aarch64-linux-gnu/libc.so.6 +196: 59# 0x0000FFFFA88D229C in /lib/aarch64-linux-gnu/libc.so.6 196: 60# __libc_start_main in /lib/aarch64-linux-gnu/libc.so.6 196: 61# _start in /usr/bin/python3 196: ---------- 196: **** 196: -198: [12:43:08] +198: [21:38:24] 198: 198: **** 198: Pre-condition Violation @@ -32933,23 +32954,23 @@ 198: 2# RDKit::Trajectory::addConformersToMol(RDKit::ROMol&, int, int) in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu//lib/libRDKitTrajectory.so.1 198: 3# boost::python::objects::caller_py_function_impl > >::operator()(_object*, _object*) in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/rdkit/Chem/rdtrajectory.so 198: 4# boost::python::objects::function::call(_object*, _object*) const in /lib/aarch64-linux-gnu/libboost_python313.so.1.83.0 -198: 5# 0x0000FFFF86D32680 in /lib/aarch64-linux-gnu/libboost_python313.so.1.83.0 +198: 5# 0x0000FFFFBA632680 in /lib/aarch64-linux-gnu/libboost_python313.so.1.83.0 198: 6# boost::python::detail::exception_handler::operator()(boost::function0 const&) const in /lib/aarch64-linux-gnu/libboost_python313.so.1.83.0 198: 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-202409.4/obj-aarch64-linux-gnu/rdkit/Chem/rdmolfiles.so 198: 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-202409.4/obj-aarch64-linux-gnu/rdkit/Chem/rdmolfiles.so 198: 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-202409.4/obj-aarch64-linux-gnu/rdkit/Chem/rdCIPLabeler.so 198: 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-202409.4/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so -198: 11# 0x0000FFFF847A9FA0 in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so -198: 12# 0x0000FFFF847A9F38 in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so -198: 13# 0x0000FFFF847A9EC8 in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so -198: 14# 0x0000FFFF847A9E60 in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so -198: 15# 0x0000FFFF847A9DF8 in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so +198: 11# 0x0000FFFFB80A9FA0 in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so +198: 12# 0x0000FFFFB80A9F38 in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so +198: 13# 0x0000FFFFB80A9EC8 in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so +198: 14# 0x0000FFFFB80A9E60 in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so +198: 15# 0x0000FFFFB80A9DF8 in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so 198: 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-202409.4/obj-aarch64-linux-gnu/rdkit/rdBase.so 198: 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-202409.4/obj-aarch64-linux-gnu/rdkit/rdBase.so 198: 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-202409.4/obj-aarch64-linux-gnu/rdkit/rdBase.so 198: 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-202409.4/obj-aarch64-linux-gnu/rdkit/rdBase.so 198: 20# boost::python::handle_exception_impl(boost::function0) in /lib/aarch64-linux-gnu/libboost_python313.so.1.83.0 -198: 21# 0x0000FFFF86D2F25C in /lib/aarch64-linux-gnu/libboost_python313.so.1.83.0 +198: 21# 0x0000FFFFBA62F25C in /lib/aarch64-linux-gnu/libboost_python313.so.1.83.0 198: 22# _PyObject_MakeTpCall in /usr/bin/python3 198: 23# _PyEval_EvalFrameDefault in /usr/bin/python3 198: 24# 0x000000000052F1D8 in /usr/bin/python3 @@ -32981,13 +33002,13 @@ 198: 50# 0x0000000000621C6C in /usr/bin/python3 198: 51# Py_RunMain in /usr/bin/python3 198: 52# Py_BytesMain in /usr/bin/python3 -198: 53# 0x0000FFFF8751229C in /lib/aarch64-linux-gnu/libc.so.6 +198: 53# 0x0000FFFFBAE1229C in /lib/aarch64-linux-gnu/libc.so.6 198: 54# __libc_start_main in /lib/aarch64-linux-gnu/libc.so.6 198: 55# _start in /usr/bin/python3 198: ---------- 198: **** 198: -198: .[12:43:08] +198: .[21:38:24] 198: 198: **** 198: Pre-condition Violation @@ -33001,23 +33022,23 @@ 198: 2# RDKit::Trajectory::addConformersToMol(RDKit::ROMol&, int, int) in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu//lib/libRDKitTrajectory.so.1 198: 3# boost::python::objects::caller_py_function_impl > >::operator()(_object*, _object*) in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/rdkit/Chem/rdtrajectory.so 198: 4# boost::python::objects::function::call(_object*, _object*) const in /lib/aarch64-linux-gnu/libboost_python313.so.1.83.0 -198: 5# 0x0000FFFF86D32680 in /lib/aarch64-linux-gnu/libboost_python313.so.1.83.0 +198: 5# 0x0000FFFFBA632680 in /lib/aarch64-linux-gnu/libboost_python313.so.1.83.0 198: 6# boost::python::detail::exception_handler::operator()(boost::function0 const&) const in /lib/aarch64-linux-gnu/libboost_python313.so.1.83.0 198: 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-202409.4/obj-aarch64-linux-gnu/rdkit/Chem/rdmolfiles.so 198: 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-202409.4/obj-aarch64-linux-gnu/rdkit/Chem/rdmolfiles.so 198: 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-202409.4/obj-aarch64-linux-gnu/rdkit/Chem/rdCIPLabeler.so 198: 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-202409.4/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so -198: 11# 0x0000FFFF847A9FA0 in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so -198: 12# 0x0000FFFF847A9F38 in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so -198: 13# 0x0000FFFF847A9EC8 in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so -198: 14# 0x0000FFFF847A9E60 in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so -198: 15# 0x0000FFFF847A9DF8 in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so +198: 11# 0x0000FFFFB80A9FA0 in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so +198: 12# 0x0000FFFFB80A9F38 in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so +198: 13# 0x0000FFFFB80A9EC8 in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so +198: 14# 0x0000FFFFB80A9E60 in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so +198: 15# 0x0000FFFFB80A9DF8 in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so 198: 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-202409.4/obj-aarch64-linux-gnu/rdkit/rdBase.so 198: 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-202409.4/obj-aarch64-linux-gnu/rdkit/rdBase.so 198: 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-202409.4/obj-aarch64-linux-gnu/rdkit/rdBase.so 198: 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-202409.4/obj-aarch64-linux-gnu/rdkit/rdBase.so 198: 20# boost::python::handle_exception_impl(boost::function0) in /lib/aarch64-linux-gnu/libboost_python313.so.1.83.0 -198: 21# 0x0000FFFF86D2F25C in /lib/aarch64-linux-gnu/libboost_python313.so.1.83.0 +198: 21# 0x0000FFFFBA62F25C in /lib/aarch64-linux-gnu/libboost_python313.so.1.83.0 198: 22# _PyObject_MakeTpCall in /usr/bin/python3 198: 23# _PyEval_EvalFrameDefault in /usr/bin/python3 198: 24# 0x000000000052F1D8 in /usr/bin/python3 @@ -33049,13 +33070,14 @@ 198: 50# 0x0000000000621C6C in /usr/bin/python3 198: 51# Py_RunMain in /usr/bin/python3 198: 52# Py_BytesMain in /usr/bin/python3 -198: 53# 0x0000FFFF8751229C in /lib/aarch64-linux-gnu/libc.so.6 +198: 53# 0x0000FFFFBAE1229C in /lib/aarch64-linux-gnu/libc.so.6 198: 54# __libc_start_main in /lib/aarch64-linux-gnu/libc.so.6 198: 55# _start in /usr/bin/python3 198: ---------- 198: **** 198: -198: .[12:43:09] +187: bulk, no symmetry +198: .[21:38:24] 198: 198: **** 198: Range Error @@ -33070,23 +33092,23 @@ 198: 3# RDKit::getSnapshot_wrap(RDKit::Trajectory*, unsigned int) in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/rdkit/Chem/rdtrajectory.so 198: 4# boost::python::objects::caller_py_function_impl, boost::mpl::vector3 > >::operator()(_object*, _object*) in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/rdkit/Chem/rdtrajectory.so 198: 5# boost::python::objects::function::call(_object*, _object*) const in /lib/aarch64-linux-gnu/libboost_python313.so.1.83.0 -198: 6# 0x0000FFFF86D32680 in /lib/aarch64-linux-gnu/libboost_python313.so.1.83.0 +198: 6# 0x0000FFFFBA632680 in /lib/aarch64-linux-gnu/libboost_python313.so.1.83.0 198: 7# boost::python::detail::exception_handler::operator()(boost::function0 const&) const in /lib/aarch64-linux-gnu/libboost_python313.so.1.83.0 198: 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-202409.4/obj-aarch64-linux-gnu/rdkit/Chem/rdmolfiles.so 198: 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-202409.4/obj-aarch64-linux-gnu/rdkit/Chem/rdmolfiles.so 198: 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-202409.4/obj-aarch64-linux-gnu/rdkit/Chem/rdCIPLabeler.so 198: 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-202409.4/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so -198: 12# 0x0000FFFF847A9FA0 in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so -198: 13# 0x0000FFFF847A9F38 in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so -198: 14# 0x0000FFFF847A9EC8 in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so -198: 15# 0x0000FFFF847A9E60 in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so -198: 16# 0x0000FFFF847A9DF8 in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so +198: 12# 0x0000FFFFB80A9FA0 in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so +198: 13# 0x0000FFFFB80A9F38 in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so +198: 14# 0x0000FFFFB80A9EC8 in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so +198: 15# 0x0000FFFFB80A9E60 in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so +198: 16# 0x0000FFFFB80A9DF8 in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so 198: 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-202409.4/obj-aarch64-linux-gnu/rdkit/rdBase.so 198: 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-202409.4/obj-aarch64-linux-gnu/rdkit/rdBase.so 198: 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-202409.4/obj-aarch64-linux-gnu/rdkit/rdBase.so 198: 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-202409.4/obj-aarch64-linux-gnu/rdkit/rdBase.so 198: 21# boost::python::handle_exception_impl(boost::function0) in /lib/aarch64-linux-gnu/libboost_python313.so.1.83.0 -198: 22# 0x0000FFFF86D2F25C in /lib/aarch64-linux-gnu/libboost_python313.so.1.83.0 +198: 22# 0x0000FFFFBA62F25C in /lib/aarch64-linux-gnu/libboost_python313.so.1.83.0 198: 23# _PyObject_MakeTpCall in /usr/bin/python3 198: 24# _PyEval_EvalFrameDefault in /usr/bin/python3 198: 25# 0x000000000052F1D8 in /usr/bin/python3 @@ -33118,13 +33140,13 @@ 198: 51# 0x0000000000621C6C in /usr/bin/python3 198: 52# Py_RunMain in /usr/bin/python3 198: 53# Py_BytesMain in /usr/bin/python3 -198: 54# 0x0000FFFF8751229C in /lib/aarch64-linux-gnu/libc.so.6 +198: 54# 0x0000FFFFBAE1229C in /lib/aarch64-linux-gnu/libc.so.6 198: 55# __libc_start_main in /lib/aarch64-linux-gnu/libc.so.6 198: 56# _start in /usr/bin/python3 198: ---------- 198: **** 198: -198: .[12:43:09] +198: .[21:38:24] 198: 198: **** 198: Pre-condition Violation @@ -33138,23 +33160,23 @@ 198: 2# RDKit::readAmberTrajectory(std::__cxx11::basic_string, std::allocator > const&, RDKit::Trajectory&) in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu//lib/libRDKitTrajectory.so.1 198: 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-202409.4/obj-aarch64-linux-gnu/rdkit/Chem/rdtrajectory.so 198: 4# boost::python::objects::function::call(_object*, _object*) const in /lib/aarch64-linux-gnu/libboost_python313.so.1.83.0 -198: 5# 0x0000FFFF86D32680 in /lib/aarch64-linux-gnu/libboost_python313.so.1.83.0 +198: 5# 0x0000FFFFBA632680 in /lib/aarch64-linux-gnu/libboost_python313.so.1.83.0 198: 6# boost::python::detail::exception_handler::operator()(boost::function0 const&) const in /lib/aarch64-linux-gnu/libboost_python313.so.1.83.0 198: 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-202409.4/obj-aarch64-linux-gnu/rdkit/Chem/rdmolfiles.so 198: 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-202409.4/obj-aarch64-linux-gnu/rdkit/Chem/rdmolfiles.so 198: 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-202409.4/obj-aarch64-linux-gnu/rdkit/Chem/rdCIPLabeler.so 198: 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-202409.4/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so -198: 11# 0x0000FFFF847A9FA0 in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so -198: 12# 0x0000FFFF847A9F38 in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so -198: 13# 0x0000FFFF847A9EC8 in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so -198: 14# 0x0000FFFF847A9E60 in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so -198: 15# 0x0000FFFF847A9DF8 in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so +198: 11# 0x0000FFFFB80A9FA0 in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so +198: 12# 0x0000FFFFB80A9F38 in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so +198: 13# 0x0000FFFFB80A9EC8 in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so +198: 14# 0x0000FFFFB80A9E60 in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so +198: 15# 0x0000FFFFB80A9DF8 in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so 198: 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-202409.4/obj-aarch64-linux-gnu/rdkit/rdBase.so 198: 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-202409.4/obj-aarch64-linux-gnu/rdkit/rdBase.so 198: 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-202409.4/obj-aarch64-linux-gnu/rdkit/rdBase.so 198: 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-202409.4/obj-aarch64-linux-gnu/rdkit/rdBase.so 198: 20# boost::python::handle_exception_impl(boost::function0) in /lib/aarch64-linux-gnu/libboost_python313.so.1.83.0 -198: 21# 0x0000FFFF86D2F25C in /lib/aarch64-linux-gnu/libboost_python313.so.1.83.0 +198: 21# 0x0000FFFFBA62F25C in /lib/aarch64-linux-gnu/libboost_python313.so.1.83.0 198: 22# _PyObject_MakeTpCall in /usr/bin/python3 198: 23# _PyEval_EvalFrameDefault in /usr/bin/python3 198: 24# 0x000000000052F1D8 in /usr/bin/python3 @@ -33186,13 +33208,13 @@ 198: 50# 0x0000000000621C6C in /usr/bin/python3 198: 51# Py_RunMain in /usr/bin/python3 198: 52# Py_BytesMain in /usr/bin/python3 -198: 53# 0x0000FFFF8751229C in /lib/aarch64-linux-gnu/libc.so.6 +198: 53# 0x0000FFFFBAE1229C in /lib/aarch64-linux-gnu/libc.so.6 198: 54# __libc_start_main in /lib/aarch64-linux-gnu/libc.so.6 198: 55# _start in /usr/bin/python3 198: ---------- 198: **** 198: -198: ..[12:43:09] +198: ..[21:38:24] 198: 198: **** 198: Pre-condition Violation @@ -33206,23 +33228,23 @@ 198: 2# RDKit::readGromosTrajectory(std::__cxx11::basic_string, std::allocator > const&, RDKit::Trajectory&) in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu//lib/libRDKitTrajectory.so.1 198: 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-202409.4/obj-aarch64-linux-gnu/rdkit/Chem/rdtrajectory.so 198: 4# boost::python::objects::function::call(_object*, _object*) const in /lib/aarch64-linux-gnu/libboost_python313.so.1.83.0 -198: 5# 0x0000FFFF86D32680 in /lib/aarch64-linux-gnu/libboost_python313.so.1.83.0 +198: 5# 0x0000FFFFBA632680 in /lib/aarch64-linux-gnu/libboost_python313.so.1.83.0 198: 6# boost::python::detail::exception_handler::operator()(boost::function0 const&) const in /lib/aarch64-linux-gnu/libboost_python313.so.1.83.0 198: 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-202409.4/obj-aarch64-linux-gnu/rdkit/Chem/rdmolfiles.so 198: 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-202409.4/obj-aarch64-linux-gnu/rdkit/Chem/rdmolfiles.so 198: 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-202409.4/obj-aarch64-linux-gnu/rdkit/Chem/rdCIPLabeler.so 198: 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-202409.4/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so -198: 11# 0x0000FFFF847A9FA0 in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so -198: 12# 0x0000FFFF847A9F38 in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so -198: 13# 0x0000FFFF847A9EC8 in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so -198: 14# 0x0000FFFF847A9E60 in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so -198: 15# 0x0000FFFF847A9DF8 in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so +198: 11# 0x0000FFFFB80A9FA0 in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so +198: 12# 0x0000FFFFB80A9F38 in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so +198: 13# 0x0000FFFFB80A9EC8 in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so +198: 14# 0x0000FFFFB80A9E60 in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so +198: 15# 0x0000FFFFB80A9DF8 in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so 198: 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-202409.4/obj-aarch64-linux-gnu/rdkit/rdBase.so 198: 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-202409.4/obj-aarch64-linux-gnu/rdkit/rdBase.so 198: 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-202409.4/obj-aarch64-linux-gnu/rdkit/rdBase.so 198: 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-202409.4/obj-aarch64-linux-gnu/rdkit/rdBase.so 198: 20# boost::python::handle_exception_impl(boost::function0) in /lib/aarch64-linux-gnu/libboost_python313.so.1.83.0 -198: 21# 0x0000FFFF86D2F25C in /lib/aarch64-linux-gnu/libboost_python313.so.1.83.0 +198: 21# 0x0000FFFFBA62F25C in /lib/aarch64-linux-gnu/libboost_python313.so.1.83.0 198: 22# _PyObject_MakeTpCall in /usr/bin/python3 198: 23# _PyEval_EvalFrameDefault in /usr/bin/python3 198: 24# 0x000000000052F1D8 in /usr/bin/python3 @@ -33254,13 +33276,13 @@ 198: 50# 0x0000000000621C6C in /usr/bin/python3 198: 51# Py_RunMain in /usr/bin/python3 198: 52# Py_BytesMain in /usr/bin/python3 -198: 53# 0x0000FFFF8751229C in /lib/aarch64-linux-gnu/libc.so.6 +198: 53# 0x0000FFFFBAE1229C in /lib/aarch64-linux-gnu/libc.so.6 198: 54# __libc_start_main in /lib/aarch64-linux-gnu/libc.so.6 198: 55# _start in /usr/bin/python3 198: ---------- 198: **** 198: -198: .[12:43:09] +198: .[21:38:24] 198: 198: **** 198: Pre-condition Violation @@ -33274,23 +33296,23 @@ 198: 2# RDKit::Snapshot::getPoint2D(unsigned int) const in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu//lib/libRDKitTrajectory.so.1 198: 3# boost::python::objects::caller_py_function_impl > >::operator()(_object*, _object*) in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/rdkit/Chem/rdtrajectory.so 198: 4# boost::python::objects::function::call(_object*, _object*) const in /lib/aarch64-linux-gnu/libboost_python313.so.1.83.0 -198: 5# 0x0000FFFF86D32680 in /lib/aarch64-linux-gnu/libboost_python313.so.1.83.0 +198: 5# 0x0000FFFFBA632680 in /lib/aarch64-linux-gnu/libboost_python313.so.1.83.0 198: 6# boost::python::detail::exception_handler::operator()(boost::function0 const&) const in /lib/aarch64-linux-gnu/libboost_python313.so.1.83.0 198: 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-202409.4/obj-aarch64-linux-gnu/rdkit/Chem/rdmolfiles.so 198: 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-202409.4/obj-aarch64-linux-gnu/rdkit/Chem/rdmolfiles.so 198: 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-202409.4/obj-aarch64-linux-gnu/rdkit/Chem/rdCIPLabeler.so 198: 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-202409.4/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so -198: 11# 0x0000FFFF847A9FA0 in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so -198: 12# 0x0000FFFF847A9F38 in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so -198: 13# 0x0000FFFF847A9EC8 in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so -198: 14# 0x0000FFFF847A9E60 in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so -198: 15# 0x0000FFFF847A9DF8 in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so +198: 11# 0x0000FFFFB80A9FA0 in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so +198: 12# 0x0000FFFFB80A9F38 in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so +198: 13# 0x0000FFFFB80A9EC8 in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so +198: 14# 0x0000FFFFB80A9E60 in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so +198: 15# 0x0000FFFFB80A9DF8 in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so 198: 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-202409.4/obj-aarch64-linux-gnu/rdkit/rdBase.so 198: 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-202409.4/obj-aarch64-linux-gnu/rdkit/rdBase.so 198: 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-202409.4/obj-aarch64-linux-gnu/rdkit/rdBase.so 198: 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-202409.4/obj-aarch64-linux-gnu/rdkit/rdBase.so 198: 20# boost::python::handle_exception_impl(boost::function0) in /lib/aarch64-linux-gnu/libboost_python313.so.1.83.0 -198: 21# 0x0000FFFF86D2F25C in /lib/aarch64-linux-gnu/libboost_python313.so.1.83.0 +198: 21# 0x0000FFFFBA62F25C in /lib/aarch64-linux-gnu/libboost_python313.so.1.83.0 198: 22# _PyObject_MakeTpCall in /usr/bin/python3 198: 23# _PyEval_EvalFrameDefault in /usr/bin/python3 198: 24# 0x000000000052F1D8 in /usr/bin/python3 @@ -33322,13 +33344,13 @@ 198: 50# 0x0000000000621C6C in /usr/bin/python3 198: 51# Py_RunMain in /usr/bin/python3 198: 52# Py_BytesMain in /usr/bin/python3 -198: 53# 0x0000FFFF8751229C in /lib/aarch64-linux-gnu/libc.so.6 +198: 53# 0x0000FFFFBAE1229C in /lib/aarch64-linux-gnu/libc.so.6 198: 54# __libc_start_main in /lib/aarch64-linux-gnu/libc.so.6 198: 55# _start in /usr/bin/python3 198: ---------- 198: **** 198: -198: [12:43:09] +198: [21:38:24] 198: 198: **** 198: Pre-condition Violation @@ -33342,23 +33364,23 @@ 198: 2# RDKit::Snapshot::getPoint2D(unsigned int) const in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu//lib/libRDKitTrajectory.so.1 198: 3# boost::python::objects::caller_py_function_impl > >::operator()(_object*, _object*) in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/rdkit/Chem/rdtrajectory.so 198: 4# boost::python::objects::function::call(_object*, _object*) const in /lib/aarch64-linux-gnu/libboost_python313.so.1.83.0 -198: 5# 0x0000FFFF86D32680 in /lib/aarch64-linux-gnu/libboost_python313.so.1.83.0 +198: 5# 0x0000FFFFBA632680 in /lib/aarch64-linux-gnu/libboost_python313.so.1.83.0 198: 6# boost::python::detail::exception_handler::operator()(boost::function0 const&) const in /lib/aarch64-linux-gnu/libboost_python313.so.1.83.0 198: 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-202409.4/obj-aarch64-linux-gnu/rdkit/Chem/rdmolfiles.so 198: 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-202409.4/obj-aarch64-linux-gnu/rdkit/Chem/rdmolfiles.so 198: 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-202409.4/obj-aarch64-linux-gnu/rdkit/Chem/rdCIPLabeler.so 198: 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-202409.4/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so -198: 11# 0x0000FFFF847A9FA0 in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so -198: 12# 0x0000FFFF847A9F38 in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so -198: 13# 0x0000FFFF847A9EC8 in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so -198: 14# 0x0000FFFF847A9E60 in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so -198: 15# 0x0000FFFF847A9DF8 in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so +198: 11# 0x0000FFFFB80A9FA0 in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so +198: 12# 0x0000FFFFB80A9F38 in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so +198: 13# 0x0000FFFFB80A9EC8 in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so +198: 14# 0x0000FFFFB80A9E60 in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so +198: 15# 0x0000FFFFB80A9DF8 in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so 198: 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-202409.4/obj-aarch64-linux-gnu/rdkit/rdBase.so 198: 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-202409.4/obj-aarch64-linux-gnu/rdkit/rdBase.so 198: 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-202409.4/obj-aarch64-linux-gnu/rdkit/rdBase.so 198: 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-202409.4/obj-aarch64-linux-gnu/rdkit/rdBase.so 198: 20# boost::python::handle_exception_impl(boost::function0) in /lib/aarch64-linux-gnu/libboost_python313.so.1.83.0 -198: 21# 0x0000FFFF86D2F25C in /lib/aarch64-linux-gnu/libboost_python313.so.1.83.0 +198: 21# 0x0000FFFFBA62F25C in /lib/aarch64-linux-gnu/libboost_python313.so.1.83.0 198: 22# _PyObject_MakeTpCall in /usr/bin/python3 198: 23# _PyEval_EvalFrameDefault in /usr/bin/python3 198: 24# 0x000000000052F1D8 in /usr/bin/python3 @@ -33390,13 +33412,13 @@ 198: 50# 0x0000000000621C6C in /usr/bin/python3 198: 51# Py_RunMain in /usr/bin/python3 198: 52# Py_BytesMain in /usr/bin/python3 -198: 53# 0x0000FFFF8751229C in /lib/aarch64-linux-gnu/libc.so.6 +198: 53# 0x0000FFFFBAE1229C in /lib/aarch64-linux-gnu/libc.so.6 198: 54# __libc_start_main in /lib/aarch64-linux-gnu/libc.so.6 198: 55# _start in /usr/bin/python3 198: ---------- 198: **** 198: -198: .[12:43:09] +198: .[21:38:24] 198: 198: **** 198: Range Error @@ -33411,23 +33433,23 @@ 198: 3# RDKit::getSnapshot_wrap(RDKit::Trajectory*, unsigned int) in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/rdkit/Chem/rdtrajectory.so 198: 4# boost::python::objects::caller_py_function_impl, boost::mpl::vector3 > >::operator()(_object*, _object*) in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/rdkit/Chem/rdtrajectory.so 198: 5# boost::python::objects::function::call(_object*, _object*) const in /lib/aarch64-linux-gnu/libboost_python313.so.1.83.0 -198: 6# 0x0000FFFF86D32680 in /lib/aarch64-linux-gnu/libboost_python313.so.1.83.0 +198: 6# 0x0000FFFFBA632680 in /lib/aarch64-linux-gnu/libboost_python313.so.1.83.0 198: 7# boost::python::detail::exception_handler::operator()(boost::function0 const&) const in /lib/aarch64-linux-gnu/libboost_python313.so.1.83.0 198: 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-202409.4/obj-aarch64-linux-gnu/rdkit/Chem/rdmolfiles.so 198: 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-202409.4/obj-aarch64-linux-gnu/rdkit/Chem/rdmolfiles.so 198: 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-202409.4/obj-aarch64-linux-gnu/rdkit/Chem/rdCIPLabeler.so 198: 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-202409.4/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so -198: 12# 0x0000FFFF847A9FA0 in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so -198: 13# 0x0000FFFF847A9F38 in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so -198: 14# 0x0000FFFF847A9EC8 in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so -198: 15# 0x0000FFFF847A9E60 in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so -198: 16# 0x0000FFFF847A9DF8 in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so +198: 12# 0x0000FFFFB80A9FA0 in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so +198: 13# 0x0000FFFFB80A9F38 in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so +198: 14# 0x0000FFFFB80A9EC8 in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so +198: 15# 0x0000FFFFB80A9E60 in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so +198: 16# 0x0000FFFFB80A9DF8 in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so 198: 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-202409.4/obj-aarch64-linux-gnu/rdkit/rdBase.so 198: 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-202409.4/obj-aarch64-linux-gnu/rdkit/rdBase.so 198: 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-202409.4/obj-aarch64-linux-gnu/rdkit/rdBase.so 198: 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-202409.4/obj-aarch64-linux-gnu/rdkit/rdBase.so 198: 21# boost::python::handle_exception_impl(boost::function0) in /lib/aarch64-linux-gnu/libboost_python313.so.1.83.0 -198: 22# 0x0000FFFF86D2F25C in /lib/aarch64-linux-gnu/libboost_python313.so.1.83.0 +198: 22# 0x0000FFFFBA62F25C in /lib/aarch64-linux-gnu/libboost_python313.so.1.83.0 198: 23# _PyObject_MakeTpCall in /usr/bin/python3 198: 24# _PyEval_EvalFrameDefault in /usr/bin/python3 198: 25# 0x000000000052F1D8 in /usr/bin/python3 @@ -33459,13 +33481,13 @@ 198: 51# 0x0000000000621C6C in /usr/bin/python3 198: 52# Py_RunMain in /usr/bin/python3 198: 53# Py_BytesMain in /usr/bin/python3 -198: 54# 0x0000FFFF8751229C in /lib/aarch64-linux-gnu/libc.so.6 +198: 54# 0x0000FFFFBAE1229C in /lib/aarch64-linux-gnu/libc.so.6 198: 55# __libc_start_main in /lib/aarch64-linux-gnu/libc.so.6 198: 56# _start in /usr/bin/python3 198: ---------- 198: **** 198: -198: [12:43:09] +198: [21:38:24] 198: 198: **** 198: Range Error @@ -33479,23 +33501,23 @@ 198: 2# RDKit::Snapshot::getPoint2D(unsigned int) const in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu//lib/libRDKitTrajectory.so.1 198: 3# boost::python::objects::caller_py_function_impl > >::operator()(_object*, _object*) in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/rdkit/Chem/rdtrajectory.so 198: 4# boost::python::objects::function::call(_object*, _object*) const in /lib/aarch64-linux-gnu/libboost_python313.so.1.83.0 -198: 5# 0x0000FFFF86D32680 in /lib/aarch64-linux-gnu/libboost_python313.so.1.83.0 +198: 5# 0x0000FFFFBA632680 in /lib/aarch64-linux-gnu/libboost_python313.so.1.83.0 198: 6# boost::python::detail::exception_handler::operator()(boost::function0 const&) const in /lib/aarch64-linux-gnu/libboost_python313.so.1.83.0 198: 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-202409.4/obj-aarch64-linux-gnu/rdkit/Chem/rdmolfiles.so 198: 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-202409.4/obj-aarch64-linux-gnu/rdkit/Chem/rdmolfiles.so 198: 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-202409.4/obj-aarch64-linux-gnu/rdkit/Chem/rdCIPLabeler.so 198: 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-202409.4/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so -198: 11# 0x0000FFFF847A9FA0 in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so -198: 12# 0x0000FFFF847A9F38 in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so -198: 13# 0x0000FFFF847A9EC8 in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so -198: 14# 0x0000FFFF847A9E60 in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so -198: 15# 0x0000FFFF847A9DF8 in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so +198: 11# 0x0000FFFFB80A9FA0 in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so +198: 12# 0x0000FFFFB80A9F38 in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so +198: 13# 0x0000FFFFB80A9EC8 in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so +198: 14# 0x0000FFFFB80A9E60 in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so +198: 15# 0x0000FFFFB80A9DF8 in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so 198: 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-202409.4/obj-aarch64-linux-gnu/rdkit/rdBase.so 198: 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-202409.4/obj-aarch64-linux-gnu/rdkit/rdBase.so 198: 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-202409.4/obj-aarch64-linux-gnu/rdkit/rdBase.so 198: 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-202409.4/obj-aarch64-linux-gnu/rdkit/rdBase.so 198: 20# boost::python::handle_exception_impl(boost::function0) in /lib/aarch64-linux-gnu/libboost_python313.so.1.83.0 -198: 21# 0x0000FFFF86D2F25C in /lib/aarch64-linux-gnu/libboost_python313.so.1.83.0 +198: 21# 0x0000FFFFBA62F25C in /lib/aarch64-linux-gnu/libboost_python313.so.1.83.0 198: 22# _PyObject_MakeTpCall in /usr/bin/python3 198: 23# _PyEval_EvalFrameDefault in /usr/bin/python3 198: 24# 0x000000000052F1D8 in /usr/bin/python3 @@ -33527,13 +33549,13 @@ 198: 50# 0x0000000000621C6C in /usr/bin/python3 198: 51# Py_RunMain in /usr/bin/python3 198: 52# Py_BytesMain in /usr/bin/python3 -198: 53# 0x0000FFFF8751229C in /lib/aarch64-linux-gnu/libc.so.6 +198: 53# 0x0000FFFFBAE1229C in /lib/aarch64-linux-gnu/libc.so.6 198: 54# __libc_start_main in /lib/aarch64-linux-gnu/libc.so.6 198: 55# _start in /usr/bin/python3 198: ---------- 198: **** 198: -198: .[12:43:09] +198: .[21:38:24] 198: 198: **** 198: Range Error @@ -33548,23 +33570,23 @@ 198: 3# RDKit::getSnapshot_wrap(RDKit::Trajectory*, unsigned int) in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/rdkit/Chem/rdtrajectory.so 198: 4# boost::python::objects::caller_py_function_impl, boost::mpl::vector3 > >::operator()(_object*, _object*) in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/rdkit/Chem/rdtrajectory.so 198: 5# boost::python::objects::function::call(_object*, _object*) const in /lib/aarch64-linux-gnu/libboost_python313.so.1.83.0 -198: 6# 0x0000FFFF86D32680 in /lib/aarch64-linux-gnu/libboost_python313.so.1.83.0 +198: 6# 0x0000FFFFBA632680 in /lib/aarch64-linux-gnu/libboost_python313.so.1.83.0 198: 7# boost::python::detail::exception_handler::operator()(boost::function0 const&) const in /lib/aarch64-linux-gnu/libboost_python313.so.1.83.0 198: 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-202409.4/obj-aarch64-linux-gnu/rdkit/Chem/rdmolfiles.so 198: 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-202409.4/obj-aarch64-linux-gnu/rdkit/Chem/rdmolfiles.so 198: 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-202409.4/obj-aarch64-linux-gnu/rdkit/Chem/rdCIPLabeler.so 198: 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-202409.4/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so -198: 12# 0x0000FFFF847A9FA0 in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so -198: 13# 0x0000FFFF847A9F38 in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so -198: 14# 0x0000FFFF847A9EC8 in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so -198: 15# 0x0000FFFF847A9E60 in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so -198: 16# 0x0000FFFF847A9DF8 in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so +198: 12# 0x0000FFFFB80A9FA0 in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so +198: 13# 0x0000FFFFB80A9F38 in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so +198: 14# 0x0000FFFFB80A9EC8 in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so +198: 15# 0x0000FFFFB80A9E60 in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so +198: 16# 0x0000FFFFB80A9DF8 in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so 198: 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-202409.4/obj-aarch64-linux-gnu/rdkit/rdBase.so 198: 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-202409.4/obj-aarch64-linux-gnu/rdkit/rdBase.so 198: 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-202409.4/obj-aarch64-linux-gnu/rdkit/rdBase.so 198: 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-202409.4/obj-aarch64-linux-gnu/rdkit/rdBase.so 198: 21# boost::python::handle_exception_impl(boost::function0) in /lib/aarch64-linux-gnu/libboost_python313.so.1.83.0 -198: 22# 0x0000FFFF86D2F25C in /lib/aarch64-linux-gnu/libboost_python313.so.1.83.0 +198: 22# 0x0000FFFFBA62F25C in /lib/aarch64-linux-gnu/libboost_python313.so.1.83.0 198: 23# _PyObject_MakeTpCall in /usr/bin/python3 198: 24# _PyEval_EvalFrameDefault in /usr/bin/python3 198: 25# 0x000000000052F1D8 in /usr/bin/python3 @@ -33596,13 +33618,13 @@ 198: 51# 0x0000000000621C6C in /usr/bin/python3 198: 52# Py_RunMain in /usr/bin/python3 198: 53# Py_BytesMain in /usr/bin/python3 -198: 54# 0x0000FFFF8751229C in /lib/aarch64-linux-gnu/libc.so.6 +198: 54# 0x0000FFFFBAE1229C in /lib/aarch64-linux-gnu/libc.so.6 198: 55# __libc_start_main in /lib/aarch64-linux-gnu/libc.so.6 198: 56# _start in /usr/bin/python3 198: ---------- 198: **** 198: -198: [12:43:09] +198: [21:38:24] 198: 198: **** 198: Pre-condition Violation @@ -33616,23 +33638,23 @@ 198: 2# RDKit::Snapshot::getPoint2D(unsigned int) const in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu//lib/libRDKitTrajectory.so.1 198: 3# boost::python::objects::caller_py_function_impl > >::operator()(_object*, _object*) in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/rdkit/Chem/rdtrajectory.so 198: 4# boost::python::objects::function::call(_object*, _object*) const in /lib/aarch64-linux-gnu/libboost_python313.so.1.83.0 -198: 5# 0x0000FFFF86D32680 in /lib/aarch64-linux-gnu/libboost_python313.so.1.83.0 +198: 5# 0x0000FFFFBA632680 in /lib/aarch64-linux-gnu/libboost_python313.so.1.83.0 198: 6# boost::python::detail::exception_handler::operator()(boost::function0 const&) const in /lib/aarch64-linux-gnu/libboost_python313.so.1.83.0 198: 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-202409.4/obj-aarch64-linux-gnu/rdkit/Chem/rdmolfiles.so 198: 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-202409.4/obj-aarch64-linux-gnu/rdkit/Chem/rdmolfiles.so 198: 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-202409.4/obj-aarch64-linux-gnu/rdkit/Chem/rdCIPLabeler.so 198: 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-202409.4/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so -198: 11# 0x0000FFFF847A9FA0 in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so -198: 12# 0x0000FFFF847A9F38 in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so -198: 13# 0x0000FFFF847A9EC8 in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so -198: 14# 0x0000FFFF847A9E60 in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so -198: 15# 0x0000FFFF847A9DF8 in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so +198: 11# 0x0000FFFFB80A9FA0 in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so +198: 12# 0x0000FFFFB80A9F38 in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so +198: 13# 0x0000FFFFB80A9EC8 in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so +198: 14# 0x0000FFFFB80A9E60 in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so +198: 15# 0x0000FFFFB80A9DF8 in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so 198: 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-202409.4/obj-aarch64-linux-gnu/rdkit/rdBase.so 198: 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-202409.4/obj-aarch64-linux-gnu/rdkit/rdBase.so 198: 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-202409.4/obj-aarch64-linux-gnu/rdkit/rdBase.so 198: 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-202409.4/obj-aarch64-linux-gnu/rdkit/rdBase.so 198: 20# boost::python::handle_exception_impl(boost::function0) in /lib/aarch64-linux-gnu/libboost_python313.so.1.83.0 -198: 21# 0x0000FFFF86D2F25C in /lib/aarch64-linux-gnu/libboost_python313.so.1.83.0 +198: 21# 0x0000FFFFBA62F25C in /lib/aarch64-linux-gnu/libboost_python313.so.1.83.0 198: 22# _PyObject_MakeTpCall in /usr/bin/python3 198: 23# _PyEval_EvalFrameDefault in /usr/bin/python3 198: 24# 0x000000000052F1D8 in /usr/bin/python3 @@ -33664,13 +33686,13 @@ 198: 50# 0x0000000000621C6C in /usr/bin/python3 198: 51# Py_RunMain in /usr/bin/python3 198: 52# Py_BytesMain in /usr/bin/python3 -198: 53# 0x0000FFFF8751229C in /lib/aarch64-linux-gnu/libc.so.6 +198: 53# 0x0000FFFFBAE1229C in /lib/aarch64-linux-gnu/libc.so.6 198: 54# __libc_start_main in /lib/aarch64-linux-gnu/libc.so.6 198: 55# _start in /usr/bin/python3 198: ---------- 198: **** 198: -198: [12:43:09] +198: [21:38:24] 198: 198: **** 198: Pre-condition Violation @@ -33684,23 +33706,23 @@ 198: 2# RDKit::Snapshot::getPoint2D(unsigned int) const in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu//lib/libRDKitTrajectory.so.1 198: 3# boost::python::objects::caller_py_function_impl > >::operator()(_object*, _object*) in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/rdkit/Chem/rdtrajectory.so 198: 4# boost::python::objects::function::call(_object*, _object*) const in /lib/aarch64-linux-gnu/libboost_python313.so.1.83.0 -198: 5# 0x0000FFFF86D32680 in /lib/aarch64-linux-gnu/libboost_python313.so.1.83.0 +198: 5# 0x0000FFFFBA632680 in /lib/aarch64-linux-gnu/libboost_python313.so.1.83.0 198: 6# boost::python::detail::exception_handler::operator()(boost::function0 const&) const in /lib/aarch64-linux-gnu/libboost_python313.so.1.83.0 198: 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-202409.4/obj-aarch64-linux-gnu/rdkit/Chem/rdmolfiles.so 198: 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-202409.4/obj-aarch64-linux-gnu/rdkit/Chem/rdmolfiles.so 198: 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-202409.4/obj-aarch64-linux-gnu/rdkit/Chem/rdCIPLabeler.so 198: 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-202409.4/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so -198: 11# 0x0000FFFF847A9FA0 in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so -198: 12# 0x0000FFFF847A9F38 in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so -198: 13# 0x0000FFFF847A9EC8 in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so -198: 14# 0x0000FFFF847A9E60 in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so -198: 15# 0x0000FFFF847A9DF8 in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so +198: 11# 0x0000FFFFB80A9FA0 in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so +198: 12# 0x0000FFFFB80A9F38 in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so +198: 13# 0x0000FFFFB80A9EC8 in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so +198: 14# 0x0000FFFFB80A9E60 in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so +198: 15# 0x0000FFFFB80A9DF8 in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so 198: 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-202409.4/obj-aarch64-linux-gnu/rdkit/rdBase.so 198: 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-202409.4/obj-aarch64-linux-gnu/rdkit/rdBase.so 198: 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-202409.4/obj-aarch64-linux-gnu/rdkit/rdBase.so 198: 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-202409.4/obj-aarch64-linux-gnu/rdkit/rdBase.so 198: 20# boost::python::handle_exception_impl(boost::function0) in /lib/aarch64-linux-gnu/libboost_python313.so.1.83.0 -198: 21# 0x0000FFFF86D2F25C in /lib/aarch64-linux-gnu/libboost_python313.so.1.83.0 +198: 21# 0x0000FFFFBA62F25C in /lib/aarch64-linux-gnu/libboost_python313.so.1.83.0 198: 22# _PyObject_MakeTpCall in /usr/bin/python3 198: 23# _PyEval_EvalFrameDefault in /usr/bin/python3 198: 24# 0x000000000052F1D8 in /usr/bin/python3 @@ -33732,7 +33754,7 @@ 198: 50# 0x0000000000621C6C in /usr/bin/python3 198: 51# Py_RunMain in /usr/bin/python3 198: 52# Py_BytesMain in /usr/bin/python3 -198: 53# 0x0000FFFF8751229C in /lib/aarch64-linux-gnu/libc.so.6 +198: 53# 0x0000FFFFBAE1229C in /lib/aarch64-linux-gnu/libc.so.6 198: 54# __libc_start_main in /lib/aarch64-linux-gnu/libc.so.6 198: 55# _start in /usr/bin/python3 198: ---------- @@ -33740,152 +33762,81 @@ 198: 198: . 198: ---------------------------------------------------------------------- -198: Ran 9 tests in 0.211s +198: Ran 9 tests in 0.380s 198: 198: OK 198: Testing Trajectory wrapper -188/236 Test #198: pyTestTrajectory ....................... Passed 0.51 sec -test 200 - Start 200: pyTestThreads +187/236 Test #198: pyTestTrajectory ....................... Passed 0.92 sec +test 199 + Start 199: pyTestSGroups -200: Test command: /usr/bin/python3 "/build/reproducible-path/rdkit-202409.4/Code/GraphMol/Wrap/testThreads.py" -200: Working Directory: /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/GraphMol/Wrap -200: Test timeout computed to be: 1500 +199: Test command: /usr/bin/python3 "/build/reproducible-path/rdkit-202409.4/Code/GraphMol/Wrap/testSGroups.py" +199: Working Directory: /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/GraphMol/Wrap +199: Test timeout computed to be: 1500 +187: [21:38:25] Relabelling existing label 199: ............. 199: ---------------------------------------------------------------------- -199: Ran 13 tests in 0.029s +199: Ran 13 tests in 0.024s 199: 199: OK 199: Testing SubstanceGroups wrapper -189/236 Test #199: pyTestSGroups .......................... Passed 0.50 sec +187: Best mapping +188/236 Test #199: pyTestSGroups .......................... Passed 0.44 sec +test 200 + Start 200: pyTestThreads + +200: Test command: /usr/bin/python3 "/build/reproducible-path/rdkit-202409.4/Code/GraphMol/Wrap/testThreads.py" +200: Working Directory: /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/GraphMol/Wrap +200: Test timeout computed to be: 1500 +196: ....................[21:38:25] Explicit valence for atom # 1 F, 2, is greater than permitted +196: [21:38:25] Explicit valence for atom # 6 F, 2, is greater than permitted +196: [21:38:25] Can't kekulize mol. Unkekulized atoms: 3 4 5 +189/236 Test #187: testRGroupDecomp ....................... Passed 6.37 sec test 201 Start 201: pyTestMultithreadedMolSupplier 201: Test command: /usr/bin/python3 "/build/reproducible-path/rdkit-202409.4/Code/GraphMol/Wrap/testMultithreadedMolSupplier.py" 201: Working Directory: /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/GraphMol/Wrap 201: Test timeout computed to be: 1500 -175: ..[12:43:09] -175: -175: **** -175: Invariant Violation -175: molzip: bond info not properly setup for bgn atom with label:1 -175: Violation occurred on line 995 in file ./Code/GraphMol/ChemTransforms/MolFragmenter.cpp -175: Failed Expression: bond.a -175: ---------- -175: Stacktrace: -175: 0# Invar::Invariant::toString[abi:cxx11]() const in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu//lib/libRDKitRDGeneral.so.1 -175: 1# Invar::operator<<(std::ostream&, Invar::Invariant const&) in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu//lib/libRDKitRDGeneral.so.1 -175: 2# RDKit::molzip(RDKit::ROMol const&, RDKit::ROMol const&, RDKit::MolzipParams const&, std::optional, std::allocator > > >&) in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu//lib/libRDKitChemTransforms.so.1 -175: 3# RDKit::molzip(RDKit::ROMol const&, RDKit::ROMol const&, RDKit::MolzipParams const&) in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu//lib/libRDKitChemTransforms.so.1 -175: 4# RDKit::molzip(RDKit::ROMol const&, RDKit::MolzipParams const&) in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu//lib/libRDKitChemTransforms.so.1 -175: 5# RDKit::SynthonSpaceSearch::SynthonSet::transferProductBondsToSynthons() in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu//lib/libRDKitSynthonSpaceSearch.so.1 -175: 6# RDKit::SynthonSpaceSearch::SynthonSpace::readTextFile(std::__cxx11::basic_string, std::allocator > const&) in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu//lib/libRDKitSynthonSpaceSearch.so.1 -175: 7# boost::python::objects::caller_py_function_impl, std::allocator > const&), boost::python::default_call_policies, boost::mpl::vector3, std::allocator > const&> > >::operator()(_object*, _object*) in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/rdkit/Chem/rdSynthonSpaceSearch.so -175: 8# boost::python::objects::function::call(_object*, _object*) const in /lib/aarch64-linux-gnu/libboost_python313.so.1.83.0 -175: 9# 0x0000FFFF99FA2680 in /lib/aarch64-linux-gnu/libboost_python313.so.1.83.0 -175: 10# boost::python::detail::exception_handler::operator()(boost::function0 const&) const in /lib/aarch64-linux-gnu/libboost_python313.so.1.83.0 -175: 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-202409.4/obj-aarch64-linux-gnu/rdkit/Chem/rdmolfiles.so -175: 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-202409.4/obj-aarch64-linux-gnu/rdkit/Chem/rdmolfiles.so -175: 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-202409.4/obj-aarch64-linux-gnu/rdkit/Chem/rdCIPLabeler.so -175: 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-202409.4/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so -175: 15# 0x0000FFFF97A19FA0 in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so -175: 16# 0x0000FFFF97A19F38 in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so -175: 17# 0x0000FFFF97A19EC8 in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so -175: 18# 0x0000FFFF97A19E60 in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so -175: 19# 0x0000FFFF97A19DF8 in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so -175: 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-202409.4/obj-aarch64-linux-gnu/rdkit/rdBase.so -175: 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-202409.4/obj-aarch64-linux-gnu/rdkit/rdBase.so -175: 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-202409.4/obj-aarch64-linux-gnu/rdkit/rdBase.so -175: 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-202409.4/obj-aarch64-linux-gnu/rdkit/rdBase.so -175: 24# boost::python::handle_exception_impl(boost::function0) in /lib/aarch64-linux-gnu/libboost_python313.so.1.83.0 -175: 25# 0x0000FFFF99F9F25C in /lib/aarch64-linux-gnu/libboost_python313.so.1.83.0 -175: 26# _PyObject_MakeTpCall in /usr/bin/python3 -175: 27# 0x000000000052F2FC in /usr/bin/python3 -175: 28# _PyEval_EvalFrameDefault in /usr/bin/python3 -175: 29# 0x000000000052F1D8 in /usr/bin/python3 -175: 30# _PyEval_EvalFrameDefault in /usr/bin/python3 -175: 31# 0x00000000004AB644 in /usr/bin/python3 -175: 32# 0x000000000065E594 in /usr/bin/python3 -175: 33# _PyObject_MakeTpCall in /usr/bin/python3 -175: 34# _PyEval_EvalFrameDefault in /usr/bin/python3 -175: 35# 0x000000000052F1D8 in /usr/bin/python3 -175: 36# _PyEval_EvalFrameDefault in /usr/bin/python3 -175: 37# 0x00000000004AB644 in /usr/bin/python3 -175: 38# 0x000000000065E594 in /usr/bin/python3 -175: 39# _PyObject_MakeTpCall in /usr/bin/python3 -175: 40# _PyEval_EvalFrameDefault in /usr/bin/python3 -175: 41# 0x000000000052F1D8 in /usr/bin/python3 -175: 42# _PyEval_EvalFrameDefault in /usr/bin/python3 -175: 43# 0x00000000004AB644 in /usr/bin/python3 -175: 44# 0x000000000065E594 in /usr/bin/python3 -175: 45# _PyObject_MakeTpCall in /usr/bin/python3 -175: 46# _PyEval_EvalFrameDefault in /usr/bin/python3 -175: 47# 0x0000000000502930 in /usr/bin/python3 -175: 48# _PyObject_MakeTpCall in /usr/bin/python3 -175: 49# _PyEval_EvalFrameDefault in /usr/bin/python3 -175: 50# PyEval_EvalCode in /usr/bin/python3 -175: 51# 0x00000000005FA63C in /usr/bin/python3 -175: 52# 0x00000000005F41C4 in /usr/bin/python3 -175: 53# 0x0000000000622878 in /usr/bin/python3 -175: 54# 0x0000000000621ED4 in /usr/bin/python3 -175: 55# 0x0000000000621C6C in /usr/bin/python3 -175: 56# Py_RunMain in /usr/bin/python3 -175: 57# Py_BytesMain in /usr/bin/python3 -175: 58# 0x0000FFFF9A96229C in /lib/aarch64-linux-gnu/libc.so.6 -175: 59# __libc_start_main in /lib/aarch64-linux-gnu/libc.so.6 -175: 60# _start in /usr/bin/python3 -175: ---------- -175: **** -175: -175: [12:43:09] Error:: in reaction amide-1 :: building molecule from synthons : 1-1 (c1cc[1*]ccc1C(=O)[1*]) and 2-1 ([1*]N1CCCC1) -175: molzip: bond info not properly setup for bgn atom with label:1 -175: [12:43:09] Explicit valence for atom # 4 C, 5, is greater than permitted -175: [12:43:09] Error:: in reaction error-1 :: building molecule from synthons : 1-1 (C(=[2*])=CC=[1*]) and 2-1 (ClC([2*])=CN=[1*]) -175: Explicit valence for atom # 4 C, 5, is greater than permitted -175: . -175: ---------------------------------------------------------------------- -175: Ran 4 tests in 17.382s -175: -175: OK -190/236 Test #175: pySynthonSpaceSearch ................... Passed 17.67 sec +196: .................[21:38:25] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +174: =============================================================================== +174: All tests passed (29 assertions in 4 test cases) +174: +201: .s. +201: ---------------------------------------------------------------------- +201: Ran 3 tests in 0.325s +201: +201: OK (skipped=1) +201: Testing Smiles and SD MultithreadedMolSupplier +190/236 Test #201: pyTestMultithreadedMolSupplier ......... Passed 0.91 sec test 202 Start 202: pyTestPropertyLists 202: Test command: /usr/bin/python3 "/build/reproducible-path/rdkit-202409.4/Code/GraphMol/Wrap/testPropertyLists.py" 202: Working Directory: /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/GraphMol/Wrap 202: Test timeout computed to be: 1500 -201: .s. -201: ---------------------------------------------------------------------- -201: Ran 3 tests in 0.060s -201: -201: OK (skipped=1) -201: Testing Smiles and SD MultithreadedMolSupplier -196: ....................[12:43:09] Explicit valence for atom # 1 F, 2, is greater than permitted -196: [12:43:09] Explicit valence for atom # 6 F, 2, is greater than permitted -196: [12:43:09] Can't kekulize mol. Unkekulized atoms: 3 4 5 -191/236 Test #201: pyTestMultithreadedMolSupplier ......... Passed 0.31 sec +191/236 Test #174: testSynthonSpaceFingerprintSearch ...... Passed 34.74 sec test 203 Start 203: pyCDXMLTest 203: Test command: /usr/bin/python3 "/build/reproducible-path/rdkit-202409.4/Code/GraphMol/Wrap/test_cdxml.py" 203: Working Directory: /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/GraphMol/Wrap 203: Test timeout computed to be: 1500 -196: .................[12:43:09] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -202: [12:43:09] Value [?] for property atom.iprop.PartiallyMissingInt of atom 0 can not be parsed. Ignoring it. -202: [12:43:09] Value ? for property atom.iprop.PartiallyMissingInt of atom 3 can not be parsed. Ignoring it. -202: [12:43:09] Value $$$$ for property atom.iprop.PartiallyMissingInt of atom 4 can not be parsed. Ignoring it. -202: .[12:43:09] Value [?] for property atom.iprop.PartiallyMissingInt of atom 0 can not be parsed. Ignoring it. -202: [12:43:09] Value ? for property atom.iprop.PartiallyMissingInt of atom 3 can not be parsed. Ignoring it. -202: [12:43:09] Value $$$$ for property atom.iprop.PartiallyMissingInt of atom 4 can not be parsed. Ignoring it. -202: ...[12:43:09] Value [?] for property atom.iprop.PartiallyMissingInt of atom 0 can not be parsed. Ignoring it. -202: [12:43:09] Value ? for property atom.iprop.PartiallyMissingInt of atom 3 can not be parsed. Ignoring it. -202: [12:43:09] Value $$$$ for property atom.iprop.PartiallyMissingInt of atom 4 can not be parsed. Ignoring it. +202: [21:38:26] Value [?] for property atom.iprop.PartiallyMissingInt of atom 0 can not be parsed. Ignoring it. +202: [21:38:26] Value ? for property atom.iprop.PartiallyMissingInt of atom 3 can not be parsed. Ignoring it. +202: [21:38:26] Value $$$$ for property atom.iprop.PartiallyMissingInt of atom 4 can not be parsed. Ignoring it. +202: .[21:38:26] Value [?] for property atom.iprop.PartiallyMissingInt of atom 0 can not be parsed. Ignoring it. +202: [21:38:26] Value ? for property atom.iprop.PartiallyMissingInt of atom 3 can not be parsed. Ignoring it. +202: [21:38:26] Value $$$$ for property atom.iprop.PartiallyMissingInt of atom 4 can not be parsed. Ignoring it. +202: ...[21:38:26] Value [?] for property atom.iprop.PartiallyMissingInt of atom 0 can not be parsed. Ignoring it. +202: [21:38:26] Value ? for property atom.iprop.PartiallyMissingInt of atom 3 can not be parsed. Ignoring it. +202: [21:38:26] Value $$$$ for property atom.iprop.PartiallyMissingInt of atom 4 can not be parsed. Ignoring it. 202: . 202: ---------------------------------------------------------------------- -202: Ran 5 tests in 0.008s +202: Ran 5 tests in 0.015s 202: 202: OK -192/236 Test #202: pyTestPropertyLists .................... Passed 0.26 sec +192/236 Test #202: pyTestPropertyLists .................... Passed 0.52 sec test 204 Start 204: molStandardizeTest @@ -33894,25 +33845,25 @@ 204: Test timeout computed to be: 1500 203: . 203: ---------------------------------------------------------------------- -203: Ran 1 test in 0.006s +203: Ran 1 test in 0.019s 203: 203: OK -193/236 Test #203: pyCDXMLTest ............................ Passed 0.26 sec +193/236 Test #203: pyCDXMLTest ............................ Passed 0.62 sec test 205 Start 205: molNormalizeTest 205: Test command: /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/GraphMol/MolStandardize/molNormalizeTest 205: Working Directory: /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/GraphMol/MolStandardize 205: Test timeout computed to be: 1500 -205: [12:43:09] Can't kekulize mol. Unkekulized atoms: 3 7 8 9 -205: [12:43:09] Initializing Normalizer -205: [12:43:09] Running Normalizer -205: [12:43:09] Rule applied: BrokenazidetoN=N+=N- -205: [12:43:09] Initializing Normalizer -205: [12:43:09] Running Normalizer -205: [12:43:09] Initializing Normalizer -205: [12:43:09] Running Normalizer -194/236 Test #205: molNormalizeTest ....................... Passed 0.09 sec +205: [21:38:27] Can't kekulize mol. Unkekulized atoms: 3 7 8 9 +205: [21:38:27] Initializing Normalizer +205: [21:38:27] Running Normalizer +205: [21:38:27] Rule applied: BrokenazidetoN=N+=N- +205: [21:38:27] Initializing Normalizer +205: [21:38:27] Running Normalizer +205: [21:38:27] Initializing Normalizer +205: [21:38:27] Running Normalizer +194/236 Test #205: molNormalizeTest ....................... Passed 0.18 sec test 206 Start 206: molValidateTest @@ -33937,22 +33888,21 @@ 206: ERROR: [StereoValidation] Bond 3 has assigned stereo type, but unexpected bond order. 206: there 206: ERROR: [StereoValidation] Atom 0 has stereo bonds, but less than 3 explicit substituents. -195/236 Test #206: molValidateTest ........................ Passed 0.03 sec +195/236 Test #206: molValidateTest ........................ Passed 0.08 sec test 207 Start 207: molChargeTest 207: Test command: /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/GraphMol/MolStandardize/molChargeTest 207: Working Directory: /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/GraphMol/MolStandardize 207: Test timeout computed to be: 1500 -196/236 Test #207: molChargeTest .......................... Passed 0.05 sec +196/236 Test #207: molChargeTest .......................... Passed 0.14 sec test 208 Start 208: molTautomerTest 208: Test command: /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/GraphMol/MolStandardize/molTautomerTest 208: Working Directory: /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/GraphMol/MolStandardize 208: Test timeout computed to be: 1500 -208: [12:43:10] Tautomer enumeration stopped at 292 tautomers: max transforms reached -197/236 Test #204: molStandardizeTest ..................... Passed 0.59 sec +197/236 Test #204: molStandardizeTest ..................... Passed 1.07 sec test 209 Start 209: molStandardizeSmallTest @@ -33966,8 +33916,8 @@ 210: Test command: /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/GraphMol/MolStandardize/molFragmentTest 210: Working Directory: /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/GraphMol/MolStandardize 210: Test timeout computed to be: 1500 -210: [12:43:10] SMARTS Parse Error: syntax error while parsing: [Cl -210: [12:43:10] SMARTS Parse Error: Failed parsing SMARTS '[Cl' for input: '[Cl' +210: [21:38:28] SMARTS Parse Error: syntax error while parsing: [Cl +210: [21:38:28] SMARTS Parse Error: Failed parsing SMARTS '[Cl' for input: '[Cl' 199/236 Test #210: molFragmentTest ........................ Passed 0.04 sec test 211 Start 211: molStandardizeCatchTest @@ -33975,34 +33925,42 @@ 211: Test command: /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/GraphMol/MolStandardize/molStandardizeCatchTest 211: Working Directory: /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/GraphMol/MolStandardize 211: Test timeout computed to be: 1500 -208: [12:43:10] Tautomer enumeration stopped at 292 tautomers: max transforms reached -208: [12:43:10] Tautomer enumeration stopped at 50 tautomers: max tautomers reached -211: Randomness seeded to: 493008364 +211: Randomness seeded to: 3589111494 211: * - * - * - * m1 211: * - * - * - * m2 211: * - * - * - * m1 211: * - * - * - * m2 -211: [12:43:10] Can't kekulize mol. Unkekulized atoms: 3 7 -211: [12:43:10] Can't kekulize mol. Unkekulized atoms: 3 8 -211: [12:43:10] Can't kekulize mol. Unkekulized atoms: 2 3 4 -174: =============================================================================== -174: All tests passed (29 assertions in 4 test cases) -174: -208: [12:43:10] Tautomer enumeration stopped at 129 tautomers: canceled +211: [21:38:28] Can't kekulize mol. Unkekulized atoms: 3 7 +211: [21:38:28] Can't kekulize mol. Unkekulized atoms: 3 8 +211: [21:38:28] Can't kekulize mol. Unkekulized atoms: 2 3 4 +208: [21:38:28] Tautomer enumeration stopped at 292 tautomers: max transforms reached +208: [21:38:28] Tautomer enumeration stopped at 292 tautomers: max transforms reached +208: [21:38:28] Tautomer enumeration stopped at 50 tautomers: max tautomers reached +208: [21:38:29] Tautomer enumeration stopped at 83 tautomers: canceled 208: Enumeration was canceled due to timeout (50 ms) -200/236 Test #174: testSynthonSpaceFingerprintSearch ...... Passed 21.67 sec +208: 375 +208: Enumeration has completed +208: [21:38:29] Tautomer enumeration stopped at 85 tautomers: canceled +208: CN=c1cc[nH]cn1 +208: CN=c1ccnc[nH]1 +208: CNc1ccncn1 +208: res: CNc1ccncn1 +208: CN=c1cccc[nH]1 +208: CNc1ccccn1 +208: res: CNc1ccccn1 +200/236 Test #208: molTautomerTest ........................ Passed 3.04 sec test 212 Start 212: molStandardizePipelineTest 212: Test command: /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/GraphMol/MolStandardize/molStandardizePipelineTest 212: Working Directory: /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/GraphMol/MolStandardize 212: Test timeout computed to be: 1500 -212: Randomness seeded to: 402236231 +212: Randomness seeded to: 3425311833 212: 1 Counts line too short: '' on line4 212: 1 Could not instantiate a valid molecule from input 212: 8 Molecule has no atoms -212: [12:43:10] Explicit valence for atom # 1 N, 4, is greater than permitted -212: [12:43:10] Explicit valence for atom # 1 N, 4, is greater than permitted +212: [21:38:30] Explicit valence for atom # 1 N, 4, is greater than permitted +212: [21:38:30] Explicit valence for atom # 1 N, 4, is greater than permitted 212: 8 Explicit valence for atom # 1 N, 4, is greater than permitted 212: 128 An error occurred while preparing the molecule for standardization. 212: 8 The molecule contains an unknown isotope: 3C @@ -34017,13 +33975,13 @@ 212: 4 Bond 3 of dative type is not allowed 212: 4 Enhanced stereochemistry features are not allowed 212: 8 The radical at atom 0 is not allowed -212: [12:43:10] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +212: [21:38:30] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 212: 16 The molecule includes non-null Z coordinates 212: 32 Atom 0 too close to bond 2 212: 32 The length of bond 3 between atoms 0 and 3 exceeds a configured limit 212: 64 Atom 0 has 3 explicit substituents and multiple stereo bonds 212: 64 Atom 0 has adjacent stereo bonds with like orientation -212: [12:43:10] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +212: [21:38:30] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 212: 16 The molecule includes non-null Z coordinates 212: 64 Atom 0 has adjacent stereo bonds with like orientation 212: 32 The length of bond 16 between atoms 16 and 1 exceeds a configured limit @@ -34069,395 +34027,108 @@ 212: 16777216 Double bond 2 was assigned an undefined/unknown stereochemical configuration 212: 16777216 The "wavy" style of bond 3 was removed 212: 16777216 The representation of some functional groups was adjusted. -212: [12:43:10] Can't kekulize mol. Unkekulized atoms: 2 3 5 -208: 375 -208: Enumeration has completed +212: [21:38:31] Can't kekulize mol. Unkekulized atoms: 2 3 5 212: =============================================================================== 212: All tests passed (268 assertions in 5 test cases) 212: -201/236 Test #212: molStandardizePipelineTest ............. Passed 0.13 sec +201/236 Test #212: molStandardizePipelineTest ............. Passed 0.18 sec test 213 Start 213: pyMolStandardize 213: Test command: /usr/bin/python3 "/build/reproducible-path/rdkit-202409.4/Code/GraphMol/MolStandardize/Wrap/testMolStandardize.py" 213: Working Directory: /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/GraphMol/MolStandardize/Wrap 213: Test timeout computed to be: 1500 -208: [12:43:11] Tautomer enumeration stopped at 130 tautomers: canceled -208: CN=c1cc[nH]cn1 -208: CN=c1ccnc[nH]1 -208: CNc1ccncn1 -208: res: CNc1ccncn1 -208: CN=c1cccc[nH]1 -208: CNc1ccccn1 -208: res: CNc1ccccn1 -213: .....[12:43:11] Tautomer enumeration stopped at 292 tautomers: max transforms reached -213: [12:43:11] Tautomer enumeration stopped at 50 tautomers: max tautomers reached -202/236 Test #208: molTautomerTest ........................ Passed 1.48 sec +175: ..[21:38:31] +175: +175: **** +175: Invariant Violation +175: molzip: bond info not properly setup for bgn atom with label:1 +175: Violation occurred on line 995 in file ./Code/GraphMol/ChemTransforms/MolFragmenter.cpp +175: Failed Expression: bond.a +175: ---------- +175: Stacktrace: +175: 0# Invar::Invariant::toString[abi:cxx11]() const in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu//lib/libRDKitRDGeneral.so.1 +175: 1# Invar::operator<<(std::ostream&, Invar::Invariant const&) in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu//lib/libRDKitRDGeneral.so.1 +175: 2# RDKit::molzip(RDKit::ROMol const&, RDKit::ROMol const&, RDKit::MolzipParams const&, std::optional, std::allocator > > >&) in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu//lib/libRDKitChemTransforms.so.1 +175: 3# RDKit::molzip(RDKit::ROMol const&, RDKit::ROMol const&, RDKit::MolzipParams const&) in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu//lib/libRDKitChemTransforms.so.1 +175: 4# RDKit::molzip(RDKit::ROMol const&, RDKit::MolzipParams const&) in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu//lib/libRDKitChemTransforms.so.1 +175: 5# RDKit::SynthonSpaceSearch::SynthonSet::transferProductBondsToSynthons() in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu//lib/libRDKitSynthonSpaceSearch.so.1 +175: 6# RDKit::SynthonSpaceSearch::SynthonSpace::readTextFile(std::__cxx11::basic_string, std::allocator > const&) in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu//lib/libRDKitSynthonSpaceSearch.so.1 +175: 7# boost::python::objects::caller_py_function_impl, std::allocator > const&), boost::python::default_call_policies, boost::mpl::vector3, std::allocator > const&> > >::operator()(_object*, _object*) in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/rdkit/Chem/rdSynthonSpaceSearch.so +175: 8# boost::python::objects::function::call(_object*, _object*) const in /lib/aarch64-linux-gnu/libboost_python313.so.1.83.0 +175: 9# 0x0000FFFF89DA2680 in /lib/aarch64-linux-gnu/libboost_python313.so.1.83.0 +175: 10# boost::python::detail::exception_handler::operator()(boost::function0 const&) const in /lib/aarch64-linux-gnu/libboost_python313.so.1.83.0 +175: 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-202409.4/obj-aarch64-linux-gnu/rdkit/Chem/rdmolfiles.so +175: 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-202409.4/obj-aarch64-linux-gnu/rdkit/Chem/rdmolfiles.so +175: 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-202409.4/obj-aarch64-linux-gnu/rdkit/Chem/rdCIPLabeler.so +175: 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-202409.4/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so +175: 15# 0x0000FFFF87819FA0 in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so +175: 16# 0x0000FFFF87819F38 in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so +175: 17# 0x0000FFFF87819EC8 in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so +175: 18# 0x0000FFFF87819E60 in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so +175: 19# 0x0000FFFF87819DF8 in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so +175: 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-202409.4/obj-aarch64-linux-gnu/rdkit/rdBase.so +175: 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-202409.4/obj-aarch64-linux-gnu/rdkit/rdBase.so +175: 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-202409.4/obj-aarch64-linux-gnu/rdkit/rdBase.so +175: 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-202409.4/obj-aarch64-linux-gnu/rdkit/rdBase.so +175: 24# boost::python::handle_exception_impl(boost::function0) in /lib/aarch64-linux-gnu/libboost_python313.so.1.83.0 +175: 25# 0x0000FFFF89D9F25C in /lib/aarch64-linux-gnu/libboost_python313.so.1.83.0 +175: 26# _PyObject_MakeTpCall in /usr/bin/python3 +175: 27# 0x000000000052F2FC in /usr/bin/python3 +175: 28# _PyEval_EvalFrameDefault in /usr/bin/python3 +175: 29# 0x000000000052F1D8 in /usr/bin/python3 +175: 30# _PyEval_EvalFrameDefault in /usr/bin/python3 +175: 31# 0x00000000004AB644 in /usr/bin/python3 +175: 32# 0x000000000065E594 in /usr/bin/python3 +175: 33# _PyObject_MakeTpCall in /usr/bin/python3 +175: 34# _PyEval_EvalFrameDefault in /usr/bin/python3 +175: 35# 0x000000000052F1D8 in /usr/bin/python3 +175: 36# _PyEval_EvalFrameDefault in /usr/bin/python3 +175: 37# 0x00000000004AB644 in /usr/bin/python3 +175: 38# 0x000000000065E594 in /usr/bin/python3 +175: 39# _PyObject_MakeTpCall in /usr/bin/python3 +175: 40# _PyEval_EvalFrameDefault in /usr/bin/python3 +175: 41# 0x000000000052F1D8 in /usr/bin/python3 +175: 42# _PyEval_EvalFrameDefault in /usr/bin/python3 +175: 43# 0x00000000004AB644 in /usr/bin/python3 +175: 44# 0x000000000065E594 in /usr/bin/python3 +175: 45# _PyObject_MakeTpCall in /usr/bin/python3 +175: 46# _PyEval_EvalFrameDefault in /usr/bin/python3 +175: 47# 0x0000000000502930 in /usr/bin/python3 +175: 48# _PyObject_MakeTpCall in /usr/bin/python3 +175: 49# _PyEval_EvalFrameDefault in /usr/bin/python3 +175: 50# PyEval_EvalCode in /usr/bin/python3 +175: 51# 0x00000000005FA63C in /usr/bin/python3 +175: 52# 0x00000000005F41C4 in /usr/bin/python3 +175: 53# 0x0000000000622878 in /usr/bin/python3 +175: 54# 0x0000000000621ED4 in /usr/bin/python3 +175: 55# 0x0000000000621C6C in /usr/bin/python3 +175: 56# Py_RunMain in /usr/bin/python3 +175: 57# Py_BytesMain in /usr/bin/python3 +175: 58# 0x0000FFFF8A76229C in /lib/aarch64-linux-gnu/libc.so.6 +175: 59# __libc_start_main in /lib/aarch64-linux-gnu/libc.so.6 +175: 60# _start in /usr/bin/python3 +175: ---------- +175: **** +175: +175: [21:38:31] Error:: in reaction amide-1 :: building molecule from synthons : 1-1 (c1cc[1*]ccc1C(=O)[1*]) and 2-1 ([1*]N1CCCC1) +175: molzip: bond info not properly setup for bgn atom with label:1 +175: [21:38:31] Explicit valence for atom # 4 C, 5, is greater than permitted +175: [21:38:31] Error:: in reaction error-1 :: building molecule from synthons : 1-1 (C(=[2*])=CC=[1*]) and 2-1 (ClC([2*])=CN=[1*]) +175: Explicit valence for atom # 4 C, 5, is greater than permitted +175: . +175: ---------------------------------------------------------------------- +175: Ran 4 tests in 31.971s +175: +175: OK +202/236 Test #175: pySynthonSpaceSearch ................... Passed 32.48 sec test 214 Start 214: testScaffoldNetwork 214: Test command: /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/GraphMol/ScaffoldNetwork/testScaffoldNetwork 214: Working Directory: /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/GraphMol/ScaffoldNetwork 214: Test timeout computed to be: 1500 -213: .[12:43:11] Tautomer enumeration stopped at 91 tautomers: canceled -213: Enumeration was canceled due to timeout (50 ms) -203/236 Test #200: pyTestThreads .......................... Passed 2.89 sec -test 215 - Start 215: pyScaffoldNetwork - -215: Test command: /usr/bin/python3 "/build/reproducible-path/rdkit-202409.4/Code/GraphMol/ScaffoldNetwork/Wrap/testScaffoldNetwork.py" -215: Working Directory: /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/GraphMol/ScaffoldNetwork/Wrap -215: Test timeout computed to be: 1500 -214: Randomness seeded to: 1250472847 -214: =============================================================================== -214: All tests passed (273 assertions in 19 test cases) -214: -204/236 Test #214: testScaffoldNetwork .................... Passed 0.67 sec -test 216 - Start 216: pyScaffoldNetworkPickling - -216: Test command: /usr/bin/python3 "/build/reproducible-path/rdkit-202409.4/Code/GraphMol/ScaffoldNetwork/Wrap/testPickleScaffoldNetwork.py" -216: Working Directory: /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/GraphMol/ScaffoldNetwork/Wrap -216: Test timeout computed to be: 1500 -215: ....... -215: ---------------------------------------------------------------------- -215: Ran 7 tests in 0.024s -215: -215: OK -213: Enumeration has completed -205/236 Test #215: pyScaffoldNetwork ...................... Passed 0.26 sec -test 217 - Start 217: testMolEnumerator - -217: Test command: /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/GraphMol/MolEnumerator/testMolEnumerator -217: Working Directory: /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/GraphMol/MolEnumerator -217: Test timeout computed to be: 1500 -213: [12:43:12] Tautomer enumeration stopped at 91 tautomers: canceled -217: Randomness seeded to: 568572144 -217: [12:43:12] can only enumerate SRUs with CONNECT=HT or CONNECT=HH -217: =============================================================================== -217: All tests passed (321 assertions in 16 test cases) -217: -206/236 Test #217: testMolEnumerator ...................... Passed 0.05 sec -test 218 - Start 218: pyMolEnumerator - -218: Test command: /usr/bin/python3 "/build/reproducible-path/rdkit-202409.4/Code/GraphMol/MolEnumerator/Wrap/rough_test.py" -218: Working Directory: /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/GraphMol/MolEnumerator/Wrap -218: Test timeout computed to be: 1500 -216: . -216: ---------------------------------------------------------------------- -216: Ran 1 test in 0.008s -216: -216: OK -207/236 Test #216: pyScaffoldNetworkPickling .............. Passed 0.24 sec -test 219 - Start 219: testAbbreviations - -219: Test command: /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/GraphMol/Abbreviations/testAbbreviations -219: Working Directory: /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/GraphMol/Abbreviations -219: Test timeout computed to be: 1500 -219: Randomness seeded to: 764267448 -219: [12:43:12] SMARTS Parse Error: syntax error while parsing: *fail -219: [12:43:12] SMARTS Parse Error: Failed parsing SMARTS '*fail' for input: '*fail' -219: [12:43:12] no suitable SubstanceGroups found -219: =============================================================================== -219: All tests passed (195 assertions in 12 test cases) -219: -208/236 Test #219: testAbbreviations ...................... Passed 0.03 sec -test 220 - Start 220: pyAbbreviations - -220: Test command: /usr/bin/python3 "/build/reproducible-path/rdkit-202409.4/Code/GraphMol/Abbreviations/Wrap/testAbbreviations.py" -220: Working Directory: /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/GraphMol/Abbreviations/Wrap -220: Test timeout computed to be: 1500 -213: ..........[12:43:12] Explicit valence for atom # 1 N, 4, is greater than permitted -213: [12:43:12] Explicit valence for atom # 1 N, 4, is greater than permitted -213: [12:43:12] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -213: [12:43:12] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -218: ... -218: ---------------------------------------------------------------------- -218: Ran 3 tests in 0.008s -218: -218: OK -209/236 Test #218: pyMolEnumerator ........................ Passed 0.24 sec -test 221 - Start 221: generalizedSubstructCatch - -221: Test command: /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/GraphMol/GeneralizedSubstruct/generalizedSubstructCatch -221: Working Directory: /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/GraphMol/GeneralizedSubstruct -221: Test timeout computed to be: 1500 -220: ....... -220: ---------------------------------------------------------------------- -220: Ran 7 tests in 0.028s -220: -220: OK -221: Randomness seeded to: 1866849843 -221: =============================================================================== -221: All tests passed (486 assertions in 10 test cases) -221: -210/236 Test #221: generalizedSubstructCatch .............. Passed 0.14 sec -test 222 - Start 222: pyGeneralizedSubstruct - -222: Test command: /usr/bin/python3 "/build/reproducible-path/rdkit-202409.4/Code/GraphMol/GeneralizedSubstruct/Wrap/testGeneralizedSubstruct.py" -222: Working Directory: /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/GraphMol/GeneralizedSubstruct/Wrap -222: Test timeout computed to be: 1500 -211/236 Test #220: pyAbbreviations ........................ Passed 0.33 sec -test 223 - Start 223: testMolProcessing - -223: Test command: /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/GraphMol/MolProcessing/testMolProcessing -223: Working Directory: /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/GraphMol/MolProcessing -223: Test timeout computed to be: 1500 -222: ....... -222: ---------------------------------------------------------------------- -222: Ran 7 tests in 0.091s -222: -222: OK -212/236 Test #222: pyGeneralizedSubstruct ................. Passed 0.35 sec -test 224 - Start 224: pyMolProcessing - -224: Test command: /usr/bin/python3 "/build/reproducible-path/rdkit-202409.4/Code/GraphMol/MolProcessing/Wrap/testMolProcessing.py" -224: Working Directory: /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/GraphMol/MolProcessing/Wrap -224: Test timeout computed to be: 1500 -213: ............[12:43:13] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -213: [12:43:13] Warning: ambiguous stereochemistry - opposing bonds have opposite wedging - at atom 1 ignored. -213: [12:43:13] Warning: ambiguous stereochemistry - opposing bonds have opposite wedging - at atom 1 ignored. -213: ........[12:43:13] Explicit valence for atom # 1 O, 3, is greater than permitted -213: .. -213: ---------------------------------------------------------------------- -213: Ran 38 tests in 2.149s -213: -213: OK -213: done -213/236 Test #213: pyMolStandardize ....................... Passed 2.40 sec -test 225 - Start 225: testMIF - -225: Test command: /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/GraphMol/MolInteractionFields/testMIF -225: Working Directory: /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/GraphMol/MolInteractionFields -225: Test timeout computed to be: 1500 -225: Randomness seeded to: 1972641363 -225: =============================================================================== -225: All tests passed (27926 assertions in 8 test cases) -225: -214/236 Test #225: testMIF ................................ Passed 0.04 sec -test 226 - Start 226: pyMIF - -226: Test command: /usr/bin/python3 "/build/reproducible-path/rdkit-202409.4/Code/GraphMol/MolInteractionFields/Wrap/testMIF.py" -226: Working Directory: /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/GraphMol/MolInteractionFields/Wrap -226: Test timeout computed to be: 1500 -224: .. -224: ---------------------------------------------------------------------- -224: Ran 2 tests in 0.185s -224: -224: OK -215/236 Test #224: pyMolProcessing ........................ Passed 0.42 sec -test 227 - Start 227: testQuery - -227: Test command: /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/Query/testQuery -227: Working Directory: /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/Query -227: Test timeout computed to be: 1500 -227: Query -227: Query2 -227: Equality -227: Greater -227: GreaterEqual -227: Less -227: LessEqual -227: Open Range -227: Closed Range -227: Float -227: With Tolerance -227: Set -227: And -227: Or -227: XOr -227: pointer and copy foo -227: Set2 -216/236 Test #227: testQuery .............................. Passed 0.00 sec -test 228 - Start 228: testMatCalc - -228: Test command: /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/DataManip/MetricMatrixCalc/testMatCalc -228: Working Directory: /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/DataManip/MetricMatrixCalc -228: Test timeout computed to be: 1500 -228: 1.68022e+08 -228: 1.73149e+08 -228: 1.05549e+08 -228: 7.20603e+07 -228: 1.41535e+08 -228: 1.08592e+08 -228: 1.11334e+08 -228: 2.05553e+08 -228: 1.54962e+08 -228: 8.08231e+07 -228: 5.61421e+07 -228: 1.28874e+08 -228: 1.59011e+08 -228: 8.69902e+07 -228: 1.31367e+08 -228: 2.27389e+08 -228: 1.60289e+08 -228: 7.79813e+07 -228: 1.61001e+08 -228: 2.07599e+08 -228: 2.24432e+08 -228: 1.39725e+08 -228: 2.42614e+08 -228: 1.77578e+08 -228: 1.05908e+08 -228: 9.06742e+07 -228: 1.8087e+08 -228: 1.98182e+08 -228: 2.03052e+08 -228: 1.7673e+08 -228: 9.32798e+07 -228: 1.37969e+08 -228: 1.83778e+08 -228: 2.1228e+08 -228: 5.06157e+07 -228: 1.566e+08 -228: 2.37142e+08 -228: 1.49345e+08 -228: 7.05819e+07 -228: 1.71633e+08 -228: 1.96817e+08 -228: 2.18246e+08 -228: 9.49496e+07 -228: 2.25618e+08 -228: 1.30219e+08 -217/236 Test #228: testMatCalc ............................ Passed 0.00 sec -test 229 - Start 229: pyMatCalc - -229: Test command: /usr/bin/python3 "/build/reproducible-path/rdkit-202409.4/Code/DataManip/MetricMatrixCalc/Wrap/testMatricCalc.py" -229: Working Directory: /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/DataManip/MetricMatrixCalc/Wrap -229: Test timeout computed to be: 1500 -226: ....... -226: ---------------------------------------------------------------------- -226: Ran 7 tests in 0.039s -226: -226: OK -226: Testing MIF wrapper -218/236 Test #226: pyMIF .................................. Passed 0.29 sec -test 230 - Start 230: testSimDivPickers - -230: Test command: /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/SimDivPickers/testSimDivPickers -230: Working Directory: /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/SimDivPickers -230: Test timeout computed to be: 1500 -230: [12:43:13] ------------------------------------- -230: [12:43:13] Testing github issue 1421: MaxMinPicker picking non-existent element. -230: [12:43:13] Done -230: [12:43:13] ------------------------------------- -230: [12:43:13] Testing github issue 2245: MinMax Diversity picker seeding shows deterministic / non-random behaviour. -230: [12:43:13] Done -219/236 Test #230: testSimDivPickers ...................... Passed 0.00 sec -test 231 - Start 231: pickersTestsCatch - -231: Test command: /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/SimDivPickers/pickersTestsCatch -231: Working Directory: /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/SimDivPickers -231: Test timeout computed to be: 1500 -146: [12:43:13] done -231: Randomness seeded to: 4108648646 -231: =============================================================================== -231: All tests passed (21267 assertions in 1 test case) -231: -220/236 Test #231: pickersTestsCatch ...................... Passed 0.05 sec -test 232 - Start 232: pySimDivPickers - -232: Test command: /usr/bin/python3 "/build/reproducible-path/rdkit-202409.4/Code/SimDivPickers/Wrap/testPickers.py" -232: Working Directory: /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/SimDivPickers/Wrap -232: Test timeout computed to be: 1500 -229: ..... -229: ---------------------------------------------------------------------- -229: Ran 5 tests in 0.165s -229: -229: OK -221/236 Test #229: pyMatCalc .............................. Passed 0.36 sec -test 233 - Start 233: pyRanker - -233: Test command: /usr/bin/python3 "/build/reproducible-path/rdkit-202409.4/Code/ML/InfoTheory/Wrap/testRanker.py" -233: Working Directory: /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/ML/InfoTheory/Wrap -233: Test timeout computed to be: 1500 -232: [12:43:13] the useCache argument is deprecated and ignored -233: ..[12:43:14] -233: -233: **** -233: Invariant Violation -233: Can't rank more bits than the ensemble size -233: Violation occurred on line 156 in file ./Code/ML/InfoTheory/InfoBitRanker.cpp -233: Failed Expression: num <= dp_maskBits->getNumOnBits() -233: ---------- -233: Stacktrace: -233: 0# Invar::Invariant::toString[abi:cxx11]() const in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu//lib/libRDKitRDGeneral.so.1 -233: 1# Invar::operator<<(std::ostream&, Invar::Invariant const&) in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu//lib/libRDKitRDGeneral.so.1 -233: 2# RDInfoTheory::InfoBitRanker::getTopN(unsigned int) in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu//lib/libRDKitInfoTheory.so.1 -233: 3# RDInfoTheory::getTopNbits(RDInfoTheory::InfoBitRanker*, int) in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/rdkit/ML/InfoTheory/rdInfoTheory.so -233: 4# boost::python::objects::caller_py_function_impl > >::operator()(_object*, _object*) in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/rdkit/ML/InfoTheory/rdInfoTheory.so -233: 5# boost::python::objects::function::call(_object*, _object*) const in /lib/aarch64-linux-gnu/libboost_python313.so.1.83.0 -233: 6# 0x0000FFFFAB1A2680 in /lib/aarch64-linux-gnu/libboost_python313.so.1.83.0 -233: 7# boost::python::detail::exception_handler::operator()(boost::function0 const&) const in /lib/aarch64-linux-gnu/libboost_python313.so.1.83.0 -233: 8# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/rdkit/rdBase.so -233: 9# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/rdkit/rdBase.so -233: 10# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/rdkit/rdBase.so -233: 11# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/rdkit/rdBase.so -233: 12# boost::python::handle_exception_impl(boost::function0) in /lib/aarch64-linux-gnu/libboost_python313.so.1.83.0 -233: 13# 0x0000FFFFAB19F25C in /lib/aarch64-linux-gnu/libboost_python313.so.1.83.0 -233: 14# _PyObject_MakeTpCall in /usr/bin/python3 -233: 15# _PyEval_EvalFrameDefault in /usr/bin/python3 -233: 16# 0x000000000052F1D8 in /usr/bin/python3 -233: 17# _PyEval_EvalFrameDefault in /usr/bin/python3 -233: 18# 0x00000000004AB644 in /usr/bin/python3 -233: 19# 0x000000000065E594 in /usr/bin/python3 -233: 20# _PyObject_MakeTpCall in /usr/bin/python3 -233: 21# _PyEval_EvalFrameDefault in /usr/bin/python3 -233: 22# 0x000000000052F1D8 in /usr/bin/python3 -233: 23# _PyEval_EvalFrameDefault in /usr/bin/python3 -233: 24# 0x00000000004AB644 in /usr/bin/python3 -233: 25# 0x000000000065E594 in /usr/bin/python3 -233: 26# _PyObject_MakeTpCall in /usr/bin/python3 -233: 27# _PyEval_EvalFrameDefault in /usr/bin/python3 -233: 28# 0x000000000052F1D8 in /usr/bin/python3 -233: 29# _PyEval_EvalFrameDefault in /usr/bin/python3 -233: 30# 0x00000000004AB644 in /usr/bin/python3 -233: 31# 0x000000000065E594 in /usr/bin/python3 -233: 32# _PyObject_MakeTpCall in /usr/bin/python3 -233: 33# _PyEval_EvalFrameDefault in /usr/bin/python3 -233: 34# 0x0000000000502930 in /usr/bin/python3 -233: 35# _PyObject_MakeTpCall in /usr/bin/python3 -233: 36# _PyEval_EvalFrameDefault in /usr/bin/python3 -233: 37# PyEval_EvalCode in /usr/bin/python3 -233: 38# 0x00000000005FA63C in /usr/bin/python3 -233: 39# 0x00000000005F41C4 in /usr/bin/python3 -233: 40# 0x0000000000622878 in /usr/bin/python3 -233: 41# 0x0000000000621ED4 in /usr/bin/python3 -233: 42# 0x0000000000621C6C in /usr/bin/python3 -233: 43# Py_RunMain in /usr/bin/python3 -233: 44# Py_BytesMain in /usr/bin/python3 -233: 45# 0x0000FFFFAD63229C in /lib/aarch64-linux-gnu/libc.so.6 -233: 46# __libc_start_main in /lib/aarch64-linux-gnu/libc.so.6 -233: 47# _start in /usr/bin/python3 -233: ---------- -233: **** -233: -233: ... -233: ---------------------------------------------------------------------- -233: Ran 5 tests in 0.013s -233: -233: OK -232: ...[12:43:14] the useCache argument is deprecated and ignored -232: [12:43:14] the useCache argument is deprecated and ignored -232: .[12:43:14] the useCache argument is deprecated and ignored -186: ......[12:43:14] +186: ......[21:38:31] 186: 186: **** 186: Pre-condition Violation @@ -34478,25 +34149,25 @@ 186: 9# RDKit::SubstructMatch(RDKit::ROMol const&, RDKit::ROMol const&, RDKit::SubstructMatchParameters const&) in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu//lib/libRDKitSubstructMatch.so.1 186: 10# bool RDKit::SubstructMatch(RDKit::ROMol const&, RDKit::ROMol const&, std::vector, std::allocator > >&, bool, bool, bool) in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so 186: 11# bool RDKit::HasSubstructMatch(RDKit::ROMol const&, RDKit::ROMol const&, bool, bool, bool) in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so -186: 12# 0x0000FFFFA40BF930 in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so +186: 12# 0x0000FFFFA9FEF930 in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so 186: 13# boost::python::objects::function::call(_object*, _object*) const in /lib/aarch64-linux-gnu/libboost_python313.so.1.83.0 -186: 14# 0x0000FFFFA6682680 in /lib/aarch64-linux-gnu/libboost_python313.so.1.83.0 +186: 14# 0x0000FFFFAC5B2680 in /lib/aarch64-linux-gnu/libboost_python313.so.1.83.0 186: 15# boost::python::detail::exception_handler::operator()(boost::function0 const&) const in /lib/aarch64-linux-gnu/libboost_python313.so.1.83.0 186: 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-202409.4/obj-aarch64-linux-gnu/rdkit/Chem/rdmolfiles.so 186: 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-202409.4/obj-aarch64-linux-gnu/rdkit/Chem/rdmolfiles.so 186: 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-202409.4/obj-aarch64-linux-gnu/rdkit/Chem/rdCIPLabeler.so 186: 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-202409.4/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so -186: 20# 0x0000FFFFA4019FA0 in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so -186: 21# 0x0000FFFFA4019F38 in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so -186: 22# 0x0000FFFFA4019EC8 in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so -186: 23# 0x0000FFFFA4019E60 in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so -186: 24# 0x0000FFFFA4019DF8 in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so +186: 20# 0x0000FFFFA9F49FA0 in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so +186: 21# 0x0000FFFFA9F49F38 in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so +186: 22# 0x0000FFFFA9F49EC8 in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so +186: 23# 0x0000FFFFA9F49E60 in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so +186: 24# 0x0000FFFFA9F49DF8 in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so 186: 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-202409.4/obj-aarch64-linux-gnu/rdkit/rdBase.so 186: 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-202409.4/obj-aarch64-linux-gnu/rdkit/rdBase.so 186: 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-202409.4/obj-aarch64-linux-gnu/rdkit/rdBase.so 186: 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-202409.4/obj-aarch64-linux-gnu/rdkit/rdBase.so 186: 29# boost::python::handle_exception_impl(boost::function0) in /lib/aarch64-linux-gnu/libboost_python313.so.1.83.0 -186: 30# 0x0000FFFFA667F25C in /lib/aarch64-linux-gnu/libboost_python313.so.1.83.0 +186: 30# 0x0000FFFFAC5AF25C in /lib/aarch64-linux-gnu/libboost_python313.so.1.83.0 186: 31# _PyObject_MakeTpCall in /usr/bin/python3 186: 32# _PyEval_EvalFrameDefault in /usr/bin/python3 186: 33# 0x000000000052F1D8 in /usr/bin/python3 @@ -34528,15 +34199,16 @@ 186: 59# 0x0000000000621C6C in /usr/bin/python3 186: 60# Py_RunMain in /usr/bin/python3 186: 61# Py_BytesMain in /usr/bin/python3 -186: 62# 0x0000FFFFA706229C in /lib/aarch64-linux-gnu/libc.so.6 +186: 62# 0x0000FFFFACF9229C in /lib/aarch64-linux-gnu/libc.so.6 186: 63# __libc_start_main in /lib/aarch64-linux-gnu/libc.so.6 186: 64# _start in /usr/bin/python3 186: ---------- 186: **** 186: -186: [12:43:14] +186: [21:38:31] 186: 186: **** +213: .....[21:38:31] Tautomer enumeration stopped at 292 tautomers: max transforms reached 186: Pre-condition Violation 186: RingInfo not initialized 186: Violation occurred on line 129 in file ./Code/GraphMol/RingInfo.cpp @@ -34546,7 +34218,7 @@ 186: 0# Invar::Invariant::toString[abi:cxx11]() const in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu//lib/libRDKitRDGeneral.so.1 186: 1# Invar::operator<<(std::ostream&, Invar::Invariant const&) in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu//lib/libRDKitRDGeneral.so.1 186: 2# RDKit::RingInfo::numBondRings(unsigned int) const in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu//lib/libRDKitGraphMol.so.1 -186: 3# 0x0000FFFFA3B70848 in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu//lib/libRDKitGraphMol.so.1 +186: 3# 0x0000FFFFA9AA0848 in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu//lib/libRDKitGraphMol.so.1 186: 4# Queries::EqualityQuery::Match(RDKit::Bond const*) const in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu//lib/libRDKitGraphMol.so.1 186: 5# RDKit::bondCompat(RDKit::Bond const*, RDKit::Bond const*, RDKit::SubstructMatchParameters const&) in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu//lib/libRDKitSubstructMatch.so.1 186: 6# boost::detail::VF2SubState const, RDKit::detail::AtomLabelFunctor, RDKit::detail::BondLabelFunctor, RDKit::MolMatchFinalCheckFunctor>::IsFeasiblePair(unsigned int, unsigned int) in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu//lib/libRDKitSubstructMatch.so.1 @@ -34556,25 +34228,25 @@ 186: 10# RDKit::SubstructMatch(RDKit::ROMol const&, RDKit::ROMol const&, RDKit::SubstructMatchParameters const&) in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu//lib/libRDKitSubstructMatch.so.1 186: 11# bool RDKit::SubstructMatch(RDKit::ROMol const&, RDKit::ROMol const&, std::vector, std::allocator > >&, bool, bool, bool) in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so 186: 12# bool RDKit::HasSubstructMatch(RDKit::ROMol const&, RDKit::ROMol const&, bool, bool, bool) in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so -186: 13# 0x0000FFFFA40BF930 in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so +186: 13# 0x0000FFFFA9FEF930 in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so 186: 14# boost::python::objects::function::call(_object*, _object*) const in /lib/aarch64-linux-gnu/libboost_python313.so.1.83.0 -186: 15# 0x0000FFFFA6682680 in /lib/aarch64-linux-gnu/libboost_python313.so.1.83.0 +186: 15# 0x0000FFFFAC5B2680 in /lib/aarch64-linux-gnu/libboost_python313.so.1.83.0 186: 16# boost::python::detail::exception_handler::operator()(boost::function0 const&) const in /lib/aarch64-linux-gnu/libboost_python313.so.1.83.0 186: 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-202409.4/obj-aarch64-linux-gnu/rdkit/Chem/rdmolfiles.so 186: 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-202409.4/obj-aarch64-linux-gnu/rdkit/Chem/rdmolfiles.so 186: 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-202409.4/obj-aarch64-linux-gnu/rdkit/Chem/rdCIPLabeler.so 186: 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-202409.4/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so -186: 21# 0x0000FFFFA4019FA0 in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so -186: 22# 0x0000FFFFA4019F38 in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so -186: 23# 0x0000FFFFA4019EC8 in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so -186: 24# 0x0000FFFFA4019E60 in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so -186: 25# 0x0000FFFFA4019DF8 in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so +186: 21# 0x0000FFFFA9F49FA0 in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so +186: 22# 0x0000FFFFA9F49F38 in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so +186: 23# 0x0000FFFFA9F49EC8 in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so +186: 24# 0x0000FFFFA9F49E60 in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so +186: 25# 0x0000FFFFA9F49DF8 in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so 186: 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-202409.4/obj-aarch64-linux-gnu/rdkit/rdBase.so 186: 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-202409.4/obj-aarch64-linux-gnu/rdkit/rdBase.so 186: 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-202409.4/obj-aarch64-linux-gnu/rdkit/rdBase.so 186: 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-202409.4/obj-aarch64-linux-gnu/rdkit/rdBase.so 186: 30# boost::python::handle_exception_impl(boost::function0) in /lib/aarch64-linux-gnu/libboost_python313.so.1.83.0 -186: 31# 0x0000FFFFA667F25C in /lib/aarch64-linux-gnu/libboost_python313.so.1.83.0 +186: 31# 0x0000FFFFAC5AF25C in /lib/aarch64-linux-gnu/libboost_python313.so.1.83.0 186: 32# _PyObject_MakeTpCall in /usr/bin/python3 186: 33# _PyEval_EvalFrameDefault in /usr/bin/python3 186: 34# 0x000000000052F1D8 in /usr/bin/python3 @@ -34606,41 +34278,69 @@ 186: 60# 0x0000000000621C6C in /usr/bin/python3 186: 61# Py_RunMain in /usr/bin/python3 186: 62# Py_BytesMain in /usr/bin/python3 -186: 63# 0x0000FFFFA706229C in /lib/aarch64-linux-gnu/libc.so.6 +186: 63# 0x0000FFFFACF9229C in /lib/aarch64-linux-gnu/libc.so.6 186: 64# __libc_start_main in /lib/aarch64-linux-gnu/libc.so.6 186: 65# _start in /usr/bin/python3 186: ---------- 186: **** 186: -222/236 Test #233: pyRanker ............................... Passed 0.22 sec -test 234 - Start 234: testChemicalFeatures +213: [21:38:31] Tautomer enumeration stopped at 50 tautomers: max tautomers reached +213: .[21:38:31] Tautomer enumeration stopped at 91 tautomers: canceled +213: Enumeration was canceled due to timeout (50 ms) +214: Randomness seeded to: 1788760172 +214: =============================================================================== +214: All tests passed (273 assertions in 19 test cases) +214: +203/236 Test #214: testScaffoldNetwork .................... Passed 1.05 sec +test 215 + Start 215: pyScaffoldNetwork -234: Test command: /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/ChemicalFeatures/testChemicalFeatures -234: Working Directory: /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/ChemicalFeatures -234: Test timeout computed to be: 1500 -234: ----------------------------------------- -234: Test1 -234: Done -223/236 Test #234: testChemicalFeatures ................... Passed 0.00 sec -test 235 - Start 235: pyFeatures +215: Test command: /usr/bin/python3 "/build/reproducible-path/rdkit-202409.4/Code/GraphMol/ScaffoldNetwork/Wrap/testScaffoldNetwork.py" +215: Working Directory: /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/GraphMol/ScaffoldNetwork/Wrap +215: Test timeout computed to be: 1500 +213: Enumeration has completed +213: [21:38:32] Tautomer enumeration stopped at 91 tautomers: canceled +215: ....... +215: ---------------------------------------------------------------------- +215: Ran 7 tests in 0.027s +215: +215: OK +204/236 Test #215: pyScaffoldNetwork ...................... Passed 0.29 sec +test 216 + Start 216: pyScaffoldNetworkPickling -235: Test command: /usr/bin/python3 "/build/reproducible-path/rdkit-202409.4/Code/ChemicalFeatures/Wrap/testFeatures.py" -235: Working Directory: /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/ChemicalFeatures/Wrap -235: Test timeout computed to be: 1500 -223: Randomness seeded to: 1970278242 -223: =============================================================================== -223: All tests passed (203 assertions in 1 test case) -223: -224/236 Test #223: testMolProcessing ...................... Passed 1.47 sec -test 236 - Start 236: pythonProjectTests +216: Test command: /usr/bin/python3 "/build/reproducible-path/rdkit-202409.4/Code/GraphMol/ScaffoldNetwork/Wrap/testPickleScaffoldNetwork.py" +216: Working Directory: /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/GraphMol/ScaffoldNetwork/Wrap +216: Test timeout computed to be: 1500 +213: ..........[21:38:32] Explicit valence for atom # 1 N, 4, is greater than permitted +213: [21:38:32] Explicit valence for atom # 1 N, 4, is greater than permitted +213: [21:38:32] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +213: [21:38:32] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +216: . +216: ---------------------------------------------------------------------- +216: Ran 1 test in 0.008s +216: +216: OK +205/236 Test #216: pyScaffoldNetworkPickling .............. Passed 0.28 sec +test 217 + Start 217: testMolEnumerator -236: Test command: /usr/bin/python3 "-m" "pytest" -236: Working Directory: /build/reproducible-path/rdkit-202409.4/Projects -236: Test timeout computed to be: 1500 -196: ..[12:43:14] +217: Test command: /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/GraphMol/MolEnumerator/testMolEnumerator +217: Working Directory: /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/GraphMol/MolEnumerator +217: Test timeout computed to be: 1500 +217: Randomness seeded to: 786587888 +217: [21:38:32] can only enumerate SRUs with CONNECT=HT or CONNECT=HH +217: =============================================================================== +217: All tests passed (321 assertions in 16 test cases) +217: +206/236 Test #217: testMolEnumerator ...................... Passed 0.13 sec +test 218 + Start 218: pyMolEnumerator + +218: Test command: /usr/bin/python3 "/build/reproducible-path/rdkit-202409.4/Code/GraphMol/MolEnumerator/Wrap/rough_test.py" +218: Working Directory: /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/GraphMol/MolEnumerator/Wrap +218: Test timeout computed to be: 1500 +196: ..[21:38:33] 196: 196: **** 196: Pre-condition Violation @@ -34654,7 +34354,7 @@ 196: 2# RDKit::Atom::getOwningMol() const in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so 196: 3# boost::python::objects::caller_py_function_impl, boost::mpl::vector2 > >::operator()(_object*, _object*) in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so 196: 4# boost::python::objects::function::call(_object*, _object*) const in /lib/aarch64-linux-gnu/libboost_python313.so.1.83.0 -196: 5# 0x0000FFFFBCB72680 in /lib/aarch64-linux-gnu/libboost_python313.so.1.83.0 +196: 5# 0x0000FFFFA7AC2680 in /lib/aarch64-linux-gnu/libboost_python313.so.1.83.0 196: 6# boost::python::detail::exception_handler::operator()(boost::function0 const&) const in /lib/aarch64-linux-gnu/libboost_python313.so.1.83.0 196: 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-202409.4/obj-aarch64-linux-gnu/rdkit/Chem/rdSLNParse.so 196: 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-202409.4/obj-aarch64-linux-gnu/rdkit/Chem/rdChemReactions.so @@ -34665,17 +34365,17 @@ 196: 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-202409.4/obj-aarch64-linux-gnu/rdkit/Chem/rdmolfiles.so 196: 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-202409.4/obj-aarch64-linux-gnu/rdkit/Chem/rdCIPLabeler.so 196: 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-202409.4/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so -196: 16# 0x0000FFFFBA5F9FA0 in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so -196: 17# 0x0000FFFFBA5F9F38 in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so -196: 18# 0x0000FFFFBA5F9EC8 in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so -196: 19# 0x0000FFFFBA5F9E60 in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so -196: 20# 0x0000FFFFBA5F9DF8 in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so +196: 16# 0x0000FFFFA5549FA0 in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so +196: 17# 0x0000FFFFA5549F38 in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so +196: 18# 0x0000FFFFA5549EC8 in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so +196: 19# 0x0000FFFFA5549E60 in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so +196: 20# 0x0000FFFFA5549DF8 in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so 196: 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-202409.4/obj-aarch64-linux-gnu/rdkit/rdBase.so 196: 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-202409.4/obj-aarch64-linux-gnu/rdkit/rdBase.so 196: 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-202409.4/obj-aarch64-linux-gnu/rdkit/rdBase.so 196: 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-202409.4/obj-aarch64-linux-gnu/rdkit/rdBase.so 196: 25# boost::python::handle_exception_impl(boost::function0) in /lib/aarch64-linux-gnu/libboost_python313.so.1.83.0 -196: 26# 0x0000FFFFBCB6F25C in /lib/aarch64-linux-gnu/libboost_python313.so.1.83.0 +196: 26# 0x0000FFFFA7ABF25C in /lib/aarch64-linux-gnu/libboost_python313.so.1.83.0 196: 27# _PyObject_MakeTpCall in /usr/bin/python3 196: 28# _PyEval_EvalFrameDefault in /usr/bin/python3 196: 29# 0x000000000052F1D8 in /usr/bin/python3 @@ -34707,13 +34407,13 @@ 196: 55# 0x0000000000621C6C in /usr/bin/python3 196: 56# Py_RunMain in /usr/bin/python3 196: 57# Py_BytesMain in /usr/bin/python3 -196: 58# 0x0000FFFFBD98229C in /lib/aarch64-linux-gnu/libc.so.6 +196: 58# 0x0000FFFFA88D229C in /lib/aarch64-linux-gnu/libc.so.6 196: 59# __libc_start_main in /lib/aarch64-linux-gnu/libc.so.6 196: 60# _start in /usr/bin/python3 196: ---------- 196: **** 196: -196: [12:43:14] +196: [21:38:33] 196: 196: **** 196: Pre-condition Violation @@ -34727,7 +34427,7 @@ 196: 2# RDKit::AtomGetNeighbors(RDKit::Atom*) in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so 196: 3# boost::python::objects::caller_py_function_impl > >::operator()(_object*, _object*) in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so 196: 4# boost::python::objects::function::call(_object*, _object*) const in /lib/aarch64-linux-gnu/libboost_python313.so.1.83.0 -196: 5# 0x0000FFFFBCB72680 in /lib/aarch64-linux-gnu/libboost_python313.so.1.83.0 +196: 5# 0x0000FFFFA7AC2680 in /lib/aarch64-linux-gnu/libboost_python313.so.1.83.0 196: 6# boost::python::detail::exception_handler::operator()(boost::function0 const&) const in /lib/aarch64-linux-gnu/libboost_python313.so.1.83.0 196: 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-202409.4/obj-aarch64-linux-gnu/rdkit/Chem/rdSLNParse.so 196: 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-202409.4/obj-aarch64-linux-gnu/rdkit/Chem/rdChemReactions.so @@ -34738,17 +34438,17 @@ 196: 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-202409.4/obj-aarch64-linux-gnu/rdkit/Chem/rdmolfiles.so 196: 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-202409.4/obj-aarch64-linux-gnu/rdkit/Chem/rdCIPLabeler.so 196: 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-202409.4/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so -196: 16# 0x0000FFFFBA5F9FA0 in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so -196: 17# 0x0000FFFFBA5F9F38 in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so -196: 18# 0x0000FFFFBA5F9EC8 in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so -196: 19# 0x0000FFFFBA5F9E60 in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so -196: 20# 0x0000FFFFBA5F9DF8 in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so +196: 16# 0x0000FFFFA5549FA0 in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so +196: 17# 0x0000FFFFA5549F38 in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so +196: 18# 0x0000FFFFA5549EC8 in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so +196: 19# 0x0000FFFFA5549E60 in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so +196: 20# 0x0000FFFFA5549DF8 in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so 196: 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-202409.4/obj-aarch64-linux-gnu/rdkit/rdBase.so 196: 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-202409.4/obj-aarch64-linux-gnu/rdkit/rdBase.so 196: 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-202409.4/obj-aarch64-linux-gnu/rdkit/rdBase.so 196: 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-202409.4/obj-aarch64-linux-gnu/rdkit/rdBase.so 196: 25# boost::python::handle_exception_impl(boost::function0) in /lib/aarch64-linux-gnu/libboost_python313.so.1.83.0 -196: 26# 0x0000FFFFBCB6F25C in /lib/aarch64-linux-gnu/libboost_python313.so.1.83.0 +196: 26# 0x0000FFFFA7ABF25C in /lib/aarch64-linux-gnu/libboost_python313.so.1.83.0 196: 27# _PyObject_MakeTpCall in /usr/bin/python3 196: 28# _PyEval_EvalFrameDefault in /usr/bin/python3 196: 29# 0x000000000052F1D8 in /usr/bin/python3 @@ -34780,13 +34480,13 @@ 196: 55# 0x0000000000621C6C in /usr/bin/python3 196: 56# Py_RunMain in /usr/bin/python3 196: 57# Py_BytesMain in /usr/bin/python3 -196: 58# 0x0000FFFFBD98229C in /lib/aarch64-linux-gnu/libc.so.6 +196: 58# 0x0000FFFFA88D229C in /lib/aarch64-linux-gnu/libc.so.6 196: 59# __libc_start_main in /lib/aarch64-linux-gnu/libc.so.6 196: 60# _start in /usr/bin/python3 196: ---------- 196: **** 196: -196: [12:43:14] +196: [21:38:33] 196: 196: **** 196: Pre-condition Violation @@ -34800,7 +34500,7 @@ 196: 2# RDKit::AtomGetBonds(RDKit::Atom*) in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so 196: 3# boost::python::objects::caller_py_function_impl > >::operator()(_object*, _object*) in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so 196: 4# boost::python::objects::function::call(_object*, _object*) const in /lib/aarch64-linux-gnu/libboost_python313.so.1.83.0 -196: 5# 0x0000FFFFBCB72680 in /lib/aarch64-linux-gnu/libboost_python313.so.1.83.0 +196: 5# 0x0000FFFFA7AC2680 in /lib/aarch64-linux-gnu/libboost_python313.so.1.83.0 196: 6# boost::python::detail::exception_handler::operator()(boost::function0 const&) const in /lib/aarch64-linux-gnu/libboost_python313.so.1.83.0 196: 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-202409.4/obj-aarch64-linux-gnu/rdkit/Chem/rdSLNParse.so 196: 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-202409.4/obj-aarch64-linux-gnu/rdkit/Chem/rdChemReactions.so @@ -34811,17 +34511,17 @@ 196: 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-202409.4/obj-aarch64-linux-gnu/rdkit/Chem/rdmolfiles.so 196: 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-202409.4/obj-aarch64-linux-gnu/rdkit/Chem/rdCIPLabeler.so 196: 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-202409.4/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so -196: 16# 0x0000FFFFBA5F9FA0 in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so -196: 17# 0x0000FFFFBA5F9F38 in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so -196: 18# 0x0000FFFFBA5F9EC8 in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so -196: 19# 0x0000FFFFBA5F9E60 in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so -196: 20# 0x0000FFFFBA5F9DF8 in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so +196: 16# 0x0000FFFFA5549FA0 in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so +196: 17# 0x0000FFFFA5549F38 in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so +196: 18# 0x0000FFFFA5549EC8 in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so +196: 19# 0x0000FFFFA5549E60 in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so +196: 20# 0x0000FFFFA5549DF8 in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so 196: 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-202409.4/obj-aarch64-linux-gnu/rdkit/rdBase.so 196: 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-202409.4/obj-aarch64-linux-gnu/rdkit/rdBase.so 196: 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-202409.4/obj-aarch64-linux-gnu/rdkit/rdBase.so 196: 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-202409.4/obj-aarch64-linux-gnu/rdkit/rdBase.so 196: 25# boost::python::handle_exception_impl(boost::function0) in /lib/aarch64-linux-gnu/libboost_python313.so.1.83.0 -196: 26# 0x0000FFFFBCB6F25C in /lib/aarch64-linux-gnu/libboost_python313.so.1.83.0 +196: 26# 0x0000FFFFA7ABF25C in /lib/aarch64-linux-gnu/libboost_python313.so.1.83.0 196: 27# _PyObject_MakeTpCall in /usr/bin/python3 196: 28# _PyEval_EvalFrameDefault in /usr/bin/python3 196: 29# 0x000000000052F1D8 in /usr/bin/python3 @@ -34853,13 +34553,13 @@ 196: 55# 0x0000000000621C6C in /usr/bin/python3 196: 56# Py_RunMain in /usr/bin/python3 196: 57# Py_BytesMain in /usr/bin/python3 -196: 58# 0x0000FFFFBD98229C in /lib/aarch64-linux-gnu/libc.so.6 +196: 58# 0x0000FFFFA88D229C in /lib/aarch64-linux-gnu/libc.so.6 196: 59# __libc_start_main in /lib/aarch64-linux-gnu/libc.so.6 196: 60# _start in /usr/bin/python3 196: ---------- 196: **** 196: -196: [12:43:14] +196: [21:38:33] 196: 196: **** 196: Pre-condition Violation @@ -34873,7 +34573,7 @@ 196: 2# RDKit::AtomIsInRing(RDKit::Atom const*) in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so 196: 3# boost::python::objects::caller_py_function_impl > >::operator()(_object*, _object*) in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so 196: 4# boost::python::objects::function::call(_object*, _object*) const in /lib/aarch64-linux-gnu/libboost_python313.so.1.83.0 -196: 5# 0x0000FFFFBCB72680 in /lib/aarch64-linux-gnu/libboost_python313.so.1.83.0 +196: 5# 0x0000FFFFA7AC2680 in /lib/aarch64-linux-gnu/libboost_python313.so.1.83.0 196: 6# boost::python::detail::exception_handler::operator()(boost::function0 const&) const in /lib/aarch64-linux-gnu/libboost_python313.so.1.83.0 196: 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-202409.4/obj-aarch64-linux-gnu/rdkit/Chem/rdSLNParse.so 196: 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-202409.4/obj-aarch64-linux-gnu/rdkit/Chem/rdChemReactions.so @@ -34884,17 +34584,17 @@ 196: 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-202409.4/obj-aarch64-linux-gnu/rdkit/Chem/rdmolfiles.so 196: 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-202409.4/obj-aarch64-linux-gnu/rdkit/Chem/rdCIPLabeler.so 196: 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-202409.4/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so -196: 16# 0x0000FFFFBA5F9FA0 in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so -196: 17# 0x0000FFFFBA5F9F38 in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so -196: 18# 0x0000FFFFBA5F9EC8 in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so -196: 19# 0x0000FFFFBA5F9E60 in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so -196: 20# 0x0000FFFFBA5F9DF8 in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so +196: 16# 0x0000FFFFA5549FA0 in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so +196: 17# 0x0000FFFFA5549F38 in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so +196: 18# 0x0000FFFFA5549EC8 in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so +196: 19# 0x0000FFFFA5549E60 in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so +196: 20# 0x0000FFFFA5549DF8 in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so 196: 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-202409.4/obj-aarch64-linux-gnu/rdkit/rdBase.so 196: 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-202409.4/obj-aarch64-linux-gnu/rdkit/rdBase.so 196: 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-202409.4/obj-aarch64-linux-gnu/rdkit/rdBase.so 196: 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-202409.4/obj-aarch64-linux-gnu/rdkit/rdBase.so 196: 25# boost::python::handle_exception_impl(boost::function0) in /lib/aarch64-linux-gnu/libboost_python313.so.1.83.0 -196: 26# 0x0000FFFFBCB6F25C in /lib/aarch64-linux-gnu/libboost_python313.so.1.83.0 +196: 26# 0x0000FFFFA7ABF25C in /lib/aarch64-linux-gnu/libboost_python313.so.1.83.0 196: 27# _PyObject_MakeTpCall in /usr/bin/python3 196: 28# _PyEval_EvalFrameDefault in /usr/bin/python3 196: 29# 0x000000000052F1D8 in /usr/bin/python3 @@ -34926,13 +34626,13 @@ 196: 55# 0x0000000000621C6C in /usr/bin/python3 196: 56# Py_RunMain in /usr/bin/python3 196: 57# Py_BytesMain in /usr/bin/python3 -196: 58# 0x0000FFFFBD98229C in /lib/aarch64-linux-gnu/libc.so.6 +196: 58# 0x0000FFFFA88D229C in /lib/aarch64-linux-gnu/libc.so.6 196: 59# __libc_start_main in /lib/aarch64-linux-gnu/libc.so.6 196: 60# _start in /usr/bin/python3 196: ---------- 196: **** 196: -196: [12:43:14] +196: [21:38:33] 196: 196: **** 196: Pre-condition Violation @@ -34946,7 +34646,7 @@ 196: 2# RDKit::AtomIsInRingSize(RDKit::Atom const*, int) in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so 196: 3# boost::python::objects::caller_py_function_impl > >::operator()(_object*, _object*) in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so 196: 4# boost::python::objects::function::call(_object*, _object*) const in /lib/aarch64-linux-gnu/libboost_python313.so.1.83.0 -196: 5# 0x0000FFFFBCB72680 in /lib/aarch64-linux-gnu/libboost_python313.so.1.83.0 +196: 5# 0x0000FFFFA7AC2680 in /lib/aarch64-linux-gnu/libboost_python313.so.1.83.0 196: 6# boost::python::detail::exception_handler::operator()(boost::function0 const&) const in /lib/aarch64-linux-gnu/libboost_python313.so.1.83.0 196: 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-202409.4/obj-aarch64-linux-gnu/rdkit/Chem/rdSLNParse.so 196: 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-202409.4/obj-aarch64-linux-gnu/rdkit/Chem/rdChemReactions.so @@ -34957,17 +34657,17 @@ 196: 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-202409.4/obj-aarch64-linux-gnu/rdkit/Chem/rdmolfiles.so 196: 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-202409.4/obj-aarch64-linux-gnu/rdkit/Chem/rdCIPLabeler.so 196: 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-202409.4/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so -196: 16# 0x0000FFFFBA5F9FA0 in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so -196: 17# 0x0000FFFFBA5F9F38 in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so -196: 18# 0x0000FFFFBA5F9EC8 in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so -196: 19# 0x0000FFFFBA5F9E60 in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so -196: 20# 0x0000FFFFBA5F9DF8 in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so +196: 16# 0x0000FFFFA5549FA0 in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so +196: 17# 0x0000FFFFA5549F38 in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so +196: 18# 0x0000FFFFA5549EC8 in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so +196: 19# 0x0000FFFFA5549E60 in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so +196: 20# 0x0000FFFFA5549DF8 in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so 196: 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-202409.4/obj-aarch64-linux-gnu/rdkit/rdBase.so 196: 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-202409.4/obj-aarch64-linux-gnu/rdkit/rdBase.so 196: 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-202409.4/obj-aarch64-linux-gnu/rdkit/rdBase.so 196: 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-202409.4/obj-aarch64-linux-gnu/rdkit/rdBase.so 196: 25# boost::python::handle_exception_impl(boost::function0) in /lib/aarch64-linux-gnu/libboost_python313.so.1.83.0 -196: 26# 0x0000FFFFBCB6F25C in /lib/aarch64-linux-gnu/libboost_python313.so.1.83.0 +196: 26# 0x0000FFFFA7ABF25C in /lib/aarch64-linux-gnu/libboost_python313.so.1.83.0 196: 27# _PyObject_MakeTpCall in /usr/bin/python3 196: 28# _PyEval_EvalFrameDefault in /usr/bin/python3 196: 29# 0x000000000052F1D8 in /usr/bin/python3 @@ -34999,13 +34699,13 @@ 196: 55# 0x0000000000621C6C in /usr/bin/python3 196: 56# Py_RunMain in /usr/bin/python3 196: 57# Py_BytesMain in /usr/bin/python3 -196: 58# 0x0000FFFFBD98229C in /lib/aarch64-linux-gnu/libc.so.6 +196: 58# 0x0000FFFFA88D229C in /lib/aarch64-linux-gnu/libc.so.6 196: 59# __libc_start_main in /lib/aarch64-linux-gnu/libc.so.6 196: 60# _start in /usr/bin/python3 196: ---------- 196: **** 196: -196: .....[12:43:14] +196: .....[21:38:33] 196: 196: **** 196: Range Error @@ -35019,7 +34719,7 @@ 196: 2# RDKit::RWMol::addBond(unsigned int, unsigned int, RDKit::Bond::BondType) in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu//lib/libRDKitGraphMol.so.1 196: 3# boost::python::objects::caller_py_function_impl > >::operator()(_object*, _object*) in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so 196: 4# boost::python::objects::function::call(_object*, _object*) const in /lib/aarch64-linux-gnu/libboost_python313.so.1.83.0 -196: 5# 0x0000FFFFBCB72680 in /lib/aarch64-linux-gnu/libboost_python313.so.1.83.0 +196: 5# 0x0000FFFFA7AC2680 in /lib/aarch64-linux-gnu/libboost_python313.so.1.83.0 196: 6# boost::python::detail::exception_handler::operator()(boost::function0 const&) const in /lib/aarch64-linux-gnu/libboost_python313.so.1.83.0 196: 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-202409.4/obj-aarch64-linux-gnu/rdkit/Chem/rdSLNParse.so 196: 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-202409.4/obj-aarch64-linux-gnu/rdkit/Chem/rdChemReactions.so @@ -35030,17 +34730,17 @@ 196: 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-202409.4/obj-aarch64-linux-gnu/rdkit/Chem/rdmolfiles.so 196: 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-202409.4/obj-aarch64-linux-gnu/rdkit/Chem/rdCIPLabeler.so 196: 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-202409.4/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so -196: 16# 0x0000FFFFBA5F9FA0 in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so -196: 17# 0x0000FFFFBA5F9F38 in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so -196: 18# 0x0000FFFFBA5F9EC8 in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so -196: 19# 0x0000FFFFBA5F9E60 in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so -196: 20# 0x0000FFFFBA5F9DF8 in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so +196: 16# 0x0000FFFFA5549FA0 in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so +196: 17# 0x0000FFFFA5549F38 in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so +196: 18# 0x0000FFFFA5549EC8 in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so +196: 19# 0x0000FFFFA5549E60 in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so +196: 20# 0x0000FFFFA5549DF8 in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so 196: 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-202409.4/obj-aarch64-linux-gnu/rdkit/rdBase.so 196: 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-202409.4/obj-aarch64-linux-gnu/rdkit/rdBase.so 196: 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-202409.4/obj-aarch64-linux-gnu/rdkit/rdBase.so 196: 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-202409.4/obj-aarch64-linux-gnu/rdkit/rdBase.so 196: 25# boost::python::handle_exception_impl(boost::function0) in /lib/aarch64-linux-gnu/libboost_python313.so.1.83.0 -196: 26# 0x0000FFFFBCB6F25C in /lib/aarch64-linux-gnu/libboost_python313.so.1.83.0 +196: 26# 0x0000FFFFA7ABF25C in /lib/aarch64-linux-gnu/libboost_python313.so.1.83.0 196: 27# _PyObject_MakeTpCall in /usr/bin/python3 196: 28# _PyEval_EvalFrameDefault in /usr/bin/python3 196: 29# 0x000000000052F1D8 in /usr/bin/python3 @@ -35072,55 +34772,49 @@ 196: 55# 0x0000000000621C6C in /usr/bin/python3 196: 56# Py_RunMain in /usr/bin/python3 196: 57# Py_BytesMain in /usr/bin/python3 -196: 58# 0x0000FFFFBD98229C in /lib/aarch64-linux-gnu/libc.so.6 +196: 58# 0x0000FFFFA88D229C in /lib/aarch64-linux-gnu/libc.so.6 196: 59# __libc_start_main in /lib/aarch64-linux-gnu/libc.so.6 196: 60# _start in /usr/bin/python3 196: ---------- 196: **** 196: -235: .. -235: ---------------------------------------------------------------------- -235: Ran 2 tests in 0.001s -235: -235: OK -235: Testing ChemicalFeatures Wrapper code: -196: ......[12:43:14] SMILES Parse Error: unclosed ring for input: 'c1ccccc' -196: [12:43:14] ERROR: Smiles parse error on line 0 -196: [12:43:14] ERROR: Cannot create molecule from : 'c1ccccc' -196: [12:43:14] SMILES Parse Error: extra open parentheses while parsing: C(C -196: [12:43:14] SMILES Parse Error: check for mistakes around position 2: -196: [12:43:14] C(C -196: [12:43:14] ~^ -196: [12:43:14] SMILES Parse Error: Failed parsing SMILES 'C(C' for input: 'C(C' -196: [12:43:14] ERROR: Smiles parse error on line 3 -196: [12:43:14] ERROR: Cannot create molecule from : 'C(C' -196: [12:43:14] Explicit valence for atom # 1 C, 5, is greater than permitted -196: [12:43:14] ERROR: Could not sanitize molecule on line 6 -196: [12:43:14] ERROR: Explicit valence for atom # 1 C, 5, is greater than permitted -196: [12:43:14] SMILES Parse Error: unclosed ring for input: 'c1ccccc' -196: [12:43:14] ERROR: Smiles parse error on line 0 -196: [12:43:14] ERROR: Cannot create molecule from : 'c1ccccc' -196: [12:43:14] SMILES Parse Error: extra open parentheses while parsing: C(C -196: [12:43:14] SMILES Parse Error: check for mistakes around position 2: -196: [12:43:14] C(C -196: [12:43:14] ~^ -196: [12:43:14] SMILES Parse Error: Failed parsing SMILES 'C(C' for input: 'C(C' -196: [12:43:14] ERROR: Smiles parse error on line 3 -196: [12:43:14] ERROR: Cannot create molecule from : 'C(C' -196: [12:43:14] SMILES Parse Error: unclosed ring for input: 'C1C(Cl)CCCC' -196: [12:43:14] ERROR: Smiles parse error on line 6 -196: [12:43:14] ERROR: Cannot create molecule from : 'C1C(Cl)CCCC' -196: [12:43:14] Explicit valence for atom # 1 F, 2, is greater than permitted -196: [12:43:14] ERROR: Could not sanitize molecule ending on line 21 -196: [12:43:14] ERROR: Explicit valence for atom # 1 F, 2, is greater than permitted -196: [12:43:14] ERROR: EOF hit while reading atoms -196: [12:43:14] ERROR: moving to the beginning of the next molecule -196: [12:43:14] Explicit valence for atom # 1 F, 2, is greater than permitted -196: [12:43:14] ERROR: Could not sanitize molecule ending on line 21 -196: [12:43:14] ERROR: Explicit valence for atom # 1 F, 2, is greater than permitted -196: [12:43:14] ERROR: EOF hit while reading atoms -196: [12:43:14] ERROR: moving to the beginning of the next molecule -196: ....[12:43:14] +196: ......[21:38:33] SMILES Parse Error: unclosed ring for input: 'c1ccccc' +196: [21:38:33] ERROR: Smiles parse error on line 0 +196: [21:38:33] ERROR: Cannot create molecule from : 'c1ccccc' +196: [21:38:33] SMILES Parse Error: extra open parentheses while parsing: C(C +196: [21:38:33] SMILES Parse Error: check for mistakes around position 2: +196: [21:38:33] C(C +196: [21:38:33] ~^ +196: [21:38:33] SMILES Parse Error: Failed parsing SMILES 'C(C' for input: 'C(C' +196: [21:38:33] ERROR: Smiles parse error on line 3 +196: [21:38:33] ERROR: Cannot create molecule from : 'C(C' +196: [21:38:33] Explicit valence for atom # 1 C, 5, is greater than permitted +196: [21:38:33] ERROR: Could not sanitize molecule on line 6 +196: [21:38:33] ERROR: Explicit valence for atom # 1 C, 5, is greater than permitted +196: [21:38:33] SMILES Parse Error: unclosed ring for input: 'c1ccccc' +196: [21:38:33] ERROR: Smiles parse error on line 0 +196: [21:38:33] ERROR: Cannot create molecule from : 'c1ccccc' +196: [21:38:33] SMILES Parse Error: extra open parentheses while parsing: C(C +196: [21:38:33] SMILES Parse Error: check for mistakes around position 2: +196: [21:38:33] C(C +196: [21:38:33] ~^ +196: [21:38:33] SMILES Parse Error: Failed parsing SMILES 'C(C' for input: 'C(C' +196: [21:38:33] ERROR: Smiles parse error on line 3 +196: [21:38:33] ERROR: Cannot create molecule from : 'C(C' +196: [21:38:33] SMILES Parse Error: unclosed ring for input: 'C1C(Cl)CCCC' +196: [21:38:33] ERROR: Smiles parse error on line 6 +196: [21:38:33] ERROR: Cannot create molecule from : 'C1C(Cl)CCCC' +196: [21:38:33] Explicit valence for atom # 1 F, 2, is greater than permitted +196: [21:38:33] ERROR: Could not sanitize molecule ending on line 21 +196: [21:38:33] ERROR: Explicit valence for atom # 1 F, 2, is greater than permitted +196: [21:38:33] ERROR: EOF hit while reading atoms +196: [21:38:33] ERROR: moving to the beginning of the next molecule +196: [21:38:33] Explicit valence for atom # 1 F, 2, is greater than permitted +196: [21:38:33] ERROR: Could not sanitize molecule ending on line 21 +196: [21:38:33] ERROR: Explicit valence for atom # 1 F, 2, is greater than permitted +196: [21:38:33] ERROR: EOF hit while reading atoms +196: [21:38:33] ERROR: moving to the beginning of the next molecule +196: ....[21:38:33] 196: 196: **** 196: Pre-condition Violation @@ -35134,7 +34828,7 @@ 196: 2# RDKit::RingInfo::numRings() const in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu//lib/libRDKitGraphMol.so.1 196: 3# boost::python::objects::caller_py_function_impl > >::operator()(_object*, _object*) in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so 196: 4# boost::python::objects::function::call(_object*, _object*) const in /lib/aarch64-linux-gnu/libboost_python313.so.1.83.0 -196: 5# 0x0000FFFFBCB72680 in /lib/aarch64-linux-gnu/libboost_python313.so.1.83.0 +196: 5# 0x0000FFFFA7AC2680 in /lib/aarch64-linux-gnu/libboost_python313.so.1.83.0 196: 6# boost::python::detail::exception_handler::operator()(boost::function0 const&) const in /lib/aarch64-linux-gnu/libboost_python313.so.1.83.0 196: 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-202409.4/obj-aarch64-linux-gnu/rdkit/Chem/rdSLNParse.so 196: 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-202409.4/obj-aarch64-linux-gnu/rdkit/Chem/rdChemReactions.so @@ -35145,17 +34839,17 @@ 196: 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-202409.4/obj-aarch64-linux-gnu/rdkit/Chem/rdmolfiles.so 196: 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-202409.4/obj-aarch64-linux-gnu/rdkit/Chem/rdCIPLabeler.so 196: 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-202409.4/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so -196: 16# 0x0000FFFFBA5F9FA0 in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so -196: 17# 0x0000FFFFBA5F9F38 in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so -196: 18# 0x0000FFFFBA5F9EC8 in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so -196: 19# 0x0000FFFFBA5F9E60 in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so -196: 20# 0x0000FFFFBA5F9DF8 in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so +196: 16# 0x0000FFFFA5549FA0 in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so +196: 17# 0x0000FFFFA5549F38 in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so +196: 18# 0x0000FFFFA5549EC8 in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so +196: 19# 0x0000FFFFA5549E60 in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so +196: 20# 0x0000FFFFA5549DF8 in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so 196: 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-202409.4/obj-aarch64-linux-gnu/rdkit/rdBase.so 196: 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-202409.4/obj-aarch64-linux-gnu/rdkit/rdBase.so 196: 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-202409.4/obj-aarch64-linux-gnu/rdkit/rdBase.so 196: 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-202409.4/obj-aarch64-linux-gnu/rdkit/rdBase.so 196: 25# boost::python::handle_exception_impl(boost::function0) in /lib/aarch64-linux-gnu/libboost_python313.so.1.83.0 -196: 26# 0x0000FFFFBCB6F25C in /lib/aarch64-linux-gnu/libboost_python313.so.1.83.0 +196: 26# 0x0000FFFFA7ABF25C in /lib/aarch64-linux-gnu/libboost_python313.so.1.83.0 196: 27# _PyObject_MakeTpCall in /usr/bin/python3 196: 28# _PyEval_EvalFrameDefault in /usr/bin/python3 196: 29# 0x000000000052F1D8 in /usr/bin/python3 @@ -35187,13 +34881,13 @@ 196: 55# 0x0000000000621C6C in /usr/bin/python3 196: 56# Py_RunMain in /usr/bin/python3 196: 57# Py_BytesMain in /usr/bin/python3 -196: 58# 0x0000FFFFBD98229C in /lib/aarch64-linux-gnu/libc.so.6 +196: 58# 0x0000FFFFA88D229C in /lib/aarch64-linux-gnu/libc.so.6 196: 59# __libc_start_main in /lib/aarch64-linux-gnu/libc.so.6 196: 60# _start in /usr/bin/python3 196: ---------- 196: **** 196: -196: .............[12:43:14] +196: .............[21:38:33] 196: 196: **** 196: Range Error @@ -35207,7 +34901,7 @@ 196: 2# RDKit::ROMol::getAtomWithIdx(unsigned int) in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu//lib/libRDKitGraphMol.so.1 196: 3# boost::python::objects::caller_py_function_impl >, boost::mpl::vector3 > >::operator()(_object*, _object*) in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so 196: 4# boost::python::objects::function::call(_object*, _object*) const in /lib/aarch64-linux-gnu/libboost_python313.so.1.83.0 -196: 5# 0x0000FFFFBCB72680 in /lib/aarch64-linux-gnu/libboost_python313.so.1.83.0 +196: 5# 0x0000FFFFA7AC2680 in /lib/aarch64-linux-gnu/libboost_python313.so.1.83.0 196: 6# boost::python::detail::exception_handler::operator()(boost::function0 const&) const in /lib/aarch64-linux-gnu/libboost_python313.so.1.83.0 196: 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-202409.4/obj-aarch64-linux-gnu/rdkit/Chem/rdSLNParse.so 196: 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-202409.4/obj-aarch64-linux-gnu/rdkit/Chem/rdChemReactions.so @@ -35218,17 +34912,17 @@ 196: 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-202409.4/obj-aarch64-linux-gnu/rdkit/Chem/rdmolfiles.so 196: 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-202409.4/obj-aarch64-linux-gnu/rdkit/Chem/rdCIPLabeler.so 196: 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-202409.4/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so -196: 16# 0x0000FFFFBA5F9FA0 in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so -196: 17# 0x0000FFFFBA5F9F38 in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so -196: 18# 0x0000FFFFBA5F9EC8 in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so -196: 19# 0x0000FFFFBA5F9E60 in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so -196: 20# 0x0000FFFFBA5F9DF8 in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so +196: 16# 0x0000FFFFA5549FA0 in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so +196: 17# 0x0000FFFFA5549F38 in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so +196: 18# 0x0000FFFFA5549EC8 in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so +196: 19# 0x0000FFFFA5549E60 in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so +196: 20# 0x0000FFFFA5549DF8 in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so 196: 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-202409.4/obj-aarch64-linux-gnu/rdkit/rdBase.so 196: 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-202409.4/obj-aarch64-linux-gnu/rdkit/rdBase.so 196: 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-202409.4/obj-aarch64-linux-gnu/rdkit/rdBase.so 196: 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-202409.4/obj-aarch64-linux-gnu/rdkit/rdBase.so 196: 25# boost::python::handle_exception_impl(boost::function0) in /lib/aarch64-linux-gnu/libboost_python313.so.1.83.0 -196: 26# 0x0000FFFFBCB6F25C in /lib/aarch64-linux-gnu/libboost_python313.so.1.83.0 +196: 26# 0x0000FFFFA7ABF25C in /lib/aarch64-linux-gnu/libboost_python313.so.1.83.0 196: 27# _PyObject_MakeTpCall in /usr/bin/python3 196: 28# _PyEval_EvalFrameDefault in /usr/bin/python3 196: 29# 0x000000000052F1D8 in /usr/bin/python3 @@ -35260,76 +34954,407 @@ 196: 55# 0x0000000000621C6C in /usr/bin/python3 196: 56# Py_RunMain in /usr/bin/python3 196: 57# Py_BytesMain in /usr/bin/python3 -196: 58# 0x0000FFFFBD98229C in /lib/aarch64-linux-gnu/libc.so.6 +196: 58# 0x0000FFFFA88D229C in /lib/aarch64-linux-gnu/libc.so.6 196: 59# __libc_start_main in /lib/aarch64-linux-gnu/libc.so.6 196: 60# _start in /usr/bin/python3 196: ---------- 196: **** 196: -196: ...[12:43:14] Can't kekulize mol. Unkekulized atoms: 0 1 2 3 4 -225/236 Test #235: pyFeatures ............................. Passed 0.24 sec -196: ............................[12:43:14] SMILES Parse Error: unclosed ring for input: 'C1CC' +196: ...[21:38:33] Can't kekulize mol. Unkekulized atoms: 0 1 2 3 4 +218: ... +218: ---------------------------------------------------------------------- +218: Ran 3 tests in 0.014s +218: +218: OK +207/236 Test #218: pyMolEnumerator ........................ Passed 0.37 sec +test 219 + Start 219: testAbbreviations + +219: Test command: /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/GraphMol/Abbreviations/testAbbreviations +219: Working Directory: /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/GraphMol/Abbreviations +219: Test timeout computed to be: 1500 +196: ............................[21:38:33] SMILES Parse Error: unclosed ring for input: 'C1CC' 196: ......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| -196: 863 -196: ..[12:43:14] WARNING: not removing hydrogen atom without neighbors -196: [12:43:14] WARNING: not removing hydrogen atom with dummy atom neighbors -196: [12:43:14] WARNING: not removing hydrogen atom with wedged bond -196: [12:43:14] WARNING: not removing hydrogen atom without neighbors -196: [12:43:14] WARNING: not removing hydrogen atom with dummy atom neighbors -196: ......[12:43:14] Explicit valence for atom # 1 F, 2, is greater than permitted -196: [12:43:14] Can't kekulize mol. Unkekulized atoms: 0 1 2 -196: .[12:43:14] Explicit valence for atom # 1 F, 2, is greater than permitted -196: [12:43:14] Explicit valence for atom # 1 F, 2, is greater than permitted -196: [12:43:14] Explicit valence for atom # 1 F, 2, is greater than permitted -196: [12:43:14] Explicit valence for atom # 1 F, 2, is greater than permitted -196: [12:43:14] Can't kekulize mol. Unkekulized atoms: 0 1 2 -196: [12:43:14] Can't kekulize mol. Unkekulized atoms: 0 1 2 -196: [12:43:14] Can't kekulize mol. Unkekulized atoms: 0 1 2 -196: ..........[12:43:14] SMARTS Parse Error: syntax error while parsing: CCC |$foo;;bar$| ourname -196: [12:43:14] SMARTS Parse Error: Failed parsing SMARTS 'CCC |$foo;;bar$| ourname' for input: 'CCC |$foo;;bar$| ourname' -196: .[12:43:14] SMILES Parse Error: syntax error while parsing: CCC |$foo;;bar$| ourname -196: [12:43:14] SMILES Parse Error: check for mistakes around position 4: -196: [12:43:14] CCC |$foo;;bar$| ourname -196: [12:43:14] ~~~^ -196: [12:43:14] SMILES Parse Error: Failed parsing SMILES 'CCC |$foo;;bar$| ourname' for input: 'CCC |$foo;;bar$| ourname' -196: ..[12:43:14] SMILES Parse Error: syntax error while parsing: error -196: [12:43:14] SMILES Parse Error: check for mistakes around position 1: -196: [12:43:14] error -196: [12:43:14] ^ -196: [12:43:14] SMILES Parse Error: Failed parsing SMILES 'error' for input: 'error' -196: [12:43:14] SMILES Parse Error: Failed parsing SMILES 'd' for input: 'd' -196: [12:43:14] SMARTS Parse Error: Failed parsing SMARTS 'error' for input: 'error' -196: [12:43:14] SMARTS Parse Error: Failed parsing SMARTS 'd' for input: 'd' -196: .........................[12:43:14] SMILES Parse Error: syntax error while parsing: garbage_0 -196: [12:43:14] SMILES Parse Error: check for mistakes around position 1: -196: [12:43:14] garbage_0 -196: [12:43:14] ^ -196: [12:43:14] SMILES Parse Error: Failed parsing SMILES 'garbage_0' for input: 'garbage_0' -196: [12:43:14] SMILES Parse Error: syntax error while parsing: garbage_2 -196: [12:43:14] SMILES Parse Error: check for mistakes around position 1: -196: [12:43:14] garbage_2 -196: [12:43:14] ^ -196: [12:43:14] SMILES Parse Error: Failed parsing SMILES 'garbage_2' for input: 'garbage_2' -196: [12:43:14] SMILES Parse Error: syntax error while parsing: garbage_4 -196: [12:43:14] SMILES Parse Error: check for mistakes around position 1: -196: [12:43:14] garbage_4 -196: [12:43:14] ^ -196: [12:43:14] SMILES Parse Error: Failed parsing SMILES 'garbage_4' for input: 'garbage_4' +196: 643 +196: ..[21:38:33] WARNING: not removing hydrogen atom without neighbors +196: [21:38:33] WARNING: not removing hydrogen atom with dummy atom neighbors +196: [21:38:33] WARNING: not removing hydrogen atom with wedged bond +196: [21:38:33] WARNING: not removing hydrogen atom without neighbors +196: [21:38:33] WARNING: not removing hydrogen atom with dummy atom neighbors +219: Randomness seeded to: 4113478183 +219: [21:38:33] SMARTS Parse Error: syntax error while parsing: *fail +219: [21:38:33] SMARTS Parse Error: Failed parsing SMARTS '*fail' for input: '*fail' +219: [21:38:33] no suitable SubstanceGroups found +219: =============================================================================== +219: All tests passed (195 assertions in 12 test cases) +219: +208/236 Test #219: testAbbreviations ...................... Passed 0.06 sec +test 220 + Start 220: pyAbbreviations + +220: Test command: /usr/bin/python3 "/build/reproducible-path/rdkit-202409.4/Code/GraphMol/Abbreviations/Wrap/testAbbreviations.py" +220: Working Directory: /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/GraphMol/Abbreviations/Wrap +220: Test timeout computed to be: 1500 +196: ......[21:38:33] Explicit valence for atom # 1 F, 2, is greater than permitted +196: [21:38:33] Can't kekulize mol. Unkekulized atoms: 0 1 2 +196: .[21:38:33] Explicit valence for atom # 1 F, 2, is greater than permitted +196: [21:38:33] Explicit valence for atom # 1 F, 2, is greater than permitted +196: [21:38:33] Explicit valence for atom # 1 F, 2, is greater than permitted +196: [21:38:33] Explicit valence for atom # 1 F, 2, is greater than permitted +196: [21:38:33] Can't kekulize mol. Unkekulized atoms: 0 1 2 +196: [21:38:33] Can't kekulize mol. Unkekulized atoms: 0 1 2 +196: [21:38:33] Can't kekulize mol. Unkekulized atoms: 0 1 2 +196: ..........[21:38:33] SMARTS Parse Error: syntax error while parsing: CCC |$foo;;bar$| ourname +196: [21:38:33] SMARTS Parse Error: Failed parsing SMARTS 'CCC |$foo;;bar$| ourname' for input: 'CCC |$foo;;bar$| ourname' +196: .[21:38:33] SMILES Parse Error: syntax error while parsing: CCC |$foo;;bar$| ourname +196: [21:38:33] SMILES Parse Error: check for mistakes around position 4: +196: [21:38:33] CCC |$foo;;bar$| ourname +196: [21:38:33] ~~~^ +196: [21:38:33] SMILES Parse Error: Failed parsing SMILES 'CCC |$foo;;bar$| ourname' for input: 'CCC |$foo;;bar$| ourname' +196: ..[21:38:33] SMILES Parse Error: syntax error while parsing: error +196: [21:38:33] SMILES Parse Error: check for mistakes around position 1: +196: [21:38:33] error +196: [21:38:33] ^ +196: [21:38:33] SMILES Parse Error: Failed parsing SMILES 'error' for input: 'error' +196: [21:38:33] SMILES Parse Error: Failed parsing SMILES 'd' for input: 'd' +196: [21:38:33] SMARTS Parse Error: Failed parsing SMARTS 'error' for input: 'error' +196: [21:38:33] SMARTS Parse Error: Failed parsing SMARTS 'd' for input: 'd' +196: .........................[21:38:33] SMILES Parse Error: syntax error while parsing: garbage_0 +196: [21:38:33] SMILES Parse Error: check for mistakes around position 1: +196: [21:38:33] garbage_0 +196: [21:38:33] ^ +196: [21:38:33] SMILES Parse Error: Failed parsing SMILES 'garbage_0' for input: 'garbage_0' +196: [21:38:33] SMILES Parse Error: syntax error while parsing: garbage_2 +196: [21:38:33] SMILES Parse Error: check for mistakes around position 1: +196: [21:38:33] garbage_2 +196: [21:38:33] ^ +196: [21:38:33] SMILES Parse Error: Failed parsing SMILES 'garbage_2' for input: 'garbage_2' +196: [21:38:33] SMILES Parse Error: syntax error while parsing: garbage_4 +196: [21:38:33] SMILES Parse Error: check for mistakes around position 1: +196: [21:38:33] garbage_4 +196: [21:38:33] ^ +196: [21:38:33] SMILES Parse Error: Failed parsing SMILES 'garbage_4' for input: 'garbage_4' 196: ........... 196: ---------------------------------------------------------------------- -196: Ran 278 tests in 6.160s +196: Ran 278 tests in 9.847s 196: 196: OK 196: supplier: 196: supplier: 196: supplier: -226/236 Test #196: pyGraphMolWrap ......................... Passed 6.51 sec +209/236 Test #196: pyGraphMolWrap ......................... Passed 10.56 sec +test 221 + Start 221: generalizedSubstructCatch + +221: Test command: /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/GraphMol/GeneralizedSubstruct/generalizedSubstructCatch +221: Working Directory: /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/GraphMol/GeneralizedSubstruct +221: Test timeout computed to be: 1500 +220: ....... +220: ---------------------------------------------------------------------- +220: Ran 7 tests in 0.013s +220: +220: OK +210/236 Test #220: pyAbbreviations ........................ Passed 0.36 sec +test 222 + Start 222: pyGeneralizedSubstruct + +222: Test command: /usr/bin/python3 "/build/reproducible-path/rdkit-202409.4/Code/GraphMol/GeneralizedSubstruct/Wrap/testGeneralizedSubstruct.py" +222: Working Directory: /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/GraphMol/GeneralizedSubstruct/Wrap +222: Test timeout computed to be: 1500 +221: Randomness seeded to: 1354032881 +221: =============================================================================== +221: All tests passed (486 assertions in 10 test cases) +221: +211/236 Test #221: generalizedSubstructCatch .............. Passed 0.15 sec +test 223 + Start 223: testMolProcessing + +223: Test command: /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/GraphMol/MolProcessing/testMolProcessing +223: Working Directory: /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/GraphMol/MolProcessing +223: Test timeout computed to be: 1500 +213: ............[21:38:33] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +213: [21:38:33] Warning: ambiguous stereochemistry - opposing bonds have opposite wedging - at atom 1 ignored. +213: [21:38:33] Warning: ambiguous stereochemistry - opposing bonds have opposite wedging - at atom 1 ignored. +213: ........[21:38:34] Explicit valence for atom # 1 O, 3, is greater than permitted +222: ....... +222: ---------------------------------------------------------------------- +222: Ran 7 tests in 0.099s +222: +222: OK +212/236 Test #222: pyGeneralizedSubstruct ................. Passed 0.35 sec +test 224 + Start 224: pyMolProcessing + +224: Test command: /usr/bin/python3 "/build/reproducible-path/rdkit-202409.4/Code/GraphMol/MolProcessing/Wrap/testMolProcessing.py" +224: Working Directory: /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/GraphMol/MolProcessing/Wrap +224: Test timeout computed to be: 1500 +213: .. +213: ---------------------------------------------------------------------- +213: Ran 38 tests in 2.866s +213: +213: OK +213: done +213/236 Test #213: pyMolStandardize ....................... Passed 3.25 sec +test 225 + Start 225: testMIF + +225: Test command: /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/GraphMol/MolInteractionFields/testMIF +225: Working Directory: /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/GraphMol/MolInteractionFields +225: Test timeout computed to be: 1500 +225: Randomness seeded to: 2942518004 +225: =============================================================================== +225: All tests passed (27926 assertions in 8 test cases) +225: +214/236 Test #225: testMIF ................................ Passed 0.08 sec +test 226 + Start 226: pyMIF + +226: Test command: /usr/bin/python3 "/build/reproducible-path/rdkit-202409.4/Code/GraphMol/MolInteractionFields/Wrap/testMIF.py" +226: Working Directory: /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/GraphMol/MolInteractionFields/Wrap +226: Test timeout computed to be: 1500 +146: [21:38:34] done +226: ....... +226: ---------------------------------------------------------------------- +226: Ran 7 tests in 0.043s +226: +226: OK +226: Testing MIF wrapper +215/236 Test #226: pyMIF .................................. Passed 0.32 sec +test 227 + Start 227: testQuery + +227: Test command: /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/Query/testQuery +227: Working Directory: /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/Query +227: Test timeout computed to be: 1500 +227: Query +227: Query2 +227: Equality +227: Greater +227: GreaterEqual +227: Less +227: LessEqual +227: Open Range +227: Closed Range +227: Float +227: With Tolerance +227: Set +227: And +227: Or +227: XOr +227: pointer and copy foo +227: Set2 +216/236 Test #227: testQuery .............................. Passed 0.01 sec +test 228 + Start 228: testMatCalc + +228: Test command: /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/DataManip/MetricMatrixCalc/testMatCalc +228: Working Directory: /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/DataManip/MetricMatrixCalc +228: Test timeout computed to be: 1500 +228: 1.68022e+08 +228: 1.73149e+08 +228: 1.05549e+08 +228: 7.20603e+07 +228: 1.41535e+08 +228: 1.08592e+08 +228: 1.11334e+08 +228: 2.05553e+08 +228: 1.54962e+08 +228: 8.08231e+07 +228: 5.61421e+07 +228: 1.28874e+08 +228: 1.59011e+08 +228: 8.69902e+07 +228: 1.31367e+08 +228: 2.27389e+08 +228: 1.60289e+08 +228: 7.79813e+07 +228: 1.61001e+08 +228: 2.07599e+08 +228: 2.24432e+08 +228: 1.39725e+08 +228: 2.42614e+08 +228: 1.77578e+08 +228: 1.05908e+08 +228: 9.06742e+07 +228: 1.8087e+08 +228: 1.98182e+08 +228: 2.03052e+08 +228: 1.7673e+08 +228: 9.32798e+07 +228: 1.37969e+08 +228: 1.83778e+08 +228: 2.1228e+08 +228: 5.06157e+07 +228: 1.566e+08 +228: 2.37142e+08 +228: 1.49345e+08 +228: 7.05819e+07 +228: 1.71633e+08 +228: 1.96817e+08 +228: 2.18246e+08 +228: 9.49496e+07 +228: 2.25618e+08 +228: 1.30219e+08 +217/236 Test #228: testMatCalc ............................ Passed 0.02 sec +test 229 + Start 229: pyMatCalc + +229: Test command: /usr/bin/python3 "/build/reproducible-path/rdkit-202409.4/Code/DataManip/MetricMatrixCalc/Wrap/testMatricCalc.py" +229: Working Directory: /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/DataManip/MetricMatrixCalc/Wrap +229: Test timeout computed to be: 1500 +229: ..... +229: ---------------------------------------------------------------------- +229: Ran 5 tests in 0.189s +229: +229: OK +218/236 Test #229: pyMatCalc .............................. Passed 0.42 sec +test 230 + Start 230: testSimDivPickers + +230: Test command: /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/SimDivPickers/testSimDivPickers +230: Working Directory: /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/SimDivPickers +230: Test timeout computed to be: 1500 +230: [21:38:35] ------------------------------------- +230: [21:38:35] Testing github issue 1421: MaxMinPicker picking non-existent element. +230: [21:38:35] Done +230: [21:38:35] ------------------------------------- +230: [21:38:35] Testing github issue 2245: MinMax Diversity picker seeding shows deterministic / non-random behaviour. +230: [21:38:35] Done +219/236 Test #230: testSimDivPickers ...................... Passed 0.01 sec +test 231 + Start 231: pickersTestsCatch + +231: Test command: /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/SimDivPickers/pickersTestsCatch +231: Working Directory: /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/SimDivPickers +231: Test timeout computed to be: 1500 +231: Randomness seeded to: 3101681282 +231: =============================================================================== +231: All tests passed (21267 assertions in 1 test case) +231: +220/236 Test #231: pickersTestsCatch ...................... Passed 0.07 sec +test 232 + Start 232: pySimDivPickers + +232: Test command: /usr/bin/python3 "/build/reproducible-path/rdkit-202409.4/Code/SimDivPickers/Wrap/testPickers.py" +232: Working Directory: /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/SimDivPickers/Wrap +232: Test timeout computed to be: 1500 +224: .. +224: ---------------------------------------------------------------------- +224: Ran 2 tests in 0.947s +224: +224: OK +221/236 Test #224: pyMolProcessing ........................ Passed 1.28 sec +test 233 + Start 233: pyRanker + +233: Test command: /usr/bin/python3 "/build/reproducible-path/rdkit-202409.4/Code/ML/InfoTheory/Wrap/testRanker.py" +233: Working Directory: /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/ML/InfoTheory/Wrap +233: Test timeout computed to be: 1500 +232: [21:38:35] the useCache argument is deprecated and ignored +232: ...[21:38:35] the useCache argument is deprecated and ignored +232: [21:38:35] the useCache argument is deprecated and ignored +232: .[21:38:35] the useCache argument is deprecated and ignored +233: ..[21:38:35] +233: +233: **** +233: Invariant Violation +233: Can't rank more bits than the ensemble size +233: Violation occurred on line 156 in file ./Code/ML/InfoTheory/InfoBitRanker.cpp +233: Failed Expression: num <= dp_maskBits->getNumOnBits() +233: ---------- +233: Stacktrace: +233: 0# Invar::Invariant::toString[abi:cxx11]() const in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu//lib/libRDKitRDGeneral.so.1 +233: 1# Invar::operator<<(std::ostream&, Invar::Invariant const&) in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu//lib/libRDKitRDGeneral.so.1 +233: 2# RDInfoTheory::InfoBitRanker::getTopN(unsigned int) in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu//lib/libRDKitInfoTheory.so.1 +233: 3# RDInfoTheory::getTopNbits(RDInfoTheory::InfoBitRanker*, int) in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/rdkit/ML/InfoTheory/rdInfoTheory.so +233: 4# boost::python::objects::caller_py_function_impl > >::operator()(_object*, _object*) in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/rdkit/ML/InfoTheory/rdInfoTheory.so +233: 5# boost::python::objects::function::call(_object*, _object*) const in /lib/aarch64-linux-gnu/libboost_python313.so.1.83.0 +233: 6# 0x0000FFFFA9D42680 in /lib/aarch64-linux-gnu/libboost_python313.so.1.83.0 +233: 7# boost::python::detail::exception_handler::operator()(boost::function0 const&) const in /lib/aarch64-linux-gnu/libboost_python313.so.1.83.0 +233: 8# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/rdkit/rdBase.so +233: 9# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/rdkit/rdBase.so +233: 10# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/rdkit/rdBase.so +233: 11# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/rdkit/rdBase.so +233: 12# boost::python::handle_exception_impl(boost::function0) in /lib/aarch64-linux-gnu/libboost_python313.so.1.83.0 +233: 13# 0x0000FFFFA9D3F25C in /lib/aarch64-linux-gnu/libboost_python313.so.1.83.0 +233: 14# _PyObject_MakeTpCall in /usr/bin/python3 +233: 15# _PyEval_EvalFrameDefault in /usr/bin/python3 +233: 16# 0x000000000052F1D8 in /usr/bin/python3 +233: 17# _PyEval_EvalFrameDefault in /usr/bin/python3 +233: 18# 0x00000000004AB644 in /usr/bin/python3 +233: 19# 0x000000000065E594 in /usr/bin/python3 +233: 20# _PyObject_MakeTpCall in /usr/bin/python3 +233: 21# _PyEval_EvalFrameDefault in /usr/bin/python3 +233: 22# 0x000000000052F1D8 in /usr/bin/python3 +233: 23# _PyEval_EvalFrameDefault in /usr/bin/python3 +233: 24# 0x00000000004AB644 in /usr/bin/python3 +233: 25# 0x000000000065E594 in /usr/bin/python3 +233: 26# _PyObject_MakeTpCall in /usr/bin/python3 +233: 27# _PyEval_EvalFrameDefault in /usr/bin/python3 +233: 28# 0x000000000052F1D8 in /usr/bin/python3 +233: 29# _PyEval_EvalFrameDefault in /usr/bin/python3 +233: 30# 0x00000000004AB644 in /usr/bin/python3 +233: 31# 0x000000000065E594 in /usr/bin/python3 +233: 32# _PyObject_MakeTpCall in /usr/bin/python3 +233: 33# _PyEval_EvalFrameDefault in /usr/bin/python3 +233: 34# 0x0000000000502930 in /usr/bin/python3 +233: 35# _PyObject_MakeTpCall in /usr/bin/python3 +233: 36# _PyEval_EvalFrameDefault in /usr/bin/python3 +233: 37# PyEval_EvalCode in /usr/bin/python3 +233: 38# 0x00000000005FA63C in /usr/bin/python3 +233: 39# 0x00000000005F41C4 in /usr/bin/python3 +233: 40# 0x0000000000622878 in /usr/bin/python3 +233: 41# 0x0000000000621ED4 in /usr/bin/python3 +233: 42# 0x0000000000621C6C in /usr/bin/python3 +233: 43# Py_RunMain in /usr/bin/python3 +233: 44# Py_BytesMain in /usr/bin/python3 +233: 45# 0x0000FFFFAC1D229C in /lib/aarch64-linux-gnu/libc.so.6 +233: 46# __libc_start_main in /lib/aarch64-linux-gnu/libc.so.6 +233: 47# _start in /usr/bin/python3 +233: ---------- +233: **** +233: +233: ... +233: ---------------------------------------------------------------------- +233: Ran 5 tests in 0.014s +233: +233: OK +222/236 Test #233: pyRanker ............................... Passed 0.27 sec +test 234 + Start 234: testChemicalFeatures + +234: Test command: /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/ChemicalFeatures/testChemicalFeatures +234: Working Directory: /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/ChemicalFeatures +234: Test timeout computed to be: 1500 +234: ----------------------------------------- +234: Test1 +234: Done +223/236 Test #234: testChemicalFeatures ................... Passed 0.00 sec +test 235 + Start 235: pyFeatures + +235: Test command: /usr/bin/python3 "/build/reproducible-path/rdkit-202409.4/Code/ChemicalFeatures/Wrap/testFeatures.py" +235: Working Directory: /build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu/Code/ChemicalFeatures/Wrap +235: Test timeout computed to be: 1500 +235: .. +235: ---------------------------------------------------------------------- +235: Ran 2 tests in 0.001s +235: +235: OK +235: Testing ChemicalFeatures Wrapper code: +224/236 Test #235: pyFeatures ............................. Passed 0.30 sec +test 236 + Start 236: pythonProjectTests + +236: Test command: /usr/bin/python3 "-m" "pytest" +236: Working Directory: /build/reproducible-path/rdkit-202409.4/Projects +236: Test timeout computed to be: 1500 232: ....... 232: ---------------------------------------------------------------------- -232: Ran 11 tests in 0.787s +232: Ran 11 tests in 0.746s 232: 232: OK -227/236 Test #232: pySimDivPickers ........................ Passed 1.00 sec +225/236 Test #232: pySimDivPickers ........................ Passed 0.98 sec 236: ============================= test session starts ============================== 236: platform linux -- Python 3.13.1, pytest-8.3.4, pluggy-1.5.0 236: rootdir: /build/reproducible-path/rdkit-202409.4/Projects @@ -35337,21 +35362,34 @@ 236: plugins: typeguard-4.4.1 236: collected 12 items 236: -146: [12:43:13] --------------------------------- -146: [12:43:13] test github issue 256: handling of zero-atom molecules +226/236 Test #200: pyTestThreads .......................... Passed 11.51 sec +146: [21:38:34] --------------------------------- +146: [21:38:34] test github issue 256: handling of zero-atom molecules 146: -146: [12:43:13] --------------------------------- -146: [12:43:13] test embedder callback function -146: [12:43:13] --------------------------------- -146: [12:43:13] test multi-threaded multi-conf embedding +146: [21:38:34] --------------------------------- +146: [21:38:34] test embedder callback function +146: [21:38:34] --------------------------------- +146: [21:38:34] test multi-threaded multi-conf embedding 146: -146: [12:43:15] --------------------------------- -146: [12:43:15] test github issue 563: Incorrect ring stereochemistry after embedding +146: [21:38:37] --------------------------------- +146: [21:38:37] test github issue 563: Incorrect ring stereochemistry after embedding 146: 146: CNC[C@H]1CC[C@H](C[NH3+])CC1 +223: Randomness seeded to: 4262901521 +223: =============================================================================== +223: All tests passed (203 assertions in 1 test case) +223: +227/236 Test #223: testMolProcessing ...................... Passed 3.28 sec +146: [21:38:37] --------------------------------- +146: [21:38:37] test github issue 568: Incorrect stereochemistry after embedding +146: +146: C1=NC[C@]2(CN3CC[C@@H]2C3)O1 +146: O=C(O)[C@@H]1[C@H](C(=O)O)[C@H]2CC[C@@H]1O2 +146: O=C(CCc1ccccc1)OC[C@H]1C[C@@H]2O[C@H]1[C@H]1C(=O)OC(=O)[C@H]12 +146: Cn1cc(C2=NC[C@]3(CN4CC[C@@H]3C4)O2)c2ccccc21 186: ............. 186: ---------------------------------------------------------------------- -186: Ran 19 tests in 13.243s +186: Ran 19 tests in 25.122s 186: 186: OK 186: Testing atom rings @@ -35359,38 +35397,35 @@ 186: searching atom rings 186: searching bond rings 186: done -228/236 Test #186: pySubstructLibrary ..................... Passed 13.93 sec -146: [12:43:16] --------------------------------- -146: [12:43:16] test github issue 568: Incorrect stereochemistry after embedding -146: -146: C1=NC[C@]2(CN3CC[C@@H]2C3)O1 -146: O=C(O)[C@@H]1[C@H](C(=O)O)[C@H]2CC[C@@H]1O2 -146: O=C(CCc1ccccc1)OC[C@H]1C[C@@H]2O[C@H]1[C@H]1C(=O)OC(=O)[C@H]12 -146: Cn1cc(C2=NC[C@]3(CN4CC[C@@H]3C4)O2)c2ccccc21 146: Nc1ncnc2c1ncn2[C@@H]1C=C(CO)[C@@H](O)[C@H]1O +228/236 Test #186: pySubstructLibrary ..................... Passed 25.77 sec 146: CO[C@H]1[C@@H](N)[C@@H](O)[C@@H](O)[C@H]1O 146: CO[C@@H]1[C@@H](N)[C@@H](O)[C@@H](O)[C@H]1O 146: CCS[C@@H]1[C@@H](N)[C@@H](O)[C@@H](O)[C@H]1O 146: CCCCC[C@H](O)/C=C/[C@@]1(F)[C@H](O)C[C@H](O)[C@@H]1C/C=C\CCCC(=O)OC 146: CCCCC[C@@H](O)/C=C/[C@@]1(F)[C@H](C/C=C\CCCC(=O)OC)[C@H](O)C[C@@H]1O 146: CNC(=O)Oc1cccc2c1OC[C@@H]1CCN(C)[C@H]21 -211: [12:43:19] Explicit valence for atom # 0 Br, 1, is greater than permitted -211: =============================================================================== -211: All tests passed (38344 assertions in 51 test cases) -211: -229/236 Test #211: molStandardizeCatchTest ................ Passed 9.20 sec 146: CNC(=O)Oc1ccc2c(c1)[C@@H]1[C@@H](CCN1C)CO2 146: CN1CC[C@H]2COc3c(O)cccc3[C@H]21 146: CC(=O)C[C@@]12CCC[C@H]1[C@@H]1CCC3=CC(=O)CC[C@@H]3[C@H]1CC2 +211: [21:38:41] Explicit valence for atom # 0 Br, 1, is greater than permitted +211: =============================================================================== +211: All tests passed (38344 assertions in 51 test cases) +211: +229/236 Test #211: molStandardizeCatchTest ................ Passed 13.17 sec 146: O=C(O)[C@@H]1C[C@H]2C[C@@H](CCc3nn[nH]n3)CC[C@H]2CN1 146: COc1ccc2c(c1)OC[C@@H](N1CCC(O)(c3ccc(F)cc3)CC1)[C@H]2O 146: Oc1ccc2c(c1)OC[C@@H](N1CCC(Cc3ccccc3)CC1)[C@H]2O 146: Oc1ccc2c(c1)OC[C@H](N1CCC(O)(c3ccccc3)CC1)[C@@H]2O +171: =============================================================================== +171: All tests passed (93 assertions in 5 test cases) +171: +230/236 Test #171: testRascalCluster ...................... Passed 57.29 sec 146: CC(=O)c1ccc2c(c1)[C@@]13CCCC[C@H]1[C@@H](C2)N(CC1CC1)CC3 147: =============================================================================== 147: All tests passed (12738 assertions in 19 test cases) 147: -230/236 Test #147: distGeomHelpersCatch ................... Passed 40.62 sec +231/236 Test #147: distGeomHelpersCatch ................... Passed 67.10 sec 146: CC(=O)O[C@@H]1CC[C@@H]2CN3CCc4cc5c(cc4[C@@H]3C[C@@H]2C1)OCO5 146: COc1cc2c(cc1OC)[C@@H]1C[C@@H]3C[C@H](O)CC[C@@H]3CN1CC2 146: N#C[C@@H]1C[C@@H]2CN3CCc4cc5c(cc4[C@@H]3C[C@@H]2C[C@@H]1O)OCO5 @@ -35400,10 +35435,43 @@ 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-] -171: =============================================================================== -171: All tests passed (93 assertions in 5 test cases) -171: -231/236 Test #171: testRascalCluster ...................... Passed 39.59 sec +170: =============================================================================== +170: All tests passed (2931 assertions in 29 test cases) +170: +232/236 Test #170: testRascalMCES ......................... Passed 66.98 sec +146: [21:38:51] Molecule does not have explicit Hs. Consider calling AddHs() +146: [21:38:47] --------------------------------- +146: [21:38:47] test github issue 696: Bad 1-4 bounds matrix elements in highly constrained system +146: [21:38:47] --------------------------------- +146: [21:38:47] More ChEMBL molecules failing bounds smoothing. +146: [21:38:47] --------------------------------- +146: [21:38:47] ugly conformations can be generated for highly constrained ring systems. +146: [21:38:47] --------------------------------- +146: [21:38:47] test embed parameters structure. +146: [21:38:47] --------------------------------- +146: [21:38:47] test github 1227: Hs being used in RMSD filtering. +146: [21:38:47] --------------------------------- +146: [21:38:47] Failure to embed larger aromatic rings. +146: [21:38:49] --------------------------------- +146: [21:38:49] Deterministic with large random seeds +146: [21:38:50] --------------------------------- +146: [21:38:50] Github #1990: seg fault after RemoveHs +146: [21:38:50] --------------------------------- +146: [21:38:50] Github #2246: Use coordMap when starting embedding from random coords +146: [21:38:51] --------------------------------- +146: [21:38:51] Providing a distance bounds matrix. +146: [21:38:51] --------------------------------- +146: [21:38:51] Disabling fragmentation. +146: [21:38:51] --------------------------------- +146: [21:38:51] Using symmetry in conformation pruning. +146: [21:38:51] --------------------------------- +146: [21:38:51] Force trans amides. +146: [21:38:51] --------------------------------- +146: [21:38:51] test missing Hs warning. +146: [21:38:51] --------------------------------- +146: [21:38:51] basic H bond support. +146: [21:38:51] ******************************************************* +233/236 Test #146: testDistGeomHelpers .................... Passed 74.89 sec 236: DbCLI/UnitTestDbCLI.py ............ [100%] 236: 236: =============================== warnings summary =============================== @@ -35412,57 +35480,20 @@ 236: decBase = declarative_base() 236: 236: -- Docs: https://docs.pytest.org/en/stable/how-to/capture-warnings.html -236: ======================== 12 passed, 1 warning in 15.00s ======================== -232/236 Test #236: pythonProjectTests ..................... Passed 15.46 sec -146: [12:43:30] Molecule does not have explicit Hs. Consider calling AddHs() -146: [12:43:26] --------------------------------- -146: [12:43:26] test github issue 696: Bad 1-4 bounds matrix elements in highly constrained system -146: [12:43:26] --------------------------------- -146: [12:43:26] More ChEMBL molecules failing bounds smoothing. -146: [12:43:26] --------------------------------- -146: [12:43:26] ugly conformations can be generated for highly constrained ring systems. -146: [12:43:26] --------------------------------- -146: [12:43:26] test embed parameters structure. -146: [12:43:26] --------------------------------- -146: [12:43:26] test github 1227: Hs being used in RMSD filtering. -146: [12:43:26] --------------------------------- -146: [12:43:26] Failure to embed larger aromatic rings. -146: [12:43:27] --------------------------------- -146: [12:43:27] Deterministic with large random seeds -146: [12:43:29] --------------------------------- -146: [12:43:29] Github #1990: seg fault after RemoveHs -146: [12:43:29] --------------------------------- -146: [12:43:29] Github #2246: Use coordMap when starting embedding from random coords -146: [12:43:30] --------------------------------- -146: [12:43:30] Providing a distance bounds matrix. -146: [12:43:30] --------------------------------- -146: [12:43:30] Disabling fragmentation. -146: [12:43:30] --------------------------------- -146: [12:43:30] Using symmetry in conformation pruning. -146: [12:43:30] --------------------------------- -146: [12:43:30] Force trans amides. -146: [12:43:30] --------------------------------- -146: [12:43:30] test missing Hs warning. -146: [12:43:30] --------------------------------- -146: [12:43:30] basic H bond support. -146: [12:43:30] ******************************************************* -233/236 Test #146: testDistGeomHelpers .................... Passed 48.46 sec -170: =============================================================================== -170: All tests passed (2931 assertions in 29 test cases) -170: -234/236 Test #170: testRascalMCES ......................... Passed 47.71 sec -5: [12:43:34] Finished: testMultipleTimes() -5: [12:43:34] -5: ----------------------------------------- -235/236 Test #5: testConcurrentQueue .................... Passed 59.69 sec +236: ======================== 12 passed, 1 warning in 15.48s ======================== +234/236 Test #236: pythonProjectTests ..................... Passed 15.98 sec 173: =============================================================================== 173: All tests passed (215 assertions in 18 test cases) 173: -236/236 Test #173: testSynthonSpaceSubstructureSearch ..... Passed 54.46 sec +235/236 Test #173: testSynthonSpaceSubstructureSearch ..... Passed 71.53 sec +5: [21:39:09] Finished: testMultipleTimes() +5: [21:39:09] +5: ----------------------------------------- +236/236 Test #5: testConcurrentQueue .................... Passed 103.19 sec 100% tests passed, 0 tests failed out of 236 -Total Test time (real) = 67.15 sec +Total Test time (real) = 103.27 sec make[2]: Leaving directory '/build/reproducible-path/rdkit-202409.4/obj-aarch64-linux-gnu' make[1]: Leaving directory '/build/reproducible-path/rdkit-202409.4' create-stamp debian/debhelper-build-stamp @@ -38088,42 +38119,42 @@ 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 byteaout: 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 errmsg_internal: 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 PyErr_SetObject used by debian/librdkit1t64/usr/lib/libRDKitRDBoost.so.1.2024.09.4 found in none of the libraries -dpkg-shlibdeps: warning: symbol PyExc_ValueError used by debian/librdkit1t64/usr/lib/libRDKitRDBoost.so.1.2024.09.4 found in none of the libraries -dpkg-shlibdeps: warning: symbol _Py_Dealloc used by debian/librdkit1t64/usr/lib/libRDKitRDBoost.so.1.2024.09.4 found in none of the libraries +dpkg-shlibdeps: warning: symbol PyExc_KeyError used by debian/librdkit1t64/usr/lib/libRDKitRDBoost.so.1.2024.09.4 found in none of the libraries +dpkg-shlibdeps: warning: symbol PyExc_RuntimeError used by debian/librdkit1t64/usr/lib/libRDKitRDBoost.so.1.2024.09.4 found in none of the libraries +dpkg-shlibdeps: warning: symbol PyLong_FromLong used by debian/librdkit1t64/usr/lib/libRDKitRDBoost.so.1.2024.09.4 found in none of the libraries +dpkg-shlibdeps: warning: symbol PyObject_CallFunction used by debian/librdkit1t64/usr/lib/libRDKitRDBoost.so.1.2024.09.4 found in none of the libraries dpkg-shlibdeps: warning: symbol PyLong_FromUnsignedLong used by debian/librdkit1t64/usr/lib/libRDKitRDBoost.so.1.2024.09.4 found in none of the libraries -dpkg-shlibdeps: warning: symbol _Py_NoneStruct used by debian/librdkit1t64/usr/lib/libRDKitRDBoost.so.1.2024.09.4 found in none of the libraries +dpkg-shlibdeps: warning: symbol PyExc_ValueError used by debian/librdkit1t64/usr/lib/libRDKitRDBoost.so.1.2024.09.4 found in none of the libraries dpkg-shlibdeps: warning: symbol PyObject_IsTrue used by debian/librdkit1t64/usr/lib/libRDKitRDBoost.so.1.2024.09.4 found in none of the libraries -dpkg-shlibdeps: warning: symbol PyObject_CallFunction used by debian/librdkit1t64/usr/lib/libRDKitRDBoost.so.1.2024.09.4 found in none of the libraries dpkg-shlibdeps: warning: symbol PyErr_SetString used by debian/librdkit1t64/usr/lib/libRDKitRDBoost.so.1.2024.09.4 found in none of the libraries -dpkg-shlibdeps: warning: symbol PyExc_RuntimeError used by debian/librdkit1t64/usr/lib/libRDKitRDBoost.so.1.2024.09.4 found in none of the libraries -dpkg-shlibdeps: warning: symbol PyExc_KeyError used by debian/librdkit1t64/usr/lib/libRDKitRDBoost.so.1.2024.09.4 found in none of the libraries +dpkg-shlibdeps: warning: symbol _Py_Dealloc used by debian/librdkit1t64/usr/lib/libRDKitRDBoost.so.1.2024.09.4 found in none of the libraries +dpkg-shlibdeps: warning: symbol PyExc_IndexError used by debian/librdkit1t64/usr/lib/libRDKitRDBoost.so.1.2024.09.4 found in none of the libraries dpkg-shlibdeps: warning: 2 other similar warnings have been skipped (use -v to see them all) dh_installdeb -O--buildsystem=cmake dh_gencontrol -O--buildsystem=cmake -dpkg-gencontrol: warning: Depends field of package rdkit-data: substitution variable ${shlibs:Depends} used, but is not defined -dpkg-gencontrol: warning: package rdkit-data: substitution variable ${python3:Depends} unused, but is defined dpkg-gencontrol: warning: Depends field of package rdkit-doc: substitution variable ${shlibs:Depends} used, but is not defined -dpkg-gencontrol: warning: Depends field of package librdkit-dev: substitution variable ${shlibs:Depends} used, but is not defined dpkg-gencontrol: warning: Provides field of package python3-rdkit: substitution variable ${python3:Provides} used, but is not defined -dpkg-gencontrol: warning: package postgresql-17-rdkit: substitution variable ${python3:Depends} unused, but is defined -dpkg-gencontrol: warning: package librdkit1t64: substitution variable ${python3:Depends} unused, but is defined +dpkg-gencontrol: warning: Depends field of package librdkit-dev: substitution variable ${shlibs:Depends} used, but is not defined dpkg-gencontrol: warning: package librdkit-dev: substitution variable ${python3:Depends} unused, but is defined +dpkg-gencontrol: warning: package librdkit1t64: substitution variable ${python3:Depends} unused, but is defined dpkg-gencontrol: warning: package rdkit-doc: substitution variable ${python3:Depends} unused, but is defined dpkg-gencontrol: warning: Provides field of package python3-rdkit: substitution variable ${python3:Provides} used, but is not defined -dpkg-gencontrol: warning: package postgresql-17-rdkit: substitution variable ${python3:Depends} unused, but is defined +dpkg-gencontrol: warning: Depends field of package rdkit-data: substitution variable ${shlibs:Depends} used, but is not defined dpkg-gencontrol: warning: package librdkit1t64: substitution variable ${python3:Depends} unused, but is defined +dpkg-gencontrol: warning: package rdkit-data: substitution variable ${python3:Depends} unused, but is defined +dpkg-gencontrol: warning: package postgresql-17-rdkit: substitution variable ${python3:Depends} unused, but is defined +dpkg-gencontrol: warning: package postgresql-17-rdkit: substitution variable ${python3:Depends} unused, but is defined dh_md5sums -O--buildsystem=cmake dh_builddeb -O--buildsystem=cmake dpkg-deb: building package 'python3-rdkit' in '../python3-rdkit_202409.4-1_arm64.deb'. dpkg-deb: building package 'python3-rdkit-dbgsym' in '../python3-rdkit-dbgsym_202409.4-1_arm64.deb'. dpkg-deb: building package 'rdkit-data' in '../rdkit-data_202409.4-1_all.deb'. -dpkg-deb: building package 'rdkit-doc' in '../rdkit-doc_202409.4-1_all.deb'. dpkg-deb: building package 'librdkit1t64' in '../librdkit1t64_202409.4-1_arm64.deb'. dpkg-deb: building package 'librdkit1t64-dbgsym' in '../librdkit1t64-dbgsym_202409.4-1_arm64.deb'. dpkg-deb: building package 'librdkit-dev' in '../librdkit-dev_202409.4-1_arm64.deb'. +dpkg-deb: building package 'rdkit-doc' in '../rdkit-doc_202409.4-1_all.deb'. dpkg-deb: building package 'postgresql-17-rdkit' in '../postgresql-17-rdkit_202409.4-1_arm64.deb'. dpkg-deb: building package 'postgresql-17-rdkit-dbgsym' in '../postgresql-17-rdkit-dbgsym_202409.4-1_arm64.deb'. dpkg-genbuildinfo --build=binary -O../rdkit_202409.4-1_arm64.buildinfo @@ -38133,12 +38164,14 @@ dpkg-buildpackage: info: binary-only upload (no source included) dpkg-genchanges: info: including full source code in upload I: copying local configuration +I: user script /srv/workspace/pbuilder/3933652/tmp/hooks/B01_cleanup starting +I: user script /srv/workspace/pbuilder/3933652/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/2869322 and its subdirectories -I: Current time: Wed Jan 15 12:46:32 -12 2025 -I: pbuilder-time-stamp: 1736988392 +I: removing directory /srv/workspace/pbuilder/3933652 and its subdirectories +I: Current time: Wed Feb 18 21:41:53 +14 2026 +I: pbuilder-time-stamp: 1771400513